Neuroscience 298 (2015) 220–292

iTRAQ-BASED QUANTITATIVE ANALYSIS OF HIPPOCAMPAL POSTSYNAPTIC DENSITY-ASSOCIATED PROTEINS IN A RAT CHRONIC MILD STRESS MODEL OF DEPRESSION

X. HAN, a,b,c W. SHAO, a,b,c Z. LIU, a,b,c S. FAN, a,b,c displayed differences in the abundance of several types of J. YU, b,c J. CHEN, b,c R. QIAO, b,c J. ZHOU b,c* AND proteins. A detailed protein functional analysis pointed to a,b,c,d P. XIE * a role for PSD-associated proteins involved in signaling a Department of Neurology, The First Affiliated Hospital, and regulatory functions. Within the PSD, the N-methyl-D-as- Chongqing Medical University, Chongqing, China partate (NMDA) receptor subunit NR2A and its downstream targets contribute to CMS susceptibility. Further analysis b Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China of disease relevance indicated that the PSD contains a com- c plex set of proteins of known relevance to mental illnesses Chongqing Key Laboratory of Neurobiology, Chongqing, China including depression. In sum, these findings provide novel d Department of Neurology, Yongchuan Hospital, Chongqing insights into the contribution of PSD-associated proteins Medical University, Chongqing, China to stress susceptibility and further advance our understand- ing of the role of hippocampal synaptic plasticity in MDD. Ó 2015 IBRO. Published by Elsevier Ltd. All rights reserved. Abstract—Major depressive disorder (MDD) is a prevalent psychiatric mood illness and a major cause of disability and suicide worldwide. However, the underlying pathophys- iology of MDD remains poorly understood due to its hetero- Key words: major depressive disorder, chronic mild stress, genic nature. Extensive pre-clinical research suggests that hippocampus, postsynaptic density, iTRAQ, proteomics. many molecular alterations associated with MDD preferen- tially localize to the postsynaptic density (PSD). Here, we used a rodent chronic mild stress (CMS) model to generate susceptible and unsusceptible subpopulations. Proteomic INTRODUCTION analysis using an isobaric tag for relative and absolute quantitation (iTRAQ) and tandem mass spectrometry was Major depressive disorder (MDD) is a common and performed to identify differentially expressed proteins in debilitating mental illness affecting approximately 2.5% enriched PSD preparations from the hippocampi of different of the general population and is predicted to be the groups. More than 1500 proteins were identified and quanti- number two cause of illness worldwide by 2020 fied, and 74 membrane proteins were differentially (Lecrubier, 2001). Symptoms of the illness include cogni- expressed. Of these membrane proteins, 51 (69%) were iden- tive impairment and memory loss, implicating synaptic tified by SynaptomeDB search as having a predicted PSD dysfunction in the pathophysiology of MDD (Levens and localization. The unbiased profiles identified several PSD Gotlib, 2009; Barabassy et al., 2010; Boyle et al., 2010). candidate proteins that may be related to CMS vulnerability or insusceptibility, and these two CMS phenotypes This possibility is supported by animal studies demon- strating a reduction of dendritic spine numbers and hip- pocampal neuronal function (Radley et al., 2006; Liu *Correspondence to: J. Zhou, Institute of Neuroscience and the and Aghajanian, 2008). Postmortem studies have sug- Collaborative Innovation Center for Brain Science, Chongqing Med- gested that somatodendritic, axonal, synaptic, and glial ical University, No. 1 Yixue Road, Yuzhong District, Chongqing cell number changes are all involved in the inhibition of 400016, China. P. Xie, Department of Neurology, The First Affiliated adult hippocampal neurogenesis (D’Sa and Duman, Hospital, Chongqing Medical University, No. 1 Yixue Road, Yuzhong District, Chongqing 400016, China. Tel: +86-23-68485490; fax: 2002; Sheline et al., 2003; Pittenger and Duman, 2008; +86-23-68485111. Lorenzetti et al., 2009). This is also consistent with brain E-mail addresses: [email protected] (J. Zhou), xiepeng@ imaging studies that have reported a reduction in hip- cqmu.edu.cn (P. Xie). pocampal volume in postmortem animal models of either These authors contributed equally to this work. Abbreviations: 2DE, two-dimensional gel-electrophoresis; ANOVA, stress or depression (D’Sa and Duman, 2002; Pittenger analysis of variance; CMS, chronic mild stress; DAVID, database for and Duman, 2008). In animal models, stress-induced hip- annotation, visualization and integrated discovery; FASP, filter-aided pocampal neuropathological changes may be summa- sample preparation method; FDR, false discovery rate; FST, forced swim test; GO, gene ontology; GRAVY, grand average hydropathicity; rized as follows: loss of dendritic spines, decrease in the HCD, higher energy collisional dissociation; iTRAQ, isobaric tag for number and length of dendrites, loss of synapses, loss relative and absolute quantitation; MDD, major depressive disorder; of glia, and the impairment of neurogenesis (D’Sa and MW, molecular weight; NMDA, N-methyl-D-aspartate; Nrgn, Duman, 2002; Sheline et al., 2003; Pittenger and neurogranin; pI, isoelectric point; PSD, postsynaptic density; SCX, strong cation exchange; SPT, sucrose preference test; TMDs, Duman, 2008). To date, however, the protein substrates transmembrane domains; UniProt, universal protein resource. involved in synaptic plasticity in the hippocampus of http://dx.doi.org/10.1016/j.neuroscience.2015.04.006 0306-4522/Ó 2015 IBRO. Published by Elsevier Ltd. All rights reserved.

220 X. Han et al. / Neuroscience 298 (2015) 220–292 221

MDD have not been well-explored (Czeh and Lucassen, molecular mechanism(s) underlying the abnormal 2007). synaptic plasticity observed in MDD. Recent studies have used molecular profiling technologies to examine the brains of postmortem EXPERIMENTAL PROCEDURES depressed patients and rodent models of depression. Several groups have used microarray approaches to Ethics statement demonstrate abnormalities in the expression of This study was approved by the Ethics Committee of the transcripts related to synaptic transmission, particularly Chongqing Medical University (Chongqing, China), and glutamate and GABAergic signaling, in the brains of all procedures of animal care and treatment were in depressed patients with or without suicide, especially in accordance with the National Institutes of Health the frontal and limbic regions (Choudary et al., 2005; Guidelines for Animal Research (Guide for the Care and Sequeira et al., 2007, 2009; Klempan et al., 2009). A num- Use of Laboratory Animals). Special care was taken to ber of proteomic studies investigating the overall level of minimize the number and suffering of animals. hippocampal tissue from various stress systems have shown that stressful events alter the expression of proteins with roles in energy metabolism, neurogenesis, synaptic Animals and CMS treatment plasticity, and neurotransmission (Martins-de-Souza Eighty-one healthy adult male Sprague–Dawley rats, et al., 2010; Martins-de-Souza et al., 2012a,b). Although purchased from the animal facility at the Chongqing it is unclear whether altering these molecular dysregula- Medical University (Chongqing, China), were housed tions can affect overall hippocampal structure and function, individually, given access to food and water ad libitum, there is evidence that significant changes occur at the sub- and maintained on a 12-h light/dark cycle (light from cellular level, particularly at neuronal synapses. 7:30 to 19:30) at a constant temperature of 21–22 °C Because of the complexity of the central nervous and humidity of 55 ± 5% (unless otherwise noted). system, the uses of fractionation enrichment techniques Animal weight was approximately 165 g when are usually necessary to achieve a reliable quantitation adaptation for sucrose consumption was initiated and of low-abundance proteins. Within the synapse, the approximately 250 g at the start of the stress regime. postsynaptic site contains a high concentration of The rats were allowed one week to acclimate to the proteins, including receptors and their intracellular environment and then 1% sucrose solution was given to signaling components that receive and transduce them, as well as water for five weeks for sucrose synaptic information. This postsynaptic electron-dense habituation. During this period, sucrose preference of all structure, termed the postsynaptic density (PSD), is a rats was tested twice weekly during the first three highly-organized structure attached to the postsynaptic weeks and once weekly during the last two weeks. neuronal terminal and is comprised of a complex According to the sucrose intakes of the three final network of cytoskeletal scaffolding and signaling baseline tests, the rats were divided randomly into two proteins. These proteins facilitate the movement of groups and placed in separate rooms. Stress groups receptor and signaling complexes. The PSD is critical to were exposed to a four-week CMS procedure, whereas normal neurotransmission but is also critical to adaptive the control group was left undisturbed. behaviors such as learning and memory. It has been The CMS protocol was performed according to the strongly implicated in neuropsychiatric disorders (Jay procedure described in our previous studies (Hu et al., et al., 2004), such as MDD, through its roles in synaptic 2013; Yang et al., 2013). In short, rats were subjected plasticity and cognitive function (Duric et al., 2013). to a variety of mild stress factors: paired housing, a 45° Although constituents of the PSD have been implicated cage tilt along the vertical axis, a soiled cage (with in MDD using conventional detection techniques 300 ml water spilled into bedding), exposure to an empty (Kinnunen et al., 2003; Duric et al., 2013), no study has water bottle immediately following a period of acute water yet focused on exploring global changes in the hippocam- deprivation, stroboscopic illumination (300 flashes/min), pal PSD fraction through the use of a high-throughput pro- continuous overnight illumination, and white noise. The teomic screen. procedure including the time and length of stressors are In this study, using quantitative proteomics, we described in Appendix Table 1. At the end of every week, examined changes in the expression levels of the sucrose preference of all of the rats was assessed, hippocampal PSD-associated proteins in a chronic mild and the forced swim test (FST) was carried out in the final stress (CMS) rat model of depression. This model week. generates CMS-susceptible and unsusceptible subpopulations, reflecting the two hedonic responses to Sucrose preference test (SPT) CMS. To measure the relative changes in protein expression, we used isobaric tag for relative and The SPT was conducted as a measure of the anhedonic absolute quantitation (iTRAQ) followed by tandem mass effect of CMS. A two-bottle preference test was used, spectrometric (LC-MS/MS) analysis. Our large-scale where the rats had access to both water and a 1% subcellular proteome profiles identified several sucrose solution for 24 h during a no-stress period. The differential PSD-associated proteins that may be positions of the two bottles (on the left and right sides of specifically related to stress vulnerability. These data the cages) were randomly varied. All fluid consumption should provide a valuable resource for deciphering the was recorded by weighing the two bottles before testing 222 X. Han et al. / Neuroscience 298 (2015) 220–292 and after 24 h. The sucrose preference was calculated with each pool originating from three or four rats according to the following formula: sucrose preference = (Henningsen et al., 2012; Hu et al., 2013). sucrose intake (g)/(sucrose intake (g) + water intake (g)).

FST Extraction and digestion of proteins The FST was performed as described previously with The obtained PSD pellet was dissolved using a sample slight modifications (Porsolt et al., 1977). The rats were buffer (4% SDS, 10 mM DTT, 150 mM Tris–HCl, pH placed individually in a cylinder (40 cm in height 20 cm 8.0). The lysate was boiled in water for 5 min and then in diameter) filled with water (24 ± 1 °C) to a height of centrifuged at 40,000g for 15 min. Protein 30 cm. A 15-min pretest period was followed 24 h later concentrations were determined using a bicinchoninic by a 5-min test period during which the total immobility acid (BCA) protein assay kit according to the time was recorded. The test was monitored by a video manufacturer’s instructions (Pierce, USA). Bovine serum surveillance system. Water in the cylinders was changed albumin (BSA) was used as the standard. Subsequent before each trial. protein digestion was performed using the filter-aided sample preparation method (FASP) in a 10-kDa molecular weight cut-off centrifugation filter (Sartorius) Statistical analysis of SPT and FST data (Wisniewski et al., 2009a,b). The sample was diluted with Statistical analyses were carried out using SPSS 16.0. 200 ll of UA buffer (8 M urea, 150 mM Tris–HCl, pH 8.0) Data from the SPT and FST were analyzed by a one- and then centrifuged at 14,000g for 30 min. This step was way repeated measured analyses of variance (ANOVA) repeated once. Then, 100 ll of 50 mM iodoacetamide in followed by a post hoc LSD test. A p-value of less than UA buffer was added to the filters, and the samples were 0.05 was considered to be statistically significant. incubated in darkness for 30 min. Filters were washed Statistics were presented as mean ± standard errors twice with 100 ll of UA buffer followed by two washes with (SE). 100 ll of dissolution buffer (50 mM triethylammonium bicarbonate, pH 8.5). Proteins were digested overnight in a 40 ll dissolution buffer using trypsin (Promega) at Preparation of hippocampal PSD fractions an enzyme-to-protein ratio of 1:50 at 37 °C. The released PSD fractions were obtained using a biomedical method peptides were collected by centrifugation at 14,000g for essentially as previously reported (Phillips et al., 2001; 10 min followed by two washes with dissolution buffer. Abul-Husn et al., 2009; Hu et al., 2013; Focking et al., 2014). Rats were sacrificed by decapitation and the brains rapidly removed. The fresh hippocampal tissue samples iTRAQ labeling and strong cation exchange (SCX) were collected and pooled. Using a motor-operated fractionation Teflon-glass grinder, the pooled tissues were homoge- nized on icein solution A (0.32 M sucrose, 1 mM MgCl2, The tryptic peptides were labeled with an iTRAQ-8plex kit and 0.1 mM CaCl2) containing a protease inhibitor cock- (Applied Biosystems, Foster City, CA) according to the tail (Sigma–Aldrich, St. Louis, MO, USA), respectively. manufacturer’s protocol. Samples from the control group All the following fractionation steps were carried out at were labeled with reagents 115 and 118, samples from 4 °C unless otherwise specified. Homogenates were cen- the susceptible group were labeled with reagents 114 trifuged at 1400g for 10 min, and the resultant pellet was and 117, and samples from the unsusceptible group then homogenized again. The second centrifugation was were labeled with reagents 113 and 116. The incubation performed at 710g for 10 min. Supernatants were pooled was allowed to proceed at room temperature for 2 h and and centrifuged at 12,000g for 30 min. The resulting pellet then stopped by the addition of 10 mM KH2PO4, 25% was suspended for a second time in solution B (0.32 M ACN, pH 3.0. Subsequently, all the three labeled- sucrose and 0.1 mM CaCl2) then layered over the samples were pooled, vacuum-dried and further 1.2 M/1.0 M/0.85 M sucrose gradient (10 ml each). After fractionated offline using SCX chromatography. Briefly, ultracentrifugation (himac cp 80 wx, Hitachi Koki, Japan) the peptides were dissolved and loaded onto a at 82,500g for 2 h, the synaptosome fraction from the Polysulfoethyl 4.6 100 mm column (5 lm, 200 A˚ , 1.2 M/1.0 M interface was collected. To obtain PSD frac- PolyLC Inc., MD, USA) at a flow rate of 1 ml/min. A tions, an aliquot solution (synaptosomal fraction) was suitable gradient elution was applied to separate diluted with ice-cold 0.1 mM CaCl2 and brought to an peptides at a flow rate of 1 ml/min with elution buffer equal volume of 2hypotonic buffer (40 mM Tris–HCl (10 mM KH2PO4, 500 mM KCl in 25% acetonitrile, pH pH 8, 2% Triton X-100, 0.2 mM CaCl2) containing pro- 3.0). Eluted peptides were collected and desalted by an tease and phosphatase inhibitor cocktails. This solution offline fraction collector. The resulting 30 fractions were was mixed by inversion and incubated on a shaker for combined to 10 pools and desalted on C18 Cartridges 20 min at 4 °C. The PSD pellet was collected by centrifu- (Emporeä SPE Cartridges C18 (standard density), bed gation at 40,000g for 20 min at 4 °C and then stored at I.D. 7 mm, volume 3 ml, Sigma, St. Louis, MO, USA). 80 °C before use in the proteomic analysis. The follow- Each final fraction was concentrated by a vacuum ing iTRAQ-labeling proteomic experiment was conducted concentrator and reconstituted with 40 ll of 0.1% formic on six sample pools corresponding to the three groups acid for LC-MS/MS analysis. X. Han et al. / Neuroscience 298 (2015) 220–292 223

LC-MS/MS analysis determined by comparing the intensities of reporter ion signals also present in the MS/MS scan. The results SCX fractions were used for LC-MS/MS analysis and were then exported into Microsoft Excel for manual data loaded on a pre-column (20 mm 100 lm; 5 lm-C18). interpretation. To minimize false positive results, a strict Reversed phase chromatography was performed using cutoff for protein identification was applied with FDR the Thermo EASY-nLC 1000 (Thermo Fisher Scientific, <1% as listed in Appendix Table 2. The resulting data San Jose, CA, USA) with a binary buffer system set was autobias-corrected to eliminate any variations consisting of 0.1% formic acid (buffer A) and 84% ACN imparted due to unequal mixing of the different labeled in 0.1% formic acid (buffer B). An analytical column samples. This correction is based on the assumption (100 mm 75 lm; 3 lm-C18) was used. The online LC that the expression of most proteins did not change. This separation used a gradient from 0% to 35% buffer B for bias correction mitigates the systematic error arising 100 min, then 35–100% buffer B for 8 min, and then from samples from each experimental condition that 100% buffer B for 12 min. The flow rate was 250 nl/min. were not combined in exactly equal amounts. The The column was operated at a constant temperature of software identified the median average protein ratio and 35 °C regulated by an in-house designed oven with a corrected it to unity and then applied this factor to all Peltier element. Peptides eluted from LC were directly quantification results. Proteins were considered for injected into the coupled Q-Exactive mass spectrometer quantification if at least two unique peptides had a (Thermo Fisher Scientific) via the nanoelectrospray confidence interval of P95%. The proteins for further source (Thermo Fisher Scientific). A full MS scan was analysis were filtered with a p-value of less than 0.05 operated in the data-dependent mode and acquired over and 1.2-fold changes (>1.20 or <0.83) relative to the range m/z 300–1800 with a mass resolution of control as shown in Appendix Table 3 (Ren et al., 2013). 70,000 at m/z 200. Up to the top ten most abundant isotope patterns with a charge of P2 from the survey scan were selected with an isolation window of 1.6 Th Bioinformatics analysis and fragmented by higher energy collisional dissociation The theoretical molecular weight (MW) and isoelectric (HCD) with normalized collision energies of 25. The point (pI) of the identified proteins were retrieved from maximum ion injection times for the survey scan and Mascot output files. The mapping of putative the MS/MS scans were 20 and 60 ms, respectively, and transmembrane domains (TMDs) for identified proteins the ion target value for both scan modes was set to 106. was carried out using the TMHMM 2.0 program based In this mode of operation, MS/MS scans were acquired on the transmembrane hidden Markov model (http:// with a mass resolution of 17,500 at m/z 200 and an www.cbs.dtu.dk/services/TMHMM) by submitting the isolation window of 2 m/z. Furthermore, since virtually all FASTA files (Krogh et al., 2001). The grand average scans ‘‘time out’’ at 60 ms due to the high target value, hydropathicity (GRAVY) values for identified proteins the maximum ion signal in the fragmentation spectra is were analyzed using the ProtParam tool (available at obtained. http://web.expasy.org/protparam)(Zhou et al., 2008). The subcellular location (especially membrane associa- Data analysis tion) and function of the identified differential proteins were elucidated by the gene ontology (GO) component Mascot 2.2 (Matrix Science, Boston, MA, USA) and and functional terms, respectively. The GO annotation Proteome Discoverer 1.3 (Thermo Fisher Scientific) associated with a given gene list was obtained using the software were used to simultaneously identify and Universal Protein Resource (UniProt) (http://www.uni- quantify proteins based on the UniProt_Rat release prot.org) and the Database for Annotation, Visualization 2013_03 database of 41,766 protein sequences. To and Integrated Discovery (DAVID) 6.7 Bioinformatics tool calculate the false discovery rate (FDR) of peptide (http://david.abcc.ncifcrf.gov)(Huang da et al., 2009). identification, the search was performed using the Then, the more detailed description of these differential ‘‘decoy’’ option in Mascot. The user-defined search membrane proteins with regard to synaptic components parameters were as follows: sample type as iTRAQ was derived from SynaptomeDB (http://psychiatry.igm. 8-plex (peptide-labeled), enzyme as trypsin, selection jhmi.edu/SynaptomeDB/)(Pirooznia et al., 2012). only of tryptic peptides with two missed cleavages, variable modifications of methionine oxidation, fixed modification of carbamidomethyl cysteine, peptide mass RESULTS tolerance of ±20 ppm, and fragment mass tolerance of CMS model and sucrose preference and behavioral 0.1 Da. Proteome Discoverer 1.3 software was used to assessment extract the peak intensity of each expected iTRAQ reporter ion from each analyzed fragmentation spectrum. The CMS rat model employed here is one of the most The search parameters were as follows: peptide FDR widely-used animal models for inducing depression-like <1%, the use of only unique peptides, rejection of all behavior. In this study, sucrose preference was applied quantification values if not all quantification channels are to assess CMS-induced anhedonic-like (susceptible) present, normalization on protein median, normalization and CMS-resilient (unsusceptible) behavior of rats. After all peptide ratios by the median protein ratio, and median a four-week exposure to CMS, the stressed rats protein ratio = 1 after normalization. The relative showing a <10% decrease in sucrose preference were quantity of a peptide among the different samples was regarded as being unsusceptible. The stressed rats 224 X. Han et al. / Neuroscience 298 (2015) 220–292 were sorted into susceptible and unsusceptible groups based on a median split of their sucrose preference (median = 82.0%) with the susceptible group being defined as rats exhibiting a sucrose preference below the median. Subsequent ANOVA analysis showed that the sucrose preference of the susceptible group was significantly decreased when compared to the control and unsusceptible groups (F(2,18) = 56.423, p < 0.001, Fig. 1A). The sucrose measurement indicated that rats exposed to CMS could be segregated into susceptible and unsusceptible populations. This segregation was further confirmed by subsequent behavioral testing. As assessed by the FST, the susceptible rats spent more time immobile compared with the control and unsusceptible groups (F(2,18) = 19.692; p < 0.001), indicating that they developed a despair-like behavior by the end of the CMS exposure (Fig. 1B). There was no significant difference in either SPT (p = 0.895) or FST (p = 0.53) between the control and unsusceptible groups. Taken together, the anhedonia as SPT in susceptible rats was accompanied by increased immobility in the FST. The CMS paradigm described here offers a testable preclinical model that may be helpful in defining some stress-induced molecular aspects of MDD. iTRAQ-based quantitative proteomic analysis of Fig. 1. Sucrose preference and forced swim testing. Four-week hippocampal PSD exposure to CMS resulted in a significantly decreased sucrose preference and increased immobility time in susceptible rats when To study the effect of CMS on the expression of compared to control and unsusceptible rats (n =7,⁄p < 0.001). hippocampal PSD-associated proteins, a PSD-enriched subfraction was prepared by a combination of least one ratio with a p-value <0.05 (Ren et al., 2013) subcellular fractionation and Triton solubilization as (Appendix Table 3). described previously. Next, we used differential isotopic labeling with the iTRAQ reagent to quantitate differences in protein levels by tandem high-resolution Identity categorization of differential proteins mass spectrometry (Zhan et al., 2014). An overview of the iTRAQ experimental design and workflow conducted The accession numbers of the 113 differential proteins is shown in Fig. 2. PSD proteins from the control and identified from both the susceptible and unsusceptible stress animals were labeled using iTRAQ reagents, and groups were uploaded into the UniProt and DAVID then the labeled peptides were subjected to SCX fraction- databases for categorization of subcellular localization ation and quantitatively profiled by LC-MS/MS using based on their GO annotations. In terms of cellular Q-Exactive mass spectrometer. The expression level compartmentalization, 74 (65%) of the commonly changes of proteins were indicated by the ratios of label- differential proteins were initially defined as membrane- ing tags (control: 115/118; susceptible: 113/116; unsus- associated components (Fig. 3, left). Of these membrane ceptible: 114/117). The acquired MS/MS spectra were proteins, 24 contained one or more TMDs predicted by analyzed by database searching and stringent data filter- TMHMM, and 14 exhibited a positive GRAVY value that ing. In both the control and CMS conditions, a total of was recognized as a relatively hydrophobic marker. To 1531 proteins were identified and quantitated with at least further investigate their relationship to the PSD, the one unique peptide and 1% FDR (see Appendix Table 2). detailed subtype localization of 74 differential membrane Among them, 558 were identified by a single peptide and proteins were further investigated through an integrated not analyzed further. The remaining 973 (64%) proteins database called SynaptomeDB (Pirooznia et al., 2012). with two or more unique peptides (95% confidence) were SynaptomeDB compiled the synaptic protein list from a selected for further analysis. The change in relative con- review of all peer-reviewed proteomics studies, as well centration of any given protein for susceptible and unsus- from as publicly available databases that included proteins ceptible groups compared to the controls was obtained in the post-synapse, the pre-synapse, the presynaptic from iTRAQ 8-plex reporter ion ratios by a weighted aver- active zone, and the synaptic vesicle, and provided a age of all confidently identified peptides assigned to any detailed and experimentally verified annotation of all known given protein. iTRAQ reporter ratios of 1.2 and 0.83 were synaptic proteins. Of these membrane proteins, 52 (70%) set as the cut-off value for protein changes. A total of 113 were identified by the SynaptomeDB search as having a significantly altered proteins hits (either down- or up-regu- predicted synapse-specific localization (see Appendix lated) were found responsive to CMS, all of which had at Table 3). As shown in Fig. 3 (right), 12, 11, 5, and 51 X. Han et al. / Neuroscience 298 (2015) 220–292 225

simultaneously found in other regions, suggesting that they remain associated with these regions due to multiple localization.

Functional classification and disease relevance of differential PSD proteins We applied iTRAQ technology to profile the hippocampal PSD proteome of a rodent depressive model in order to identify postsynaptic proteins specific to depression as well as increase our understanding of the signaling events underlying the pathology of MDD. Of the 51 PSD-associated proteins found, 37 were up-regulated and 14 were down-regulated in both susceptible and unsusceptible groups as compared to controls (Table 1). The results, analyzed as Venn diagrams (Fig. 4A), revealed that the susceptible phenotype was far more closely associated with the distinct up-regulation of protein groups at the hippocampal PSD. Among the 37 PSD-associated proteins found in the susceptible group, nine had similar changes to the unsusceptible group, while the remaining 28 proteins defined a unique phenotypic response to stress. To gain initial insights into the potential functions of these differential PSD-associated proteins, we classified Fig. 2. Sample preparation and iTRAQ labeling for examining PSD each protein into both susceptible and unsusceptible proteomic changes. Hippocampal PSD fractions from the three groups into 10 different functional categories on the experimental groups (control, susceptible, and unsusceptible) were basis of their GO function annotations and literature prepared through a biochemical fractionation approach and subjected surveys (Ashburner et al., 2000), though this classification to 8-plex iTRAQ. Peptides from the control group were labeled with iTRAQ reagents having 115 and 118 reporters, peptides from the could not be strict due to the multiple functions of a protein susceptible group were labeled with the iTRAQ reagent having 113 (Zhou et al., 2010)(Fig. 4B). The proteins were involved and 116 reporters, and peptides from the unsusceptible group were in an extensive set of synaptic functions, including signal- labeled with the iTRAQ reagent having 114 and 117 reporters. After ing, regulatory, transporter, trafficking, etc. Notably, those labeling, peptides from all six samples were separately combined and proteins involved in trafficking were not found in the fractionated by strong cation exchange (SCX) chromatography. Each fraction was then analyzed by LC-MS/MS by a Q-exactive mass unsusceptible group. To further investigate the relation- spectrometer. ship between functional clusters and expressional alter- ations, the dysregulated phenotypes of these proteins in proteins were compartmentalized to the presynapse, each category were systematically analyzed in the form presynaptic active zone, synaptic vesicle, and PSD, of a heatmap. Fig. 4C displays a summary of altered pro- respectively. A four-way Venn diagram approach was used teins in each functional category, which emphasizes the to display the overlap between these categories, and mul- unique dysregulations of protein expressions in the hip- tiple overlapping sets were found. Not surprisingly, the vast pocampal PSD of susceptible or unsusceptible groups. majority of the 52 proteins were associated with PSD. It A larger group of proteins were significantly changed in should be noted that the subcellular localization of 36 pro- susceptible rats when compared to unsusceptible rats, teins was distinct from PSD. At the same time, we also indicating that the progression of an anhedonic-like observed that some postsynaptic proteins were response to stress is more complex than a resilient

Fig. 3. Ontology analysis of differentially expressed proteins. (A) Pie chart showing the distribution of differentially expressed proteins by cellular components, which summarizes the percentages of membrane, non-membrane, and unknown proteins. Cellular location was determined by GO annotations from UniProt/DAVID database. (B) Venn diagram showing the detailed synaptic localization of all differential membrane-associated proteins based upon the above prediction and their overlap in terms of synaptome categories including presynaptic proteins, presynaptic active zone, synaptic vesicles, and postsynaptic density by SynaptomeDB search. 226 X. Han et al. / Neuroscience 298 (2015) 220–292

Table 1. Hippocampal PSD-associated proteins perturbed by CMS. Summary table showing significantly upregulated (") or downregulated (;) proteins found in the susceptible and unsusceptible groups relative to the control

Accession Protein name Gene Unique % Susceptible Unsusceptible Function number name peptides Sequence coverage

Proteins differentially expressed only in the susceptible group G3V7Y3_RAT ATP synthase subunit delta, Atp5d 3 16.7 " M Transporter mitochondrial UN13A_RAT Isoform 3 of Protein unc-13 homolog A Unc13a 2 1.8 " M Trafficking CNKR2_RAT Connector enhancer of kinase Cnksr2 2 2.8 " M Signaling suppressor of ras 2 D3ZT16_RAT Protein Map6d1 Map6d1 2 15.7 " M Regulatory PACN1_RAT Protein kinase C and casein kinase Pacsin1 7 21.5 " M Regulatory substrate in neurons protein 1 Q99P36_RAT Protein Syt7 Syt7 2 6.9 " M Transporter LRRC7_RAT Isoform 5 of Leucine-rich repeat- Lrrc7 6 6.4 " M Regulatory containing protein 7 B5DEG8_RAT LOC685144 protein Sec24c 2 3.3 " M Transporter B0BNK1_RAT Protein Rab5c Rab5c 3 15.1 ; M Signaling Q7TP78_RAT Aa2-258 Ndufa8 4 20.1 ; M Metabolic CADH2_RAT Cadherin-2 Cdh2 3 5.6 " M Cell adhesion PP1A_RAT Serine/threonine-protein phosphatase Ppp1ca 4 13.3 ; M Signaling PP1-alpha catalytic subunit G3V8K2_RAT Guanine nucleotide-binding protein Gng3 2 3.2 " M Signaling subunit gamma D3ZMM4_RAT ERC protein 2 Erc2 4 6.5 " M Regulatory ANXA6_RAT Annexin A6 Anxa6 2 2.2 ; M Transporter Q76LU9_RAT Glutathione peroxidase Gpx4 2 13.0 " M Metabolic VAMP2_RAT Vesicle-associated membrane protein 2 Vamp2 3 35.3 " M Trafficking DLGP2_RAT Disks large-associated protein 2 Dlgap2 2 2.8 " M Signaling M2OM_RAT Mitochondrial 2-oxoglutarate/malate Slc25a11 2 8.0 " M Receptor/ carrier protein Carrier NEUG_RAT Neurogranin Nrgn 3 26.9 " M Signaling D4A5X7_RAT Ganglioside-induced differentiation- Gdap1 5 14.0 " M Other associated-protein 1 (Predicted) PPIB_RAT Peptidyl-prolyl cis–trans isomerase B Ppib 4 18.98 ; M Other DNM1L_RAT Isoform 5 of Dynamin-1-like protein Dnm1 l 4 7.1 " M Regulatory D3ZQL7_RAT Protein Tppp Tppp 3 15.6 " M Regulatory A9UMV9_RAT Ndufa7 protein Ndufa7 8 52.7 " M Metabolic RTN3_RAT Reticulon-3 Rtn3 6 10.6 " M Trafficking G3V6T1_RAT Protein Copa Copa 2 2.4 " M Transporter G3V728_RAT 4-nitrophenylphosphatase domain and Nipsnap1 5 17.6 " M Trafficking non-neuronal SNAP25-like protein homolog 1 (C. elegans), isoform CRA_b

Proteins differentially expressed only in the unsusceptible group ODP2_RAT Dihydrolipoyllysine-residue Dlat 12 18.8 M " Metabolic acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial CD9_RAT CD9 antigen Cd9 2 10.2 M ; Cell adhesion F1LUE2_RAT Calcium/calmodulin-dependent protein Camk2 g 8 16.7 M " Signaling kinase type II subunit gamma (Fragment) KAD1_RAT Adenylate kinase isoenzyme 1 Ak1 5 32.0 M " Metabolic PRDX1_RAT Peroxiredoxin-1 Prdx1 8 34.7 M " Regulatory D4A376_RAT Ras-related protein Rab-12 Rab12 2 21.4 M ; Signaling B2CZC8_RAT Glutamate receptor, metabotropic 5, Grm5 2 1.6 M " Receptor/ isoform CRA_a Carrier ATP5H_RAT ATP synthase subunit d, mitochondrial Atp5 h 8 44.7 M " Transporter VATB2_RAT V-type proton ATPase subunit B, brain Atp6v1b2 13 29.9 M " Transporter isoform CNTP1_RAT Contactin-associated protein 1 Cntnap1 2 3.1 M ; Cell (Fragment) adhesion ADDG_RAT Isoform 1 of Gamma-adducin Add3 2 4.8 M ; Cytoskeletal X. Han et al. / Neuroscience 298 (2015) 220–292 227

Table 1 (continued)

Accession Protein name Gene Unique % Susceptible Unsusceptible Function number name peptides Sequence coverage

D3ZRF5_RAT Protein Slc25a22 Slc25a22 10 34.1 M " Receptor/ Carrier AATM_RAT Aspartate aminotransferase, Got2 17 38.8 M " Metabolic mitochondrial D3ZD09_RAT Cytochrome c oxidase subunit 6B1 Cox6b1 3 37.2 M " Metabolic Proteins differentially expressed in both susceptible and unsusceptible groups DNJA2_RAT DnaJ homolog subfamily A member 2 Dnaja2 2 5.6 ;; Chaperone F1LSL8_RAT Protein Sptbn4 Sptbn4 3 1.4 ;; Cytoskeletal NMDE1_RAT Glutamate receptor ionotropic, NMDA 2A Grin2a 2 2.0 ;; Receptor/ Carrier G3V8C3_RAT Vimentin Vim 2 3.4 ;; Cytoskeletal CX7A2_RAT Cytochrome c oxidase subunit 7A2, Cox7a2 2 18.1 ;; Metabolic mitochondrial B1VKB4_RAT Synaptopodin Synpo 3 7.6 "" Regulatory KCC2B_RAT Calcium/calmodulin-dependent protein Camk2b 15 31.9 "" Signaling kinase type II subunit beta VATE1_RAT V-type proton ATPase subunit E 1 Atp6v1e1 7 22.6 "" Transporter Q91ZE7_RAT Band 3 anion exchange protein Slc4a1 3 4.8 "" Transporter response, and that the two stress phenotypes show differ- on specific proteins and pathways associated with ences in the abundance of several different types of pro- depression, novel molecular targets that may be involved teins. Some protein systems, such as signaling and in the pathogenesis of MDD are still being investigated. regulation, were markedly dysregulated in the susceptible Our previous study carried out a two-dimensional gel- group, implicating the association with significant depres- electrophoresis (2DE) proteomic analysis of hippocampal sion-like behaviors. synaptosomal fractions and found 19 differential proteins We also carried out a literature search to explore the in a CMS rodent model of depression (Hu et al., 2013). relevance of the 51 differential PSD-associated proteins Generally, it is difficult to quantify global protein expres- to mental illnesses. As shown in Fig. 5 and Appendix sion using the conventional 2DE technique because sev- Table 4, many of these proteins have been reported in eral proteins can migrate together and isoforms of the different disease states that can affect mood states such same protein can migrate to different places. Moreover, as depression, anxiety, schizophrenia, Alzheimer’s our previous results are somewhat biased toward abun- disease, and Huntington’s disease. Thirteen proteins dant, soluble proteins, and only a small number of differ- have been found to be associated with depression, ten ential membrane proteins (particularly those with TMDs of which were altered in depressed human patients and and high hydrophobicity) were detected. This type of pro- eight of which were altered in animal models of tein is generally underrepresented in the 2DE, mainly due depression. The dysregulation of these proteins was to their poor solubility in the starting buffer and protein primarily in the hippocampus and prefrontal/frontal aggregation during the isoelectric focusing step (Santoni cortex. Furthermore, twenty-nine proteins have been et al., 2000a,b; Rabilloud, 2009; Zhou et al., 2010). implicated in four major mental illnesses (i.e., nine in Therefore, in order to discover lower abundance and anxiety, 15 in schizophrenia, 17 in Alzheimer’s disease, more hydrophobic membrane proteins, herein we and eight in Huntington’s disease) with some proteins, utilized a gel-free shotgun proteomic approach through such as Grin2a and Grm5, being related to multiple combining PSD enrichment and FASP-based peptide mood disorders (probably due to the diversity of their preparation. In this approach, the PSD was enriched by synaptic function). common isolation methods (Phillips et al., 2001; Abul- Husn et al., 2009; Focking et al., 2014), then a strong DISCUSSION SDS extraction was used to maximize the solubility of the hydrophobic proteins (Wisniewski et al., 2009b; A series of both preclinical and clinical studies has shown Zhou et al., 2010). Meanwhile, we took advantage of the hippocampal synapse to be affected in depressed FASP-based direct digestion to efficiently remove the subjects (Henningsen et al., 2012; Martins-de-Souza SDS (Wisniewski et al., 2009b), thereby improving the et al., 2012a,b; Duric et al., 2013; Martins-de-Souza, identification of highly hydrophobic membrane proteins 2014). Although some nascent efforts have been made as well as minimizing the experimental variance to investigate any potential molecular dysregulations to (Wisniewski et al., 2009a). The resulting tryptic peptides explain these effects (Duman, 2002, 2009), no direct cau- were labeled using iTRAQ reagents for MS-based quanti- sal relation has been established between these changes tative analysis. and depressed behavior (Martins-de-Souza et al., 2010; CMS is considered one of the more valid rodent Martins-de-Souza, 2014). Given this lack of knowledge models of depression. By exposing rats to the CMS 228 X. Han et al. / Neuroscience 298 (2015) 220–292

Fig. 4. Differential expression analysis of hippocampal PSD-associated proteins. (A) Venn diagrams showing the number of uniquely-regulated proteins in susceptible and unsusceptible groups as compared to controls with the overlap depicting proteins that were identically regulated by both conditions. Upregulated (red) and downregulated (green) proteins are shown separately. (B) Pie chart showing the classification of these differential PSD-associated proteins identified from susceptible and unsusceptible groups. The number of proteins in each category is indicated. (C) Up- or down-regulated proteins are indicated by red and green hues, respectively. The color intensity indicates the protein expressional level as displayed (top right). Histograms denote the expression trend of representative proteins. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.) regime, we selected rat groups with different stress rodent depression model. Initial differential data were response phenotypes through decreased sucrose screened out by a SynaptomeDB search. A total of 52 preference and increased immobility, which provides proteins were found to be relevant to synapses, of which evidence of depression-like status. A graded effect of 51 were defined as PSD-associated proteins. Our stress exposure is expected, and a distinction into purification method is enriched with respect to susceptible and unsusceptible rats provides a useful histologically-confirmed PSD proteins and has been approach for identifying potential biomarkers specific for shown to be valid for the PSD in rodents and post- anhedonia as opposed to general stress-related effects. mortem human brain tissue (Phillips et al., 2001; Abul- The resulting hippocampal PSD proteome was analyzed Husn et al., 2009; Focking et al., 2014). However, there by quantitative proteomics, and numerous differential are some proteins co-isolated that are known to be presy- proteins from the two different CMS-response naptic or mitochondrial in origin. These proteins might be phenotypes were identified. tightly bound to the PSD component and were therefore Our investigation’s purpose was to focus on the co-purified with the PSD (Peng et al., 2004; Yoshimura analysis of hippocampal PSD protein changes in the et al., 2004). But, this does not indicate that these proteins X. Han et al. / Neuroscience 298 (2015) 220–292 229

cytoskeletal proteins. To some extent, excessive levels of excitatory amino acids – such as glutamate – could lead to the down-regulation of N-methyl-D-aspartate (NMDA) receptor subunits. In the present study, levels of the NMDA receptor subunit NR2A (Grin2a) and CamKIIbeta (Camk2b, as a potential calcium signal) were similarly changed in the two groups compared to the con- trol group, suggesting CMS-induced dysfunction of the glutaminergic system in the hippocampus. However, the differential expression of many NMDA receptor downstream targets involved in glutamate signaling (Sanhueza and Lisman, 2013) were distinctly affected in susceptible rats, such as densin-180 (Lrrc7), protein kinases (Pacsin1, Nrgn), a small GTPase (Rab5c), and a G-protein (Gng3). Densin-180 is suffi- ciently abundant in the PSD (Apperson et al., 1996) and has been reported to bind directly to CaMKII and regulate Fig. 5. Differentially expressed PSD-associated proteins related to mental disorders. The associations between the differentially both NMDA receptor-dependent and metabotropic gluta- expressed proteins and mental disorders, such as depression, mate receptor-dependent long-term depression (Quitsch anxiety, Alzheimer’s disease, schizophrenia, and Huntington’s et al., 2005). In susceptible rats, the up-regulation of den- disease were analyzed. Detailed protein descriptions and related sin-180 suggests that the alteration of long-term potentia- literature have been summarized in Appendix Table 4. tion (which is generally dependent on NMDA receptor function) is critical to synaptic plasticity. Notably, densin- are unimportant or non-functional in synapses or in MDD 180 was also found to be associated with other mental ill- development. Indeed, dendritic mitochondria have been nesses including schizophrenia and autism (Carlisle et al., reported to contribute to neuron morphogenesis and 2011). Nrgn (neurogranin) is a neuron-specific postsynap- synaptic plasticity (Li et al., 2004), and mitochondrial dys- tic protein. As a Ca2+-sensitive calmodulin (CaM) reser- function may play an important role in MDD and other psy- voir and a protein kinase C (PKC) substrate, Nrgn chiatric disorders (Lin and Beal, 2006; Rezin et al., 2009). regulates the availability of calmodulin in axons and den- Here, both susceptible and unsusceptible rats were dritic spines (Kubota et al., 2007; Zhong et al., 2009; Diez- analyzed in order to discover several PSD-associated Guerra, 2010). Nrgn plays an important role in synaptic protein groups specifically related to CMS susceptibility. plasticity, learning, and memory and has been found to There were similar abundance changes between these be related to spatial learning tasks with anxiety-related two subgroups, and there was not a single protein components (Miyakawa et al., 2001; Wilcoxon et al., whose abundance was changed in opposite directions in 2007). Taken together, alterations of these key proteins these two subgroups. These overlapping proteins in the involved in signal transduction and regulation appear to two groups may only be as a result of exposure to result in specific dysregulation in processes underlying stress, and while those altered differentially may synaptic plasticity (i.e., endocytosis, long-term potentia- mediate differences in behavior. More importantly, our tion, and calcium signaling) in susceptible rats. As the pre- proteomic data revealed a significant number of proteins sent analysis was restricted to the hippocampus, that show changes in levels that are only specific to depression-specific alterations of PSD-associated pro- either susceptible or unsusceptible groups, suggesting teins occurring in other brain regions (such as the pre- differences in the stress response mechanism in these frontal cortex and amygdala) require further two phenotypes. Further functional analysis of PSD- investigation in future studies. associated proteins indicated that, in terms of protein expression levels in the hippocampal PSD micro- domain, the susceptible group had a distinct proteome CONCLUSION profile. In susceptible rats, some biological processes were heavily affected by CMS, such as signaling and In conclusion, we used a broad discovery approach to regulation. Notably, these processes have been profile the effects of CMS on the PSD-enriched previously implicated in both stress responses and in proteome isolated from the rat hippocampus. The MDD (Kinnunen et al., 2003; Carboni et al., 2006; Mu unbiased profiles identified several protein changes et al., 2007; Kang et al., 2012). within the PSD that may be related to stress Recent studies have found that CMS can induce vulnerability or insusceptibility. Proteomic analysis depression-like behaviors in rats and increase glutamate supports the importance of the PSD in the pathogenesis concentration in the hippocampus (Lou et al., 2010). In of stress-related disorders and, in particular, points to a general, the postsynaptic membrane in the brain’s excita- role for PSD-associated proteins involved in signaling tory synapses is specialized for responding rapidly to glu- and regulation. Taken together, these findings provide tamate released from the presynaptic terminal. The novel insights into the PSD’s contribution to stress postsynaptic membrane is associated with the PSD, susceptibility and mechanisms underlying NMDA which contains a high concentration of glutamate recep- receptor function and long-term potentiation that are tors and an ordered array of signaling, regulatory, and responsible for this contribution. 230 X. Han et al. / Neuroscience 298 (2015) 220–292

Acknowledgments—We thank Dr. Chenrui Hou (Shanghai Focking M, Lopez LM, English JA, Dicker P, Wolff A, Brindley E, Institute for Biological Sciences, Chinese Academy of Wynne K, Cagney G, Cotter DR (2014) Proteomic and genomic Sciences) for his assistance with the mass spectrometric analy- evidence implicates the postsynaptic density in schizophrenia. sis. We thank the scientific editors at Impactys (www.im- Mol Psychiatry 20:424–432. pactys.com) for editing and proofreading this manuscript. This Henningsen K, Palmfeldt J, Christiansen S, Baiges I, Bak S, Jensen work was supported by grants from the National Basic ON, Gregersen N, Wiborg O (2012) Candidate hippocampal biomarkers of susceptibility and resilience to stress in a rat model Research Program of China (‘‘973 program’’, Grant No. of depression. Mol Cell Proteomics 11. 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Appendix Table 1. Time and length of stressors used in the CMS procedure

Sunday Monday Tuesday Wednesday Thursday Friday Saturday

Paired housing ? 10:00 21:00 17:00 12:00 ? Cage tilt 45° 13:00–19:00 Soiled cage 19:00 ? 12:00 Water deprivation 18:00 ? 10:00 Empty water bottle 10:00–11:00 Strobe light 13:00–18:00 18:00-20:00 Continuous lighting 18:00 ? 10:00 19:00 ? 12:00 White noise 12:00–15:00 3 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 232

Appendix Table 2. A list of all identified and quantified proteins (1531 proteins) with at least one unique peptide (95% confidence) determined from the susceptible and unsusceptible groups. MW, molecular weight; pI, isoelectric point; TMDs, transmembrane domains; GRAVY, grand average hydropathicity

Accession Protein description Peptides Unique % MW (Da) pI TMDs GRAVY Susceptible 113/115 Unsusceptible 114/ Susceptible 116/118 Unsusceptible 117/ number peptides Sequence 115 118 coverage Ratio p-Value Ratio p-Value Ratio p-Value Ratio p-Value

Q2TVU3_RAT TID1 OS = Rattus norvegicus 1 1 3.5 49411.56 9.41 0 0.435 8.85655 4.71E89 2.73994 2.35E15 5.94148 8.76E42 1.44815 0.107306 GN = Dnaja3 PE = 2 SV = 1 D3ZPU2_RAT Protein Dnajb14 OS = Rattus 1 1 4.2 42346.12 8.83 0 0.762 7.17252 1.34E55 0.83651 0.384806 5.32796 2.19E32 1.60146 0.030475 norvegicus GN = Dnajb14 PE = 4 SV = 1 DGLA_RAT Sn1-specific diacylglycerol lipase alpha 2 2 3.5 115300.1 6 5 0.077 3.60509 4.14E11 3.86442 6.96E39 1.26976 0.521404 0.666667 0.132887 OS = Rattus norvegicus GN = Dagla PE = 2 SV = 1 Q7M079_RAT Calcium-binding protein 4 (Fragment) 1 1 100.0 1977.99 3.8 0 1.239 4.93312 1.69E23 0.71722 0.133523 4.70244 4.46E24 0.630599 0.096027 OS = Rattus norvegicus GN = Hsp90b1 PE = 1 SV = 1 SYN3_RAT Synapsin-3 OS = Rattus norvegicus 1 1 4.2 63347.91 9.47 0 0.531 2.45201 0.000257 3.42466 2.45E28 5.9807 1.99E42 3.10362 3.28E14 GN = Syn3 PE = 1 SV = 1 G3V8E2_RAT Protein Fam40a OS = Rattus 1 1 2.5 95608.78 5.83 0 0.395 2.80513 5.20E06 2.36942 4.55E10 1.86153 0.022881 0.985606 0.941235 norvegicus GN = Fam40a PE = 4 SV = 1 06 3.96524 6.21E16 1.49719 0.073864 B1VKB4_RAT Synaptopodin OS = Rattus norvegicus 4 3 7.6 96717.32 9.69 0 0.711 3.47943 3.43E10 2.04391 2.02E GN = Synpo PE = 2 SV = 1 F1LVC3_RAT Protein Rab6b (Fragment) OS = Rattus 1 1 7.5 21067.66 5.18 0 0.462 3.72706 4.83E12 1.73373 0.000842 2.0798 0.003999 1.12458 0.658271 norvegicus GN = Rab6b PE = 3 SV = 1 F1M471_RAT Protein Epm2aip1 (Fragment) 1 1 3.7 52757.04 5.51 0 0.151 1.93157 0.020023 1.96824 1.05E05 2.09538 0.003487 1.08546 0.763344 OS = Rattus norvegicus GN = Epm2aip1 PE = 4 SV = 1 DCMC_RAT Malonyl-CoA decarboxylase, 1 1 2.6 54761.41 8.96 0 0.225 3.51253 1.98E10 1.14455 0.512449 2.90003 2.70E07 1.07967 0.779328 mitochondrial OS = Rattus norvegicus GN = Mlycd PE = 2 SV = 1 Q4KM71_RAT Splicing factor proline/glutamine rich 1 1 1.4 75485.88 9.45 0 1.13 3.34636 2.88E09 1.12399 0.574536 3.97971 4.47E16 1.27139 0.330903 (Polypyrimidine tract binding protein associated) OS = Rattus norvegicus GN = Sfpq PE = 2 SV = 1 FAF2_RAT FAS-associated factor 2 OS = Rattus 1 1 5.5 41079.08 5.71 0 0.739 3.04 2.52E07 1.20504 0.352086 3.14699 5.70E09 1.19112 0.494914 norvegicus GN = Faf2 PE = 2 SV = 1 D3ZKT0_RAT Protein LOC362419 OS = Rattus 1 1 6.5 37785.35 9.06 0 0.14 1.33426 0.423253 2.77315 6.87E16 0.876574 0.616899 0.571385 0.053638 norvegicus GN = Tamm41 PE = 4 SV = 1 D3ZF07_RAT Protein RGD1562402 OS = Rattus 1 1 8.1 16587.22 10.99 0 0.599 2.80205 5.40E06 1.30913 0.16013 3.43551 3.54E11 1.3329 0.232333 norvegicus GN = RGD1562402 PE = 3 SV = 1 LMBD1_RAT Probable lysosomal cobalamin 1 1 3.4 61017.62 7.87 9 0.374 2.09364 0.006149 1.83561 0.000143 4.39788 1.70E20 2.13751 4.15E05 transporter OS = Rattus norvegicus GN = Lmbrd1 PE = 2 SV = 1 Q5XFV9_RAT Rps16 protein (Fragment) OS = Rattus 2 2 13.2 17899.83 10.21 0 0.342 3.11855 8.48E08 1.22029 0.317311 2.41858 0.000137 1.14013 0.618171 norvegicus GN = Rps16 PE = 2 SV = 1 3 2 7.6 35994.52 5.07 0 0.593 2.35611 0.00065 1.5469 0.012861 1.82125 0.03045 0.924053 0.726697 IMPCT_RAT ProteinGN IMPACT = Impact OS = PERattus = 2 SV =norvegicus 1 D4AE42_RAT Uncharacterized protein OS = Rattus 1 1 4.8 17165 10.37 0 1.011 0.975207 0.880645 2.48618 1.33E11 1.33235 0.415614 1.02699 0.928285 norvegicus GN = Rpl26-ps1 PE = 3 SV = 1 CP4F4_RAT Cytochrome P450 4F4 OS = Rattus 2 2 4.0 60822.84 7.24 2 0.142 1.30014 0.475429 1.88387 5.76E 05 4.32687 1.05E 19 1.47305 0.089076 norvegicusGN = Cyp4f4 PE = 3 SV = 1 D3ZGZ1_RAT SH3-containing GRB2-like protein 3- 1 1 1.6 85964.97 8.5 0 0.572 2.84222 3.30E 06 1.15806 0.473653 2.14129 0.002304 0.821632 0.418834 interacting protein 1 OSRattus = norvegicus GN = Sgip1 PE = 2 SV = 1 ABCB6_RAT ATP-binding cassette sub-family B 1 1 2.6 93303.75 8.54 8 0.144 1.29891 0.477372 1.14792 0.502613 1.9267 0.014072 0.956039 0.836636 member 6, mitochondrial OSRattus = norvegicusGN = Abcb6 PE = 2 SV = 1 Q6RKB3_RAT Fasciclin II transmembrane protein 1 1 2.0 93180.5 5.64 1 0.426 2.67256 2.47E 05 0.641767 0.05748 1.45143 0.253083 0.396004 0.006616 isoform OS = Rattus norvegicus GN = Ncam2 PE = 2 SV = 1 THOC1_RAT THO complex subunit 1 OSRattus = 1 1 2.0 75419.11 4.89 0 0.608 2.98959 4.97E 07 0.860993 0.459597 2.78511 1.39E 06 1.15112 0.590505 norvegicusGN = Thoc1 PE = 2 SV = 1 B1H271_RAT Mitochondrial coenzyme A transporter2 1 5.4 35185.3 9.86 1 0.054 2.57105 7.53E 05 1.67045 0.002286 1.81188 0.032491 1.04947 0.864103 SLC25A42 OSRattus = norvegicus

GN = Slc25a42 PE = 2 SV = 1 220–292 (2015) 298 Neuroscience / al. et Han X. D3ZJL5_RAT Uncharacterized protein OSRattus = 1 1 4.9 44851.74 5.65 0 0.746 2.11849 0.00506 0.847917 0.418683 1.38028 0.343934 0.620959 0.087707 norvegicusPE = 4 SV = 1 D3ZII1_RAT Protein Rftn2 OS =Rattus norvegicus 2 2 8.5 54746.58 5.25 0 0.552 2.32033 0.000905 1.05318 0.811212 1.59251 0.125398 0.745962 0.251171 GN = Rftn2 PE = 4 SV = 1 Q4V7D4_RAT Family with sequence similarity 126, 1 1 2.6 50824.28 7.63 0 0.292 2.23092 0.002 1.23344 0.289188 1.62719 0.103464 0.780583 0.321014 member B OS =Rattus norvegicus GN = Fam126b PE = 2 SV = 1 SKP1_RAT S-phase kinase-associated protein 1 2 2 11.0 18671.82 4.4 0 0.716 2.32185 0.000892 1.36503 0.097071 1.99347 0.008296 1.19424 0.487824 OSRattus = norvegicus GN = Skp1 PE = 2 SV = 3 DJB11_RAT DnaJ homolog subfamily B member 11 1 1 4.8 40494.5 5.92 1 0.556 1.80835 0.044292 2.05251 1.66E 06 1.26401 0.531773 1.32224 0.247726 OSRattus = norvegicus GN = Dnajb11 PE = 2 SV = 1 ERMIN_RAT Ermin OSRattus = norvegicus 1 1 6.7 32227.57 4.64 0 1.199 1.48112 0.239688 1.47877 0.029459 1.36696 0.363019 1.06691 0.814891 GN = Ermn PE = 1 SV = 1 VAMP2_RAT Vesicle-associated membrane protein 2 13 3 35.3 12690.64 7.84 1 0.004 2.18637 0.002916 1.26408 0.23036 1.47564 0.226375 0.900461 0.648942 OSRattus = norvegicus GN = Vamp2 PE = 1 SV = 2 PHYD1_RAT Phytanoyl-CoA dioxygenase domain- 1 1 4.8 34567.93 5.62 0 0.192 3.0144 3.57E 07 1.35865 0.10306 1.10767 0.846517 0.665702 0.131776 containing protein 1 (Fragment) OS =Rattus norvegicus GN = Phyhd1 PE = 2 SV = 1 Q6IMZ5_RAT Tropomodulin 1 OSRattus = 1 1 4.7 40453.56 4.97 0 0.562 1.87652 0.028863 1.06334 0.77552 2.10193 0.003289 0.994964 0.974646 norvegicus GN = Tmod1 PE = 2 SV = 1 TSSC1_RAT Protein TSSC1 OS =Rattus 1 1 4.4 43156.4 4.9 0 0.425 1.83591 0.037372 1.04295 0.847509 1.98387 0.008968 0.992256 0.964968 norvegicus GN = Tssc1 PE = 2 SV = 1 D3ZWL6_RAT Adenosylhomocysteinase OS =Rattus 1 1 4.1 56395.14 8.49 0 0.261 2.16324 0.003529 1.29745 0.176549 1.28191 0.499836 0.700463 0.176573 norvegicusGN = Ahcyl2 PE = 2 SV = 1 B2RZ27_RAT Protein Sh3bgrl3 OS =Rattus 2 2 29.0 10476.63 5.02 0 0.522 2.12015 0.004994 0.879848 0.522351 2.37561 0.00022 0.861222 0.528005 norvegicus GN = Sh3bgrl3 PE = 4 SV = 1 G3V8K2_RAT Guanine nucleotide-binding protein 3 2 32.0 8304.69 7.65 0 0.121 1.96822 0.015541 0.715778 0.131559 1.50322 0.198474 0.650938 0.115652 subunit gamma OS =Rattus norvegicus GN = Gng3 PE = 3 SV = 1

(continued on next page) 233 3 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 234

F1LSR8_RAT Voltage-dependent calcium channel 2 1 1.8 122164.9 5.55 0 0.227 1.97583 0.01473 1.22106 0.315606 1.47817 0.223703 0.872279 0.560899 subunit alpha-2/delta-3 OS = Rattus norvegicusGN = Cacna2d3 PE = 2 SV = 1 Q76LU9_RAT Glutathione peroxidase OS =Rattus 3 2 13.0 29111.31 10.31 0 0.875 2.07201 0.007263 1.22491 0.307243 1.97087 0.009955 0.930798 0.7495 norvegicusGN = Gpx4 PE = 2 SV = 2 TM40L_RAT Mitochondrial import receptor subunit 1 1 4.9 34048.49 6.59 0 0.056 2.29508 0.001138 1.60191 0.006179 1.11139 0.838471 0.860438 0.525712 TOM40B OS =Rattus norvegicus GN = Tomm40l PE = 1 SV = 1 PRS8_RAT 26S protease regulatory subunit 8 1 1 4.7 45625.51 7.11 0 0.322 1.7687 0.056126 2.55022 1.70E 12 1.95547 0.011249 2.73394 4.05E 10 OSRattus = norvegicus GN = Psmc5 PE = 1 SV = 1 TRXR2_RAT Thioredoxin reductase 2, mitochondrial1 1 2.5 56424.14 8.82 0 0.112 2.40491 0.000408 1.3145 0.152981 1.44394 0.261768 1.00692 0.986005 OSRattus = norvegicus GN = Txnrd2 PE = 1 SV = 3 PSA1_RAT Proteasome subunit alpha type-1 1 1 7.6 29517.18 6.14 0 0.431 2.43401 0.000308 1.06923 0.755046 1.23881 0.578401 0.622141 0.088695 OSRattus = norvegicus GN = Psma1 PE = 1 SV = 2 INP4B_RAT Isoform 2 of Type II inositol 3,4- 1 1 1.4 106484.1 5.69 0 0.349 2.39871 0.000434 1.51367 0.019478 1.57203 0.139956 0.992241 0.964917 bisphosphate 4-phosphatase OSRattus = norvegicus GN = Inpp4b D3ZT16_RAT Protein Map6d1 OS =Rattus 3 2 15.7 20412.55 9.94 0 0.516 1.84475 0.035356 1.27709 0.20814 1.67856 0.076706 1.0115 0.972804 norvegicus GN = Map6d1 PE = 4 SV = 1 RASA3_RAT Ras GTPase-activating protein 3 2 2 4.4 96016.32 7.25 0 0.448 1.76814 0.056309 1.18363 0.40484 1.11332 0.834317 0.655559 0.120522 OSRattus = norvegicus GN = Rasa3 PE = 2 SV = 1 F1MAH8_RAT Protein Clip1 OS =Rattus norvegicus 1 1 1.2 148277 5.24 0 0.824 1.80089 0.046344 1.4772 0.029998 1.08215 0.902041 0.730694 0.224015 GN = Clip1 PE = 2 SV = 1 D4A4F9_RAT Protein LOC682489 OS =Rattus 1 1 9.2 15018.64 6.7 1 0.916 1.50073 0.220252 0.873242 0.499876 2.19778 0.001355 0.8625 0.531757 norvegicus GN = LOC682489 PE = 4 SV = 1 Q498C9_RAT Protein Zfp207 OS = Rattus norvegicus 1 1 2.6 52778.28 9.2 0 0.649 1.57734 0.155183 1.08967 0.685412 1.49444 0.20707 0.727066 0.217883 GN = Zfp207 PE = 4 SV = 1 NSF1C_RAT NSFL1 cofactor p47 OS =Rattus 2 2 9.2 40679.45 5.04 0 0.638 1.77483 0.054139 1.07763 0.726166 1.621 0.107141 0.724476 0.213579 norvegicus GN = Nsfl1c PE = 1 SV = 1 F1LRA1_RAT Protein ERGIC-53 OS =Rattus 1 1 3.9 57819.18 5.68 1 0.544 1.68408 0.090265 1.12778 0.562815 1.23221 0.590934 0.691296 0.163785 norvegicus GN = Lman1 PE = 2 SV = 1 ARP2_RAT Actin-related protein 2 OS =Rattus 6 3 15.7 32490.99 6.15 0 0.123 2.04618 0.00883 1.13564 0.538932 1.79542 0.036362 0.945658 0.800489 norvegicusGN = Actr2 PE = 2 SV = 1 RL3_RAT 60S ribosomal protein L3 OS =Rattus 1 1 2.7 46135.41 10.22 0 0.645 1.74559 0.064161 1.09027 0.683425 1.91923 0.014901 0.824801 0.427051 norvegicusGN = Rpl3 PE = 1 SV = 3 G3V7H5_RAT E74-like factor 2, isoform CRA_b 1 1 1.7 56937.79 9.08 0 0.312 2.03132 0.009862 1.06264 0.777972 1.85439 0.024089 0.833457 0.449971 OSRattus = norvegicus GN = Elf2 PE = 3 SV = 1 F1M084_RAT 1-phosphatidylinositol 4,5-bisphosphate 1 1 1.3 124392.1 5.88 0 0.59 1.16813 0.706462 1.14931 0.498576 1.57908 0.134806 0.925822 0.732655 phosphodiesterase beta-1 (Fragment) OSRattus = norvegicus GN = Plcb1 PE = 2 SV = 1 CADM2_RAT Cell adhesion molecule 2 (Fragment) 4 3 15.1 39608.36 5.13 0 0.216 1.79388 0.04834 1.08379 0.705208 1.19242 0.66894 0.601753 0.072865 OSRattus = norvegicus GN = Cadm2 PE = 2 SV = 1 G3V7I3_RAT ATPase type 13A1 (Predicted), isoform 1 1 1.4 131914 8.37 0 0.11 1.48434 0.236417 0.925753 0.691514 1.72741 0.056774 0.977157 0.911163 CRA_a OS =Rattus norvegicus GN = Atp13a1 PE = 3 SV = 1 PAGR1_RAT PAXIP1-associated glutamate-rich 1 1 3.2 27682.86 4.52 0 0.985 2.01362 0.011231 1.52063 0.017888 1.95133 0.011622 1.31478 0.25893 protein 1 OS = Rattus norvegicus GN = PAGR1 PE = 2 SV = 2 HD_RAT Huntingtin OS = Rattus norvegicus 1 1 0.5 343758 5.91 0 0.065 1.3652 0.378974 1.65521 0.002874 1.67731 0.077279 1.23543 0.39952 GN = Htt PE = 1 SV = 1 MT3_RAT Metallothionein-3 OS = Rattus 1 1 19.7 6809.04 8.04 0 0.458 1.78583 0.050725 0.843035 0.403976 2.07143 0.004302 0.866048 0.542241 norvegicus GN = Mt3 PE = 2 SV = 1 GP158_RAT Probable G-protein coupled receptor 1 1 1.1 134457.2 8.3 0 0.461 1.86981 0.030141 0.97524 0.892677 1.40174 0.314568 0.820801 0.416693 158 OS = Rattus norvegicus GN = Gpr158 PE = 3 SV = 1 D3ZMM4_RAT ERC protein 2 OS = Rattus norvegicus 5 4 6.5 98023.61 6.41 0 0.949 1.97706 0.014603 1.26546 0.227926 1.26531 0.52941 0.855664 0.511851 GN = Erc2 PE = 4 SV = 1 LRRC7_RAT Isoform 5 of Leucine-rich repeat- 6 6 6.4 158648.5 6.01 0 0.647 1.8738 0.029374 0.756778 0.1967 1.37116 0.356938 0.659188 0.124459 containing protein 7 OS = Rattus norvegicus GN = Lrrc7 G3V7Y3_RAT ATP synthase subunit delta, 10 3 16.7 17562.79 5.16 0 0.211 1.81525 0.042467 1.18238 0.408058 2.16807 0.001796 1.18527 0.508343 mitochondrial OS = Rattus norvegicus GN = Atp5d PE = 3 SV = 1 GATA_RAT Glutamyl-tRNA(Gln) amidotransferase 1 1 3.4 56837.03 5.61 0 0.086 2.06135 0.007877 2.22253 2.62E08 0.693767 0.285413 0.700628 0.17681 subunit A, mitochondrial OS = Rattus norvegicus GN = Qrsl1 PE = 2 SV = 1 G3V8U9_RAT Proteasome subunit beta type 1 1 5.7 29228.03 5.65 0 0.161 2.15818 0.003678 1.5844 0.007852 1.59085 0.126531 1.29446 0.291159 OS = Rattus norvegicus GN = Psmb4 220–292 (2015) 298 Neuroscience / al. et Han X. PE = 3 SV = 1 D3ZHL1_RAT Protein Ksr1 OS = Rattus norvegicus 1 1 1.7 96731.86 8.88 0 0.526 1.76505 0.057335 1.24511 0.265681 1.27536 0.511396 0.82771 0.434678 GN = Ksr1 PE = 2 SV = 1 ARF5_RAT ADP-ribosylation factor 5 OS = Rattus 1 1 5.6 20529.42 6.3 0 0.204 1.80781 0.044438 1.14613 0.507817 1.76742 0.043848 1.26353 0.345203 norvegicus GN = Arf5 PE = 1 SV = 2 PJA2_RAT E3 ubiquitin-protein ligase Praja-2 1 1 2.6 77920.02 4.34 0 0.844 1.65748 0.103934 1.25961 0.238359 4.54038 3.91E22 3.29302 1.33E16 OS = Rattus norvegicus GN = Pja2 PE = 2 SV = 1 D3Z8X1_RAT Uncharacterized protein OS = Rattus 1 1 4.1 27354.92 9.92 0 0.537 2.01764 0.010906 1.63513 0.003859 1.42953 0.279063 1.16594 0.554097 norvegicus PE = 4 SV = 1 Q91ZE7_RAT Band 3 anion exchange protein 5 3 4.8 94311.68 5.83 10 0.327 1.43918 0.28521 2.31773 1.99E09 2.38937 0.000189 3.28321 1.79E16 OS = Rattus norvegicus GN = Slc4a1 PE = 2 SV = 1 1 1 1.0 221416 4.79 0 0.41 1.76939 0.055897 0.871478 0.493962 1.09017 0.884529 0.521787 0.031398 B2LYI9_RAT TenascinGN = Tnc C PE OS = = 2Rattus SV = norvegicus 1

UN13A_RAT Isoform 3 of Protein unc-13 homolog A OS = Rattus norvegicus 3 2 1.8 194360.9 5.15 0 0.554 1.81562 0.042369 1.28698 0.192316 2.07493 0.004173 1.05959 0.835476 GN = Unc13a STMN1_RAT Stathmin OS = Rattus norvegicus GN = Stmn1 PE = 1 SV = 2 2 2 16.1 17288.28 5.76 0 1.313 2.00308 0.012124 1.07894 0.7217 1.91688 0.01517 1.06063 0.832535 PPM1F_RAT Protein phosphatase 1F OS = Rattus norvegicus GN = Ppm1f 1 1 3.3 49164.92 5.19 0 0.22 1.02976 0.981407 1.59773 0.006545 2.04845 0.005245 1.31689 0.255723 PE = 2 SV = 1 CNKR2_RAT Connector enhancer of kinase suppressor of ras 2 OS = Rattus 5 2 2.8 109695.9 6.09 0 0.776 1.82396 0.040251 0.722787 0.141321 1.49871 0.202854 0.680763 0.149966 norvegicus GN = Cnksr2 PE = 2 SV = 1 RTN3_RAT Reticulon-3 OS = Rattus norvegicus GN = Rtn3 PE = 1 SV = 1 7 6 10.6 101515.7 5 3 0.409 1.56595 0.163808 1.21607 0.32671 1.89721 0.017599 0.970207 0.886517 A1E5S7_RAT Nel-like 2 splice variant OS = Rattus norvegicus GN = Nell2 1 1 2.5 86433.29 5.48 0 0.38 1.62766 0.121157 1.04999 0.82249 1.07486 0.918004 0.670958 0.137919 PE = 2 SV = 1 DLGP2_RAT Disks large-associated protein 2 OS = Rattus norvegicus 3 2 2.8 118977.2 6.3 0 0.868 2.28604 0.001234 1.21635 0.326083 1.33779 0.407061 0.67704 0.1453 GN = Dlgap2 PE = 1 SV = 3 SHAN3_RAT Isoform 1 of SH3 and multiple ankyrin repeat domains protein 3 4 4 3.4 192384.5 9 0 0.57 1.63122 0.11899 1.03526 0.875052 1.63912 0.096667 0.969209 0.882985 OS = Rattus norvegicus GN = Shank3 SRBS2_RAT Sorbin and SH3 domain-containing protein 2 OS = Rattus 1 1 1.5 134055.9 8.7 0 0.869 1.62436 0.12319 1.19641 0.372799 1.91145 0.015809 0.848395 0.491119 norvegicus GN = Sorbs2 PE = 1 SV = 2 B2GUZ3_RAT Mthfd1l protein OS = Rattus norvegicus GN = Mthfd1l PE = 2 2 2 2.6 105840.9 7.29 0 0.092 1.67336 0.095587 1.42632 0.052575 2.27685 0.000621 1.41568 0.135387 SV = 1 F1M5F9_RAT Protein Efr3b (Fragment) OS = Rattus norvegicus GN = Efr3b 2 2 3.8 87513.01 6.39 0 0.175 1.95817 0.016673 1.12943 0.55776 1.28001 0.503185 0.750393 0.259466 PE = 2 SV = 1 F1M5B8_RAT Protein Astn1 (Fragment) OS = Rattus norvegicus GN = Astn1 5 3 4.0 135268.2 5.25 0 0.331 2.4942 0.000168 0.851422 0.429436 1.56489 0.145331 1.09681 0.732311 PE = 4 SV = 1 (continued on next page) 235 3 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 236

CADH2_RAT Cadherin-2 OS = Rattus norvegicus GN = Cdh2 PE = 1 SV = 1 6 3 5.6 99685.04 4.61 1 0.347 1.90336 0.024202 1.14542 0.509898 1.60723 0.115683 0.902012 0.65395 DPYL4_RAT Dihydropyrimidinase-related protein 4 OS =Rattus norvegicus 3 3 6.3 64173.55 6.58 0 0.176 1.72952 0.07029 1.03332 0.882011 1.46078 0.242516 0.849002 0.492835 GN = Dpysl4 PE = 2 SV = 1 TXNL1_RAT Thioredoxin-like protein 1 OS =Rattus norvegicus GN = Txnl1 3 3 13.9 33600.59 4.81 0 0.293 1.70413 0.08095 1.17343 0.43154 1.19978 0.654202 0.790155 0.342372 PE = 2 SV = 1 D3ZQL7_RAT Protein Tppp OS =Rattus norvegicus GN = Tppp PE = 4 SV = 1 9 3 15.6 23546.3 9.45 0 0.748 1.75205 0.061826 1.20499 0.35222 1.84113 0.02648 1.09131 0.747308 D4AD48_RAT Protein Dcun1d2 OS =Rattus norvegicus GN = Dcun1d2 PE = 4 1 1 6.6 29999.76 5.39 0 0.51 1.6502 0.107944 1.10267 0.642434 1.25126 0.555122 0.765088 0.288322 SV = 1 CTL2_RAT Choline transporter-like protein 2 OS =Rattus norvegicus 2 2 3.4 79274.95 8.91 0 0.419 1.7416 0.065641 1.07982 0.718686 1.45309 0.251183 0.881428 0.588842 GN = Slc44a2 PE = 2 SV = 1 Q3ZB99_RAT Tight junction protein 2 OS =Rattus norvegicus GN = Tjp2 2 2 2.8 131355.7 6.29 0 0.919 1.6873 0.088712 0.853568 0.436097 1.54261 0.163108 0.686789 0.157759 PE = 2 SV = 1 G3V9J8_RAT Glycerol-3-phosphate acyltransferase 1, mitochondrial 1 1 1.9 93726.48 8.32 0 0.151 2.5354 0.00011 2.13699 2.28E 07 0.776896 0.417967 1.02049 0.946955 OSRattus = norvegicus GN = Gpam PE = 4 SV = 1 F1M281_RAT Calcium-transporting ATPase type 2C member 1 (Fragment) 1 1 2.0 97013.02 6.3 0 0.176 1.0531 0.933943 1.27577 0.210322 1.39711 0.320762 0.733833 0.22942 OSRattus = norvegicus GN = Atp2c1 PE = 2 SV = 1 Q99P36_RAT Protein Syt7 OS = Rattus norvegicus GN = Syt7 PE = 2 SV = 1 2 2 6.9 58160.81 9.35 1 0.532 1.86126 0.031841 1.03799 0.865262 1.46107 0.242198 0.944809 0.797551 F1LP46_RAT ATP-dependent RNA helicase SUPV3L1, mitochondrial (Fragment) 1 1 2.8 77826.52 6.7 0 0.277 1.80117 0.046264 0.884369 0.538023 1.16362 0.727792 0.694991 0.168854 OSRattus = norvegicus GN = Supv3l1 PE = 2 SV = 1 LRC8C_RAT Leucine-rich repeat-containing protein 8C OS =Rattus norvegicus 1 1 2.0 92461.61 7.97 0 0.098 1.48343 0.237331 1.02343 0.917668 1.30435 0.46129 0.755454 0.26917 GN = Lrrc8c PE = 2 SV = 1 Q6IRL2_RAT Mitofusin 2 OS =Rattus norvegicus GN = Mfn2 PE = 2 SV = 1 1 1 2.5 86179.92 6.41 1 0.291 1.47726 0.243647 1.05333 0.810664 1.25845 0.54188 0.801189 0.368094 D4ADS9_RAT Protein Efr3a OS =Rattus norvegicus GN = Efr3a PE = 4 1 1 1.7 92522.89 6.36 0 0.153 1.74617 0.063948 1.52498 0.016951 1.3084 0.454518 1.30878 0.268174 SV = 1 D4A0V6_RAT Protein Anln OS =Rattus norvegicus GN = Anln PE = 4 SV = 1 1 1 1.4 122559.9 8.08 0 0.572 1.76994 0.055717 1.23914 0.277538 1.09198 0.88058 0.700717 0.176939 ECI1_RAT Enoyl-CoA delta isomerase 1, mitochondrial OS =Rattus 1 1 5.5 32254.03 9.55 0 0.156 1.55879 0.169415 1.21546 0.328074 1.01258 0.938095 0.739199 0.238872 norvegicusGN = Eci1 PE = 1 SV = 1 PDE2A_RAT cGMP-dependent 3’,5’-cyclic phosphodiesterase (Fragment) 4 4 5.4 103262 5.24 0 0.202 1.66889 0.09788 1.06243 0.778701 1.15934 0.73667 0.774479 0.307857 OSRattus = norvegicus GN = Pde2a PE = 2 SV = 1 BCAS1_RAT Isoform 5 of Breast carcinoma-amplified sequence 1 homolog 4 4 10.0 63711.01 7.7 0 0.949 1.61726 0.127661 1.4599 0.036499 1.24658 0.56381 0.979225 0.918514 OSRattus = norvegicus GN = Bcas1 D4A1Q9_RAT Protein Ttll12 OS =Rattus norvegicus GN = Ttll12 PE = 4 1 1 2.2 73897.12 5.39 0 0.396 0.492556 0.080909 1.07713 0.727873 2.00349 0.007643 0.461202 0.015374 SV = 1 PACN1_RAT Protein kinase C and casein kinase substrate in neurons protein 1 9 7 21.5 50448.57 5.15 0 1.02 1.8529 0.033581 1.15996 0.468306 1.24948 0.558424 0.640845 0.105552 OSRattus = norvegicus GN = Pacsin1 PE = 1 SV = 1 NCKX2_RAT Sodium/potassium/calcium exchanger 2 OS =Rattus norvegicus 3 2 3.4 74655.81 5.93 11 0.209 1.62693 0.1216 0.930795 0.711296 2.10525 0.003193 0.988757 0.952479 GN = Slc24a2 PE = 2 SV = 1 B5DEG8_RAT LOC685144 protein OS =Rattus norvegicus GN = Sec24c 2 2 3.3 118522.8 6.71 0 0.228 1.88383 0.027522 1.10479 0.635558 1.74991 0.049162 1.1784 0.524372 PE = 2 SV = 1 D4ABB2_RAT Megalencephalic leukoencephalopathy with subcortical cysts 1 1 1 4.7 44305.25 8.36 0 0.324 1.44628 0.277118 1.17155 0.436564 0.996406 0.898206 0.790703 0.343623 homolog (Human) (Predicted) OS =Rattus norvegicus GN = Mlc1 PE = 4 SV = 1 Q9ES33_RAT Protein Dkk3 OS =Rattus norvegicus GN = Dkk3 PE = 2 SV = 1 1 1 5.1 30762.82 4.57 0 0.579 1.43235 0.293143 1.08292 0.708164 1.59021 0.126972 1.03616 0.902014 F1LZ81_RAT Protein Dock4 OS =Rattus norvegicus GN = Dock4 PE = 2 3 2 1.4 225192.8 8.09 0 0.355 1.4342 0.290985 1.31483 0.152548 1.14599 0.764646 0.742164 0.244211 SV = 1 D3ZNY3_RAT Methylmalonic aciduria (Cobalamin deficiency) cblA type 1 1 3.9 46329.24 9.64 0 0.209 1.8094 0.044012 1.09255 0.675799 1.14519 0.766322 0.916108 0.700147 (Predicted), isoform CRA_a OS =Rattus norvegicus GN = Mmaa PE = 4 SV = 1 D4A9Z6_RAT Mitochondrial ribosomal protein S35 (Predicted) OS =Rattus 2 1 5.9 36206.27 9.26 0 0.572 1.56707 0.162942 1.09888 0.654849 0.970649 0.835264 0.595434 0.068457 norvegicusGN = Mrps35 PE = 4 SV = 1 P5I11_RAT Tumor protein p53-inducible protein 11 OS =Rattus norvegicus 1 1 7.9 20938.52 9.43 4 0.341 1.45648 0.265773 1.20895 0.342945 1.26382 0.5321 0.845727 0.483625 GN = Tp53i11 PE = 2 SV = 1 CYLD_RAT Ubiquitin carboxyl-terminal hydrolase CYLD OS = Rattus 2 2 2.9 106711.4 5.44 0 0.354 1.7638 0.057754 1.05168 0.816491 2.0484 0.005246 1.24799 0.374631 norvegicusGN = Cyld PE = 2 SV = 1 CX6C2_RAT CX6C2_RAT Cytochrome c oxidase subunit 6C-2 OS =Rattus 10 2 27.6 8454.83 10.07 1 0.108 1.7896 0.049595 0.980969 0.916695 1.94724 0.012 1.09994 0.723818 norvegicusGN = Cox6c2 PE = 1 SV = 3 G3V728_RAT G3V728_RAT 4-nitrophenylphosphatase domain and non-neuronal 10 5 17.6 33345.9 9.44 0 0.596 1.63347 0.117636 1.17614 0.424343 2.07727 0.004089 1.38827 0.16324 SNAP25-like protein homolog 1 (C. elegans), isoform CRA_b OSRattus = norvegicus GN = Nipsnap1 PE = 4 SV = 1 D3ZSN7_RAT Protein Slc25a44 OS = Rattus norvegicus GN = Slc25a44 1 1 4.8 37878.66 9.68 0 0.018 1.83193 0.038312 1.07859 0.722897 1.22658 0.601702 0.819609 0.413636 PE = 3 SV = 1 DNM1L_RAT Isoform 5 of Dynamin-1-like protein OS = Rattus norvegicus 5 4 7.1 82538.89 6.51 0 0.266 1.69747 0.083952 1.24623 0.263505 1.79993 0.035264 1.37945 0.173072 GN = Dnm1l ROGDI_RAT Protein rogdi homolog OS = Rattus norvegicus GN = Rogdi 1 1 7.3 32204.74 8.32 0 0.102 1.70329 0.081325 1.01697 0.941053 1.30611 0.458349 0.960696 0.852971 PE = 2 SV = 1 CH037_RAT Protein C8orf37 homolog OS = Rattus norvegicus PE = 2 SV = 1 1 1 7.1 23770.5 6.44 0 0.728 1.32057 0.443768 1.01818 0.936673 1.0356 0.995106 0.624104 0.090355

SCFD1_RAT Sec1 family domain-containing protein 1 OS = Rattus 1 1 2.6 43970.84 5.72 0 0.728 1.57714 0.155334 1.07365 0.739818 1.69457 0.069622 1.15572 0.579081 norvegicus GN = Scfd1 PE = 2 SV = 1 D3ZDX5_RAT Protein Plxnb1 OS = Rattus norvegicus GN = Plxnb1 PE = 4 5 4 3.3 231808.5 5.37 0 0.142 1.69039 0.087245 0.95116 0.793054 1.07533 0.916974 0.666946 0.13321 SV = 1 ITM2B_RAT Integral membrane protein 2B OS = Rattus norvegicus 1 1 7.1 30313.6 5.14 1 0.095 1.50921 0.212214 1.25391 0.248857 1.00096 0.909421 0.766518 0.291242 GN = Itm2b PE = 2 SV = 1 CLVS2_RAT Clavesin-2 OS = Rattus norvegicus GN = Clvs2 PE = 1 1 1 5.5 37915.92 5.69 0 0.368 1.46861 0.252694 1.07353 0.740207 2.45634 8.93E-05 1.41466 0.136353 SV = 1 PRIO_RAT Major prion protein OS = Rattus norvegicus GN = Prnp 11 3 8.7 27803.89 9.32 2 0.597 1.65754 0.103897 1.03291 0.883482 1.53044 0.173482 0.948695 0.811025 PE = 1 SV = 2 D4A899_RAT Protein Vps13a OS = Rattus norvegicus GN = Vps13a PE = 2 1 1 0.3 347445.7 5.56 0 0.171 1.89316 0.02589 1.27983 0.203668 1.33913 0.404976 1.014 0.965607

SV = 1 220–292 (2015) 298 Neuroscience / al. et Han X. CDK5_RAT Cyclin-dependent kinase 5 OS = Rattus norvegicus 1 1 5.5 33254.06 7.57 0 0.298 1.58362 0.150577 0.940048 0.748097 1.46097 0.242309 0.736956 0.234887 GN = Cdk5 PE = 1 SV = 1 NUCB2_RAT Nucleobindin-2 OS = Rattus norvegicus GN = Nucb2 PE = 2 1 1 3.1 50089.67 5.02 0 1.063 1.60425 0.13618 1.12006 0.586809 1.22089 0.612692 0.725228 0.214823 SV = 1 D4AEC2_RAT Protein Camsap1l1 OS = Rattus norvegicus GN = Camsap2 1 1 1.0 165610.2 6.6 0 0.752 1.11746 0.804723 1.42615 0.052668 0.944691 0.772881 0.783869 0.328244 PE = 4 SV = 1 D3ZVA6_RAT Protein Bola2 OS = Rattus norvegicus GN = Bola2 PE = 3 2 2 22.1 10214.47 5.57 0 0.681 1.47525 0.245724 1.11312 0.608727 1.34054 0.402779 0.758399 0.274929 SV = 1 CATA_RAT Catalase OS = Rattus norvegicus GN = Cat PE = 1 SV = 3 16 1 5 3.0 8.9 59756.49 92171.01 7.07 6.39 0 0 0.6390.501 1.30763 1.71541 0.463688 0.076064 1.34653 1.02292 0.11526 0.919521 1.08191 1.26638 0.902571 0.527484 1.06428 0.825948 0.822259 0.430049 DLG3_RAT Isoform Short of Disks large homolog 3 OS = Rattus norvegicus LRC8A_RATGN Leucine-rich = Dlg3 repeat-containing protein 8A OS = Rattus 1 1 2.2 94160.53 8.15 4 0.119 1.83012 0.038746 0.916497 0.655755 1.14783 0.760762 0.660882 0.12633 norvegicus GN = Lrrc8a PE = 2 SV = 1 OXR1_RAT Oxidation resistance protein 1 OS = Rattus norvegicus 5 3 5.6 92808.97 5.01 0 0.703 1.5342 0.189752 1.18083 0.412052 1.22712 0.600668 0.754241 0.266822 GN = Oxr1 PE = 1 SV = 3 PLRKT_RAT Plasminogen receptor (KT) OS = Rattus norvegicus 4 1 6.8 17312.13 9.48 0 0.286 1.25101 0.556373 1.42072 0.05576 2.34975 0.00029 1.72628 0.008936 GN = Plgrkt PE = 1 SV = 1 A9UMV9_RAT Ndufa7 protein OS = Rattus norvegicus GN = Ndufa7 PE = 4 11 8 52.7 12500.31 10.48 0 0.662 1.66864 0.098011 1.0147 0.949279 1.84332 0.026072 0.853033 0.504295 SV = 1 NB5R3_RAT Isoform 2 of NADH-cytochrome b5 reductase 3 OS = Rattus 2 2 9.5 34865.15 8.56 0 0.16 1.24571 0.565506 1.28882 0.189479 1.92744 0.013993 1.12624 0.653927 norvegicus GN = Cyb5r3 UGGG1_RAT UDP-glucose:glycoprotein glucosyltransferase 1 OS = Rattus 1 1 1.0 176428.5 5.43 0 0.317 1.66263 0.101166 1.20882 0.343259 0.969525 0.832538 0.848009 0.490031 norvegicus GN = Uggt1 PE = 1 SV = 2 RIMB2_RAT RIMS-binding protein 2 OS = Rattus norvegicus GN = Rimbp2 1 1 1.6 115612.9 5.06 0 0.581 1.50928 0.212152 1.07588 0.732148 1.0876 0.890128 0.738086 0.236889 PE = 1 SV = 2 CSPG2_RAT Versican core protein (Fragments) OS = Rattus norvegicus 9 4 2.0 300004.3 4.49 0 0.551 1.46411 0.257493 0.859754 0.455628 1.39443 0.324381 0.735065 0.231566 GN = Vcan PE = 2 SV = 2 PCCA_RAT Propionyl-CoA carboxylase alpha chain, mitochondrial 4 4 7.3 81621.88 7.6 0 0.216 1.54909 0.177234 1.22819 0.300205 1.3667 0.363406 1.12155 0.666205 OS = Rattus norvegicus GN = Pcca PE = 1 SV = 3 RAB6A_RAT Ras-related protein Rab-6A OS = Rattus norvegicus 2 2 11.1 23589.51 5.42 0 0.416 1.60292 0.137077 1.02735 0.903531 1.59069 0.12664 1.0372 0.899058 GN = Rab6a PE = 2 SV = 2 PLCL1_RAT Inactive phospholipase C-like protein 1 OS = Rattus norvegicus 1 1 1.3 122771.1 5.47 0 0.341 0.886596 0.657743 2.37851 3.49E10 0.835177 0.529434 1.39156 0.159693 GN = Plcl1 PE = 1 SV = 1 Q8CHN5_RAT Epididymal secretory protein 1 OS = Rattus norvegicus 1 1 10.7 16363.87 7.55 0 0.038 0.817822 0.502635 1.33053 0.133072 0.910086 0.692012 0.697516 0.172384 GN = Npc2 PE = 2 SV = 1 HPLN2_RAT Hyaluronan and proteoglycan link protein 2 OS = Rattus 11 6 20.5 38046.09 9.3 0 0.296 1.59861 0.140003 1.41672 0.058135 1.33494 0.411535 1.28439 0.308088 norvegicus GN = Hapln2 PE = 2 SV = 1 CSPG5_RAT Chondroitin sulfate proteoglycan 5 OS = Rattus norvegicus 2 1 2.8 60957.89 4.41 2 0.449 1.84924 0.034369 1.07307 0.74179 1.33367 0.413534 0.839102 0.465288

GN = Cspg5 PE = 1 SV = 1 237 (continued on next page) 3 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 238

PPT1_RAT Palmitoyl-protein thioesterase 1 (Fragment) OS = Rattus 3 2 11.8 31531.1 6.72 0 0.197 1.63154 0.118793 1.90674 3.68E 05 0.947669 0.779973 1.54995 0.047937 norvegicusGN = Ppt1 PE = 4 SV = 1 NEGR1_RAT Neuronal growth regulator 1 OSRattus = norvegicus 1 1 3.7 37857.63 6.1 0 0.071 0.717555 0.31646 1.01929 0.932657 4.23923 9.43E 19 3.85032 8.46E 25 GN = Negr1 PE = 1 SV = 1 M2OM_RAT Mitochondrial 2-oxoglutarate/malate carrier protein 6 2 8.0 34132.51 9.89 0 0.101 1.42587 0.300805 1.09563 0.665571 1.74927 0.049367 1.12853 0.647992 OSRattus = norvegicus GN = Slc25a11 PE = 2 SV = 3 NEUG_RAT Neurogranin OS = Rattus norvegicus GN = Nrgn PE = 1 4 3 26.9 7496.25 6.53 0 0.612 1.58853 0.147048 1.03698 0.868888 1.76185 0.045485 1.1586 0.571999 SV = 1 HNRH1_RAT Protein Hnrph1 OS =Rattus norvegicus GN = Hnrph1 PE = 2 2 2 5.5 51218.21 6.21 0 0.564 1.55516 0.172309 0.926022 0.692565 1.41711 0.294586 0.919357 0.710963 SV = 1 Q5RJN0_RAT NADH dehydrogenase (Ubiquinone) Fe-S protein 7 7 3 22.5 23944.78 10.02 0 0.042 1.59913 0.139651 0.946884 0.775663 1.37804 0.347104 0.865329 0.540108 OSRattus = norvegicus GN = Ndufs7 PE = 2 SV = 1 D3ZCF8_RAT Uncharacterized protein OS =Rattus norvegicus 2 2 12.5 26377.12 5.02 0 0.056 1.61308 0.130355 1.23777 0.280308 1.08782 0.889657 0.854257 0.507803 GN = Abca8a PE = 4 SV = 1 FKB1A_RAT Peptidyl-prolyl cis-trans isomerase FKBP1A OS = Rattus 2 2 15.7 11922.49 7.89 0 0.38 1.41737 0.311065 0.906068 0.616392 1.82527 0.029609 0.989835 0.956326 norvegicusGN = Fkbp1a PE = 1 SV = 3 AL9A1_RAT 4-trimethylaminobutyraldehyde dehydrogenase OS =Rattus 5 3 9.4 56468.48 6.94 0 0.032 1.6109 0.131775 1.22083 0.316132 1.18859 0.676651 1.00323 0.996626 norvegicusGN = Aldh9a1 PE = 3 SV = 1 G3V982_RAT Engulfment and cell motility 2, ced-12 homolog (C. elegans), 2 2 4.4 82426.88 5.66 0 0.327 1.31261 0.455961 1.17671 0.422846 1.44829 0.256703 1.1127 0.689591 isoform CRA_c OS =Rattus norvegicus GN = Elmo2 PE = 4 SV = 1 KCNA6_RAT Potassium voltage-gated channel subfamily A member 6 1 1 3.0 58883.22 5 4 0.082 1.42463 0.302293 0.903676 0.607511 1.27509 0.511883 1.14854 0.596948 OSRattus = norvegicus GN = Kcna6 PE = 2 SV = 1 SCPDL_RAT Saccharopine dehydrogenase-like oxidoreductase OS =Rattus 2 2 9.9 35411.12 8.09 0 0.12 1.85696 0.032727 1.39332 0.07376 1.55531 0.152779 1.42393 0.127764 norvegicusGN = Sccpdh PE = 2 SV = 1 GABT_RAT 4-aminobutyrate aminotransferase, mitochondrial OS =Rattus 18 8 22.8 56455.15 8.15 0 0.285 1.67752 0.093494 1.46937 0.032803 1.07932 0.908233 1.01557 0.961099 norvegicusGN = Abat PE = 1 SV = 3 Q06QG6_RAT NADH-ubiquinone oxidoreductase chain 5 OS =Rattus 7 3 7.9 68587.28 9.34 15 0.621 1.68515 0.089746 1.54435 0.013287 1.2839 0.496345 1.39349 0.157635 norvegicusGN = Mt-nd5 PE = 3 SV = 1 F1LPP6_RAT A-kinase anchor protein 5 OS = Rattus norvegicus 3 2 4.8 75970.73 4.73 0 0.688 1.68349 0.090553 1.16145 0.464166 0.934815 0.749505 0.721798 0.209195 GN = Akap5 PE = 2 SV = 1 GDE1_RAT Glycerophosphodiester phosphodiesterase 1 OS =Rattus 1 1 4.5 37633.74 6.26 0 0.089 1.60357 0.136636 0.88088 0.525907 1.52989 0.173962 0.990551 0.958882 norvegicusGN = Gde1 PE = 1 SV = 2 F1M787_RAT Catenin delta-2 OS =Rattus norvegicus GN = Ctnnd2 PE = 2 4 4 5.2 121665.4 8.44 0 0.514 1.51666 0.205328 0.939742 0.746868 1.72244 0.058581 0.818361 0.41045 SV = 1 VATE1_RAT V-type proton ATPase subunit E 1 OS =Rattus norvegicus 12 7 22.6 26128.12 8.44 0 0.49 1.56403 0.165295 1.61803 0.00493 1.94464 0.012247 1.96348 0.000519 GN = Atp6v1e1 PE = 1 SV = 1 F1LNN7_RAT Neurocan core protein OS =Rattus norvegicus GN = Ncan 15 9 7.8 135654.5 5.29 0 0.476 1.59294 0.143936 0.919224 0.666213 1.63022 0.101705 1.20059 0.473548 PE = 2 SV = 1 Q8R2H0_RAT Protein Atp6v1g2 OS =Rattus norvegicus GN = Atp6v1g2 4 3 28.6 12164.29 5.84 0 0.938 1.51278 0.20889 1.00905 0.969781 1.04904 0.974739 0.676383 0.144489 PE = 2 SV = 1 DHSB_RAT Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, 5 5 18.1 31829.64 8.96 0 0.37 1.41043 0.319598 1.66788 0.002377 2.72809 3.03E 06 3.20927 1.61E-15 mitochondrial OS =Rattus norvegicus GN = Sdhb PE = 2 SV = 2 G3V6T1_RAT Protein Copa OSRattus = norvegicus GN = Copa PE = 4 2 2 2.4 138358.3 7.69 0 0.279 1.6798 0.092359 1.03846 0.863568 2.06645 0.004493 1.52781 0.057695 SV = 1 STXB5_RAT Isoform 3 of Syntaxin-binding protein 5 OS =Rattus norvegicus 3 3 5.4 121741.4 6.46 0 0.289 1.65701 0.104187 1.07344 0.740529 1.01672 0.948317 0.801543 0.36894 GN = Stxbp5 NFASC_RAT Neurofascin OS =Rattus norvegicus GN = Nfasc PE = 1 34 15 18.0 138002.6 5.79 2 0.513 1.40231 0.329785 0.978168 0.904942 1.3026 0.464232 0.896419 0.63597 SV = 2 DCLK1_RAT Serine/threonine-protein kinase DCLK1 OS =Rattus 3 3 9.7 47680.29 5.52 0 0.408 1.46234 0.259394 1.20543 0.351168 1.38168 0.34197 1.12843 0.64824 norvegicusGN = Dclk1 PE = 2 SV = 1 D3ZNN0_RAT Protein Sbf1 OS =Rattus norvegicus GN = Sbf1 PE = 4 3 2 1.5 175668.8 8.37 0 0.316 1.62372 0.123591 1.27744 0.207568 0.966773 0.825874 1.01211 0.971052 SV = 1 O35791_RAT RhoA (Fragment) OS =Rattus norvegicus GN = Rhoa PE = 2 10 4 25.3 19686.18 4.89 0 0.475 1.46183 0.259945 1.0664 0.764863 1.44978 0.254983 0.947952 0.808443 SV = 1 B0BN83_RAT Armadillo repeat-containing protein 1 OS =Rattus norvegicus 3 2 5.3 31204.1 5.41 0 0.316 1.43645 0.288367 1.15136 0.492676 1.25835 0.542076 1.1866 0.505285 GN = Armc1 PE = 2 SV = 1 F1LSM3_RAT WD repeat-containing protein 44 (Fragment) OS = Rattus 1 1 1.6 98996.55 5.53 0 0.67 1.82255 0.040603 1.69091 0.001669 0.889315 0.645041 0.687325 0.158467 norvegicus GN = Wdr44 PE = 2 SV = 1 Q6IRH7_RAT ClpB caseinolytic peptidase B homolog (E. coli) OS = Rattus 1 1 2.4 75678.49 8.68 0 0.454 1.52123 0.201186 0.935377 0.729442 0.915226 0.703829 0.686575 0.157477 norvegicus GN = Clpb PE = 2 SV = 1 ABLM2_RAT Actin-binding LIM protein 2 OS = Rattus norvegicus 2 1 2.3 68552.57 8.36 0 0.549 1.4695 0.251755 1.17799 0.419478 1.16608 0.722689 0.778882 0.317311 GN = Ablim2 PE = 2 SV = 1 BAG5_RAT BAG family molecular chaperone regulator 5 OS = Rattus 2 1 4.5 51029.89 5.84 0 0.483 1.50338 0.21772 1.12089 0.584186 0.990875 0.884622 0.710837 0.191928 norvegicus GN = Bag5 PE = 1 SV = 1 KCC2B_RAT Calcium/calmodulin-dependent protein kinase type II subunit 55 15 31.9 60401.11 6.73 0 0.353 1.73409 0.068502 1.34355 0.118429 1.83977 0.026737 1.56141 0.043456 beta OS = Rattus norvegicus GN = Camk2b PE = 1 SV = 1 F1LVV3_RAT Uncharacterized protein (Fragment) OS = Rattus norvegicus 1 1 2.5 70961.21 7.47 0 0.379 1.37857 0.360748 1.12111 0.5835 0.931139 0.740862 0.657919 0.123071 PE = 4 SV = 1 F1LRK4_RAT Protein Grsf1 OS = Rattus norvegicus GN = Grsf1 PE = 2 1 1 3.3 53200.94 6.9 0 0.42 1.51419 0.20759 1.15603 0.47937 1.42935 0.279294 1.03779 0.897351 SV = 1 D3ZGN2_RAT Copine 5 protein OS = Rattus norvegicus GN = Cpne5 PE = 2 1 1 3.2 65605.57 5.49 0 0.282 1.16902 0.704785 1.16745 0.447654 1.23264 0.590114 0.86266 0.532227 SV = 1 PPP5_RAT Serine/threonine-protein phosphatase 5 OS = Rattus 1 1 2.2 56916.08 5.84 0 0.509 1.38804 0.348192 1.1414 0.521719 1.5267 0.176769 0.993869 0.970732 norvegicus GN = Ppp5c PE = 2 SV = 1 RTN4R_RAT Reticulon-4 receptor OS = Rattus norvegicus GN = Rtn4r 1 1 2.5 50850.66 9.14 0 0.175 1.10297 0.833481 1.51549 0.01905 1.06798 0.933102 0.831009 0.443421 PE = 1 SV = 2 220–292 (2015) 298 Neuroscience / al. et Han X. D4A8U7_RAT Dynactin subunit 1 OS = Rattus norvegicus GN = Dctn1 1 1 1.1 137008.8 5.34 0 0.582 1.35026 0.399991 1.18782 0.394149 1.45986 0.243541 1.03912 0.893568 PE = 2 SV = 1 UCRI_RAT Cytochrome b-c1 complex subunit Rieske, mitochondrial 13 7 23.7 29445.36 9.04 0 0.108 1.41647 0.312156 1.0274 0.903327 1.67505 0.078331 1.11077 0.69472 OS = Rattus norvegicus GN = Uqcrfs1 PE = 1 SV = 2 RHOB_RAT Rho-related GTP-binding protein RhoB OS = Rattus 11 4 25.0 22123.15 5.1 1 0.26 1.44313 0.280688 1.25113 0.254096 1.42578 0.283699 1.02277 0.940405 norvegicus GN = Rhob PE = 1 SV = 1 CSTN1_RAT Calsyntenin-1 OS = Rattus norvegicus GN = Clstn1 PE = 2 1 1 1.6 106259.7 4.91 1 0.427 1.57098 0.159953 1.48826 0.026384 1.31028 0.4514 1.35866 0.197977 SV = 1 0.657 1.32541 0.436451 0.906027 0.616237 0.870811 0.60435 0.562313 0.048793 F1M2K6_RAT Protein Pkp4 OS = Rattus norvegicus GN = Pkp4 PE = 2 3 3 3.9 127228.6 9.24 0 Q9JMB3_RATSV Protein= 1 Epb41l3 OS = Rattus norvegicus GN = Epb41l3 14 9 9.9 119689.6 5.04 0 0.677 1.51906 0.203139 0.963577 0.844113 1.17342 0.707567 0.834105 0.451714 PE = 2 SV = 1 ACTN4_RAT Alpha-actinin-4 OS = Rattus norvegicus GN = Actn4 PE = 1 8 6 7.0 104913.8 5.27 0 0.654 1.53778 0.186683 1.107 0.628387 1.1039 0.854674 0.837242 0.460211 SV = 2 PTMS_RAT Parathymosin OS = Rattus norvegicus GN = Ptms PE = 1 3 2 22.6 11558.77 4.15 0 2.047 1.4956 0.22523 0.743625 0.173635 1.85037 0.024793 0.858662 0.520534 SV = 2 A6Y857_RAT Phospholipase C delta 1 long form OS = Rattus norvegicus 1 1 1.3 88444.11 5.82 0 0.47 1.52441 0.198332 1.30794 0.161745 1.10967 0.842203 0.75631 0.270835 GN = Plcd1 PE = 2 SV = 1 CR1L_RAT Isoform 2 of Complement component receptor 1-like protein 1 1 4.0 54785.99 5.63 0 0.174 2.06532 0.007643 0.682674 0.092343 1.35808 0.376098 0.677579 0.145969 OS = Rattus norvegicus GN = Cr1l D3ZDT1_RAT Protein Epb4.1l2 OS = Rattus norvegicus GN = Epb4.1l2 3 3 6.8 102593 5.25 0 0.806 1.32235 0.441078 0.897582 0.585148 1.36717 0.362715 0.727133 0.217995 PE = 4 SV = 1 F1M8K1_RAT Protein Pcdh1 (Fragment) OS = Rattus norvegicus 6 5 7.4 109699.9 4.85 0 0.424 1.24042 0.574662 0.858329 0.451087 1.45208 0.252337 0.940469 0.782576 GN = Pcdh1 PE = 4 SV = 1 F1M6N9_RAT Protein Pcdh1 (Fragment) OS = Rattus norvegicus 5 3 10.6 36984.28 8.14 0 1.033 1.48439 0.236366 0.858329 0.451087 1.00961 0.930757 0.78254 0.325308 GN = Pcdh1 PE = 4 SV = 1 PACS1_RAT Phosphofurin acidic cluster sorting protein 1 OS = Rattus 2 2 3.1 104699 7.61 0 0.468 1.43234 0.293154 1.19362 0.379663 0.782743 0.428486 0.785338 0.331513 norvegicus GN = Pacs1 PE = 2 SV = 1 SHAN2_RAT SH3 and multiple ankyrin repeat domains protein 2 OS = Rattus 4 4 3.3 158681.8 6.76 0 0.6 1.37845 0.360916 1.11573 0.600452 1.47999 0.221791 0.964539 0.866495 norvegicus GN = Shank2 PE = 1 SV = 2 D4A435_RAT Protein Icam5 OS = Rattus norvegicus GN = Icam5 PE = 4 8 6 10.5 96903.47 5.88 0 0.188 1.46552 0.255977 0.863622 0.468088 1.28186 0.499933 0.819045 0.412195 SV = 1 SNP25_RAT Synaptosomal-associated protein 25 OS = Rattus norvegicus 53 15 61.7 23314.87 4.66 0 0.865 1.44572 0.277749 1.01654 0.942624 1.33944 0.404486 0.924497 0.728192 GN = Snap25 PE = 1 SV = 1 B0BNF6_RAT Membrane-associated ring finger (C3HC4) 5 OS = Rattus 1 1 5.8 31231.35 9 4 0.126 1.37723 0.362548 1.04859 0.827467 1.7506 0.048945 1.16982 0.544767 norvegicus GN = March5 PE = 2 SV = 1 LPPRC_RAT Leucine-rich PPR motif-containing protein, mitochondrial 6 4 4.1 156651 6.2 0 0.183 1.61623 0.128321 1.35509 0.10653 1.27835 0.506104 1.15906 0.570866 OS = Rattus norvegicus GN = Lrpprc PE = 1 SV = 1 NLGN2_RAT Neuroligin-2 OS = Rattus norvegicus GN = Nlgn2 PE = 1 3 3 4.8 90959.88 5.78 1 0.304 1.41079 0.319153 0.849696 0.424121 1.51087 0.191195 0.964276 0.865567 239 SV = 1 (continued on next page) 4 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 240 F1LV09_RAT Uncharacterized protein (Fragment) OS = Rattus norvegicus 1 1 1.2 145320.3 4.87 0 0.556 1.39572 0.338204 0.758197 0.199316 1.61925 0.108199 1.00884 0.980453 PE = 3 SV = 1 NFL_RAT Neurofilament light polypeptide OS =Rattus norvegicus 10 8 15.7 61334.55 4.63 0 0.911 1.47951 0.241333 0.95507 0.809047 1.50888 0.193067 0.992153 0.964601 GN = Nefl PE = 1 SV = 3 D4A6H8_RAT Protein Ctnna2 OS =Rattus norvegicus GN = Ctnna2 PE = 4 4 3 8.7 52874.1 4.56 0 0.349 1.1298 0.780456 0.81304 0.320577 1.38138 0.342394 0.703244 0.180598 SV = 1 THTM_RAT 3-mercaptopyruvate sulfurtransferase OS =Rattus norvegicus 5 3 8.4 32939.8 5.88 0 0.292 1.63225 0.118369 1.20076 0.362277 1.00633 0.922665 1.02315 0.939291 GN = Mpst PE = 1 SV = 3 B2RYW3_RAT NADH dehydrogenase (Ubiquinone) 1 beta subcomplex, 9 8 4 37.4 21891.75 8.22 0 1.053 1.40427 0.32731 1.21099 0.338247 1.1114 0.83846 1.02564 0.932144 OSRattus = norvegicus GN = Ndufb9 PE = 2 SV = 1 Q5BKB9_RAT Rgs14 protein OS =Rattus norvegicus GN = Rgs14 PE = 2 2 2 8.8 41164.16 7.62 0 0.452 0.96704 0.859394 1.94754 1.62E 05 1.19827 0.657203 1.15135 0.589911 SV = 1 D3ZXA6_RAT Protein Pdpr OSRattus = norvegicus GN = Pdpr PE = 3 2 2 2.9 98817.56 6.03 0 0.233 1.51965 0.202609 1.16641 0.450479 1.23867 0.578659 0.901252 0.651493 SV = 1 F1M983_RAT Protein Cfh OS =Rattus norvegicus GN = Cfh PE = 2 SV = 1 1 1 1.3 140006.2 6.52 0 0.611 1.71847 0.074779 1.24785 0.26037 0.977932 0.852974 0.982637 0.930656 CNTP1_RAT Contactin-associated protein 1 (Fragment) OS =Rattus 4 2 3.1 149647.2 6.44 0 0.339 1.31876 0.446532 0.696924 0.107888 1.19094 0.671913 0.519136 0.030475 norvegicusGN = Cntnap1 PE = 2 SV = 1 RS14_RAT 40S ribosomal protein S14 OS =Rattus norvegicus 1 1 9.3 16258.51 10.07 0 0.503 1.26809 0.527486 0.98839 0.947912 1.12444 0.810425 0.782919 0.326144 GN = Rps14 PE = 2 SV = 3 AP180_RAT Clathrin coat assembly protein AP180 OS =Rattus norvegicus 1 1 1.6 93518.01 4.76 0 0.095 1.56581 0.163919 1.16162 0.463704 1.72293 0.058401 1.40065 0.15017 GN = Snap91 PE = 1 SV = 1 Q68HB5_RAT Protein Pcdh7 OS =Rattus norvegicus GN = Pcdh7 PE = 2 1 1 1.3 135771 5.05 2 0.484 1.78298 0.051591 0.955873 0.812344 2.05789 0.004837 1.3245 0.244407 SV = 1 G3V964_RAT Neurotrimin OS =Rattus norvegicus GN = Ntm PE = 4 13 7 20.4 38012.05 7.99 0 0.097 1.42494 0.301923 1.0253 0.910922 1.4078 0.306583 0.797103 0.358433 SV = 1 EMAL1_RAT Echinoderm microtubule-associated protein-like 1 OS =Rattus 1 1 1.7 89800.69 6.56 0 0.393 1.5807 0.152707 1.18458 0.402386 1.357 0.377715 0.899598 0.646165 norvegicusGN=Eml1PE=2SV=2 B2GV74_RAT Kinesin light chain 2 (Predicted), isoform CRA_b OS =Rattus 2 2 4.8 66943.6 6.58 0 0.698 1.49025 0.230492 0.979604 0.910965 1.27217 0.517078 0.780432 0.320683 norvegicusGN = Klc2 PE = 2 SV = 1 D4A9C3_RAT Protein Psd3 OS =Rattus norvegicus GN = Psd3 PE = 2 7 5 13.8 42285.42 9.6 0 0.902 1.27676 0.513125 1.02114 0.925953 1.27214 0.517132 1.15161 0.589262 SV = 1 D4A6R4_RAT Protein LOC100362216 OS =Rattus norvegicus 1 1 9.8 30458.04 6.92 0 0.397 1.49318 0.227595 0.922097 0.677304 1.47776 0.224136 1.0175 0.955551 GN = LOC100362216 PE = 4 SV = 1 F2Z3Q8_RAT Importin subunit beta-1 OS =Rattus norvegicus GN = Kpnb1 2 2 2.9 97183.09 4.68 0 0.097 1.3254 0.436463 1.14722 0.504658 1.47071 0.231642 1.16064 0.567002 PE = 4 SV = 1 DC1I1_RAT Cytoplasmic dynein 1 intermediate chain 1 OS =Rattus 1 1 1.9 70306.76 5.07 0 0.594 1.52205 0.200444 0.835252 0.381177 1.49977 0.201818 1.12621 0.65401 norvegicusGN = Dync1i1 PE = 2 SV = 1 ABD12_RAT Monoacylglycerol lipase ABHD12 OS =Rattus norvegicus 2 2 7.8 45295.28 8.9 0 0.309 1.28115 0.505937 0.784583 0.252679 1.26068 0.537822 0.665045 0.131023 GN = Abhd12 PE = 2 SV = 1 EMC8_RAT ER membrane protein complex subunit 8 OS =Rattus 2 2 14.5 23405.26 5.72 0 0.368 1.26067 0.539939 1.21648 0.325775 0.980325 0.858808 0.821563 0.418655 norvegicusGN=Emc8PE=2SV=1

HS71L_RAT Heat shock 70 kDa protein 1-like OS =Rattus norvegicus 9 2 4.5 70548.35 5.91 0 0.387 1.58576 0.149033 1.12748 0.563743 1.5452 0.16096 1.20426 0.465407 GN = Hspa1l PE = 2 SV = 2 OAT_RAT Ornithine aminotransferase, mitochondrial OS =Rattus 8 5 14.4 48332.06 6.53 0 0.113 1.54739 0.178628 1.15186 0.49124 0.996666 0.898848 0.769976 0.298383 norvegicusGN = Oat PE = 1 SV = 1 D4A0T0_RAT Protein Ndufb10 OS =Rattus norvegicus GN = Ndufb10 14 5 32.4 20858.36 7.57 0 0.937 1.25573 0.548313 0.978999 0.908427 1.72866 0.056327 1.23233 0.405816 PE = 4 SV = 1 D4A8H3_RAT Protein Uba6 OS =Rattus norvegicus GN = Uba6 PE = 4 1 1 1.2 117929.5 5.73 0 0.246 1.9089 0.023326 1.24382 0.268215 2.434 0.000115 2.55437 2.10E-08 SV = 1 G3V8B6_RAT 26S proteasome non-ATPase regulatory subunit 1 OS =Rattus 1 1 1.5 105698.9 5.25 0 0.227 1.21793 0.614432 1.22566 0.305623 1.19378 0.666208 1.12692 0.652163 norvegicusGN = Psmd1 PE = 4 SV = 1 D4A565_RAT NADH dehydrogenase (Ubiquinone) 1 beta subcomplex, 5 14 6 27.0 21663.84 9.46 0 0.252 1.51166 0.209929 1.07874 0.722373 1.44238 0.263614 1.20907 0.454864 (Predicted), isoform CRA_b OS =Rattus norvegicus GN = Ndufb5 PE = 4 SV = 1 Q63714_RAT GCP360 OS =Rattus norvegicus GN = Golgb1 PE = 2 1 1 0.4 364293.2 5.01 0 0.912 1.40499 0.326398 1.09508 0.667397 1.16493 0.72507 0.882431 0.591945 SV = 1 SL9A1_RAT Sodium/hydrogen exchanger 1 OS =Rattus norvegicus 2 1 1.6 91645.93 6.71 13 0.209 1.52867 0.194568 1.10977 0.619444 0.810371 0.480222 0.609498 0.078582 GN = Slc9a1 PE = 1 SV = 2 OGT1_RAT UDP-N-acetylglucosamine–peptide N- 1 1 0.9 115604.8 6.18 0 0.232 1.48709 0.233648 1.29712 0.177036 1.6902 0.071502 1.59761 0.031557 acetylglucosaminyltransferase 110 kDa subunit OS = Rattus norvegicusGN = Ogt PE = 1 SV = 1 D3ZZR9_RAT Peptidyl-prolyl cis-trans isomerase OS = Rattus norvegicus 2 2 10.0 15387.8 9.05 0 0.172 1.33689 0.419369 1.00742 0.975718 1.35188 0.385409 0.914061 0.693363 GN = Fkbp2 PE = 4 SV = 1 QCR6_RAT Cytochrome b-c1 complex subunit 6, mitochondrial OS = Rattus 21 3 37.1 10423.53 4.9 0 1.019 1.3891 0.346795 0.936334 0.73325 1.3861 0.335815 0.862006 0.530305 norvegicus GN = Uqcrh PE = 3 SV = 1 D3ZEI4_RAT Protein Hepacam OS = Rattus norvegicus GN = Hepacam 10 6 20.5 45999.26 9.66 0 0.524 1.28622 0.497686 0.906319 0.617327 1.46093 0.242352 0.852656 0.503217 PE = 4 SV = 1 GPM6B_RAT Neuronal membrane glycoprotein M6-b OS = Rattus norvegicus 11 3 8.5 36196.32 5.76 4 0.202 1.37206 0.369551 0.884257 0.537634 1.75041 0.049004 0.843147 0.476438 GN = Gpm6b PE = 4 SV = 1 D4A1G8_RAT Protein Cep170b OS = Rattus norvegicus GN = Cep170b 2 2 2.7 171693.2 6.29 0 0.88 1.19374 0.658493 0.668783 0.078973 1.15731 0.740909 0.97061 0.887943 PE = 2 SV = 1 GMFB_RAT Glia maturation factor beta OS = Rattus norvegicus 1 1 7.0 16750 5.32 0 0.606 1.48598 0.234756 1.11965 0.588075 1.42042 0.29039 0.944836 0.797646 GN=GmfbPE=2SV=1 F1LN80_RAT Uncharacterized protein (Fragment) OS = Rattus norvegicus 1 1 3.4 52008.43 7.81 0 0.172 1.72115 0.073671 1.16699 0.448919 1.4752 0.226841 1.02376 0.937552 PE = 4 SV = 1 OPCM_RAT Opioid-binding protein/cell adhesion molecule OS = Rattus 12 5 14.5 37284.93 5.99 0 0.09 1.57282 0.158566 0.966132 0.854706 1.57355 0.138832 1.05022 0.861969 norvegicus GN = Opcml PE = 4 SV = 1 D3ZZB2_RAT Protein Pex1 OS = Rattus norvegicus GN = Pex1 PE = 3 1 1 1.1 141398.2 5.9 0 0.276 1.38619 0.350621 1.19479 0.376778 1.28065 0.502049 1.03909 0.893657 SV = 1 D3ZUJ5_RAT Deoxythymidylate kinase (Predicted), isoform CRA_b 1 1 4.7 23973.2 5.67 0 0.221 1.20668 0.634754 1.27749 0.207477 1.21642 0.62138 1.02148 0.944096 OS = Rattus norvegicus GN = Dtymk PE = 3 SV = 1 220–292 (2015) 298 Neuroscience / al. et Han X. Q5VLR5_RAT BWK4 OS = Rattus norvegicus GN = Erp44 PE = 2 SV = 1 3 3 9.6 46877.51 5.09 0 0.413 1.34598 0.406126 1.2689 0.221927 1.09675 0.870193 0.984492 0.937267 G3V640_RAT Mitochondrial import inner membrane translocase subunit TIM44 2 2 6.4 51059.81 8.49 0 0.502 1.30028 0.475211 1.05097 0.819005 1.07883 0.909306 0.839645 0.466777 OS = Rattus norvegicus GN = Timm44 PE = 4 SV = 1 G3V881_RAT Leucine rich repeat neuronal 6A, isoform CRA_a OS = Rattus 4 4 7.4 69830.97 8.63 0 0.04 1.46163 0.260163 1.11088 0.615882 1.33684 0.408559 0.896793 0.637165 norvegicus GN = Lingo1 PE = 4 SV = 1 MIC25_RAT Coiled-coil-helix-coiled-coil-helix domain-containing protein 6, 5 4 19.8 20460.68 7.81 0 0.843 1.41804 0.310245 0.99898 0.992592 1.55483 0.153165 1.34998 0.209104 mitochondrial OS = Rattus norvegicus GN = Chchd6 PE = 2 SV = 1 NDRG2_RAT Protein NDRG2 OS = Rattus norvegicus GN = Ndrg2 PE = 1 4 3 13.2 40778.74 5.16 0 0.272 1.34479 0.407849 1.08929 0.686686 1.85857 0.023374 1.2535 0.364033 SV = 1 1 1 3.3 52625.87 5.23 0 0.22 1.77416 0.054355 1.30733 0.162577 0.73822 0.352309 0.719554 0.205572 D3ZP76_RAT ProteinSV = 1 Ttyh3 OS = Rattus norvegicus GN = Ttyh3 PE = 2 F1MAP9_RAT E3 ubiquitin-protein ligase HUWE1 OS = Rattus norvegicus 2 2 0.6 459716.1 5.1 0 0.36 1.29897 0.477283 1.66163 0.002611 0.942172 0.7669 1.0088 0.980581 GN = HUWE1 PE = 2 SV = 1 TSN2_RAT Tetraspanin-2 OS = Rattus norvegicus GN = Tspan2 PE = 1 1 1 5.4 24189.26 8.28 4 0.546 1.61637 0.128232 0.662015 0.073054 1.8491 0.025019 0.714966 0.198305 SV = 1 TBA1A_RAT Tubulin alpha-1A chain OS = Rattus norvegicus GN = Tuba1a 132 18 42.4 50135.07 4.94 0 0.229 1.37772 0.361891 1.15873 0.471767 1.41296 0.299902 1.21471 0.442675 PE = 1 SV = 1 B0K031_RAT 60S ribosomal protein L7 OS = Rattus norvegicus GN = Rpl7 3 2 11.2 30312.85 10.87 0 0.578 1.30208 0.472378 1.08492 0.701403 1.44161 0.264519 1.09218 0.744931 PE = 2 SV = 1 SCRN1_RAT Secernin-1 OS = Rattus norvegicus GN = Scrn1 PE = 1 5 4 11.8 46395.51 4.73 0 0.428 1.32912 0.430883 1.07604 0.731601 1.61072 0.113467 1.04322 0.881871 SV = 1 GABR2_RAT Gamma-aminobutyric acid type B receptor subunit 2 1 1 1.9 105750.3 8.95 7 0.122 1.33981 0.415087 1.21532 0.328384 0.82505 0.509038 0.724114 0.212983 OS = Rattus norvegicus GN = Gabbr2 PE = 1 SV = 2 L1CAM_RAT Neural cell adhesion molecule L1 OS = Rattus norvegicus 9 6 8.6 140876.7 5.51 0 0.477 1.43232 0.293176 1.04367 0.844966 1.21 0.633951 0.929441 0.744896 GN = L1cam PE = 2 SV = 1 VGLU1_RAT Vesicular glutamate transporter 1 OS = Rattus norvegicus 10 4 7.3 61664.67 6.96 10 0.225 1.3302 0.429282 1.04934 0.824789 1.6983 0.068052 1.23947 0.391403 GN = Slc17a7 PE = 1 SV = 1 Q4KM69_RAT COP9 (Constitutive photomorphogenic) homolog, subunit 5 1 1 5.7 37578.39 6.1 0 0.377 1.25758 0.545177 1.20907 0.342679 0.859976 0.581071 0.782235 0.324636 (Arabidopsis thaliana) OS = Rattus norvegicus GN = Cops5 PE = 2 SV = 1 D3Z8X2_RAT Protein Pcdh10 OS = Rattus norvegicus GN = Pcdh10 PE = 2 1 1 1.2 108570.9 4.82 0 0.245 1.22156 0.607921 0.785508 0.254715 1.47741 0.224506 0.894777 0.630728 SV = 1 TBA3_RAT Tubulin alpha-3 chain OS = Rattus norvegicus GN = Tuba3a 120 16 39.8 49958.99 4.98 0 0.185 1.3673 0.376078 1.11777 0.594007 1.30866 0.454083 1.06016 0.833861 PE = 2 SV = 1 TBA1B_RAT Tubulin alpha-1B chain OS = Rattus norvegicus GN = Tuba1b 135 19 42.6 50151.07 4.94 0 0.23 1.36858 0.374313 1.16373 0.457842 1.40612 0.308784 1.21569 0.440583 PE = 1 SV = 1 KCC2A_RAT Calcium/calmodulin-dependent protein kinase type II subunit 60 19 35.4 54114.1 6.61 0 0.386 1.44262 0.281269 1.26537 0.228077 1.62648 0.103885 1.36385 0.191529 alpha OS = Rattus norvegicus GN = Camk2a PE = 1 SV = 1 241 (continued on next page) 4 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 242 B1H2A6_RAT Fxr2 protein OS = Rattus norvegicus GN = Fxr2 PE = 2 1 1 2.7 74373.52 5.85 0 0.835 1.29038 0.490975 1.09891 0.654776 1.3004 0.467958 0.982164 0.928971 SV = 1 B5DF26_RAT Similar to oxysterol-binding protein-like protein 8 isoform a 1 1 2.3 93861.36 7.08 0 0.679 1.67971 0.092404 1.41266 0.060629 1.09567 0.872539 0.98854 0.951702 OSRattus = norvegicus GN = Osbpl8 PE = 2 SV = 1 D4A0T8_RAT Protein RGD1565002 OS =Rattus norvegicus 1 1 2.7 38310.26 8.55 0 0.077 1.4388 0.285643 0.760966 0.204496 1.52472 0.178527 0.866247 0.542831 GN = RGD1565002 PE = 3 SV = 1 Q6TXE9_RAT Protein Eprs OS =Rattus norvegicus GN = Eprs PE = 2 5 3 3.4 169858.9 7.29 0 0.497 1.20712 0.633952 1.1073 0.627425 1.23215 0.591043 0.970291 0.886812 SV = 1 3HIDH_RAT 3-hydroxyisobutyrate dehydrogenase, mitochondrial 3 2 10.8 35302.37 8.73 0 0.031 1.47515 0.245831 1.14263 0.51809 1.38053 0.343588 1.26763 0.3377 OSRattus = norvegicus GN = Hibadh PE = 1 SV = 3 MPP3_RAT MAGUK p55 subfamily member 3 OS = Rattus norvegicus 5 4 8.0 66587.76 6.05 0 0.528 1.50818 0.213184 0.994263 0.972679 1.46789 0.234698 1.2296 0.411397 GN = Mpp3 PE = 1 SV = 3 CC50A_RAT Cell cycle control protein 50A OS =Rattus norvegicus 1 1 5.8 37172.11 8.98 2 0.353 0.687975 0.271538 0.930486 0.710076 1.65243 0.089513 0.824257 0.425635 GN = Tmem30a PE = 2 SV = 1 PIPNB_RAT Phosphatidylinositol transfer protein beta isoform OS =Rattus 1 1 4.4 31619.69 5.88 0 0.625 0.932932 0.771908 1.05675 0.798622 0.974642 0.844965 0.723237 0.211543 norvegicusGN = Pitpnb PE = 2 SV = 1 MAP6_RAT Microtubule-associated protein 6 OS =Rattus norvegicus 14 10 19.6 100483.7 9.45 0 0.928 1.39971 0.333086 0.926361 0.693889 1.22097 0.612542 0.824547 0.426388 GN = Map6 PE = 1 SV = 1 Q99PV2_RAT Protein Stxbp3 OS =Rattus norvegicus GN = Stxbp3 PE = 2 1 1 10.0 11667.61 9.1 0 0.374 1.25562 0.548512 0.940031 0.748029 1.72749 0.056744 1.1419 0.613678 SV = 1 ACTB_RAT Actin, cytoplasmic 1 OS =Rattus norvegicus GN = Actb 154 20 49.6 41736.29 5.29 0 0.2 1.39714 0.336377 1.06805 0.759153 1.3209 0.433968 0.986223 0.943437 PE = 1 SV = 1 CSN8_RAT COP9 signalosome complex subunit 8 OS =Rattus norvegicus 1 1 6.2 23235.31 5.09 0 0.127 1.68906 0.087873 1.26676 0.225641 1.10531 0.85162 0.80568 0.3789 GN = Cops8 PE = 2 SV = 1 Q68G39_RAT PCTAIRE protein kinase 1 OS =Rattus norvegicus 2 1 2.0 55874.28 7.23 0 0.446 1.40738 0.3234 1.17113 0.43769 1.44291 0.262979 1.1638 0.559294 GN = Cdk16 PE = 2 SV = 1 NAC3_RAT Sodium/calcium exchanger 3 OS =Rattus norvegicus 1 1 1.3 103161.6 5.02 10 0.132 1.23012 0.592721 1.09287 0.674729 0.952954 0.792602 0.657733 0.122869 GN = Slc8a3 PE = 2 SV = 1 F1LQL3_RAT 60S ribosomal protein L18a (Fragment) OS = Rattus norvegicus 2 2 11.0 22318.9 10.81 0 0.605 1.36971 0.372767 1.03666 0.87003 1.4828 0.218877 1.08004 0.778298 GN = Rpl18a PE = 2 SV = 1 G3V826_RAT Transketolase OS =Rattus norvegicus GN = Tkt PE = 4 9 5 10.7 71157.78 7.54 0 0.171 1.39909 0.33388 1.02698 0.904831 1.54434 0.16167 1.04212 0.885006 SV = 1 ACTN1_RAT Alpha-actinin-1 (Fragment) OS =Rattus norvegicus 15 12 15.6 99808.87 5.41 0 0.577 1.3174 0.448602 0.865976 0.475762 1.26471 0.530505 0.913765 0.692385 GN = Actn1 PE = 2 SV = 1 Q4V7D9_RAT Protein Smpdl3b OS =Rattus norvegicus GN = Smpdl3b 1 1 2.2 51644.72 5.53 6 0.229 1.04295 0.954566 0.826364 0.356131 1.49856 0.203004 0.931172 0.750773 PE = 2 SV = 1 F1LXD6_RAT Protein Pitpnm2 (Fragment) OS =Rattus norvegicus 1 1 1.1 139593.1 7.86 0 0.418 1.41981 0.308097 1.03811 0.864817 1.48294 0.218725 1.13525 0.630641 GN = Pitpnm2 PE = 2 SV = 1 Q3T1H3_RAT Ncam1 protein OS =Rattus norvegicus GN = Ncam1 PE = 2 33 13 18.9 93572.07 4.84 0 0.417 1.3472 0.404369 0.822788 0.346353 1.26959 0.521709 0.840389 0.46882 SV = 1 D3ZSY8_RAT Protein Tbc1d10b OS =Rattus norvegicus GN = Tbc1d10b 2 2 3.5 86648.14 9.19 0 0.584 1.50382 0.217301 0.931522 0.714165 1.33937 0.40461 1.00084 0.99563 PE = 4 SV = 1 D3ZN99_RAT Protein Bai2 OS =Rattus norvegicus GN = Bai2 PE = 2 1 1 1.2 169791.1 7.49 0 0.188 1.30777 0.463467 1.04266 0.848576 1.46577 0.237004 0.814182 0.399884 SV = 1 GSK3B_RAT Glycogen synthase kinase-3 beta OS =Rattus norvegicus 1 1 5.7 46741.84 8.98 0 0.32 1.80051 0.04645 1.09058 0.682396 1.23168 0.591933 0.875138 0.569562 GN = Gsk3b PE = 1 SV = 1 RALA_RAT Ras-related protein Ral-A OS =Rattus norvegicus GN = Rala 4 3 17.0 23552.5 6.66 0 0.621 1.44418 0.279497 1.01804 0.937163 1.56119 0.148173 1.0723 0.799814 PE = 1 SV = 1 STABP_RAT STAM-binding protein OS =Rattus norvegicus GN = Stambp 1 1 2.8 48511.18 6.42 0 0.509 1.21128 0.62642 1.14545 0.509799 1.17796 0.698248 0.976047 0.90722 PE = 2 SV = 1 UBA1_RAT Ubiquitin-like modifier-activating enzyme 1 OS =Rattus 7 5 6.7 117786.4 5.36 0 0.272 1.38033 0.358397 1.01477 0.949013 1.1578 0.739877 0.889423 0.613775 norvegicusGN = Uba1 PE = 1 SV = 1 F1LQP0_RAT Cytohesin-3 (Fragment) OS =Rattus norvegicus GN = Cyth3 1 1 2.6 45489.28 5.66 0 0.637 1.17921 0.685554 0.9156 0.652328 1.43921 0.267369 0.860926 0.527138 PE = 2 SV = 1 KAP0_RAT cAMP-dependent protein kinase type I-alpha regulatory subunit 6 3 9.7 43094.47 5.27 0 0.413 1.36687 0.376668 0.901784 0.600528 1.19441 0.66494 0.838227 0.462894 OSRattus = norvegicus GN = Prkar1a PE = 2 SV = 2 D3ZPJ0_RAT Protein Shisa7 OS =Rattus norvegicus GN = Shisa7 PE = 2 2 2 4.1 56422.2 9.91 0 0.399 1.37795 0.361586 1.03244 0.885165 1.05292 0.966203 0.724371 0.213407 SV = 1 NUMBL_RAT Numb-like protein OS =Rattus norvegicus GN = Numbl 2 2 4.7 65512.12 9.07 0 0.581 1.19368 0.658603 1.06348 0.775032 1.10838 0.844986 0.918858 0.709298 PE = 1 SV = 1 UCHL3_RAT Ubiquitin carboxyl-terminal hydrolase isozyme L3 OS =Rattus 1 1 7.0 26123.32 5.01 0 0.393 1.48772 0.233012 1.32244 0.142855 0.824575 0.508092 0.81234 0.39528 norvegicusGN = Uchl3 PE = 1 SV = 1 AT1A3_RAT Sodium/potassium-transporting ATPase subunit alpha-3 200 44 41.5 111690.3 5.26 8 0.007 1.36492 0.379354 0.874667 0.504679 1.38741 0.333998 0.919092 0.710078 OS = Rattus norvegicus GN = Atp1a3 PE = 1 SV = 2 D4A781_RAT Protein Ipo5 OS = Rattus norvegicus GN = Ipo5 PE = 4 2 1 1.6 123704.8 4.85 0 0.133 1.82442 0.040137 1.39793 0.070439 0.728312 0.3366 1.07085 0.803882 SV = 1 CLCB_RAT Clathrin light chain B OS = Rattus norvegicus GN = Cltb 1 1 4.4 25117.14 4.56 0 0.871 1.30967 0.460505 0.964161 0.84653 1.48906 0.212465 1.06031 0.833442 PE = 1 SV = 1 C7C5T2_RAT 6-phosphofructokinase OS = Rattus norvegicus GN = Pfkp 8 6 8.8 85719.37 6.94 0 0.132 1.4412 0.282895 1.08656 0.695862 1.11332 0.834321 0.752686 0.263832 PE = 2 SV = 1 G3V963_RAT RCG47487, isoform CRA_b OS = Rattus norvegicus 2 2 2.8 110459.9 5.3 0 0.25 1.30328 0.470478 1.2492 0.257778 1.14157 0.773968 0.886164 0.603556 GN = Tmem132a PE = 4 SV = 1 Q99NI1_RAT Nucleoside diphosphate kinase DR-nm23 OS = Rattus 1 1 8.3 19088.75 5.98 0 0.021 1.06472 0.910369 0.921328 0.674327 1.49386 0.207646 1.17989 0.52089 norvegicus GN=Nme3PE=2SV=1 TERA_RAT Transitional endoplasmic reticulum ATPase OS = Rattus 15 10 19.7 89347.81 5.14 0 0.351 1.38893 0.347024 1.1382 0.531257 1.26256 0.534387 1.18382 0.511713 norvegicus GN = Vcp PE = 1 SV = 3 CAZA1_RAT F-actin-capping protein subunit alpha-1 OS = Rattus norvegicus 3 2 13.3 32909.37 5.43 0 0.641 1.25787 0.544683 0.954723 0.807624 0.871159 0.605105 0.760691 0.279469 GN = Capza1 PE = 1 SV = 1 G3V6P2_RAT Dihydrolipoamide S-succinyltransferase (E2 component of 2- 9 4 8.8 48898.78 8.9 0 0.165 1.52716 0.195897 1.16407 0.456923 1.50133 0.200303 0.995028 0.974874 oxo-glutarate complex), isoform CRA_a OS = Rattus norvegicus GN = Dlst PE = 3 SV = 1 AT1A2_RAT Sodium/potassium-transporting ATPase subunit alpha-2 144 37 34.8 112129 5.35 0 0.001 1.35427 0.394281 0.88386 0.536248 1.34342 0.398331 0.976457 0.908674 220–292 (2015) 298 Neuroscience / al. et Han X. OS = Rattus norvegicus GN = Atp1a2 PE = 2 SV = 1 B5DF52_RAT C1q and tumor necrosis factor related protein 4 OS = Rattus 1 1 4.3 35178.58 9.09 0 0.138 1.19994 0.647068 0.918129 0.662004 1.26409 0.531614 0.861921 0.530057 norvegicus GN = C1qtnf4 PE = 2 SV = 1 D3ZWW3_RAT Protein Rasal3 OS = Rattus norvegicus GN = Rasal3 PE = 4 1 1 0.7 114478.5 9.29 0 0.456 1.44312 0.280705 1.46912 0.032896 1.38759 0.333744 1.43412 0.118815 SV = 1 D3ZNZ8_RAT 40S ribosomal protein S27 OS = Rattus norvegicus 1 1 13.1 9470.05 9.44 0 0.467 1.37352 0.367563 0.930407 0.709765 1.3287 0.421413 0.820767 0.416607 GN = Rps27l2 PE = 3 SV = 1

CTNB1_RAT Catenin beta-1 OS = Rattus norvegicus GN = Ctnnb1 PE = 1 10 5 9.1 85453.59 5.53 0 0.178 1.26176 0.538104 0.995559 0.978148 0.809136 0.477839 0.657659 0.122788 SV = 1 ECI2_RAT Enoyl-CoA delta isomerase 2, mitochondrial OS = Rattus 4 3 8.7 43020.9 9.11 0 0.242 1.45818 0.263911 1.42322 0.054319 1.26138 0.536541 1.17301 0.537144 ATP5I_RAT ATPnorvegicus synthaseGN subunit = Eci2 e, PE mitochondrial = 1 SV = 1 OS = Rattus 3 2 32.4 8254.55 9.34 0 0.494 1.00707 0.964249 1.17739 0.421041 2.10203 0.003286 2.20621 1.38E05 norvegicus GN = Atp5i PE = 1 SV = 3 F1LS79_RAT Chondroitin sulfate proteoglycan 4 OS = Rattus norvegicus 2 2 1.3 252005 5.27 0 0.157 1.16315 0.71593 0.862628 0.464868 1.19501 0.663741 0.786167 0.333366 GN = Cspg4 PE = 2 SV = 1 D3ZES7_RAT Uncharacterized protein OS = Rattus norvegicus 4 4 3.1 212608.9 6.44 0 0.23 1.26015 0.540822 1.0273 0.903678 1.04167 0.990993 0.857647 0.517585 GN = Plxna4a PE = 4 SV = 1 Q3SWU5_RAT Protein kinase, cAMP dependent regulatory, type I, beta 5 3 8.7 40106.88 5.12 0 0.405 1.33846 0.41707 1.12039 0.585749 1.27568 0.510828 0.936601 0.769294 OS = Rattus norvegicus GN = Cyp4f18 PE = 2 SV = 1 VATL_RAT V-type proton ATPase 16 kDa proteolipid subunit OS = Rattus 1 1 11.6 15807.75 9.1 4 1.075 1.52376 0.198917 1.16609 0.451368 1.0068 0.923816 1.06299 0.825882 norvegicus GN = Atp6v0c PE = 2 SV = 1 GBLP_RAT Guanine nucleotide-binding protein subunit beta-2-like 1 1 1 5.1 35076.33 7.6 0 0.251 1.01246 0.978436 0.739516 0.16686 1.07779 0.911579 0.693602 0.166935 OS = Rattus norvegicus GN = Gnb2l1 PE = 1 SV = 3 EAA1_RAT Excitatory amino acid transporter 1 OS = Rattus norvegicus 16 4 13.1 59696.84 8.51 6 0.379 1.29243 0.487686 0.796929 0.280796 1.43637 0.270766 0.810997 0.391942 GN = Slc1a3 PE = 1 SV = 2 RS3A_RAT 40S ribosomal protein S3a OS = Rattus norvegicus 2 1 5.3 29944.59 9.75 0 0.626 1.15472 0.732081 0.987015 0.942121 0.965467 0.822714 0.933127 0.757428 GN = Rps3a PE = 1 SV = 2 D3ZPC5_RAT Protein Igsf8 OS = Rattus norvegicus GN = Igsf8 PE = 2 9 5 15.9 53802.3 6.58 0 0.137 1.4048 0.326634 0.771918 0.225936 1.19779 0.658168 0.780245 0.320276 SV = 1 IRGM_RAT Immunity-related GTPase family M protein OS = Rattus 1 1 3.9 46337.28 8.39 0 0.134 1.27875 0.509856 0.96148 0.835437 1.14573 0.765199 0.777885 0.315152 norvegicus GN = Irgm PE = 2 SV = 1 CLVS1_RAT Clavesin-1 OS = Rattus norvegicus GN = Clvs1 PE = 1 1 1 5.1 40665.99 6.32 0 0.368 1.4749 0.246088 0.93064 0.710683 1.99099 0.008464 1.47148 0.090142 SV = 1 E9PSJ4_RAT Protein Spag9 OS = Rattus norvegicus GN = Spag9 PE = 2 1 1 1.5 77754.21 4.93 0 0.382 1.25537 0.54894 0.970418 0.87254 1.41248 0.300512 1.00623 0.987987 SV = 1 B2RYT7_RAT Haloacid dehalogenase-like hydrolase domain containing 3 4 2 14.3 27793.54 6.5 0 0.082 1.18324 0.677998 1.17705 0.421933 0.862056 0.585508 0.753805 0.265981 OS = Rattus norvegicus GN = Hdhd3 PE = 2 SV = 1

SYNJ1_RAT Isoform 2 of Synaptojanin-1 OS = Rattus norvegicus 8 6 5.7 144521.4 6.97 0 0.358 1.36762 0.375626 1.07963 0.719334 1.38717 0.33433 1.11512 0.683148 243 GN = Synj1 (continued on next page) 4 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 244

BSN_RAT Protein bassoon OS = Rattus norvegicus GN = Bsn PE = 2 43 32 11.7 416591.8 7.37 0 0.828 1.32334 0.439571 0.877371 0.513863 1.4326 0.275323 0.980286 0.922287 SV = 1 D3ZQP6_RAT Protein Sema7a OS =Rattus norvegicus GN = Sema7a 2 2 5.9 75143.16 7.09 0 0.457 1.32042 0.444005 1.00206 0.995179 0.982231 0.863463 0.757317 0.272803 PE = 4 SV = 1 D4A4M0_RAT Protein Shisa6 OS =Rattus norvegicus GN = Shisa6 PE = 4 4 3 8.8 58181.89 9.51 0 0.447 1.38486 0.352378 1.06721 0.762076 1.03849 0.998002 0.762566 0.283222 SV = 1 CRTC1_RAT CREB-regulated transcription coactivator 1 OS =Rattus 2 1 2.4 66923.68 5.68 0 0.563 1.28521 0.499334 0.928836 0.703585 1.09222 0.880056 0.739825 0.239992 norvegicusGN = Crtc1 PE = 1 SV = 1 F1M6T7_RAT Protein Erich5 OS =Rattus norvegicus GN = Erich5 PE = 4 1 1 5.5 33328.31 4.62 0 1.016 1.22265 0.605986 0.873869 0.501985 1.21592 0.622369 0.708547 0.188457 SV = 1 D4ADS4_RAT Protein Mgst3 OS =Rattus norvegicus GN = Mgst3 PE = 4 21 2 15.8 16732.33 9.54 0 0.226 1.15972 0.72249 1.14889 0.499805 1.82417 0.029837 1.41488 0.136143 SV = 1 G3V6P8_RAT Guanine nucleotide-binding protein subunit gamma 9 3 59.7 7985.1 9.14 0 0.465 1.45168 0.271069 1.13379 0.544499 1.06905 0.930738 0.845944 0.484232 OS =Rattus norvegicus GN = Gng12 PE = 3 SV = 1 D3ZZ41_RAT Protein Mrps36 OS =Rattus norvegicus GN = Mrps36 3 2 13.5 11470.14 10.34 0 0.635 1.3521 0.397357 1.04494 0.84044 1.15798 0.739512 0.900932 0.650462 PE = 2 SV = 1 CNTN1_RAT Contactin-1 OS =Rattus norvegicus GN = Cntn1 PE = 1 24 15 19.8 113493.1 5.77 0 0.309 1.38108 0.3574 0.965631 0.852626 1.29835 0.471431 0.878576 0.580063 SV = 2 D3ZD86_RAT Uncharacterized protein OS =Rattus norvegicus PE = 2 1 1 0.3 622450.4 5.28 0 0.635 1.57616 0.156064 1.25526 0.246336 1.33851 0.405941 0.759671 0.277443 SV = 1 RL8_RAT 60S ribosomal protein L8 OS =Rattus norvegicus GN = Rpl8 1 1 6.2 28024.32 11.04 0 0.528 1.24904 0.559755 1.14256 0.518288 1.21875 0.616854 0.885525 0.601562 PE = 2 SV = 2 Q5PPH9_RAT Acidic (Leucine-rich) nuclear phosphoprotein 32 family, 1 1 4.9 28565.24 3.98 0 1.206 1.4802 0.240629 0.761263 0.205056 1.47728 0.224644 0.937409 0.772065 member A OS =Rattus norvegicus GN = Anp32a PE = 2 SV = 1 G3V758_RAT Contactin 2 OS =Rattus norvegicus GN = Cntn2 PE = 4 2 2 3.9 113046.5 7.57 0 0.324 1.15884 0.724174 0.924051 0.684883 1.20014 0.653475 0.944353 0.795975 SV = 1 CADM3_RAT Cell adhesion molecule 3 OS =Rattus norvegicus 11 8 29.0 42905.73 5.5 1 0.295 1.31589 0.450917 0.741743 0.170506 1.47881 0.223029 0.996397 0.979764 GN = Cadm3 PE = 2 SV = 1 F1LT49_RAT Protein Lrrc47 (Fragment) OS =Rattus norvegicus 1 1 1.7 63629.47 8.52 0 0.416 1.42952 0.296473 1.07679 0.729046 1.11537 0.829899 0.755769 0.269781 GN = Lrrc47 PE = 4 SV = 1 ODBA_RAT 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1 1 3.6 50163.89 7.68 0 0.594 0.762919 0.394315 0.824495 0.350998 1.01717 0.949429 1.26106 0.349783 (Fragment) OS =Rattus norvegicus GN = Bckdha PE = 1 SV = 1 D3ZQ23_RAT ELKS/Rab6-interacting/CAST family member 1 OS =Rattus 3 3 3.0 128317.2 5.68 0 0.983 1.14127 0.758064 0.848571 0.420678 1.29053 0.484831 0.73191 0.226098 norvegicusGN = Erc1 PE = 2 SV = 1 G3V644_RAT NADH dehydrogenase (Ubiquinone) flavoprotein 3-like, isoform 6 4 8.5 49299.2 8.82 0 0.913 1.33121 0.427772 1.17021 0.440172 1.36573 0.364824 1.17097 0.542009 CRA_a OS =Rattus norvegicus GN = Ndufv3 PE = 4 SV = 1 THIL_RAT Acetyl-CoA acetyltransferase, mitochondrial OS =Rattus 13 7 19.1 44694.51 8.92 0 0.086 1.44225 0.281691 1.17758 0.420557 1.00374 0.916275 1.31191 0.263327 norvegicusGN = Acat1 PE = 1 SV = 1 ECH1_RAT Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial 1 1 3.4 36171.3 8.14 0 0.097 1.1732 0.696865 0.872363 0.496925 1.65697 0.087171 1.15791 0.573684 OS = Rattus norvegicus GN = Ech1 PE = 1 SV = 2 D3Z8I7_RAT Glutathione S-transferase theta-1 OS =Rattus norvegicus 2 2 10.5 23380.84 9.3 0 0.267 1.23574 0.582844 1.15356 0.4864 1.33191 0.416325 1.107 0.704794 GN = Gstt1 PE = 4 SV = 1 GNAI1_RAT Guanine nucleotide-binding protein G(i) subunit alpha-1 35 10 28.0 40344.64 5.69 0 0.32 1.47663 0.2443 1.03202 0.886695 1.42893 0.279804 1.1294 0.645717 OSRattus = norvegicus GN = Gnai1 PE = 1 SV = 3 ENOG_RAT Gamma-enolase OS =Rattus norvegicus GN = Eno2 PE = 1 19 11 27.2 47139.99 5.03 0 0.183 1.28286 0.503147 1.12846 0.560733 1.31345 0.446151 1.10787 0.70246 SV = 2 GBG7_RAT Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit 5 1 20.6 7523.65 8.71 0 0.335 1.25442 0.550547 0.856583 0.445557 1.35431 0.381742 1.00684 0.986231 gamma-7 OS =Rattus norvegicus GN = Gng7 PE = 2 SV = 2 ODP2_RAT Dihydrolipoyllysine-residue acetyltransferase component of 23 12 18.8 67165.04 8.76 0 0.017 1.27995 0.507901 1.43714 0.046849 1.54527 0.160905 1.46697 0.093277 pyruvate dehydrogenase complex, mitochondrial OS =Rattus norvegicusGN = Dlat PE = 1 SV = 3 B5DFJ4_RAT Protein Vps18 OS =Rattus norvegicus GN = Vps18 PE = 2 1 1 1.2 110184.3 5.71 0 0.266 1.26426 0.533907 0.924767 0.687673 1.19819 0.657371 0.867421 0.546324 SV = 1 D4A921_RAT Protein Trim46 OS =Rattus norvegicus GN = Trim46 PE = 2 1 1 2.2 83429.61 7.85 0 0.281 0.956762 0.832797 0.816272 0.328979 1.02432 0.967141 0.704564 0.18253 SV = 1 F1LTQ2_RAT Uncharacterized protein (Fragment) OS =Rattus norvegicus 38 3 11.0 34432.01 5.32 0 0.232 1.33028 0.42916 1.02142 0.924949 1.39992 0.317003 1.00919 0.979466 PE = 3 SV = 1 D3ZT20_RAT Uncharacterized protein OS = Rattus norvegicus PE = 4 1 1 1.3 92692.03 8.74 0 0.343 1.37751 0.362183 0.911879 0.638199 1.19899 0.655782 0.864294 0.537044 SV = 1 THIKA_RAT Isoform 2 of 3-ketoacyl-CoA thiolase A, peroxisomal 1 1 5.6 38117.96 8.56 0 0.087 1.31268 0.45586 0.724212 0.143371 1.01949 0.955169 0.61581 0.083507 OS = Rattus norvegicus GN = Acaa1a ERMP1_RAT Endoplasmic reticulum metallopeptidase 1 OS = Rattus 2 2 2.6 99895.6 6.82 8 0.184 1.282 0.504546 1.11084 0.616014 1.40337 0.312409 1.02128 0.944677 norvegicus GN = Ermp1 PE = 1 SV = 1 F1LUE2_RAT Calcium/calmodulin-dependent protein kinase type II subunit 26 8 16.7 53592.45 7.39 0 0.42 1.55503 0.172409 1.51285 0.019673 1.50767 0.194218 1.7957 0.004169 gamma (Fragment) OS = Rattus norvegicus GN = Camk2g PE = 2 SV = 1 SNIP1_RAT Protein Snip OS = Rattus norvegicus GN = Snip PE = 2 22 12 13.9 134837.1 9.33 0 0.685 1.22188 0.607357 1.00107 0.998781 1.38233 0.341067 0.857597 0.51744 SV = 1 GUAD_RAT Guanine deaminase OS = Rattus norvegicus GN = Gda 6 5 12.3 51015.52 5.56 0 0.192 1.27123 0.522264 1.11596 0.599727 1.49742 0.204118 0.997279 0.982917 PE = 1 SV = 1 S6A11_RAT Sodium- and chloride-dependent GABA transporter 3 4 3 5.4 69946.25 6.66 10 0.43 1.42002 0.307841 0.978485 0.906269 1.20426 0.645291 0.87829 0.579185 OS = Rattus norvegicus GN = Slc6a11 PE = 2 SV = 1 Q63116_RAT Tyrosine-protein kinase receptor OS = Rattus norvegicus 3 3 3.5 109340.9 7.45 0 0.207 1.29411 0.485005 1.10485 0.635355 1.19306 0.66764 1.0078 0.983469 GN = Kit PE = 2 SV = 1 F1M585_RAT Protein Atp8a1 OS = Rattus norvegicus GN = Atp8a1 PE = 2 6 4 5.1 129701 6.62 0 0.018 1.33738 0.418654 1.05109 0.818581 1.33347 0.413854 0.728251 0.219872 SV = 1 KAD1_RAT Adenylate kinase isoenzyme 1 OS = Rattus norvegicus 7 5 32.0 21583.52 7.66 0 0.43 1.35191 0.397637 1.51853 0.018355 1.65882 0.08623 2.14985 3.42E05 220–292 (2015) 298 Neuroscience / al. et Han X. GN = Ak1 PE = 1 SV = 3 DREB_RAT Isoform E1 of Drebrin OS = Rattus norvegicus GN = Dbn1 12 6 11.4 72600.7 4.4 0 0.796 1.26444 0.533602 0.81448 0.324302 1.11782 0.824623 0.744467 0.248415 D3ZP47_RAT Phosphohistidine phosphatase 1 (Predicted), isoform CRA_a 4 2 16.9 14010.4 5.27 0 0.683 1.21693 0.616227 0.982566 0.923403 1.12208 0.81548 0.893384 0.626299 OS = Rattus norvegicus GN = Phpt1 PE = 4 SV = 1 G3V8F1_RAT Transporter OS = Rattus norvegicus GN = Slc6a7 PE = 3 2 2 4.1 71075.85 6.17 0 0.492 1.12846 0.783079 1.27793 0.206765 1.16029 0.734701 1.1475 0.599541 SV = 1 A1I3_RAT Alpha-1-inhibitor 3 OS = Rattus norvegicus GN = A1i3 5 2 2.2 163771.4 5.7 0 0.216 1.2853 0.499186 1.44416 0.043418 1.15607 0.743496 1.56611 0.041726 PE = 1 SV = 1 PPM1A_RAT Protein phosphatase 1A OS = Rattus norvegicus 3 3 11.0 42416.22 5.19 0 0.493 1.21536 0.619051 1.04265 0.848608 1.04253 0.98908 0.798848 0.362539 GN = Ppm1a PE = 1 SV = 1 0.522 1.25594 0.547968 0.723497 0.14234 1.14965 0.756945 0.75493 0.268154 D3ZCZ9_RAT Protein LOC679739 OS = Rattus norvegicus 14 6 59.5 13039.69 9.33 0 MCCB_RATGNMethylcrotonoyl-CoA = LOC679739 PE = carboxylase 4 SV = 1 beta chain, mitochondrial 6 4 5.9 61516.44 8.56 0 0.178 1.34743 0.404039 1.05371 0.809346 1.09523 0.873509 0.852566 0.502959 OS = Rattus norvegicus GN = Mccc2 PE = 2 SV = 1 F1LRI7_RAT AP2-associated protein kinase 1 (Fragment) OS = Rattus 6 4 5.8 98250.41 6.07 0 0.494 1.26637 0.530359 1.20141 0.360723 0.905064 0.680539 1.03133 0.915851 norvegicus GN = Aak1 PE = 2 SV = 1 D3ZUR9_RAT Leucyl-cystinyl aminopeptidase OS = Rattus norvegicus 1 1 1.7 117272.2 5.41 0 0.22 0.904282 0.700552 0.748243 0.181492 2.16811 0.001796 1.11004 0.69668 GN = Lnpep PE = 2 SV = 1 PROF1_RAT Profilin-1 OS = Rattus norvegicus GN = Pfn1 PE = 1 SV = 2 7 2 22.9 14957.06 8.46 2 0.031 1.41228 0.317311 1.40037 0.068728 1.05838 0.954198 1.06076 0.832178 D4A5X7_RAT Ganglioside-induced differentiation-associated-protein 1 10 5 14.0 41216.11 8.86 2 0.394 1.28879 0.493531 0.978039 0.904403 1.76401 0.044843 1.38893 0.162529 (Predicted) OS = Rattus norvegicus GN = Gdap1 PE = 4 SV = 1 F1LWE3_RAT Protein RGD1308124 (Fragment) OS = Rattus norvegicus 2 1 0.7 161459.5 7.57 0 0.753 1.18794 0.669246 1.00145 0.997382 1.23711 0.581611 0.920674 0.715365 GN = Nhsl1 PE = 2 SV = 1 C2D1A_RAT Coiled-coil and C2 domain-containing protein 1A OS = Rattus 1 1 1.8 103585.7 8.26 0 0.593 1.05076 0.938687 0.704957 0.117525 1.14769 0.761074 0.847722 0.489225 norvegicus GN = Cc2d1a PE = 2 SV = 2 TBA4A_RAT Tubulin alpha-4A chain OS = Rattus norvegicus 122 20 45.8 49923.86 4.95 0 0.252 1.26504 0.532601 1.19577 0.374368 1.24002 0.576111 1.09068 0.749018 GN = Tuba4a PE = 2 SV = 1 HINT3_RAT Histidine triad nucleotide-binding protein 3 OS = Rattus 2 2 23.4 19693.33 6.23 0 0.289 1.11063 0.818262 0.971881 0.878642 1.22375 0.607154 0.862725 0.532418 norvegicus GN = Hint3 PE = 2 SV = 2 F1M745_RAT Kinesin-like protein KIF2A (Fragment) OS = Rattus norvegicus 5 4 8.5 81633.23 5.92 0 0.649 1.20583 0.636305 0.859612 0.455175 1.57499 0.137778 1.31097 0.264771 GN = Kif2a PE = 2 SV = 1 D3ZI16_RAT COP9 (Constitutive photomorphogenic) homolog, subunit 6 1 1 2.3 37701.86 5.75 0 0.019 1.27733 0.512189 0.953976 0.804564 1.4899 0.211613 1.03545 0.90405 (Arabidopsis thaliana) (Predicted), isoform CRA_a OS = Rattus norvegicus GN = Cops6 PE = 4 SV = 1 D4A9F4_RAT Netrin G2 (Predicted), isoform CRA_b OS = Rattus norvegicus 2 2 4.8 66163.26 5.81 0 0.452 1.119 0.801689 1.06075 0.784586 1.22868 0.597666 0.937557 0.772573 GN = Ntng2 PE = 4 SV = 1 AT1A1_RAT Sodium/potassium-transporting ATPase subunit alpha-1 129 32 30.7 113053 5.3 10 0.002 1.27399 0.517688 0.83158 0.370702 1.47412 0.227994 0.979436 0.919264 OS = Rattus norvegicus GN = Atp1a1 PE = 1 SV = 1 245 (continued on next page) 4 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 246 MAP2_RAT Isoform MAP2b of Microtubule-associated protein 2 33 22 17.9 199050.5 4.73 0 0.802 1.24731 0.562744 0.99435 0.973046 1.41171 0.30151 1.04667 0.872038 OS = Rattus norvegicus GN = Map2 B5DF50_RAT Protein Galnt2 (Fragment) OS =Rattus norvegicus 1 1 2.6 60415.95 8.35 0 0.564 1.17284 0.697549 1.35028 0.111375 0.911497 0.695249 1.08146 0.774396 GN = Galnt2 PE = 2 SV = 1 ESTD_RAT S-formylglutathione hydrolase OS =Rattus norvegicus 3 3 13.5 31363.33 6.44 0 0.263 1.44307 0.280753 0.824163 0.350091 1.01733 0.949841 1.02105 0.945346 GN = Esd PE = 1 SV = 1 Q9JMG8_RAT Dihydropyrimidinase-related protein OS =Rattus norvegicus 8 7 15.8 61394.45 6.5 0 0.162 1.40827 0.322285 0.995535 0.978049 1.23688 0.582049 0.951395 0.820419 GN = Dpysl5 PE = 2 SV = 1 PCLO_RAT Isoform 2 of Protein piccolo OS =Rattus norvegicus 16 13 4.3 530146.2 6 0 0.806 1.27868 0.509971 0.958651 0.823764 1.29568 0.475986 0.832529 0.447481 GN = Pclo EIF3I_RAT Eukaryotic translation initiation factor 3 subunit I OS =Rattus 1 1 3.4 36460.38 5.38 0 0.408 1.24417 0.56816 0.841237 0.398637 1.60902 0.114545 1.04416 0.879192 norvegicusGN = Eif3i PE = 2 SV = 1 D3ZEG5_RAT Protein Gprin1 OS =Rattus norvegicus GN = Gprin1 PE = 4 9 7 11.4 96201.63 6.18 0 0.643 1.20785 0.632626 0.80301 0.295399 1.35584 0.379451 1.04484 0.877252 SV = 1 DCE2_RAT Glutamate decarboxylase 2 OS =Rattus norvegicus 2 2 3.9 65401.59 6.45 0 0.191 1.32056 0.443789 0.922574 0.67915 1.2467 0.563602 0.836249 0.457512 GN = Gad2 PE = 1 SV = 1 HPLN1_RAT Hyaluronan and proteoglycan link protein 1 OS =Rattus 11 5 17.2 40261.17 8.2 0 0.338 1.2955 0.482785 0.795502 0.277441 1.31769 0.43919 1.37921 0.173349 norvegicusGN = Hapln1 PE = 1 SV = 2 D3ZWX4_RAT Protein Nckipsd OS =Rattus norvegicus GN = Nckipsd 2 2 4.1 78452.44 5.67 0 0.3 1.37547 0.364922 1.12891 0.559371 1.26659 0.527107 0.979359 0.918991 PE = 4 SV = 1 OLA1_RAT Obg-like ATPase 1 OS =Rattus norvegicus GN = Ola1 1 1 4.6 44534.78 7.62 0 0.387 1.26275 0.53645 1.34588 0.115943 1.4044 0.311055 1.3708 0.183131 PE = 2 SV = 1 F1M9A2_RAT Sodium/calcium exchanger 2 OS =Rattus norvegicus 19 8 13.4 100334.7 5.1 0 0.109 1.23981 0.575738 0.993074 0.967662 1.0491 0.974622 0.78006 0.319872 GN = Slc8a2 PE = 2 SV = 1 UK114_RAT Ribonuclease UK114 OS = Rattus norvegicus GN = Hrsp12 2 1 7.3 14303.28 7.8 0 0.216 1.22914 0.594455 1.0944 0.669664 1.50899 0.192967 1.248 0.37461 PE = 1 SV = 3 F1M4V9_RAT Gamma-aminobutyric acid receptor subunit gamma-2 2 2 5.8 51680.93 8.64 0 0.114 1.23378 0.586273 0.793306 0.272332 1.14778 0.760881 0.814843 0.401544 (Fragment) OS =Rattus norvegicus GN = Gabrg2 PE = 2 SV = 1 GEPH_RAT Isoform 5 of Gephyrin OS =Rattus norvegicus GN = Gphn 2 2 5.6 79747.52 5.25 0 0.181 1.27031 0.523791 0.890234 0.558706 1.38781 0.333439 0.920393 0.714423 PALM_RAT Paralemmin, isoform CRA_b OS =Rattus norvegicus 7 5 13.0 37019.81 4.87 0 0.868 1.34275 0.41081 0.728326 0.149421 1.03895 0.996986 0.740857 0.241846 GN = Palm PE = 4 SV = 1 B7X6I3_RAT C38 protein OS =Rattus norvegicus GN = Cend1 PE = 2 8 3 19.5 15042.83 9.01 1 0.6 1.33012 0.429393 1.22225 0.313007 1.31471 0.444069 1.04517 0.876313 SV = 1 Q6P7A7_RAT Ribophorin I OS =Rattus norvegicus GN = Rpn1 PE = 2 6 5 11.2 68400.3 6.05 1 0.226 1.27027 0.523867 1.24815 0.259796 1.15199 0.75203 1.09325 0.741984 SV = 1 ABCB9_RAT Isoform 3 of ATP-binding cassette sub-family B member 9 1 1 1.3 76376.42 6.18 0 0.281 1.63877 0.114492 1.04756 0.831123 1.20208 0.64963 0.839133 0.465373 OSRattus = norvegicus GN = Abcb9 CRYL1_RAT Lambda-crystallin homolog OS = Rattus norvegicus 1 1 3.5 35340.66 5.94 0 0.103 0.965705 0.855932 2.34697 8.70E 10 1.41039 0.303222 1.1444 0.60736 GN = Cryl1 PE = 2 SV = 3 RL24_RAT 60S ribosomal protein L24 OSRattus = norvegicus 2 1 8.9 17778.75 11.26 0 0.926 1.24549 0.565884 0.986232 0.938825 1.0514 0.969556 0.869019 0.551097 GN = Rpl24 PE = 1 SV = 1

SHAN1_RAT SH3 and multiple ankyrin repeat domains protein 1 OS =Rattus 9 6 4.3 226332.4 8.52 0 0.564 1.18468 0.675324 0.991948 0.962914 1.28833 0.488631 1.01242 0.97015 norvegicusGN = Shank1 PE = 1 SV = 1 NLRX1_RAT NLR family member X1 OS =Rattus norvegicus GN = Nlrx1 3 2 3.4 107588.6 7.36 0 0.096 1.21364 0.622154 0.999351 0.994157 1.41324 0.299532 0.969951 0.885609 PE = 2 SV = 1 GNAI3_RAT Guanine nucleotide-binding protein G(k) subunit alpha OS =Rattus 24 4 11.6 40521.71 5.5 0 0.36 1.43354 0.291755 0.992608 0.965697 1.49393 0.207573 1.17972 0.521289 norvegicusGN = Gnai3 PE = 1 SV = 3 ENOB_RAT Beta-enolase OS =Rattus norvegicus GN = Eno3 PE = 1 14 5 15.7 47013.35 7.08 0 0.196 1.22381 0.603922 1.06872 0.756812 1.17744 0.699308 1.03916 0.893452 SV = 3 MAP4_RAT Microtubule-associated protein OS =Rattus norvegicus 6 4 6.9 95057.9 8.81 0 0.657 1.45755 0.264596 1.24977 0.256674 1.18779 0.678262 1.07165 0.801636 GN = Map4 PE = 2 SV = 1 NCAM1_RAT Neural cell adhesion molecule 1 OS =Rattus norvegicus 33 13 18.9 94657.19 4.83 0 0.433 1.2353 0.583611 0.856514 0.445337 1.17224 0.709983 0.896769 0.637088 GN = Ncam1 PE = 1 SV = 1 CSRP1_RAT Cysteine and glycine-rich protein 1 OS =Rattus norvegicus 4 2 14.0 20613.3 8.9 0 0.526 1.27226 0.520562 0.638455 0.055216 1.18734 0.679184 0.637209 0.102089 GN = Csrp1 PE = 2 SV = 2 Q5PQK5_RAT Radixin OS =Rattus norvegicus GN = Rdx PE = 2 SV = 1 2 2 4.5 68542.98 5.95 0 0.997 0.988887 0.916429 1.06564 0.767513 1.4745 0.227582 1.086 0.761866 AP2M1_RAT AP-2 complex subunit mu OS =Rattus norvegicus GN = Ap2m1 9 4 9.0 49388.84 9.57 0 0.258 1.27782 0.511384 0.846889 0.41556 1.1752 0.703912 0.959597 0.849109 PE = 2 SV = 1 ARPC5_RAT Actin-related protein 2/3 complex subunit 5 OS =Rattus 2 2 21.2 16320.23 5.47 0 0.404 1.35735 0.389933 1.43661 0.047114 1.36199 0.370304 1.43573 0.117448 norvegicusGN = Arpc5 PE = 1 SV = 3 D3ZPN0_RAT Protein Pcdh17 OS = Rattus norvegicus GN = Pcdh17 PE = 4 1 1 1.0 130217.4 5.03 0 0.473 1.02063 1 0.839051 0.392205 1.30712 0.456649 0.802749 0.371827 SV = 1 SC6A9_RAT Sodium- and chloride-dependent glycine transporter 1 OS = Rattus 2 1 3.5 70576.63 8.34 0 0.435 0.795642 0.457083 0.702295 0.114259 1.2216 0.611318 0.479758 0.019268 norvegicus GN = Slc6a9 PE = 2 SV = 1 COF1_RAT Cofilin-1 OS = Rattus norvegicus GN = Cfl1 PE = 1 SV = 3 15 5 28.9 18532.31 8.22 0 0.374 1.358 0.389014 1.09914 0.654019 1.48832 0.213215 1.38052 0.171851 NEUM_RAT Neuromodulin OS = Rattus norvegicus GN = Gap43 PE = 1 14 7 30.5 23603.06 4.61 0 1.306 1.32676 0.434422 0.742172 0.171217 1.22253 0.609513 0.785072 0.330918 SV = 1 D3ZFJ7_RAT Protein Emc1 OS = Rattus norvegicus GN = Emc1 PE = 2 1 1 1.7 111495.8 6.86 0 0.066 1.42217 0.305241 1.02691 0.905105 0.972213 0.839061 0.771327 0.301204 SV = 1 AQP4_RAT Aquaporin-4 OS = Rattus norvegicus GN = Aqp4 PE = 2 SV = 1 2 2 6.6 35527.9 5.75 0 0.461 1.1812 0.681823 1.01965 0.931351 1.62016 0.107646 1.14614 0.602971 PCYOX_RAT Prenylcysteine oxidase OS = Rattus norvegicus GN = Pcyox1 1 1 3.6 56286.98 6.61 0 0.099 1.03466 0.971424 1.16177 0.463286 1.03824 0.998541 0.802139 0.370365 PE = 1 SV = 1 COPB_RAT Coatomer subunit beta OS = Rattus norvegicus GN = Copb1 1 1 1.4 107009.8 5.66 0 0.093 1.51142 0.210155 1.45343 0.039222 0.737127 0.350554 0.890025 0.615674 PE = 1 SV = 1 SC11A_RAT Signal peptidase complex catalytic subunit SEC11A OS = Rattus 2 2 10.6 20598.99 9.15 2 0.119 1.8394 0.036565 1.20802 0.345103 1.33804 0.40668 1.17152 0.540691 norvegicus GN = Sec11a PE = 2 SV = 1 CCD51_RAT Coiled-coil domain-containing protein 51 OS = Rattus norvegicus 4 3 9.3 45812.78 8.22 1 0.415 1.07087 0.897936 1.13059 0.554218 1.40742 0.307079 1.10421 0.712307 GN = Ccdc51 PE = 2 SV = 2 MFF_RAT Mitochondrial fission factor OS = Rattus norvegicus GN = Mff 4 3 15.5 32800.98 6.88 0 0.461 1.08326 0.872959 1.12489 0.571749 1.23343 0.588592 1.1153 0.682679 PE = 4 SV = 1 220–292 (2015) 298 Neuroscience / al. et Han X. F1LQN3_RAT Reticulon-4 OS = Rattus norvegicus GN = Rtn4 PE = 2 SV = 1 8 6 6.9 126400.6 4.41 0 0.407 1.25768 0.545 1.01652 0.942678 1.22067 0.61312 0.927126 0.737058 F162A_RAT Protein FAM162A OS = Rattus norvegicus GN = Fam162a 1 1 7.7 17826.76 10.02 1 0.512 1.29279 0.487111 1.17104 0.437933 1.66984 0.080803 1.63979 0.021322 PE = 2 SV = 1 F1M3W5_RAT Protein Dmxl2 OS = Rattus norvegicus GN = Dmxl2 PE = 4 6 5 2.5 338164.9 5.94 0 0.309 1.16807 0.706571 1.04275 0.848221 1.14134 0.77445 0.904163 0.660919 SV = 1 CHID1_RAT Chitinase domain-containing protein 1 OS = Rattus norvegicus 3 2 4.3 44874.03 7.78 0 0.202 1.28482 0.499961 1.22824 0.300107 1.08366 0.898732 1.19295 0.490746 GN = Chid1 PE = 2 SV = 2 D4AD90_RAT Protein Agfg2 OS = Rattus norvegicus GN = Agfg2 PE = 4 1 1 4.0 48974.45 9.06 0 0.216 1.76943 0.055886 0.861835 0.462309 1.35762 0.376795 0.993756 0.970328 SV = 1 D3ZPF2_RATATCAY_RAT ProteinCaytaxin Mcat OS =OSRattus = Rattus norvegicus norvegicusGNGN = Atcay = Mcat PE PE = 1= SV 4 SV = 1= 1 1 1 4.22.7 41831.7942116.74 8.394.53 02 0.1040.472 1.214151.15472 0.621230.732077 0.9417460.934439 0.7549160.725712 1.012431.12336 0.9377110.812735 0.6655340.900184 0.1315830.648051 F1LPB9_RAT Rabphilin-3A OS = Rattus norvegicus GN = Rph3a PE = 2 8 6 17.0 75802.54 8.46 0 0.865 1.34824 0.402878 0.691896 0.102182 1.18668 0.680519 0.851997 0.501336 SV = 1 GRP78_RAT 78 kDa glucose-regulated protein OS = Rattus norvegicus 30 10 21.9 72346.1 5.07 0 0.481 1.24108 0.573521 1.21063 0.339078 1.02256 0.962783 0.987867 0.949302 GN = Hspa5 PE = 1 SV = 1 Q2IBD4_RAT Cortactin binding protein 2 OS = Rattus norvegicus GN = Cttnbp2 1 1 0.6 178765.8 8.44 0 0.475 0.924194 0.749908 1.08345 0.706366 1.80266 0.034613 1.1901 0.497238 PE = 4 SV = 1 VPP1_RAT V-type proton ATPase 116 kDa subunit a isoform 1 OS = Rattus 38 12 15.6 96326.63 6.04 6 0.025 1.233 0.587655 1.06928 0.754899 0.913633 0.70016 0.749286 0.257377 norvegicus GN = Atp6v0a1 PE = 2 SV = 1 LRC73_RAT LLeucine-rich repeat-containing protein 73 OS = Rattus norvegicus 1 1 2.9 33376.7 4.83 0 0.005 1.13771 0.764995 0.858104 0.45037 1.57177 0.140149 0.993759 0.970338 GN = Lrrc73 PE = 2 SV = 1 STIP1_RAT Stress-induced-phosphoprotein 1 OS = Rattus norvegicus 4 3 5.2 62569.41 6.4 0 0.945 1.55919 0.169093 1.2081 0.344935 1.51197 0.190166 1.74467 0.007343 GN = Stip1 PE = 1 SV = 1 I6LBW6_RAT I6LBW6_RAT Protocadherin gamma a1 OS = Rattus norvegicus 1 1 1.5 101588.8 4.78 0 0.263 1.06304 0.913779 0.986048 0.938049 0.950746 0.787319 0.826969 0.432728 GN = Pcdhga1 PE = 2 SV = 1 M0RC65_RAT Protein Cfl2 (Fragment) OS = Rattus norvegicus GN = Cfl2 14 3 17.6 18578.17 7.88 0 0.402 1.21446 0.620673 1.09131 0.679934 1.43631 0.270841 1.24495 0.380575 PE = 4 SV = 1 E9PT79_RAT Protein Tsn OS = Rattus norvegicus GN = Tsn PE = 2 SV = 1 1 1 5.4 31472.87 9.35 0 0.207 1.23547 0.583311 1.55729 0.011248 0.585673 0.160292 0.785098 0.330977 CXG2_RAT Gap junction gamma-2 protein OS = Rattus norvegicus GN = Gjc2 2 1 3.4 46989.76 6.72 3 0.212 1.23564 0.583024 1.4676 0.033468 0.786645 0.43559 0.824301 0.425748 PE = 1 SV = 2 ISCA1_RAT Iron-sulfur cluster assembly 1 homolog, mitochondrial OS = Rattus 1 1 11.6 14149.13 9.19 0 0.329 1.46982 0.251412 1.21739 0.323754 0.871306 0.605424 0.843285 0.476821 norvegicus GN = Isca1 PE = 2 SV = 1 D3Z941_RAT Protein Mars OS = Rattus norvegicus GN = Mars PE = 3 SV = 1 1 1 2.4 101580.4 6.07 0 0.245 1.49457 0.226234 1.26484 0.229011 1.47083 0.231518 1.16278 0.561763 NDUS2_RAT NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, 11 4 10.8 52560.95 6.52 0 0.27 1.24271 0.570683 1.00782 0.97425 1.02762 0.975306 0.821563 0.418656 mitochondrial OS = Rattus norvegicus GN = Ndufs2 PE = 1 SV = 1 PECR_RAT Peroxisomal trans-2-enoyl-CoA reductase OS = Rattus norvegicus 1 1 4.6 32432.78 8.89 0 0.007 1.04188 0.956745 1.23221 0.291739 0.846067 0.55182 0.76896 0.296273 GN = Pecr PE = 2 SV = 1 G3V746_RAT Glutamate receptor ionotropic, NMDA 2B OS = Rattus norvegicus 5 4 3.6 166027 6.41 0 0.388 1.2059 0.636179 1.19796 0.369034 0.892191 0.651467 1.02732 0.927342 247 GN = Grin2b PE = 4 SV = 1 (continued on next page) 4 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 248

F1LPS8_RAT Transcriptional activator protein Pur-alpha OS = Rattus norvegicus 3 2 11.8 34883.31 6.07 0 0.777 1.12355 0.792718 0.958312 0.822371 1.43924 0.267329 1.03689 0.899922 GN = Pura PE = 2 SV = 1 B2RYU2_RAT RCG45615, isoform CRA_a OS =Rattus norvegicus 1 1 11.5 17845.41 9.48 0 0.363 1.32141 0.442497 1.4534 0.039233 1.45222 0.252181 1.1873 0.503669 GN = LOC685320 PE = 2 SV = 1 QCR8_RAT Cytochrome b-c1 complex subunit 8 OS =Rattus norvegicus 14 2 25.6 9849.22 10.52 1 0.656 1.14595 0.748991 1.27881 0.205316 1.04636 0.980643 0.977584 0.912679 GN = Uqcrq PE = 3 SV = 1 NTRK3_RAT Isoform IC108 of NT-3 growth factor receptor OS =Rattus 1 1 1.8 62758.6 5.81 0 0.138 1.12979 0.780457 0.669979 0.080058 1.09043 0.883949 0.682347 0.151986 norvegicusGN = Ntrk3 D4AC36_RAT Protein Eif3f OS =Rattus norvegicus GN = Eif3f PE = 4 SV = 1 1 1 4.2 37996.79 5.24 0 0.119 1.1223 0.795182 1.7392 0.00077 0.687218 0.276336 0.460021 0.015151 D4A5J1_RAT Protein Kbtbd11 OS =Rattus norvegicus GN = Kbtbd11 PE = 4 3 3 7.0 67848.31 5.22 0 0.328 1.36007 0.386116 0.957204 0.81781 1.17035 0.713874 0.976376 0.908387 SV = 1 COX41_RAT Cytochrome c oxidase subunit 4 isoform 1, mitochondrial 52 10 38.5 19514.33 9.45 1 0.37 1.15658 0.7285 0.961919 0.837252 1.32 0.435428 0.939632 0.779696 OSRattus = norvegicus GN = Cox4i1 PE = 1 SV = 1 F1LTP6_RAT Enolase (Fragment) OS =Rattus norvegicus PE = 3 SV = 1 7 4 16.5 38504.7 7.11 0 0.113 1.20478 0.638219 1.17349 0.431378 1.15553 0.744634 1.13907 0.620877 F1LM05_RAT Protein LOC299282 OS =Rattus norvegicus GN = LOC299282 1 1 1.6 68165.54 5.31 0 0.196 1.07665 0.886262 1.26522 0.228334 1.35347 0.383004 1.34045 0.221854 PE = 2 SV = 1 EZRI_RAT Ezrin (Fragment) OS =Rattus norvegicus GN = Ezr PE = 2 3 3 4.6 69286.83 5.83 0 0.972 1.15189 0.737527 0.976393 0.897503 1.38784 0.333407 0.939699 0.779925 SV = 1 ACADV_RAT Very long-chain-specific acyl-CoA dehydrogenase, mitochondrial 2 2 5.0 68950.46 9.09 0 0.101 1.25262 0.553623 1.13954 0.527246 1.0701 0.928435 1.08404 0.767273 OSRattus = norvegicus GN = Acadvl PE = 2 SV = 1 F1M8Y2_RAT Protein Tspan7 (Fragment) OS =Rattus norvegicus GN = Tspan7 1 1 7.7 21388.63 7.02 0 0.37 1.10858 0.822333 0.534655 0.013645 1.33549 0.410678 0.661645 0.127181 PE = 2 SV = 1 MAP1A_RAT Microtubule-associated protein 1A OS =Rattus norvegicus 38 20 9.9 324060.5 4.89 0 0.833 1.16478 0.712841 0.884457 0.538332 1.10304 0.856541 0.895507 0.633056 GN = Map1a PE = 2 SV = 1 ALBU_RAT Serum albumin OS =Rattus norvegicus GN = Alb PE = 1 SV = 2 47 19 32.2 68730.1 6.09 0 0.38 1.18453 0.675586 1.73391 0.00084 1.32753 0.423292 1.81831 0.003212 PDP1_RAT [Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, 3 2 5.4 64744.67 6.44 0 0.407 1.26358 0.53504 1.21621 0.32638 0.89187 0.650747 0.815585 0.403413 mitochondrial (Fragment) OS =Rattus norvegicus GN = Pdp1 PE = 3 SV = 1 GSH0_RAT Glutamate–cysteine ligase regulatory subunit OS =Rattus 1 1 5.8 30547.51 5.36 0 0.283 1.11393 0.81172 1.24587 0.264206 0.877952 0.619918 0.945712 0.800678 norvegicusGN = Gclm PE = 1 SV = 1 D3ZTB4_RAT Protein Vps11 OS =Rattus norvegicus GN = Vps11 PE = 4 1 1 1.3 101170 6.54 0 0.471 1.1228 0.794206 0.926869 0.695874 1.25443 0.549277 0.987895 0.949402 SV = 1 B2RZ13_RAT Gprc5b protein (Fragment) OS =Rattus norvegicus GN = Gprc5b 9 4 12.1 49474.71 9.31 7 0.356 1.19759 0.651389 0.925034 0.688711 1.09309 0.878162 0.8411 0.470776 PE = 2 SV = 1 F1LPF3_RAT Choline transporter-like protein 1 (Fragment) OS = Rattus 3 3 6.7 71724.5 8.89 0 0.552 1.14303 0.754639 1.26523 0.228328 1.11709 0.826207 1.05471 0.84925 norvegicusGN = Slc44a1 PE = 2 SV = 1 NHRF2_RAT Na(+)/H(+) exchange regulatory cofactor NHE-RF2 OS = Rattus 1 1 6.3 35217.08 8.28 0 0.823 0.947035 0.807801 1.02282 0.919863 1.66122 0.085025 1.47299 0.089114 norvegicusGN = Slc9a3r2 PE = 2 SV = 1 Q6Q7Y5_RAT Galpha13 OS =Rattus norvegicus GN = Gna13 PE = 2 SV = 1 22 3 8.2 44011.09 8.41 0 0.395 1.31634 0.45022 0.974082 0.887837 1.52278 0.180267 1.16873 0.547383 AINX_RAT Alpha-internexin OS =Rattus norvegicus GN = Ina PE = 1 20 10 26.7 56114.7 5.2 0 0.649 1.32214 0.441396 1.1201 0.586656 1.21218 0.62967 1.03215 0.913483 SV = 2 KPCG_RAT Protein kinase C gamma type OS =Rattus norvegicus 20 13 25.4 78356.8 7.27 0 0.349 1.17922 0.685533 0.964255 0.84692 1.34839 0.390707 1.055 0.848422 GN = Prkcg PE = 1 SV = 1 D4ACG2_RAT IlvB (Bacterial acetolactate synthase)-like (Predicted), isoform 2 2 4.0 72269.13 8.61 0 0.204 1.13742 0.765547 1.06618 0.765637 0.93516 0.750317 0.812327 0.395246 CRA_c OS =Rattus norvegicus GN = Ilvbl PE = 3 SV = 1 NDUAB_RAT NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 6 4 29.1 14853.9 8.3 2 0.157 1.15291 0.735563 1.35012 0.111538 1.14606 0.764496 1.15026 0.592628 OS =Rattus norvegicus GN = Ndufa11 PE = 2 SV = 1 F1M951_RAT Tyrosine-protein phosphatase non-receptor type 23 OS = Rattus 2 2 1.7 182185.1 6.36 0 0.45 0.706303 0.298829 1.14407 0.513848 1.13162 0.795088 1.02032 0.947422 norvegicusGN = Ptpn23 PE = 2 SV = 1 D3ZZ99_RAT Alpha-adducin OS =Rattus norvegicus GN = Add1 PE = 2 10 9 16.9 73150.98 6.2 0 0.544 1.28807 0.494691 0.924282 0.685782 1.48896 0.212565 1.10506 0.710017 SV = 1 D3Z981_RAT Uncharacterized protein OS =Rattus norvegicus 3 3 2.1 210890.5 6.89 0 0.236 1.14157 0.75748 1.0751 0.734822 1.00732 0.925103 0.926305 0.734285 GN = RGD1560871 PE = 4 SV = 1 BEGIN_RAT Isoform 2 of Brain-enriched guanylate kinase-associated protein 1 1 1.2 66161.36 5.49 0 0.744 1.16353 0.715222 0.906046 0.616309 1.28966 0.486339 0.933382 0.758297 OSRattus = norvegicus GN = Begain D4A4D8_RAT Uncharacterized protein OS =Rattus norvegicus GN = Palm2 3 3 8.0 42040.54 5 0 0.723 1.12383 0.792169 0.998892 0.992221 1.09799 0.867499 1.02028 0.947537 PE = 4 SV = 1 B0BNE6_RAT NADH dehydrogenase (Ubiquinone) Fe-S protein 8 (Predicted), 6 4 14.6 23970.05 5.87 0 0.374 1.11959 0.800522 0.946657 0.774742 1.39392 0.325084 1.23134 0.407831 isoform CRA_a OS =Rattus norvegicus GN = Ndufs8 PE = 2 SV = 1 B4F7C7_RAT Hebp1 protein OS = Rattus norvegicus GN = Hebp1 PE = 2 1 1 6.3 21123.7 5.33 0 0.464 1.08475 0.869969 0.798698 0.284992 1.0912 0.882279 1.09625 0.73384 SV = 1 TAU_RAT Isoform Tau-F of Microtubule-associated protein tau OS = Rattus 10 8 24.3 39151.41 9.51 0 0.832 1.14131 0.75798 1.0868 0.695053 1.51776 0.18482 1.20355 0.466981 norvegicus GN = Mapt F1LST4_RAT Microtubule-associated protein OS = Rattus norvegicus 10 8 11.4 78554.06 5.91 0 0.837 1.16648 0.709596 1.0868 0.695053 1.23033 0.594524 1.03858 0.895094 GN = Mapt PE = 2 SV = 1 CSKI1_RAT Caskin-1 OS = Rattus norvegicus GN = Caskin1 PE = 1 SV = 1 4 2 2.5 150345.4 9.25 0 0.551 1.13932 0.761866 1.0313 0.88928 1.57784 0.135698 0.865117 0.539479 GBB1_RAT Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 48 9 29.1 37376.59 5.6 0 0.231 1.11755 0.804562 0.994479 0.97359 1.09575 0.872373 0.962825 0.860458 OS = Rattus norvegicus GN = Gnb1 PE = 1 SV = 4 LPPR4_RAT Lipid phosphate phosphatase-related protein type 4 OS = Rattus 3 3 4.1 83360.59 9.06 5 0.366 1.22149 0.608061 1.07739 0.727 1.36411 0.367191 1.23554 0.399304 norvegicus GN = Lppr4 PE = 2 SV = 1 F1LPG5_RAT Protein LOC688963 OS = Rattus norvegicus GN = LOC688963 8 4 36.4 15064.16 9.82 0 0.676 1.08287 0.873732 1.00073 1 1.27716 0.508204 0.973684 0.898834 PE = 2 SV = 1 PPIF_RAT Peptidyl-prolyl cis-trans isomerase F, mitochondrial OS = Rattus 3 2 15.5 21809.74 9.3 0 0.164 1.16646 0.709633 1.15838 0.472732 1.07233 0.92354 0.88898 0.612384 norvegicus GN = Ppif PE = 1 SV = 2 Q5M7T6_RAT ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d1 14 9 20.5 40300.61 4.89 0 0.093 1.16897 0.704874 1.11566 0.600657 1.14353 0.769824 1.04975 0.863296 OS = Rattus norvegicus GN = Atp6v0d1 PE = 2 SV = 1

GRAP1_RAT Isoform 2 of GRIP1-associated protein 1 OS = Rattus norvegicus 3 3 4.8 90909.92 5.15 0 0.726 1.14242 0.75583 1.01443 0.950278 1.00122 0.910066 0.764152 0.286422

GN = Gripap1 220–292 (2015) 298 Neuroscience / al. et Han X. Q6P3V9_RAT 60S ribosomal protein L4 OS = Rattus norvegicus GN = Rpl4 2 2 6.2 47300.3 11.02 0 0.651 1.29582 0.482277 0.958211 0.821954 1.30818 0.454887 0.912421 0.687947 PE = 2 SV = 1 B2GUW3_RAT Hdac11 protein OS = Rattus norvegicus GN = Hdac11 PE = 2 1 1 3.8 39337.8 7.22 0 0.199 1.18284 0.678755 0.953985 0.804601 1.08397 0.898064 0.868126 0.548428 SV = 1 B4F7A5_RAT Cd99 protein OS = Rattus norvegicus GN = Cd99 PE = 2 2 2 11.5 16588.24 4.92 2 0.481 1.16416 0.714006 1.0819 0.711623 1.21059 0.632806 1.05955 0.835568 SV = 1 D3ZDF0_RAT Neuroplastin OS = Rattus norvegicus GN = Nptn PE = 2 10 6 23.6 40939.63 7.05 0 0.46 1.17179 0.699531 0.894217 0.572966 0.945612 0.775074 0.719196 0.204997 SV = 1 Q6S396_RAT Plectin OS = Rattus norvegicus GN = Plec PE = 2 SV = 1 2912 24 7 24.6 6.7 518360 49142.67 5.6 5.48 0 0 0.6880.708 1.20178 1.15265 0.643704 0.736065 0.912704 0.963789 0.64132 0.844992 1.00549 0.957969 0.920576 0.804635 0.72261 0.850748 0.210518 0.49778 BIN1_RAT IsoformRattus AMPH2-5 norvegicus of MycGN box-dependent-interacting = Bin1 protein 1 JAGN1_RATOS Protein = jagunal homolog 1 OS = Rattus norvegicus GN = Jagn1 2 1 6.6 21101.74 9.8 3 0.242 1.25872 0.543249 1.18898 0.391231 1.32355 0.429674 1.31697 0.255598 PE = 2 SV = 1 LSAMP_RAT LSAMP_RAT Isoform 2 of Limbic system-associated membrane 16 7 22.4 39860.96 7.03 0 0.255 1.22922 0.594313 0.706556 0.119522 1.37624 0.349659 0.918938 0.709565 protein OS = Rattus norvegicus GN = Lsamp B2RYS8_RAT NADH dehydrogenase (Ubiquinone) 1 beta subcomplex 8 8 3 21.0 21958.68 5.67 0 0.705 1.34426 0.408619 0.953692 0.803403 1.29793 0.472153 1.05872 0.837915 OS = Rattus norvegicus GN = Ndufb8 PE = 2 SV = 1 B2GUY4_RAT Protein Epb49 OS = Rattus norvegicus GN = Epb49 PE = 2 2 2 5.2 45494.84 8.52 0 0.864 0.865441 0.607982 0.943376 0.761477 1.6865 0.07312 1.34775 0.212038 SV = 1 GCSH_RAT Glycine cleavage system H protein, mitochondrial OS = Rattus 1 1 6.1 18184.53 5.8 0 0.285 1.09059 0.85824 1.03227 0.885804 1.31091 0.450347 1.12827 0.648665 norvegicus GN = Gcsh PE = 2 SV = 1 ENOA_RAT Alpha-enolase OS = Rattus norvegicus GN = Eno1 PE = 1 27 14 35.3 47127.31 6.16 0 0.193 1.17115 0.700743 1.06646 0.764654 1.12278 0.813973 1.07319 0.797334 SV = 4 THEM6_RAT Protein THEM6 OS = Rattus norvegicus GN = Them6 PE = 2 5 2 12.6 23747.36 9.14 1 0.001 1.46571 0.255777 1.6903 0.001685 0.628432 0.203644 1.02494 0.934167 SV = 1 D4A7L4_RAT NADH dehydrogenase (Ubiquinone) 1 beta subcomplex, 11 3 2 25.8 17633.8 5.17 0 0.436 1.08714 0.865167 0.593568 0.031184 0.834073 0.52719 0.729673 0.222277 (Predicted) OS = Rattus norvegicus GN = Ndufb11 PE = 4 SV = 1 D3ZUX5_RAT Coiled-coil-helix-coiled-coil-helix domain containing 3 (Predicted), 6 3 12.8 26434.31 8.25 0 1.035 1.20961 0.629443 1.11778 0.593954 1.29926 0.469892 0.994661 0.973561 isoform CRA_a OS = Rattus norvegicus GN = Chchd3 PE = 4 SV = 1 ERLN2_RAT Erlin-2 OS = Rattus norvegicus GN = Erlin2 PE = 1 SV = 1 1 1 3.5 37709.93 5.54 0 0.172 1.10984 0.819814 1.29704 0.177151 1.1289 0.800889 1.07043 0.805034 D3ZUE2_RAT Coronin OS = Rattus norvegicus GN = Coro7 PE = 2 SV = 1 1 1 0.8 100780.7 5.58 0 0.292 1.11542 0.80877 1.24198 0.271866 1.33643 0.409194 1.26691 0.338999 PSB6_RAT Proteasome subunit beta type-6 OS = Rattus norvegicus 1 1 4.2 25289.37 4.85 0 0.025 1.23925 0.576701 1.14191 0.520232 1.23978 0.576571 0.958355 0.844749 GN = Psmb6 PE = 1 SV = 3 ARL8B_RAT ADP-ribosylation factor-like protein 8B OS = Rattus norvegicus 7 3 18.8 21538.78 8.67 0 0.272 1.19746 0.651637 0.957143 0.817559 1.32169 0.432691 1.18731 0.50364 GN = Arl8b PE = 2 SV = 1 NDUV2_RAT NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial 7 4 28.6 27378.04 6.23 0 0.316 1.29303 0.486733 0.997216 0.985145 1.03415 0.991488 0.874652 0.568085

OS = Rattus norvegicus GN = Ndufv2 PE = 1 SV = 2 249 (continued on next page) 5 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 250 TMOD2_RAT Tropomodulin-2 OS = Rattus norvegicus GN = Tmod2 PE = 1 5 4 15.7 39491.34 5.34 0 0.68 1.1537 0.734041 0.908772 0.626498 1.03204 0.986263 1.15622 0.577849 SV = 1 ACBG1_RAT Long-chain-fatty-acid–CoA ligase ACSBG1 OS =Rattus 2 2 3.9 80517.97 5.65 0 0.267 1.09853 0.842352 0.93178 0.715181 1.17169 0.711117 0.920299 0.714111 norvegicusGN = Acsbg1 PE = 1 SV = 1 F1LRV4_RAT Heat shock 70 kDa protein 4 OS =Rattus norvegicus 6 4 4.2 94025.38 5.13 0 0.58 1.08699 0.865453 1.17978 0.414796 1.44306 0.262804 1.49254 0.076617 GN = Hspa4 PE = 2 SV = 1 ATAD3_RAT ATPase family AAA domain-containing protein 3 OS =Rattus 6 4 7.3 66758.2 9.32 0 0.66 0.982384 0.899393 1.25652 0.244021 1.59422 0.124236 1.31286 0.261859 norvegicusGN = Atad3 PE = 1 SV = 1 F1LMM9_RAT Elongation factor G, mitochondrial OS =Rattus norvegicus 1 1 2.1 83311.6 6.76 0 0.28 1.21939 0.611803 0.898082 0.586969 0.61154 0.185596 0.437321 0.011391 GN = Gfm1 PE = 2 SV = 1 RAN_RAT GTP-binding nuclear protein Ran OS =Rattus norvegicus 2 1 4.6 24422.81 7.01 0 0.266 1.25109 0.556251 1.16956 0.441924 1.36036 0.372713 1.17763 0.526196 GN = Ran PE = 1 SV = 3 GNAS1_RAT Guanine nucleotide-binding protein G(s) subunit alpha isoforms 22 4 5.2 122885.2 4.73 0 0.564 1.312 0.456911 0.946956 0.775955 1.51603 0.186406 1.33068 0.235494 XLas OSRattus = norvegicus GN = Gnas PE = 1 SV = 3 F1M4A0_RAT Protein Tjp1 (Fragment) OS =Rattus norvegicus GN = Tjp1 2 2 1.6 195367.8 6.13 0 0.908 1.17484 0.693767 0.895743 0.578476 1.39122 0.328757 0.913305 0.690866 PE = 4 SV = 1 D4A1Y0_RAT Protein Scyl2 OS =Rattus norvegicus GN = Scyl2 PE = 2 1 1 1.3 103364.1 8.36 0 0.249 1.1357 0.768915 1.17861 0.417858 1.05638 0.9586 1.08331 0.769279 SV = 1 SCN2A_RAT Protein Scn2a1 OS =Rattus norvegicus GN = Scn2a1 PE = 2 6 4 2.0 227851.2 5.53 0 0.002 1.0952 0.849007 0.826531 0.35659 1.07277 0.922576 0.758444 0.275018 SV = 1 LAT1_RAT Large neutral amino acids transporter small subunit 1 4 3 6.3 55902.7 8.18 9 0.73 1.30889 0.461718 0.919117 0.6658 0.983587 0.866776 0.635029 0.100057 OSRattus = norvegicus GN = Slc7a5 PE = 1 SV = 2 F1MAK3_RAT Protein Rics OS = Rattus norvegicus GN = Arhgap32 PE = 4 1 1 0.5 229583.5 6.49 0 0.662 1.62639 0.121933 1.17996 0.414311 0.974465 0.844533 1.01556 0.961121 SV = 1 D4AAE9_RAT Protein Cisd2 OS =Rattus norvegicus GN = Cisd2 PE = 4 2 2 21.5 15292.92 9.68 0 0.096 1.32674 0.434457 0.945923 0.771771 1.05465 0.962396 0.819302 0.412851 SV = 1 PDXK_RAT Pyridoxal kinase OS =Rattus norvegicus GN = Pdxk PE = 1 5 4 14.1 34907.76 6.32 0 0.251 1.28539 0.499036 0.811099 0.315598 1.13896 0.779503 1.03148 0.915409 SV = 1 B5DF65_RAT Biliverdin reductase B (Flavin reductase (NADPH)) OS =Rattus 3 3 18.5 22093.99 6.29 0 0.098 1.34455 0.408198 1.19988 0.364385 0.922724 0.721197 1.03368 0.909099 norvegicusGN = LOC681468 PE = 2 SV = 1 D3ZLY4_RAT Protein Atp8b2 OS =Rattus norvegicus GN = Atp8b2 PE = 2 1 1 2.8 68235.17 6.21 0 0.935 1.01796 0.99294 0.995211 0.976682 0.790339 0.442377 0.630066 0.095551 SV = 1 PHB2_RAT Prohibitin-2 OS =Rattus norvegicus GN = Phb2 PE = 1 SV = 1 25 11 38.1 33311.97 9.83 0 0.266 1.25111 0.556214 0.949372 0.785768 1.2769 0.508661 1.05388 0.851608 VATB2_RAT V-type proton ATPase subunit B, brain isoform OS =Rattus 28 13 29.9 56550.16 5.57 0 0.176 1.19254 0.660714 1.31607 0.150929 1.24388 0.568864 1.54945 0.048142 norvegicusGN = Atp6v1b2 PE = 1 SV = 1 SYUB_RAT Beta-synuclein OS =Rattus norvegicus GN = Sncb PE = 1 13 5 39.4 14503.99 4.48 0 0.553 1.15259 0.736178 1.00956 0.967939 1.4456 0.259831 1.25593 0.359407 SV = 1 B1H262_RAT Protein phosphatase 1, regulatory subunit 9B OS =Rattus 5 4 8.5 89661.35 4.86 0 0.826 1.14335 0.754023 1.02186 0.923342 1.49733 0.204208 1.40932 0.141498 norvegicusGN = Ppp1r9b PE = 2 SV = 1 ACTZ_RAT Alpha-centractin OS =Rattus norvegicus GN = Actr1a PE = 1 3 2 7.5 42613.22 6.19 0 0.285 1.08779 0.863848 1.06044 0.785671 1.50131 0.200321 1.44818 0.107287 SV = 1 B2RYJ7_RAT ARP1 actin-related protein 1 homolog B (Yeast) OS =Rattus 3 2 6.7 42280.84 5.98 0 0.259 1.18574 0.673342 1.27723 0.207901 1.38363 0.339251 1.45139 0.10478 norvegicusGN = Actr1b PE = 2 SV = 1 DHB4_RAT Peroxisomal multifunctional enzyme type 2 OS =Rattus 5 4 7.5 79426.83 8.77 0 0.104 1.03232 0.97619 1.20062 0.362606 1.11776 0.824767 1.15087 0.591112 norvegicusGN = Hsd17b4 PE = 1 SV = 3 Q45QN0_RAT Guanine nucleotide binding protein alpha inhibiting 2 OS =Rattus 36 7 24.2 40498.57 5.28 0 0.372 1.24657 0.56401 0.870395 0.490348 1.45498 0.249038 1.08668 0.760001 norvegicusGN = Gnai2 PE = 2 SV = 1 NDUF3_RAT NADH dehydrogenase [ubiquinone] 1 alpha subcomplex 1 1 5.4 20696.2 7.73 0 0.282 1.02313 0.994925 0.932531 0.71815 1.24685 0.563318 0.973279 0.897396 assembly factor 3 OS =Rattus norvegicus GN = Ndufaf3 PE = 2 SV = 1 F136A_RAT Protein FAM136A OS =Rattus norvegicus GN = Fam136a 6 3 36.2 15624.95 7.56 0 0.504 1.21742 0.615349 1.02275 0.920112 1.52854 0.175147 1.21812 0.435402 PE = 2 SV = 1 E9PTX9_RAT Protein Slc12a2 OS =Rattus norvegicus GN = Slc12a2 PE = 4 6 4 4.2 130365 6.08 0 0.042 1.16476 0.712871 1.02371 0.916666 1.06421 0.941376 1.01592 0.960083 SV = 1 NAT8L_RAT N-acetylaspartate synthetase OS = Rattus norvegicus 2 1 4.0 32718.68 8.8 0 0.029 1.12969 0.780664 0.901155 0.598214 1.21276 0.628534 0.950776 0.818262 GN = Nat8l PE = 1 SV = 1 Q5RK10_RAT 60S ribosomal protein L13a OS = Rattus norvegicus 2 2 10.3 23445.86 11.02 0 0.441 1.2272 0.597899 0.972851 0.88269 1.60801 0.115188 1.31343 0.260988 GN = Rpl13a PE = 2 SV = 1 B2GUZ6_RAT Protein Rtn4ip1 OS =Rattus norvegicus GN = Rtn4ip1 PE = 2 1 1 3.5 43605.27 9.3 0 0.032 1.06821 0.903305 1.21095 0.338329 0.805267 0.470415 0.957082 0.840286 SV = 1 GRM7_RAT Metabotropic glutamate receptor 7 OS = Rattus norvegicus 1 1 1.8 102230.9 8.2 0 0.096 0.931437 0.76813 0.975241 0.892683 0.896976 0.662213 0.859172 0.522017 GN = Grm7 PE = 1 SV = 1 TPM3_RAT Isoform 2 of Tropomyosin alpha-3 chain OS = Rattus norvegicus 11 8 31.5 28719.66 4.69 0 1.015 1.16304 0.716155 1.06081 0.784368 1.20926 0.635426 1.10076 0.721597 GN = Tpm3 TTC19_RAT Tetratricopeptide repeat protein 19, mitochondrial OS = Rattus 1 1 4.1 41332.95 5.88 0 0.327 0.994645 0.931545 1.28629 0.193389 0.841334 0.542033 1.32491 0.243815 norvegicus GN = Ttc19 PE = 2 SV = 1 AT2B2_RAT Plasma membrane calcium-transporting ATPase 2 OS = Rattus 41 19 18.9 136809.7 5.7 8 0.166 1.12537 0.789138 0.846556 0.414554 1.36422 0.367035 0.913851 0.692672 norvegicus GN = Atp2b2 PE = 2 SV = 2 F1MAR6_RAT Protein Prodh OS = Rattus norvegicus GN = Prodh PE = 4 2 2 6.2 68121.23 6.91 0 0.347 1.0848 0.86986 1.03271 0.884218 1.11161 0.838005 0.916841 0.702584 SV = 1 PTMA_RAT Prothymosin alpha OS = Rattus norvegicus GN = Ptma PE = 1 1 1 12.5 12382.13 3.75 0 1.974 1.20435 0.639005 0.681645 0.091294 1.02328 0.964552 0.559754 0.047494 SV = 2 Q6PW39_RAT Neuronal cell adhesion molecule long isoform Nc1 OS = Rattus 7 7 7.8 133380.3 5.76 1 0.397 1.14937 0.742377 0.834719 0.379644 1.15509 0.745539 0.842769 0.475389 norvegicus GN = Nrcam PE = 2 SV = 1 PARK7_RAT Protein DJ-1 OS = Rattus norvegicus GN = Park7 PE = 1 9 5 30.7 19973.96 6.32 0 0.022 1.17284 0.697549 0.957028 0.817085 1.69545 0.069252 1.06391 0.823303 SV = 1 1433F_RAT 14-3-3 protein eta OS = Rattus norvegicus GN = Ywhah PE = 1 28 11 31.7 28211.42 4.81 0 0.607 1.21431 0.620937 1.10692 0.628648 1.35573 0.379619 1.29693 0.287106 SV = 2 UCHL1_RAT Ubiquitin carboxyl-terminal hydrolase isozyme L1 (Fragment) 8 4 24.6 24787.84 5.21 0 0.381 1.10883 0.821825 1.00486 0.985006 1.13281 0.792561 1.08152 0.77423 OS = Rattus norvegicus GN = Uchl1 PE = 2 SV = 1 LETM1_RAT LETM1 and EF-hand domain-containing protein 1, mitochondrial 8 5 10.0 83058.77 6.22 1 0.413 0.808221 0.482627 1.07664 0.729548 1.32998 0.419374 1.02659 0.929443 OS = Rattus norvegicus GN = Letm1 PE = 1 SV = 1 220–292 (2015) 298 Neuroscience / al. et Han X. Q6LBV1_RAT Rat myelin-associated glycoprotein (S-MAG) C-term OS = Rattus 4 3 30.5 18095.44 8.58 1 0.163 1.01267 0.979003 0.930957 0.711933 1.39969 0.317311 1.00241 0.998985 norvegicus GN = Mag PE = 2 SV = 1 F1M5C5_RAT Uncharacterized protein (Fragment) OS = Rattus norvegicus 1 1 4.0 22780.89 4.85 0 0.396 1.19706 0.652363 1.00592 0.981152 1.27079 0.519555 0.964826 0.867507 PE = 4 SV = 1 HIBCH_RAT 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial OS = Rattus 3 2 7.0 43024.17 8.64 0 0.231 1.17469 0.694051 1.10576 0.632397 1.21173 0.630566 1.04735 0.870126 norvegicus GN = Hibch PE = 1 SV = 2 F1M953_RAT Stress-70 protein, mitochondrial OS = Rattus norvegicus 32 14 28.4 73743.69 5.87 0 0.414 1.14658 0.747763 1.50266 0.02225 1.01228 0.93734 1.1801 0.520395 GN = Hspa9 PE = 2 SV = 1 F1M8H6_RAT Phosphatidylinositol 4-phosphate 5-kinase type-1 gamma 3 3 6.3 75612.14 5.86 0 0.454 1.13203 0.776083 0.96605 0.854366 1.23187 0.591577 1.04442 0.878451 OS = Rattus norvegicus GN = Pip5k1c PE = 2 SV = 1 10 6 12.8 51959.58 6.34 0 0.189 1.16616 0.710216 0.90231 0.602463 1.29393 0.478985 0.931288 0.751165 SAM50_RAT SortingOS = Rattus and assembly norvegicus machineryGN = Samm50 component PE 50 = homolog1 SV = 1 RTCB_RAT tRNA-splicing ligase RtcB homolog OS = Rattus norvegicus 2 2 5.9 55248.73 6.77 0 0.241 1.11105 0.817431 1.07148 0.747288 0.935201 0.750414 0.83521 0.454696 PE = 2 SV = 1 VTI1B_RAT Vesicle transport through interaction with t-SNAREs homolog 1B 1 1 5.6 26703.15 9.04 1 0.606 1.14856 0.743946 1.27039 0.219369 0.876076 0.61581 0.92358 0.725108 OS = Rattus norvegicus GN = Vti1b PE = 1 SV = 2 D4AEH9_RAT Amylo-1, 6-glucosidase, 4-alpha-glucanotransferase (Glycogen 1 1 0.9 174330.3 6.28 0 0.313 1.212 0.62511 1.01718 0.940304 0.888909 0.644137 0.803817 0.374394 debranching enzyme, glycogen storage disease type III) (Predicted), isoform CRA_a OS = Rattus norvegicus GN = Agl PE = 4 SV = 1 NFS1_RAT Cysteine desulfurase, mitochondrial OS = Rattus norvegicus 1 1 3.1 50012 8.92 0 0.222 1.19259 0.660621 1.23376 0.28852 1.30989 0.452036 0.993182 0.968277 GN = Nfs1 PE = 2 SV = 1 CRYM_RAT Thiomorpholine-carboxylate dehydrogenase OS = Rattus 4 2 5.1 33553.86 5.34 0 0.05 1.1008 0.837815 1.10503 0.634752 1.3673 0.362524 1.20639 0.460728 norvegicus GN = Crym PE = 1 SV = 1 MOBP_RAT Isoform 2 of Myelin-associated oligodendrocyte basic protein 1 1 6.5 18916.74 11.04 0 1.22 1.17628 0.691053 0.566929 0.021694 1.24658 0.563824 0.599171 0.071036 OS = Rattus norvegicus GN = Mobp F1LRL9_RAT Microtubule-associated protein 1B OS = Rattus norvegicus 29 15 8.8 269639.6 4.74 0 0.849 1.08034 0.878837 0.796805 0.280504 1.38271 0.340524 1.04584 0.874416 GN = Map1b PE = 2 SV = 1 4F2_RAT 4F2 cell-surface antigen heavy chain OS = Rattus norvegicus 5 4 7.0 58071.49 5.19 1 0.126 1.09981 0.839786 0.948685 0.782974 1.23743 0.581001 0.989271 0.954312 GN = Slc3a2 PE = 1 SV = 1 1433Z_RAT 14-3-3 protein zeta/delta OS = Rattus norvegicus GN = Ywhaz 32 11 31.4 27770.83 4.73 0 0.635 1.15054 0.740121 1.03769 0.866318 1.34456 0.396567 1.08369 0.768234 PE = 1 SV = 1 ODO1_RAT 2-oxoglutarate dehydrogenase, mitochondrial OS = Rattus 15 10 13.5 117741.4 6.55 0 0.319 1.03018 0.980558 1.24789 0.260296 0.898579 0.665831 0.912705 0.688886 norvegicus GN = Ogdh PE = 2 SV = 1 CAPZB_RAT F-actin-capping protein subunit beta OS = Rattus norvegicus 3 3 18.4 30628.4 5.69 0 0.554 1.07408 0.891457 1.32273 0.142492 1.07283 0.922457 1.24516 0.380159 GN = Capzb PE = 1 SV = 1 D3ZHX3_RAT Protein Diras2 OS = Rattus norvegicus GN = Diras2 PE = 4 2 2 16.1 22497.7 8.98 0 0.412 0.905153 0.702687 0.864421 0.470682 1.32999 0.419359 1.08127 0.774911 SV = 1 F1M8Z9_RAT Protein Rap1gds1 (Fragment) OS = Rattus norvegicus 3 3 7.0 61913.11 5.37 0 0.1 1.0716 0.896469 1.83639 0.000141 1.10156 0.859753 0.718813 0.204386 251 GN = Rap1gds1 PE = 2 SV = 1 (continued on next page) 5 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 252 AP1M1_RAT AP-1 complex subunit mu-1 OS = Rattus norvegicus 1 1 3.8 48556.29 6.82 0 0.277 1.11058 0.81836 1.04721 0.83237 0.917506 0.709095 0.975304 0.904582 GN = Ap1m1 PE = 1 SV = 3 AGAP2_RAT Arf-GAP with GTPase, ANK repeat and PH domain-containing 2 2 2.3 124436.1 9.89 0 0.425 1.15521 0.731141 1.16282 0.460364 0.97083 0.835704 1.02726 0.927515 protein 2 OS =Rattus norvegicus GN = Agap2 PE = 1 SV = 1 Q76GL9_RAT Amino acid transporter OS =Rattus norvegicus GN = Slc1a4 5 3 6.6 56137.88 6.38 10 0.529 1.08625 0.866948 0.550614 0.017218 1.32225 0.431773 0.618312 0.085527 PE = 2 SV = 1 TCPG_RAT T-complex protein 1 subunit gamma OS = Rattus norvegicus 7 6 12.3 60646.34 6.23 0 0.271 1.11993 0.799846 1.0132 0.954737 0.845469 0.550579 0.774694 0.308314 GN = Cct3 PE = 1 SV = 1 O88321_RAT Protein Psmd4 OS =Rattus norvegicus GN = Psmd4 PE = 2 2 2 9.0 39335.03 5.06 0 0.271 1.18636 0.67218 0.939631 0.746424 0.825637 0.510209 0.666832 0.133079 SV = 1 NHRF1_RAT Na(+)/H(+) exchange regulatory cofactor NHE-RF1 1 1 3.7 38829.93 5.7 0 0.774 1.00023 0.946238 0.892557 0.567002 0.972222 0.839083 0.677744 0.146175 OSRattus = norvegicus GN = Slc9a3r1 PE = 1 SV = 3 PSA3_RAT Proteasome subunit alpha type-3 OS =Rattus norvegicus 2 2 9.0 28418.93 5.29 0 0.283 1.12751 0.784942 1.41006 0.062277 1.18093 0.692192 1.43984 0.114012 GN = Psma3 PE = 1 SV = 3 Q63555_RAT SP120 OS =Rattus norvegicus GN = Hnrnpu PE = 2 SV = 1 2 2 3.8 87747.5 5.92 0 0.929 0.966426 0.857801 0.73432 0.158582 1.17013 0.71432 0.690439 0.162626 5HT1A_RAT 5-hydroxytryptamine receptor 1A OS =Rattus norvegicus 1 1 3.6 46428.66 9.16 7 0.182 1.12552 0.788838 0.784732 0.253005 0.789651 0.441109 0.620375 0.087222 GN = Htr1a PE = 3 SV = 1 SC6A1_RAT Sodium- and chloride-dependent GABA transporter 1 3 2 8.4 67000.71 8.25 12 0.468 1.12561 0.788667 0.611279 0.039304 1.12629 0.806474 0.688171 0.159588 OS =Rattus norvegicus GN = Slc6a1 PE = 1 SV = 1 D3ZFR9_RAT Protein Rdh13 OS = Rattus norvegicus GN = Rdh13 PE = 3 2 2 5.4 36407.44 9.03 0 0.113 1.08594 0.867561 0.969139 0.867212 1.00423 0.917463 0.791999 0.346589 SV = 1 HPRT_RAT Hypoxanthine-guanine phosphoribosyltransferase OS =Rattus 2 2 12.4 24476.97 6.07 0 0.102 1.15293 0.735512 0.768622 0.219322 1.34576 0.394728 1.03874 0.894639 norvegicusGN = Hprt1 PE = 1 SV = 1 PTPM1_RAT Phosphatidylglycerophosphatase and protein-tyrosine 1 1 6.7 21886.11 9.63 0 0.117 0.945317 0.803404 1.79232 0.000312 0.791481 0.444487 1.37587 0.177188 phosphatase 1 OS =Rattus norvegicus GN = Ptpmt1 PE = 2 SV = 1 Q6IMX4_RAT Lipid phosphate phosphohydrolase 3 OS =Rattus norvegicus 7 3 11.9 35232.81 9.25 6 0.144 1.10643 0.826595 0.873677 0.501338 1.25021 0.557068 1.13696 0.626264 GN = Ppap2b PE = 2 SV = 1 LRFN1_RAT Leucine-rich repeat and fibronectin type III domain-containing 2 2 3.9 81968.58 7.89 0 0.097 1.30228 0.472061 0.957133 0.817518 1.33718 0.408029 1 0.992644 protein 1 OS =Rattus norvegicus GN = Lrfn1 PE = 1 SV = 1 SYSC_RAT Serine–tRNA ligase, cytoplasmic OS =Rattus norvegicus 2 2 5.3 58587.25 5.86 0 0.525 1.21591 0.618055 1.1892 0.390677 0.861023 0.583303 0.946854 0.804633 GN = Sars PE = 1 SV = 3 WASF1_RAT Wiskott-Aldrich syndrome protein family member 1 OS =Rattus 2 2 4.7 61514.27 5.94 0 0.622 1.12031 0.799103 0.996284 0.98121 0.928745 0.73525 0.805718 0.378993 norvegicusGN = Wasf1 PE = 2 SV = 1 MAP1S_RAT Microtubule-associated protein 1S OS =Rattus norvegicus 2 2 2.8 102804.7 6.68 0 0.284 1.04262 0.955233 1.07514 0.734703 1.34442 0.396784 0.921695 0.718782 GN = Map1s PE = 1 SV = 1 F1LW39_RAT Protein Srgap3 (Fragment) OS =Rattus norvegicus 2 2 5.6 72935.11 6.46 0 0.612 1.1003 0.838809 1.34247 0.119596 0.907665 0.686471 0.875878 0.571815 GN = Srgap3 PE = 2 SV = 1 KC1G2_RAT Casein kinase 1, gamma 2, isoform CRA_a OS =Rattus 1 1 2.0 50129.61 9.1 0 0.62 0.993269 0.92793 1.47244 0.031678 0.891398 0.649691 1.21091 0.450878 norvegicusGN = Csnk1g2 PE = 3 SV = 1 F1M4D1_RAT Glyceraldehyde-3-phosphate dehydrogenase (Fragment) 9 4 17.5 23209.38 8.87 0 0.069 1.11584 0.807935 1.20385 0.354903 1.09135 0.88195 1.25312 0.364754 OSRattus = norvegicus PE = 3 SV = 1 F1LM47_RAT Protein Sucla2 (Fragment) OS =Rattus norvegicus GN = Sucla2 25 12 23.3 47286.13 6.08 0 0.026 1.13768 0.765058 1.35867 0.103039 1.50252 0.199143 1.80977 0.003547 PE = 2 SV = 1 D3ZKD9_RAT Microtubule-associated protein OS =Rattus norvegicus 10 8 26.3 37954.36 9.98 0 0.833 1.12402 0.791805 1.05558 0.802735 1.20374 0.646325 1.03435 0.907198 GN=MaptPE=2SV=1 F1LYA6_RAT Protein Abi2 (Fragment) OS =Rattus norvegicus GN = Abi2 2 2 5.8 49143.3 5.93 0 0.542 0.728346 0.334 1.14011 0.52555 1.05539 0.960773 0.796597 0.357246 PE = 2 SV = 1 D4A5I9_RAT Protein Myo6 OS =Rattus norvegicus GN = Myo6 PE = 2 6 5 6.1 145663.9 8.64 0 0.607 1.2054 0.6371 1.06241 0.778793 1.07636 0.914711 1.11161 0.692477 SV = 1 F1M7N2_RAT Ectonucleoside triphosphate diphosphohydrolase 2 OS =Rattus 1 1 4.2 60018.11 7.15 0 0.018 1.45371 0.268813 1.11039 0.617463 0.849484 0.558939 0.797593 0.359584 norvegicusGN = Entpd2 PE = 2 SV = 1 SET_RAT Protein SET OS = Rattus norvegicus GN = Set PE = 1 SV = 2 1 1 3.5 33405.41 4.22 0 1.28 1.01215 0.977616 0.891614 0.563626 1.83202 0.028241 1.72551 0.009009 COX7C_RAT Cytochrome c oxidase subunit 7C, mitochondrial OS =Rattus 6 1 14.3 7374.62 11 0 0.114 1.04196 0.956575 0.918507 0.663455 1.27575 0.5107 1.05335 0.853088 norvegicusGN = Cox7c PE = 1 SV = 2 BSCL2_RAT Seipin OS =Rattus norvegicus GN = Bscl2 PE = 2 SV = 1 1 1 2.4 42408.55 5.71 2 0.162 0.801271 0.468419 1.3123 0.155871 1.25673 0.545032 1.14592 0.603528 D3ZAX3_RAT Plasma membrane calcium-transporting ATPase 1 OS =Rattus 46 26 22.6 130647.5 5.69 0 0.193 1.12555 0.788792 0.884376 0.538048 1.25993 0.539188 0.877768 0.577587 norvegicusGN = Atp2b1 PE = 2 SV = 1 1433G_RAT 14-3-3 protein gamma OS =Rattus norvegicus GN = Ywhag 40 14 36.0 28302.27 4.8 0 0.68 1.12206 0.795659 1.03161 0.888162 1.28744 0.490177 1.17499 0.532441 PE = 1 SV = 2 VIAAT_RAT Vesicular inhibitory amino acid transporter OS =Rattus 8 3 8.8 57406.52 6.19 9 0.464 1.08532 0.86881 1.03251 0.88491 1.29835 0.471432 0.987451 0.947816 norvegicusGN = Slc32a1 PE = 1 SV = 1 F1MAL3_RAT Protein Sptb OS = Rattus norvegicus GN = Sptb PE = 4 9 8 4.6 267950.9 5.28 0 0.651 1.29256 0.487475 1.68277 0.001894 0.704423 0.300608 1.02394 0.937041 SV = 1 ETBR2_RAT Endothelin B receptor-like protein 2 OS = Rattus norvegicus 1 1 2.1 52859.15 6.97 4 0.24 1.04516 0.950065 1.0273 0.903678 1.36845 0.36085 1.34821 0.211441 GN = Gpr37l1 PE = 2 SV = 1 F1LMY3_RAT Receptor-type tyrosine-protein phosphatase zeta OS = Rattus 4 4 2.3 255368.2 4.74 0 0.42 1.05768 0.924638 1.06986 0.752877 1.57472 0.137973 1.35274 0.205516 norvegicus GN = Ptprz1 PE = 2 SV = 1 Q06C60_RAT BolA-like 1 (E. coli) (Predicted) OS = Rattus norvegicus 2 1 11.0 14403.31 9.41 0 0.191 0.731587 0.339386 1.14432 0.513128 0.928137 0.733825 0.716936 0.201402 GN = Bola1 PE = 2 SV = 1

B5DFC3_RAT Protein Sec23a OS = Rattus norvegicus GN = Sec23a PE = 2 1 1 2.2 86160.82 6.64 0 0.235 1.3562 0.391548 1.17185 0.435765 1.20097 0.651826 1.32519 0.24341 SV = 1 RAB1A_RAT Ras-related protein Rab-1A OS = Rattus norvegicus 11 3 15.6 22677.49 5.93 0 0.294 1.08477 0.869926 1.3042 0.166918 1.4539 0.250257 1.21622 0.439434 GN = Rab1A PE = 1 SV = 3 TRIM2_RAT Tripartite motif-containing protein 2 OS = Rattus norvegicus 8 6 9.3 81426.22 6.61 0 0.328 1.00332 0.954374 1.01903 0.933597 1.06205 0.94612 0.944772 0.797421 GN = Trim2 PE = 1 SV = 2 GDIB_RAT Rab GDP dissociation inhibitor beta OS = Rattus norvegicus 6 4 13.9 50536.56 5.93 0 0.304 0.796517 0.458834 1.60071 0.006282 0.76158 0.391146 1.11311 0.688499 GN = Gdi2 PE = 1 SV = 2 TTYH1_RAT Protein tweety homolog 1 OS = Rattus norvegicus GN = Ttyh1 2 1 3.1 49031.73 4.87 1 0.225 1.07282 0.894 1.0561 0.800899 0.788325 0.43867 0.897406 0.639126 PE = 2 SV = 1

Q4V8E2_RAT Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 14 1 1 4.5 34576.68 6.06 0 0.175 1.03272 0.975384 1.32982 0.133901 0.841027 0.541402 0.973556 0.898378 220–292 (2015) 298 Neuroscience / al. et Han X. OS = Rattus norvegicus GN = Psmd14 PE = 2 SV = 1 Q6P790_RAT 60S ribosomal protein L6 (Fragment) OS = Rattus norvegicus 2 2 7.1 33473.07 10.78 0 0.803 1.2303 0.592404 1.08771 0.692008 1.26699 0.526384 0.999466 0.990735 GN = Rpl6 PE = 2 SV = 1 PHB_RAT Prohibitin OS = Rattus norvegicus GN = Phb PE = 1 SV = 1 19 7 27.2 29819.71 5.57 0 0.009 1.15836 0.725097 0.960325 0.830666 1.41773 0.293801 1.12753 0.650576 BASP1_RAT Brain acid soluble protein 1 OS = Rattus norvegicus 26 10 64.6 21790.01 4.5 0 1.137 1.10738 0.824712 0.888737 0.553389 1.25885 0.541166 1.14607 0.603142 GN = Basp1 PE = 1 SV = 2 TIM10_RAT Mitochondrial import inner membrane translocase subunit Tim10 5 3 38.9 10332.88 5.89 0 0.649 1.27106 0.522554 0.852659 0.433269 0.98346 0.866466 0.804609 0.376306 OS = Rattus norvegicus GN = Timm10 PE = 3 SV = 1 SYN1_RAT Synapsin-1 OS = Rattus norvegicus GN = Syn1 PE = 1 74 19 33.4 73987.49 9.81 0 0.575 1.1268 0.786337 1.0113 0.961623 1.05661 0.958095 0.907477 0.671717 SV = 3 ATPB_RAT ATP synthase subunit beta, mitochondrial OS = Rattus 284 24 50.9 56352.87 5.18 0 0.034 1.14297 0.754761 1.09402 0.670918 1.02842 0.977291 1.00114 0.996723 norvegicus GN = Atp5b PE = 1 SV = 2 B2RYS2_RAT Cytochrome b-c1 complex subunit 7 OS = Rattus norvegicus 8 3 26.1 13558.39 9.3 0 1.05 1.0678 0.904146 1.21787 0.322681 1.27646 0.509449 1.3221 0.247947 TPM2_RAT TropomyosinGN = Uqcrb PEbeta = chain 3 SV OS = 1 = Rattus norvegicus GN = Tpm2 6 5 16.2 32740.27 4.62 0 1.067 1.11777 0.804124 0.916629 0.656258 1.38203 0.341481 1.31281 0.261939 PE = 2 SV = 1 F1LNY1_RAT Misshapen-like kinase 1 (Fragment) OS = Rattus norvegicus 4 3 3.3 146895.4 7.33 0 0.808 1.07059 0.898501 0.87658 0.511166 1.75133 0.048714 1.31482 0.25886 GN = LOC687705 PE = 2 SV = 1 AT1B1_RAT Sodium/potassium-transporting ATPase subunit beta-1 42 6 20.4 35201.17 8.83 1 0.548 1.10674 0.82599 0.791762 0.268779 1.28068 0.501994 0.937194 0.771329 OS = Rattus norvegicus GN = Atp1b1 PE = 1 SV = 1 CALR_RAT Calreticulin OS = Rattus norvegicus GN = Calr PE = 1 SV = 1 11 5 14.4 47994.87 4.33 0 1.099 1.08131 0.87689 1.14783 0.502882 1.1469 0.762719 1.29908 0.283605 CH10_RAT 10 kDa heat shock protein, mitochondrial OS = Rattus 18 8 58.8 10901.53 8.89 0 0.037 1.16843 0.705901 1.06569 0.767347 1.30868 0.45405 1.47745 0.086129 norvegicus GN = Hspe1 PE = 1 SV = 3 PRDX1_RAT Peroxiredoxin-1 OS = Rattus norvegicus GN = Prdx1 PE = 1 11 8 34.7 22109.14 8.27 0 0.222 1.26093 0.539511 1.57432 0.008989 1.07036 0.927867 1.2538 0.363457 SV = 1 DHE3_RAT Glutamate dehydrogenase 1, mitochondrial OS = Rattus 96 22 40.3 61415.21 8.05 0 0.306 1.10091 0.837599 1.12395 0.574658 1.08485 0.896132 1.0965 0.733136 norvegicus GN = Glud1 PE = 1 SV = 2 D3ZEA1_RAT Protein RGD1310819 OS = Rattus norvegicus 2 2 5.9 48317.48 9.5 0 0.961 1.04469 0.951031 1.19156 0.384763 0.945748 0.775397 1.0121 0.971075 GN = RGD1310819 PE = 2 SV = 1 F1M542_RAT Protein Adam22 (Fragment) OS = Rattus norvegicus 1 1 8.2 21947.1 8.85 0 0.458 0.920748 0.741286 0.612358 0.039852 1.52089 0.181969 0.987068 0.94645 GN = Adam22 PE = 4 SV = 1 D4A0I5_RAT Protein Dnajc6 OS = Rattus norvegicus GN = Dnajc6 PE = 2 4 3 4.6 99828.28 6.67 0 0.533 1.10551 0.828423 0.949281 0.785399 1.38177 0.341849 1.06563 0.818477 SV = 1 CAN2_RAT Calpain-2 catalytic subunit OS = Rattus norvegicus 2 1 2.6 79918.4 4.86 0 0.407 1.15553 0.730514 0.958178 0.821817 0.950318 0.786296 0.838729 0.464266 GN = Capn2 PE = 1 SV = 3 ADRO_RAT NADPH:adrenodoxin oxidoreductase, mitochondrial 3 2 3.5 54260.77 9.35 0 0.236 1.10114 0.837134 1.10611 0.631251 0.786922 0.436096 0.883502 0.595265 OS = Rattus norvegicus GN = Fdxr PE = 3 SV = 1 F1LP27_RAT Eukaryotic initiation factor 4A-II OS = Rattus norvegicus 1 1 4.8 36302.8 6.98 0 0.184 1.27561 0.515017 1.16333 0.458943 0.93854 0.758298 0.997332 0.983109

GN = Eif4a2 PE = 2 SV = 1 253 KACB_RAT Ig kappa chain C region, B allele OS = Rattus norvegicus 6 3 35.9 11600.7 4.97 0 0.453 1.10621 0.827032 1.20138 0.360795 1.35542 0.380075 1.37095 0.182953 PE = 1 SV = 1 (continued on next page) 5 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 254

PGAM1_RAT Phosphoglycerate mutase 1 OS = Rattus norvegicus 18 10 46.1 28831.64 6.67 0 0.488 1.03391 0.972964 0.978822 0.907683 1.15729 0.740945 1.06384 0.823516 GN = Pgam1 PE = 1 SV = 4 NUP98_RAT Nuclear pore complex protein Nup98-Nup96 OS =Rattus 1 1 0.4 197280.4 5.83 0 0.413 0.797387 0.46058 0.565604 0.021296 1.52517 0.178134 1.36537 0.189669 norvegicusGN = Nup98 PE = 1 SV = 2 COX5B_RAT Cytochrome c oxidase subunit 5B, mitochondrial OS =Rattus 19 4 31.8 13914.79 7.68 0 0.281 1.08129 0.876919 0.987295 0.9433 1.16912 0.716408 0.984492 0.937265 norvegicusGN = Cox5b PE = 1 SV = 2 AT2B3_RAT Isoform XE of Plasma membrane calcium-transporting ATPase 3 26 12 12.1 128293.3 5.76 0 0.089 1.09519 0.849023 0.671387 0.081351 1.25267 0.552508 0.810372 0.390396 OSRattus = norvegicus GN = Atp2b3 DCLK2_RAT Serine/threonine-protein kinase DCLK2 OS =Rattus norvegicus 3 2 6.5 40381.96 9.85 0 0.593 1.12308 0.793653 1.04065 0.855734 1.14781 0.760812 0.872068 0.560259 GN = Dclk2 PE = 4 SV = 1 ALDOA_RAT Fructose-bisphosphate aldolase OS =Rattus norvegicus 53 15 37.3 45085.75 8.03 0 0.311 1.08825 0.86294 1.02414 0.915109 1.12567 0.807788 1.15654 0.577053 GN = Aldoa PE = 3 SV = 1 PYC_RAT Pyruvate carboxylase, mitochondrial OS =Rattus norvegicus 18 10 11.2 129775.3 6.34 0 0.165 1.05539 0.929279 0.924759 0.687639 1.12587 0.807375 1.02654 0.92958 GN=PcPE=1SV=2 GRIA1_RAT Glutamate receptor 1 OS =Rattus norvegicus GN = Gria1 16 12 17.4 101577.9 7.46 0 0.194 1.09314 0.853125 0.845887 0.412529 1.11679 0.826847 1.0148 0.963297 PE = 1 SV = 2 F1M7V6_RAT Cell adhesion molecule 4 (Fragment) OS =Rattus norvegicus 6 4 16.6 40417.04 5.59 0 0.255 1.07705 0.885458 0.921156 0.673661 1.25484 0.548504 1.07861 0.782275 GN = Cadm4 PE = 2 SV = 1 D3ZKG1_RAT Protein LOC100361295 OS =Rattus norvegicus 3 3 5.9 82924.21 6.58 0 0.26 1.13628 0.767774 1.00873 0.970933 0.802377 0.464912 0.803934 0.374677 GN = LOC100361295 PE = 4 SV = 1 D4AA84_RAT Protein Cisd3 OS =Rattus norvegicus GN = Cisd3 PE = 2 1 1 11.1 15006.21 10.17 0 0.537 1.20631 0.635434 0.992168 0.963843 1.07893 0.909079 0.984893 0.938695 SV = 1 GPDA_RAT Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic 4 3 10.9 37452.12 6.16 0 0.134 1.17454 0.694348 1.15373 0.485914 1.00403 0.916973 1.22679 0.417195 OSRattus = norvegicus GN = Gpd1 PE = 1 SV = 4 F1MA36_RAT Spectrin beta chain, non-erythrocytic 2 OS = Rattus norvegicus 52 32 19.1 270936.9 5.59 0 0.643 1.12376 0.792316 0.963555 0.844021 1.06395 0.941936 0.861972 0.530207 GN = Sptbn2 PE = 2 SV = 1 THOP1_RAT Thimet oligopeptidase OS =Rattus norvegicus GN = Thop1 2 2 3.2 78384.59 5.64 0 0.435 1.0172 0.990955 0.85119 0.428718 1.19797 0.657809 0.9351 0.764162 PE = 1 SV = 4 MPCP_RAT Phosphate carrier protein, mitochondrial OS =Rattus 31 10 20.2 39444.68 9.41 0 0.062 1.10844 0.822598 1.03094 0.89059 1.26873 0.523249 1.07086 0.803846 norvegicusGN = Slc25a3 PE = 1 SV = 1 DOPD_RAT D-dopachrome decarboxylase OS = Rattus norvegicus 6 3 39.0 13133.12 6.09 0 0.044 1.13981 0.760902 0.966388 0.855769 0.902894 0.675603 0.891013 0.61879 GN = Ddt PE = 1 SV = 3 GNAO_RAT Isoform Alpha-2 of Guanine nucleotide-binding protein G(o) 77 12 33.1 40080.1 5.69 0 0.347 1.13676 0.766833 0.861003 0.459629 1.2566 0.545275 0.969986 0.885733 subunit alpha OS =Rattus norvegicus GN = Gnao1 SYUA_RAT Alpha-synuclein OS =Rattus norvegicus GN = Snca PE = 1 18 8 48.6 14515.09 4.74 0 -0.415 1.0837 0.87208 0.987501 0.944171 1.36096 0.371825 1.19026 0.496871 SV = 1 VAPB_RAT Vesicle-associated membrane protein-associated protein B 2 1 5.8 26915.89 7.64 1 0.316 1.12422 0.791404 1.14017 0.52539 0.709405 0.307894 0.853449 0.505486 OS =Rattus norvegicus GN = Vapb PE = 1 SV = 3 Q9JJ10_RAT Neuronal C-SRC tyrosine-specific protein kinase OS =Rattus 3 1 2.4 60726.12 7.95 0 0.485 0.897773 0.684676 0.867038 0.479244 1.91856 0.014977 1.5668 0.041475 norvegicusGN = Src PE = 2 SV = 1 RGRF2_RAT Ras-specific guanine nucleotide-releasing factor 2 OS =Rattus 3 3 3.1 135825.3 8.03 0 0.381 1.17149 0.700096 0.921604 0.675392 0.890587 0.647879 0.945954 0.801513 norvegicusGN = Rasgrf2 PE = 1 SV = 1 NCDN_RAT Neurochondrin OS =Rattus norvegicus GN = Ncdn PE = 1 7 4 6.7 78922.53 5.44 0 0.132 1.07683 0.885909 0.963033 0.84186 1.14608 0.764459 0.983038 0.932083 SV = 2 Q6LDS4_RAT Superoxide dismutase [Cu-Zn] OS = Rattus norvegicus 18 8 53.3 15709.21 5.88 0 0.434 1.04149 0.957531 0.938487 0.741845 1.1333 0.791504 1.0784 0.78285 GN = Sod1 PE = 2 SV = 1 MDHC_RAT Malate dehydrogenase, cytoplasmic OS =Rattus norvegicus 7 5 16.5 36482.68 6.16 0 0.059 1.07349 0.892638 1.1988 0.366994 0.94023 0.762297 1.03445 0.906896 GN = Mdh1 PE = 1 SV = 3 OPA1_RAT Isoform 2 of Dynamin-like 120 kDa protein, mitochondrial 35 18 21.4 117391.6 6.89 0 0.579 1.13829 0.76386 1.16504 0.454249 1.03983 0.995034 1.36858 0.185776 OSRattus = norvegicus GN = Opa1 TMM11_RAT Transmembrane protein 11, mitochondrial OS =Rattus 1 1 8.4 21341.32 6.98 0 0.004 1.08077 0.877974 0.636827 0.054131 2.03497 0.00588 1.52438 0.059348 norvegicusGN = Tmem11 PE = 2 SV = 1 D4ACB6_RAT Pleckstrin and Sec7 domain containing 2 (Predicted) 1 1 1.3 84554.28 5.05 0 0.575 1.10923 0.821039 0.938185 0.740639 0.951833 0.789918 0.899348 0.645358 OSRattus = norvegicus GN = Psd2 PE = 4 SV = 1 E9PSZ3_RAT Spectrin alpha chain, non-erythrocytic 1 OS =Rattus norvegicus 155 77 33.4 285036.7 5.24 0 0.794 1.07995 0.879625 1.00598 0.980941 1.11654 0.827374 0.949348 0.813292 GN = Sptan1 PE = 2 SV = 1 B0BMY7_RAT Protein tyrosine kinase 9-like (A6-related protein) (Predicted), 2 2 10.0 39472.45 6.33 0 0.482 1.12681 0.786309 1.04625 0.835754 1.45656 0.247243 1.2027 0.468854 isoform CRA_b OS =Rattus norvegicus GN = LOC684352 PE = 2 SV = 1 G3V928_RAT Protein Lrp1 OS = Rattus norvegicus GN = Lrp1 PE = 4 12 8 2.5 504884.5 5.14 0 0.507 1.1601 0.72176 0.988161 0.94695 1.01099 0.934166 0.972572 0.894891 SV = 1 G3V8T7_RAT Protein Tdrkh OS = Rattus norvegicus GN = Tdrkh PE = 4 2 2 4.5 62011.15 4.88 0 0.39 1.14657 0.747793 1.35857 0.103138 1.28811 0.489018 1.26903 0.335164 SV = 1 1433B_RAT 14-3-3 protein beta/alpha OS = Rattus norvegicus GN = Ywhab 36 10 28.5 28054.07 4.81 0 0.681 1.08158 0.876344 1.16878 0.444032 1.24271 0.571066 1.291 0.2969 PE = 1 SV = 3 COX5A_RAT Cytochrome c oxidase subunit 5A, mitochondrial OS = Rattus 12 4 17.8 16129.34 6.08 0 0.142 1.01224 0.97786 0.863506 0.46771 1.45671 0.247076 1.27764 0.31981 norvegicus GN = Cox5a PE = 1 SV = 1 CSDE1_RAT Cold shock domain-containing protein E1 OS = Rattus 2 2 2.9 88893.61 5.97 0 0.448 1.10689 0.82569 0.969587 0.869076 1.11187 0.837438 0.964358 0.865857 norvegicus GN = Csde1 PE = 2 SV = 1 B6DYQ7_RAT Glutathione S-transferase pi OS = Rattus norvegicus 3 3 14.8 23438.61 6.89 0 0.22 1.03072 0.979448 1.15901 0.470967 0.652604 0.231645 0.691347 0.163855 GN = Gstp1 PE = 2 SV = 1 AT2B4_RAT Plasma membrane calcium-transporting ATPase 4 OS = Rattus 22 9 9.4 128655.1 6.92 0 0.083 1.04206 0.95637 0.746862 0.179114 1.37185 0.355946 0.825513 0.428911 norvegicus GN = Atp2b4 PE = 2 SV = 1 CAZA2_RAT F-actin-capping protein subunit alpha-2 OS = Rattus norvegicus 8 4 19.9 32966.65 5.57 0 0.586 0.988661 0.915837 1.06517 0.769155 0.830391 0.519742 0.737094 0.235132 GN = Capza2 PE = 1 SV = 1 SUCA_RAT Succinyl-CoA ligase [ADP/GDP-forming] subunit alpha, 32 11 29.2 36147.53 9.54 1 0.028 1.12515 0.789571 1.1596 0.469314 1.06957 0.929612 1.19075 0.495744 mitochondrial OS = Rattus norvegicus GN = Suclg1 PE = 2 SV = 2 AMRP_RAT Alpha-2-macroglobulin receptor-associated protein OS = Rattus 2 2 7.5 42031.18 6.85 0 0.204 0.858416 0.591837 1.0253 0.910903 0.996399 0.898191 1.00595 0.988791 220–292 (2015) 298 Neuroscience / al. et Han X. norvegicus GN = Lrpap1 PE = 1 SV = 2 ALDOC_RAT Fructose-bisphosphate aldolase C OS = Rattus norvegicus 20 9 26.5 39283.32 6.67 0 0.204 0.974703 0.879332 0.902992 0.60498 1.13142 0.795513 0.965984 0.87159 GN = Aldoc PE = 1 SV = 3 I7EFB0_RAT Myelin basic protein transcript variant N (Fragment) OS = Rattus 123 13 51.2 22939.28 10.27 0 1.065 1.091 0.857416 0.931311 0.713331 1.25909 0.540716 1.05172 0.857721 norvegicus GN = Mbp PE = 2 SV = 1 F1LRT9_RAT Cytoplasmic dynein 1 heavy chain 1 (Fragment) OS = Rattus 19 14 5.1 416863.4 5.94 0 0.336 1.11747 0.804707 0.916593 0.656123 0.940333 0.76254 0.86267 0.532256 norvegicus GN = Dync1h1 PE = 2 SV = 1 DYHC1_RAT Cytoplasmic dynein 1 heavy chain 1 OS = Rattus norvegicus 19 15 4.2 532245.4 6.06 0 0.343 1.11747 0.804707 1.04077 0.855312 0.913604 0.700094 0.847873 0.489649 GN = Dync1h1 PE = 1 SV = 1 0.22 1.06046 0.919012 1.17193 0.435537 1.18084 0.692385 1.31009 0.266138 NSF_RAT Vesicle-fusing ATPase OS = Rattus norvegicus GN = Nsf 55 26 32.5 82651.56 6.55 0 Q6P9V1_RATPE =CD81 1 SV antigen = 1 OS = Rattus norvegicus GN = Cd81 PE = 2 5 2 16.5 25904.26 5.3 4 0.663 0.957099 0.833666 1.237 0.281882 1.14832 0.759732 1.39694 0.154002 SV = 1 Q5BJZ3_RAT Nicotinamide nucleotide transhydrogenase OS = Rattus 26 13 13.2 113868.2 8.02 12 0.274 1.04653 0.947273 1.02343 0.917663 1.24229 0.571848 1.20476 0.464318 norvegicus GN = Nnt PE = 2 SV = 1 ABCF1_RAT ATP-binding cassette sub-family F member 1 (Fragment) 1 1 1.4 92735.01 6.49 0 0.942 0.758319 0.38593 1.09764 0.658958 1.01767 0.950687 1.06665 0.815613 OS = Rattus norvegicus GN = Abcf1 PE = 2 SV = 1 Q6AYP5_RAT Protein Cadm1 (Fragment) OS = Rattus norvegicus 6 4 15.2 41945.85 4.89 0 0.33 1.08448 0.870498 0.765485 0.213155 1.30691 0.457005 0.786701 0.334563 GN = Cadm1 PE = 2 SV = 1 D4A520_RAT Protein Pptc7 OS = Rattus norvegicus GN = Pptc7 PE = 4 1 1 2.3 32846.51 5.08 0 0.151 0.948146 0.810644 1.13718 0.534283 1.24579 0.565297 1.16654 0.552654 SV = 1 G3V6S0_RAT Protein Sptbn1 OS = Rattus norvegicus GN = Sptbn1 PE = 4 76 44 24.0 274060.6 5.41 0 0.748 1.08071 0.878091 0.937992 0.739866 1.05755 0.95602 0.957812 0.842845 SV = 1 D4A831_RAT Protein Bai3 (Fragment) OS = Rattus norvegicus GN = Bai3 1 1 1.0 138902 6.44 0 0.33 1.03193 0.976998 1.06615 0.765748 1.05103 0.97036 1.05563 0.846653 PE = 2 SV = 1 D4A4G9_RAT Protein RGD1561815 OS = Rattus norvegicus 3 2 10.6 18630.59 10.35 0 1.001 1.07681 0.885956 0.951382 0.79396 1.17487 0.704589 1.00816 0.982423 GN = RGD1561815 PE = 4 SV = 1 F1M7K7_RAT Voltage-dependent calcium channel gamma-8 subunit 9 7 17.3 43250.25 9.32 0 0.098 1.09269 0.854036 1.00186 0.995925 0.881037 0.626696 0.779474 0.318597 (Fragment) OS = Rattus norvegicus GN = Cacng8 PE = 2 SV = 1 ACOT2_RAT Acyl-coenzyme A thioesterase 2, mitochondrial OS = Rattus 4 4 15.7 49700.56 7.69 0 0.172 0.973914 0.877276 1.32231 0.143012 1.26759 0.525293 1.4721 0.089719 norvegicus GN = Acot2 PE = 1 SV = 1 B1AC44_RAT Synaptotagmin III OS = Rattus norvegicus GN = Syt3 PE = 2 1 1 2.0 63383.22 6.16 0 0.298 0.946984 0.807668 1.15501 0.482253 1.03838 0.998224 1.03929 0.893071 SV = 1 EXOC3_RAT Exocyst complex component 3 OS = Rattus norvegicus 1 1 1.5 86495.61 5.79 0 0.341 1.25218 0.554374 1.07003 0.752306 0.712627 0.312667 0.803064 0.372582 GN = Exoc3 PE = 1 SV = 1 1433T_RAT 14-3-3 protein theta OS = Rattus norvegicus GN = Ywhaq 19 7 24.9 27777.97 4.69 0 0.512 1.08917 0.861094 1.2445 0.266892 1.26203 0.535362 1.66904 0.016048 PE = 1 SV = 1 AATM_RAT Aspartate aminotransferase, mitochondrial OS = Rattus 38 17 38.8 47313.74 9.13 0 0.23 1.15188 0.737529 1.22532 0.306347 1.23794 0.580036 1.76443 0.00592 255 norvegicus GN = Got2 PE = 1 SV = 2 (continued on next page) 5 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 256

CN37_RAT 2’,3’-cyclic-nucleotide 3’-phosphodiesterase OS = Rattus 69 19 29.5 47267.83 9.03 0 0.443 1.03482 0.971106 0.862894 0.465729 1.14516 0.766394 1.00756 0.984137 norvegicusGN = Cnp PE = 1 SV = 2 DLG4_RAT Disks large homolog 4 OS =Rattus norvegicus GN = Dlg4 24 14 19.1 80464.36 5.58 0 0.468 1.02601 0.989056 0.881719 0.528809 1.03163 0.985252 0.853799 0.506491 PE = 1 SV = 1 AASD1_RAT Alanyl-tRNA editing protein Aarsd1 OS =Rattus norvegicus 1 1 2.7 45092.64 6.05 0 0.334 1.22327 0.604873 0.795541 0.277533 1.1803 0.693479 0.984095 0.935851 GN = Aarsd1 PE = 2 SV = 1 GPR37_RAT Probable G-protein coupled receptor 37 OS =Rattus norvegicus 1 1 2.8 66960.65 8.36 7 0.056 1.12868 0.782639 0.503641 0.008523 0.895254 0.658338 0.506786 0.026473 GN = Gpr37 PE = 2 SV = 1 D3ZXR8_RAT Protein LOC685244 OS =Rattus norvegicus GN = LOC685244 7 7 5.8 157256.7 8.85 0 0.76 1.04629 0.947761 0.974679 0.890333 1.32887 0.42114 1.24424 0.381952 PE = 4 SV = 1 D4A8P9_RAT Uncharacterized protein OS =Rattus norvegicus PE = 3 10 7 9.5 113934.3 6.76 0 0.255 0.999674 0.944767 1.14711 0.50497 1.16714 0.720505 1.13135 0.640674 SV = 1 SERA_RAT D-3-phosphoglycerate dehydrogenase OS =Rattus norvegicus 2 2 4.3 56492.82 6.28 0 0.112 1.05236 0.935443 1.09874 0.655321 1.16359 0.727852 1.12289 0.662688 GN = Phgdh PE = 1 SV = 3 B2RZD6_RAT Ndufa4 protein OS =Rattus norvegicus GN = Ndufa4 PE = 4 17 4 40.2 9326.67 9.52 1 0.406 1.09044 0.858546 0.902725 0.603995 1.26023 0.538643 1.26405 0.344249 SV = 1 RL30_RAT 60S ribosomal protein L30 OS =Rattus norvegicus GN = Rpl30 1 1 12.2 12783.92 9.65 0 0.295 1.15931 0.723283 0.809875 0.312484 1.04331 0.987367 0.755498 0.269256 PE = 3 SV = 2 Q32PW9_RAT Psmc6 protein (Fragment) OS =Rattus norvegicus 1 1 2.9 43287.49 7.23 0 0.415 1.00011 0.94591 0.856647 0.445757 1.02307 0.964039 0.874122 0.566475 GN = Psmc6 PE = 2 SV = 1 DPYL2_RAT Dihydropyrimidinase-related protein 2 OS =Rattus norvegicus 82 16 38.3 62276.84 5.95 0 0.267 1.06229 0.915297 0.937927 0.739607 1.16565 0.723573 1.02964 0.920688 GN = Dpysl2 PE = 1 SV = 1 NDUA5_RAT NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 2 22.4 13411.62 6.84 0 0.349 1.11418 0.811212 1.25905 0.239371 1.12349 0.812471 1.37357 0.179861 5OS=Rattus norvegicus GN = Ndufa5 PE = 1 SV = 3 G3V7T8_RAT Discs, large (Drosophila) homolog-associated protein 3, isoform 4 4 6.1 105907.9 8.99 0 0.79 1.12989 0.780265 0.674726 0.084487 1.6012 0.119591 0.974576 0.901999 CRA_b OS =Rattus norvegicus GN = Dlgap3 PE = 4 SV = 1 RAB7A_RAT Ras-related protein Rab-7a OS =Rattus norvegicus 4 3 16.4 23503.51 6.4 0 0.377 1.06167 0.916545 0.986018 0.937923 2.08791 0.003724 1.98641 0.00038 GN = Rab7a PE = 1 SV = 2 D3ZSA9_RAT Protein Nomo1 OS =Rattus norvegicus GN = Nomo1 PE = 4 1 1 1.5 133441.5 5.73 0 0.151 0.859294 0.593844 0.929051 0.704431 0.700123 0.294413 0.624357 0.090571 SV = 1 LEG9_RAT Galectin-9 OS =Rattus norvegicus GN = Lgals9 PE = 2 1 1 3.4 39945.49 9.36 0 0.218 1.14751 0.745963 1.10928 0.621026 1.01516 0.944466 0.994586 0.973293 SV = 2 B2RYC4_RAT Protein Syvn1 OS =Rattus norvegicus GN = Syvn1 PE = 2 1 1 1.6 66872.25 6.6 6 0.098 1.11864 0.8024 0.798333 0.284123 1.16213 0.73087 0.903277 0.658044 SV = 1 GRIA3_RAT Glutamate receptor 3 OS =Rattus norvegicus GN = Gria3 9 6 8.5 100371.5 8.38 3 0.219 1.09146 0.856492 1.03052 0.892077 1.09834 0.866745 1.06032 0.833413 PE = 1 SV = 1 GPM6A_RAT Isoform 2 of Neuronal membrane glycoprotein M6-a OS =Rattus 18 5 13.5 29890.88 5.55 0 0.561 1.00877 0.968706 0.914511 0.648181 1.25217 0.553431 1.22585 0.419144 norvegicusGN = Gpm6a D4A678_RAT Protein Spta1 OS = Rattus norvegicus GN = Spta1 PE = 2 2 2 1.0 280071.2 4.94 0 0.769 1.13294 0.774292 1.53751 0.014493 0.775688 0.415814 1.15909 0.570788 SV = 1 D4A1B8_RAT Protein Dctn3 OS =Rattus norvegicus GN = Dctn3 PE = 4 1 1 4.3 21112.21 5.59 0 0.195 1.21621 0.617523 0.824635 0.351382 1.30857 0.454235 0.968565 0.880706 SV = 1 Q56A26_RAT Protein Opalin OS =Rattus norvegicus GN = Opalin PE = 2 2 2 21.8 15672.53 4.98 1 0.376 1.19298 0.659895 1.49147 0.025409 1.1037 0.855117 1.5213 0.060862 SV = 1 Q5XIH3_RAT NADH dehydrogenase (Ubiquinone) flavoprotein 1 OS =Rattus 19 5 13.2 50730.43 8.37 0 0.272 1.10596 0.827542 0.954899 0.808345 1.04711 0.979002 0.959914 0.85022 norvegicusGN = Ndufv1 PE = 2 SV = 1 F1M2C7_RAT Protein Ildr2 (Fragment) OS =Rattus norvegicus GN = Ildr2 1 1 1.8 64141.23 7.86 0 0.671 1.06954 0.900621 1.02685 0.90533 1.35019 0.387969 1.23018 0.41021 PE = 2 SV = 1 SNPH_RAT Syntaphilin OS =Rattus norvegicus GN = Snph PE = 4 8 4 7.3 50924.56 5.61 0 0.502 1.08301 0.873459 1.01087 0.963164 1.0281 0.976501 1.02851 0.923908 SV = 1 MYH10_RAT Myosin-10 OS =Rattus norvegicus GN = Myh10 PE = 2 17 13 7.8 233612.8 5.47 0 0.855 1.01173 0.976532 1.05932 0.789603 1.05541 0.960723 0.891174 0.619299 SV = 1 C8YL70_RAT DNA-directed polymerase delta interacting protein 2 1 1 4.4 41796.58 8.8 0 0.499 1.02013 0.998667 0.76437 0.210995 1.00325 0.915069 0.748253 0.255437 OSRattus = norvegicus GN = Poldip2 PE = 2 SV = 1 RS11_RAT 40S ribosomal protein S11 OS =Rattus norvegicus 1 1 11.4 18430.51 10.31 0 0.607 1.03085 0.979197 1.01182 0.959721 0.70545 0.3021 0.653951 0.11881 GN = Rps11 PE = 1 SV = 3 EFHD2_RAT EF-hand domain-containing protein D2 OS =Rattus norvegicus 6 4 18.8 26758.86 5.01 0 0.668 1.14034 0.759873 0.808296 0.308497 1.18209 0.689824 0.981311 0.925934 GN = Efhd2 PE = 1 SV = 1 F1LS65_RAT Signal-induced proliferation-associated 1-like protein 1 2 2 2.1 146782.5 7.7 0 0.675 1.10408 0.831273 0.923845 0.684085 0.97493 0.845665 0.814523 0.400739 (Fragment) OS =Rattus norvegicus GN = Sipa1l1 PE = 2 SV = 1 F1LY09_RAT Protein Actr3b (Fragment) OS = Rattus norvegicus 2 2 7.2 47759.24 5.68 0 0.183 1.06855 0.902631 0.986162 0.938529 1.51943 0.183296 1.29103 0.296862 GN = Actr3b PE = 2 SV = 1 D3ZAA9_RAT Protein Mpp2 OS = Rattus norvegicus GN = Mpp2 PE = 2 3 2 4.0 63354.32 5.79 0 0.35 0.988419 0.915202 0.975338 0.893087 0.754393 0.37893 0.817195 0.407485 SV = 1 D3ZC15_RAT Protein Rltpr OS = Rattus norvegicus GN = Ube2j2 PE = 2 2 2 1.6 141358.3 7.01 0 0.36 1.05383 0.932457 1.00461 0.985914 0.850531 0.561128 0.896732 0.636969 SV = 1 TMED7_RAT Transmembrane emp24 domain-containing protein 7 1 1 4.4 25478.69 6.43 0 0.208 0.917471 0.733115 1.05874 0.791646 0.966353 0.824857 1.04239 0.88423 OS = Rattus norvegicus GN = Tmed7 PE = 1 SV = 1 Q6AYB7_RAT Protein Ube2j2 OS = Rattus norvegicus GN = Ube2j2 PE = 2 1 1 25.7 4024.58 9.74 0 0.997 0.905011 0.702339 0.703494 0.115721 0.815281 0.489761 0.521343 0.031242 SV = 1 TIM9B_RAT Mitochondrial import inner membrane translocase subunit Tim9 B 2 1 16.0 11350.87 6.64 0 0.393 1.04071 0.95912 0.807565 0.306663 0.856148 0.572948 0.780948 0.321812 OS = Rattus norvegicus GN = Fxc1 PE = 3 SV = 1 NAC1_RAT Isoform 3 of Sodium/calcium exchanger 1 OS = Rattus 3 3 2.9 104155.5 4.82 0 0.035 1.0729 0.893836 0.740421 0.168335 1.10749 0.846913 0.930621 0.748899 norvegicus GN = Slc8a1 HS90B_RAT Heat shock protein HSP 90-beta OS = Rattus norvegicus 25 16 22.8 83280.25 4.97 0 0.678 1.04493 0.950544 1.1144 0.604676 1.03415 0.991505 1.29626 0.2882 GN = Hsp90ab1 PE = 1 SV = 4 PSMD2_RAT 26S proteasome non-ATPase regulatory subunit 2 OS = Rattus 2 2 2.4 100186.5 5.08 0 0.083 1.06519 0.909415 1.03478 0.876753 1.32986 0.419574 1.17469 0.533156 norvegicus GN = Psmd2 PE = 2 SV = 1 PGK1_RAT Phosphoglycerate kinase 1 OS = Rattus norvegicus GN = Pgk1 28 12 30.0 44537.97 8.02 0 0.083 1.05783 0.924345 1.15747 0.475293 0.931301 0.74124 1.07335 0.796901 PE = 1 SV = 2 220–292 (2015) 298 Neuroscience / al. et Han X. CYB5B_RAT Cytochrome b5 type B OS = Rattus norvegicus GN = Cyb5b 4 2 9.6 16264.75 4.92 0 0.626 1.00213 0.951239 0.8432 0.404468 1.0461 0.981232 0.87892 0.581118 PE = 1 SV = 2 B0K017_RAT ADP-ribosylhydrolase like 2 OS = Rattus norvegicus 2 1 3.0 39374.75 4.85 0 0.115 0.89167 0.669918 0.906689 0.618707 1.08703 0.891381 1.08133 0.774748 GN = Adprhl2 PE = 2 SV = 1

TPM1_RAT Isoform 5 of Tropomyosin alpha-1 chain OS = Rattus 16 11 41.6 28343.11 4.74 0 1.072 1.04847 0.943347 1.02397 0.915729 1.13766 0.782263 1.08918 0.753137 norvegicus GN = Tpm1 D3ZCV0_RAT Protein Actn2 OS = Rattus norvegicus GN = Actn2 PE = 4 4 4 5.8 103832.5 5.31 0 0.605 0.979459 0.891746 1.05811 0.793841 1.17725 0.699713 0.981894 0.928009 SV = 1 D4AAM0_RAT Protein Tnpo3 OS = Rattus norvegicus GN = Tnpo3 PE = 2 1 1 1.3 104861.1 5.31 0 0.035 0.773037 0.413143 0.843158 0.404343 0.68783 0.277176 0.583992 0.061032 SV = 1 70 16 40.0 46961.18 8.58 0 0.411 1.03533 0.970075 0.985316 0.93497 1.02295 0.963736 0.996794 0.981183 Q5BJT9_RAT Creatine kinase U-type, mitochondrial OS = Rattus norvegicus B4F7A3_RATGN Hspc159 = Ckmt1b protein PE = OS 2 =SVRattus = 1 norvegicus GN = Lgalsl 1 1 5.2 18955.48 5.12 0 0.023 1.07764 0.884267 0.997022 0.984325 1.06174 0.946813 1.02079 0.94607 PE = 2 SV = 1 GPC1_RAT Glypican-1 OS = Rattus norvegicus GN = Gpc1 PE = 1 5 3 8.6 61733.53 6.86 0 0.365 1.01116 0.975016 0.765437 0.213063 1.1465 0.763576 0.915989 0.699754 SV = 1 SCN3A_RAT Sodium channel protein type 3 subunit alpha OS = Rattus 2 2 1.1 221384.3 5.66 19 0.043 0.93259 0.771044 0.781953 0.246952 1.21038 0.633212 0.896192 0.635244 norvegicus GN = Scn3a PE = 1 SV = 1 MIC60_RAT Mitochondrial inner membrane protein OS = Rattus 40 22 25.1 82247.85 5.41 0 0.487 1.06113 0.917639 1.02388 0.916042 1.05883 0.953202 0.983054 0.932144 norvegicus GN = Immt PE = 2 SV = 1 Q5PQZ9_RAT NADH dehydrogenase [ubiquinone] 1 subunit C2 OS = Rattus 31 5 34.2 14358.69 9.41 1 0.472 1.05122 0.937742 1.02164 0.924159 1.03234 0.987024 0.98733 0.947386 norvegicus GN = Ndufc2 PE = 2 SV = 1 ATPO_RAT ATP synthase subunit O, mitochondrial OS = Rattus 28 9 39.0 23397.28 10.03 0 0.022 1.20314 0.64122 1.32029 0.145537 0.825988 0.510911 1.00425 0.993695 norvegicus GN = Atp5o PE = 1 SV = 1 D3ZT47_RAT Protein LOC100361389 OS = Rattus norvegicus 1 1 1.7 87275.77 8.41 0 0.355 1.01577 0.987164 1.07714 0.72783 0.756212 0.381998 0.785077 0.330931 GN = Fam171a2 PE = 4 SV = 1 Q6P2A7_RAT Flot1 protein OS = Rattus norvegicus GN = Flot1 PE = 2 6 6 19.4 47512.92 6.71 0 0.355 1.04285 0.95476 0.928896 0.703823 1.10918 0.843255 0.899516 0.645899 SV = 1 D3ZC55_RAT Heat shock 70kDa protein 12A (Predicted), isoform CRA_a 3 3 5.3 74829.44 6.18 0 0.23 0.9927 0.926435 0.792848 0.271276 1.1877 0.678446 0.821384 0.418195 OS = Rattus norvegicus GN = Hspa12a PE = 4 SV = 1 STML2_RAT Stomatin-like protein 2 OS = Rattus norvegicus GN = Stoml2 4 4 16.9 33231.56 6.25 0 0.178 1.1003 0.83882 0.82435 0.350602 1.09102 0.882664 0.824585 0.426489 PE = 2 SV = 1 D3ZJH9_RAT Malic enzyme OS = Rattus norvegicus GN = Me2 PE = 3 2 2 4.3 65350.91 7.87 0 0.148 1.20598 0.636037 1.47671 0.030166 1.0912 0.882284 1.20207 0.470262 SV = 1 Q6DGG9_RAT Calcium modulating ligand OS = Rattus norvegicus 1 1 4.1 32790.08 7.61 0 0.336 1.08521 0.869041 0.904762 0.611534 1.10131 0.860293 0.855726 0.512032 GN = Camlg PE = 2 SV = 1 CD166_RAT CD166 antigen OS = Rattus norvegicus GN = Alcam PE = 1 1 1 1.7 65021.21 5.77 1 0.37 1.0345 0.971764 0.86085 0.45914 1.30849 0.454374 1.02816 0.92492

SV = 1 257 (continued on next page) 5 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 258 AIFM1_RAT Apoptosis-inducing factor 1, mitochondrial OS = Rattus 9 7 10.0 66721.73 9.06 0 0.231 1.04034 0.959869 0.933221 0.720882 0.969105 0.831521 0.999326 0.990236 norvegicusGN = Aifm1 PE = 1 SV = 1 AMD_RAT Peptidyl-glycine alpha-amidating monooxygenase 1 1 1.5 108673.9 5.78 1 0.355 1.87884 0.02843 0.90979 0.630319 1.06162 0.947071 1.09042 0.749723 OSRattus = norvegicus GN = Pam PE = 1 SV = 1 D4A5X1_RAT Protein Stim2 OS =Rattus norvegicus GN = Stim2 PE = 4 1 1 2.5 89931.8 6.98 0 0.598 0.930966 0.766941 0.87454 0.504251 0.737469 0.351101 0.652546 0.117328 SV = 1 D4A8N2_RAT Protein Fdx1l OS =Rattus norvegicus GN = Fdx1l PE = 4 1 1 6.3 18770.01 5.62 0 0.272 0.914697 0.726225 0.897468 0.584734 0.93631 0.75303 0.792022 0.346643 SV = 1 F1LQ05_RAT Endophilin-A1 (Fragment) OS =Rattus norvegicus 7 6 20.4 38371.01 5.04 0 0.703 0.984573 0.905124 1.07451 0.736856 1.00503 0.91945 1.08696 0.759232 GN = Sh3gl2 PE = 2 SV = 1 D4AA31_RAT Protein Prcp OS =Rattus norvegicus GN = Prcp PE = 4 1 1 2.8 55561.67 6.59 0 0.201 1.0357 0.969316 0.994137 0.97215 0.838063 0.535322 0.950501 0.817304 SV = 1 Q5XIW9_RAT Flot2 protein OS =Rattus norvegicus GN = Flot2 PE = 2 4 4 12.5 38717.09 5.26 0 0.226 1.02554 0.990014 0.834746 0.379723 1.06358 0.942753 0.965901 0.871298 SV = 1 TBB4B_RAT Tubulin beta-4B chain OS =Rattus norvegicus GN = Tubb4b 133 22 48.5 49800.45 4.79 0 0.357 1.00178 0.950306 1.07032 0.751308 1.29522 0.476774 1.52877 0.057241 PE = 1 SV = 1 D4ACB8_RAT Chaperonin subunit 8 (Theta) (Predicted), isoform CRA_a 13 7 12.4 59587.88 5.38 0 0.078 1.01653 0.989168 0.889331 0.555495 1.03451 0.992402 0.984615 0.937706 OSRattus = norvegicus GN = Cct8 PE = 3 SV = 1 ACSF2_RAT Acyl-CoA synthetase family member 2, mitochondrial 1 1 3.1 67885.74 8.39 0 0.153 1.05708 0.925851 1.32514 0.139522 0.587947 0.162405 0.668622 0.135162 OSRattus = norvegicus GN = Acsf2 PE = 2 SV = 1 PAK3_RAT Serine/threonine-protein kinase PAK 3 OS =Rattus 3 3 6.8 60709.99 5.38 0 0.619 1.02812 0.98475 1.07955 0.719603 1.13091 0.796611 1.0439 0.879942 norvegicusGN = Pak3 PE = 1 SV = 1 G3V7V3_RAT Protein Slc27a4 OS =Rattus norvegicus GN = Slc27a4 3 3 5.8 72187.52 8.88 0 0.066 1.24122 0.573271 0.979837 0.911942 0.900765 0.670773 0.996768 0.98109 PE = 4 SV = 1 ATP8_RAT ATP synthase protein 8 OS =Rattus norvegicus GN = Mt- 6 1 14.9 7641.87 9.3 0 0.093 1.22423 0.60317 1.15008 0.496371 1.41512 0.297121 1.37523 0.177927 atp8 PE = 1 SV = 1 PPIA_RAT Peptidyl-prolyl cis-trans isomerase A OS =Rattus norvegicus 29 12 65.9 17874.13 8.34 0 0.326 1.01149 0.97588 1.2499 0.256441 1.26054 0.538075 1.82094 0.003115 GN = Ppia PE = 1 SV = 2 ODPB_RAT Pyruvate dehydrogenase E1 component subunit beta, 35 13 38.2 38981.71 6.2 0 0.045 1.11225 0.815047 0.913021 0.64252 0.95877 0.806564 0.856159 0.513279 mitochondrial OS =Rattus norvegicus GN = Pdhb PE = 1 SV = 2 CD44_RAT CD44 antigen OS =Rattus norvegicus GN = Cd44 PE = 2 3 2 2.7 85731.49 4.83 0 0.784 1.03976 0.961048 0.993008 0.967384 1.14139 0.774363 0.81328 0.397625 SV = 1 NRX1A_RAT Isoform 10a of Neurexin-1 OS =Rattus norvegicus 4 4 3.8 166871.6 5.65 0 0.319 1.03201 0.976823 0.784254 0.251958 0.767387 0.40119 0.669517 0.136213 GN = Nrxn1 VISL1_RAT Visinin-like protein 1 OS =Rattus norvegicus GN = Vsnl1 5 3 15.7 22142.1 5.01 0 0.502 1.16472 0.712945 0.869765 0.488253 1.40088 0.315717 2.57316 1.41E 08 PE = 1 SV = 2 F8WG73_RAT Basigin OSRattus = norvegicus GN = Bsg PE = 4 SV = 1 1 1 4.0 29713.26 5.12 0 0.232 0.999688 0.944802 1.02125 0.925561 1.13902 0.779369 1.04051 0.889606 QCR1_RAT Cytochrome b-c1 complex subunit 1, mitochondrial 48 11 26.0 52848.18 5.57 0 0.159 1.00187 0.950552 1.20085 0.362047 0.968445 0.829921 1.04198 0.885405 OSRattus = norvegicus GN = Uqcrc1 PE = 1 SV = 1 ATP5H_RAT ATP synthase subunit d, mitochondrial OS =Rattus 11 8 44.7 18763.21 6.16 0 0.702 1.13882 0.762836 1.90881 3.53E 05 1.02835 0.977119 1.92459 0.000867 norvegicusGN = Atp5h PE = 1 SV = 3 STX1B_RAT Syntaxin-1B OSRattus = norvegicus GN = Stx1b PE = 1 49 14 47.9 33244.34 5.25 1 0.694 0.993766 0.929234 0.965919 0.853821 1.15928 0.7368 1.09343 0.741519 SV = 1 D4A8L9_RAT Protein Btbd17 OS =Rattus norvegicus GN = Btbd17 PE = 4 1 1 3.6 55405.68 9.38 0 0.004 1.03219 0.97646 1.00384 0.988707 2.07582 0.004141 1.91504 0.000981 SV = 1 B5DFG5_RAT Protein Sept6 (Fragment) OS =Rattus norvegicus 13 6 18.6 48594.81 6.14 0 0.657 1.13706 0.766262 1.01018 0.965701 1.28071 0.501942 1.11127 0.693393 GN = Sept6 PE = 2 SV = 1 D3ZTR5_RAT Protein Scand3 OS =Rattus norvegicus GN = Zbed5 PE = 4 2 1 3.3 84033.6 8.9 0 0.225 1.04803 0.944235 0.78973 0.264153 1.06927 0.93027 0.859407 0.522703 SV = 1 TCPB_RAT T-complex protein 1 subunit beta OS =Rattus norvegicus 4 4 8.2 57457.69 6.01 0 0.021 0.999689 0.944806 1.06812 0.758912 0.713702 0.314272 0.657578 0.1227 GN = Cct2 PE = 1 SV = 3 NDKA_RAT Nucleoside diphosphate kinase A OS = Rattus norvegicus 11 3 25.7 17192.54 5.96 0 0.239 1.05818 0.923631 0.998551 0.99078 0.821873 0.502725 1.01717 0.956492 GN=Nme1PE=1SV=1 SEPT2_RAT Septin-2 OS =Rattus norvegicus GN = Sept2 PE = 1 10 6 20.5 41592.07 6.15 1 0.539 1.02416 0.99281 1.08055 0.716223 0.883936 0.633096 0.998058 0.985703 SV = 1 D3ZUB0_RAT Protein Rcn1 OS =Rattus norvegicus GN = Rcn1 PE = 4 1 1 4.9 38089.56 4.67 0 0.996 1.0418 0.956892 1.15173 0.491609 0.947891 0.780501 1.17357 0.535807 SV = 1 NDUAA_RAT NADH dehydrogenase [ubiquinone] 1 alpha subcomplex 10 7 20.3 40492.6 7.64 0 0.436 0.96904 0.864591 0.982353 0.922508 1.03159 0.985149 1.16496 0.556474 subunit 10, mitochondrial OS =Rattus norvegicus GN = Ndufa10 PE = 1 SV = 1 G3V8D6_RAT Tripartite motif protein 3, isoform CRA_a OS = Rattus 4 3 4.4 80759.56 8.01 0 0.314 0.959657 0.840272 0.867829 0.481849 1.03019 0.981689 0.912607 0.688563 norvegicus GN = Trim3 PE = 4 SV = 1 Q5XIA6_RAT Protein Smpd1 OS = Rattus norvegicus GN = Smpd1 PE = 2 1 1 2.4 69760.01 7.08 1 0.189 1.25193 0.554797 1.19973 0.364743 0.663236 0.24479 0.869135 0.551446 SV = 1 G3V8Q6_RAT Protein kinase, cAMP-dependent, regulatory, type 2, alpha, 11 7 24.7 45479.71 4.81 0 0.499 1.07809 0.883367 0.902208 0.602087 1.35 0.388256 1.07756 0.785195 isoform CRA_a OS = Rattus norvegicus GN = Prkar2a PE = 4 SV = 1 RPGF2_RAT Rap guanine nucleotide exchange factor 2 OS = Rattus 4 4 5.1 164514.9 6.12 0 0.657 1.02556 0.989968 0.750902 0.186132 1.16451 0.725942 1.15027 0.592603 norvegicus GN = Rapgef2 PE = 4 SV = 1 SYNPR_RAT Synaptoporin OS = Rattus norvegicus GN = Synpr PE = 2 2 1 5.3 29106.73 6.07 4 0.118 0.999279 0.943726 0.967742 0.861397 0.939488 0.76054 0.916017 0.699847 SV = 2 F1LXA0_RAT Protein Ndufa12 (Fragment) OS = Rattus norvegicus 6 4 27.7 17608.89 9.81 0 0.812 0.913559 0.723403 1.05048 0.82074 0.902079 0.673752 1.01982 0.948858 GN = Ndufa12 PE = 4 SV = 1 G3V733_RAT Synapsin II, isoform CRA_a OS = Rattus norvegicus 25 9 18.8 63411.89 8.59 0 0.457 0.889872 0.665594 1.04333 0.846167 1.17609 0.70209 1.26822 0.336619 GN = Syn2 PE = 4 SV = 1 KCRB_RAT Creatine kinase B-type OS = Rattus norvegicus GN = Ckb 17 11 32.6 42724.79 5.39 0 0.466 0.937571 0.783664 0.951867 0.795938 1.00721 0.924824 0.919401 0.71111 PE = 1 SV = 2 B1H264_RAT Protein Tbc1d17 OS = Rattus norvegicus GN = Tbc1d17 4 3 3.6 72794.57 5.09 0 0.363 0.927456 0.758098 1.04182 0.851555 1.12181 0.816052 1.19409 0.488161 PE = 2 SV = 1 ARHG2_RAT Rho guanine nucleotide exchange factor 2 OS = Rattus 4 4 5.6 111908.1 6.73 0 0.564 1.02132 0.998607 0.891053 0.561622 0.875954 0.615544 0.761207 0.280499 220–292 (2015) 298 Neuroscience / al. et Han X. norvegicus GN = Arhgef2 PE = 2 SV = 1 Q6AYD3_RAT Proliferation-associated 2G4 OS = Rattus norvegicus 1 1 2.8 43656.28 6.41 0 0.482 1.03563 0.969457 0.885942 0.543535 1.08652 0.892481 0.991038 0.960619 GN = Pa2g4 PE = 2 SV = 1 LANC1_RAT LanC-like protein 1 OS = Rattus norvegicus GN = Lancl1 4 3 11.0 45239.44 7.57 0 0.177 0.971858 0.871922 1.08616 0.697198 1.04295 0.988176 0.847051 0.487336 PE = 2 SV = 2 IMPA1_RAT Inositol monophosphatase 1 OS = Rattus norvegicus 4 4 14.4 30511.01 5.17 0 0.023 1.03631 0.968074 0.913675 0.645002 0.986515 0.873939 0.809399 0.387995 GN = Impa1 PE = 1 SV = 2 ACSL6_RAT Isoform 2 of Long-chain-fatty-acid–CoA ligase 6 OS = Rattus 10 5 8.2 80947.69 6.57 0 0.161 0.987444 0.912644 0.921601 0.675381 1.21911 0.616148 1.21591 0.440115 norvegicus GN = Acsl6 CTBP1_RAT C-terminal-binding protein 1 OS = Rattus norvegicus 2 2 7.3 47758.02 6.28 0 0.117 0.990405 0.920411 0.938144 0.740474 1.08515 0.895476 0.983072 0.932205 GN = Ctbp1 PE = 2 SV = 1 105 19 48.7 49585.25 4.78 0 0.321 1.01193 0.977055 1.30015 0.172646 1.21566 0.622858 1.54997 0.04793 B4F7C2_RAT RCG45085 OS = Rattus norvegicus GN = Tubb4 PE = 2 MACD1_RATSV O-acetyl-ADP-ribose = 1 deacetylase MACROD1 (Fragment) 1 1 5.4 28642.72 8.69 0 0.26 0.995725 0.934383 1.21455 0.330117 0.98163 0.861995 1.57478 0.038681 OS = Rattus norvegicus GN = Macrod1 PE = 2 SV = 2 D4A133_RAT Protein Atp6v1a OS = Rattus norvegicus GN = Atp6v1a 20 10 21.1 68264.26 5.42 0 0.19 0.981099 0.896033 1.0757 0.732758 0.937324 0.755422 1.07561 0.790596 PE = 3 SV = 1 S2546_RAT Solute carrier family 25 member 46 OS = Rattus norvegicus 8 5 16.5 46209.76 7.7 0 0.011 0.955899 0.830571 1.12031 0.586002 0.845594 0.550838 1.01671 0.957809 GN = Slc25a46 PE = 2 SV = 2 D3ZTW9_RAT Endonuclease G-like 1 (Predicted), isoform CRA_d 6 3 11.1 41326.34 8.86 0 0.443 0.799634 0.465107 1.0694 0.754484 0.95232 0.791084 0.874991 0.569113 OS = Rattus norvegicus GN = Exog PE = 4 SV = 1 D3ZH41_RAT Protein Ckap4 OS = Rattus norvegicus GN = Ckap4 PE = 4 2 2 4.7 63546.33 5.44 0 0.503 0.837989 0.546048 1.06612 0.765832 1.28537 0.493789 1.19451 0.487214 SV = 1 I1T7F1_RAT Amino acid transporter OS = Rattus norvegicus PE = 2 57 9 23.6 54500.7 5.86 0 0.411 0.966186 0.857179 0.78686 0.257711 1.26457 0.530756 1.04385 0.88007 SV = 1 TCPD_RAT T-complex protein 1 subunit delta OS = Rattus norvegicus 5 4 10.8 58098.8 8.24 0 0.003 1.04609 0.948174 0.86335 0.467205 1.16806 0.718595 1.04205 0.885218 GN = Cct4 PE = 1 SV = 3 TBB5_RAT Tubulin beta-5 chain OS = Rattus norvegicus GN = Tubb5 123 22 48.7 49670.28 4.78 0 0.348 1.00761 0.965671 1.25104 0.254262 1.15474 0.746271 1.44923 0.106462 PE = 1 SV = 1 F8WFM2_RAT Beta-soluble NSF attachment protein OS = Rattus norvegicus 15 9 29.5 33556.58 5.32 0 0.456 0.956897 0.833144 1.0642 0.772537 1.06938 0.930028 1.28989 0.298758 GN = Napb PE = 4 SV = 1 MP2K1_RAT Dual specificity mitogen-activated protein kinase kinase 1 3 1 3.6 43464.54 6.18 0 0.3 1.56637 0.163482 1.29622 0.178359 0.977356 0.851569 1.58754 0.034549 OS = Rattus norvegicus GN = Map2k1 PE = 1 SV = 2 D3Z9H2_RAT Hyaluronan and proteoglycan link protein 4 (Predicted) 8 5 15.8 42728.94 9.12 0 0.2 0.903164 0.697815 1.03204 0.886609 0.918461 0.711305 0.751932 0.26239 OS = Rattus norvegicus GN = Hapln4 PE = 4 SV = 1 F1LR80_RAT CaM kinase-like vesicle-associated protein OS = Rattus 7 6 13.5 54120.95 5.37 0 0.436 1.00223 0.951492 0.793858 0.273611 0.789391 0.44063 0.72055 0.207174 norvegicus GN = Camkv PE = 2 SV = 1 D3ZRF5_RAT Protein Slc25a22 OS = Rattus norvegicus GN = Slc25a22 29 10 34.1 34661.99 9.26 2 0.179 1.05736 0.925296 1.29793 0.175852 1.28026 0.50274 1.71517 0.010043 PE = 3 SV = 1 259 Q1RP74_RAT Protein Tbcb OS = Rattus norvegicus GN = Tbcb PE = 2 2 1 4.1 27247.09 4.93 0 0.537 1.24704 0.563208 1.04011 0.857671 1.14688 0.762778 1.03492 0.905574 SV = 1 (continued on next page) 6 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 260

C1TC_RAT C-1-tetrahydrofolate synthase, cytoplasmic OS = Rattus 1 1 0.8 100994.3 7.05 0 0.063 0.986652 0.910568 0.90272 0.603978 1.19819 0.657376 0.982111 0.928785 norvegicusGN = Mthfd1 PE = 1 SV = 3 Q9QXG3_RAT Syntaxin 1A OS =Rattus norvegicus GN = Stx1a PE = 2 12 6 22.6 33152.3 5.2 1 0.608 0.905248 0.70292 0.928506 0.702292 1.13649 0.784727 1.05069 0.860647 SV = 1 F1LYS1_RAT Uncharacterized protein (Fragment) OS =Rattus norvegicus 4 3 2.7 158257.5 9.65 0 0.936 0.977351 0.88624 0.90182 0.600659 1.12549 0.808179 1.12418 0.659301 PE = 2 SV = 1 HSP7C_RAT Heat shock cognate 71 kDa protein OS =Rattus norvegicus 62 21 36.8 70870.22 5.37 0 0.452 1.01779 0.992509 1.04812 0.829108 1.09402 0.876129 1.09901 0.726328 GN = Hspa8 PE = 1 SV = 1 TBB2A_RAT Tubulin beta-2A chain OS =Rattus norvegicus GN = Tubb2a 137 21 48.3 49906.45 4.78 0 0.408 1.00313 0.95387 1.25104 0.25427 1.15822 0.739016 1.36007 0.196206 PE = 1 SV = 1 KAD2_RAT Adenylate kinase 2, mitochondrial OS =Rattus norvegicus 1 1 7.1 26379.2 6.33 0 0.319 0.713824 0.31054 0.964834 0.849323 0.628931 0.204196 0.525115 0.032592 GN = Ak2 PE = 2 SV = 2 GLPK_RAT Glycerol kinase OS =Rattus norvegicus GN = Gk PE = 2 7 5 9.8 61231.83 5.64 0 0.035 1.01868 0.994839 1.14467 0.512083 1.08798 0.889312 0.980548 0.92322 SV = 1 D4A5J2_RAT 5’,3’-nucleotidase, mitochondrial (Predicted) OS = Rattus 1 1 7.2 23433.9 8.94 0 0.167 0.892511 0.671944 1.2722 0.21629 0.716619 0.31865 0.69563 0.169741 norvegicusGN = Nt5m PE = 4 SV = 1 D3Z9L0_RAT Protein Agk OS =Rattus norvegicus GN = Agk PE = 4 1 1 2.6 46768.12 8.5 0 0.281 0.960351 0.842065 0.936138 0.732469 1.05468 0.962334 0.997372 0.983251 SV = 1 G3V8G5_RAT Golgi apparatus protein 1 OS =Rattus norvegicus GN = Glg1 6 4 4.1 133551.5 6.52 0 0.48 0.975083 0.880324 0.871684 0.494649 1.124 0.811364 0.960197 0.851215 PE = 4 SV = 1 GRIA2_RAT Glutamate receptor 2 OS =Rattus norvegicus GN = Gria2 14 10 11.8 98785.84 7.48 0 0.165 0.951057 0.818114 0.848338 0.419968 1.00229 0.912684 0.888603 0.611198 PE = 4 SV = 1 B5DFK6_RAT Adaptor-related protein complex 3, delta 1 subunit, isoform 2 2 1.5 135665.3 6.73 0 0.48 0.873125 0.625862 1.1311 0.552652 1.04784 0.977386 1.08708 0.758897 CRA_b OS =Rattus norvegicus GN = Ap3d1 PE = 2 SV = 1 D4A9Q5_RAT Carboxypeptidase M (Predicted) OS =Rattus norvegicus 1 1 3.6 50319.91 8.05 0 0.298 0.778292 0.423129 0.99265 0.965875 0.673339 0.257757 0.626231 0.092183 GN = Cpm PE = 4 SV = 1 68MP_RAT 6.8 kDa mitochondrial proteolipid OS =Rattus norvegicus 1 1 11.7 6914.16 9.93 0 0.135 1.13463 0.770989 1.06027 0.786252 1.27945 0.504167 1.41278 0.138146 GN = Mp68 PE = 1 SV = 1 ATLA1_RAT Atlastin-1 OS =Rattus norvegicus GN = Atl1 PE = 1 SV = 1 2 2 3.8 63374.57 5.76 2 0.294 0.871114 0.621161 0.937418 0.737574 0.917903 0.710013 0.838788 0.464429 D3ZLD5_RAT Protein Golga3 OS =Rattus norvegicus GN = Golga3 1 1 0.8 162543 5.27 0 0.809 0.599759 0.164194 1.05513 0.804339 2.05652 0.004894 1.61242 0.027565 PE = 4 SV = 1 F1LYK8_RAT Protein Cadps2 (Fragment) OS =Rattus norvegicus 1 1 1.6 127026 5.88 0 0.426 0.701445 0.291422 0.538523 0.014445 0.665262 0.247352 0.423059 0.009477 GN = Cadps2 PE = 2 SV = 1 D3ZXK9_RAT Nucleoside phosphorylase (Mapped), isoform CRA_b 1 1 8.8 24336.33 6.65 0 0.215 1.09727 0.844859 1.05806 0.794008 1.07407 0.91974 1.09311 0.742369 OSRattus = norvegicus GN = Pnp PE = 4 SV = 1 HOME1_RAT Homer protein homolog 1 OS =Rattus norvegicus 2 2 7.7 41304.34 5.39 0 -0.807 0.850601 0.574113 0.847495 0.4174 0.989853 0.882116 0.794859 0.353194 GN = Homer1 PE = 1 SV = 2 IDH3B_RAT Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial 36 15 33.5 42353.41 8.89 0 0.133 1.02214 0.996938 1.24381 0.26823 0.959961 0.809428 1.27002 0.333367 OS =Rattus norvegicus GN = Idh3B PE = 1 SV = 1 H1UBM8_RAT Copine 4 protein OS =Rattus norvegicus GN = Cpne4 1 1 2.2 62407.45 5.92 0 0.294 0.98799 0.914077 1.16333 0.458954 0.842149 0.543713 0.86391 0.535911 PE = 2 SV = 1 ADDG_RAT Isoform 1 of Gamma-adducin OS =Rattus norvegicus 2 2 4.8 75360.54 5.75 0 0.543 1.01871 0.994928 0.702522 0.114534 0.704591 0.300852 0.51055 0.027642 GN = Add3 G3V9D3_RAT Protein sel-1 homolog 1 OS =Rattus norvegicus GN = Sel1l 1 1 1.0 88522.44 5.32 0 0.409 1.19212 0.661496 0.792676 0.270878 1.30266 0.464144 0.871875 0.559678 PE = 4 SV = 1 TBB3_RAT Tubulin beta-3 chain OS =Rattus norvegicus GN = Tubb3 91 18 39.1 50418.13 4.82 0 0.371 0.989093 0.91697 1.25815 0.241011 1.15947 0.736399 1.59416 0.032556 PE = 1 SV = 1 PEBP1_RAT Phosphatidylethanolamine-binding protein 1 OS =Rattus 7 4 20.9 20801.14 5.47 0 0.569 1.03766 0.965321 1.31668 0.150139 0.76084 0.389878 1.09818 0.728592 norvegicusGN = Pebp1 PE = 1 SV = 3 CISD1_RAT CDGSH iron-sulfur domain-containing protein 1 OS =Rattus 24 7 52.8 12096.82 8.99 1 0.378 0.967143 0.859662 0.894437 0.57376 0.969746 0.833074 0.97816 0.914727 norvegicusGN = Cisd1 PE = 3 SV = 1 D3ZVQ8_RAT Protein Gstm6 OS =Rattus norvegicus GN = Gstm6 PE = 3 5 3 9.9 27155.94 5.99 0 0.23 0.957776 0.835413 1.08784 0.691556 1.00427 0.917569 1.22342 0.424219 SV = 1 F1M9N9_RAT Protein Ank2 (Fragment) OS =Rattus norvegicus GN = Ank2 65 41 13.9 426282.8 5.04 0 0.662 0.989326 0.917579 0.942837 0.759307 0.985342 0.871067 0.918741 0.708907 PE = 2 SV = 1 THTR_RAT Thiosulfate sulfurtransferase OS =Rattus norvegicus 4 3 15.5 33406.34 7.71 0 0.439 0.989126 0.917055 1.14635 0.507187 0.766306 0.399308 1.0225 0.941176 GN = Tst PE = 1 SV = 3 F1LZ38_RAT Protein Tenm4 OS =Rattus norvegicus GN = Tenm4 PE = 2 2 2 1.2 314168.7 6.04 0 0.403 1.13275 0.774663 1.00409 0.987808 1.28998 0.485786 0.880761 0.586783 SV = 1 D4A7D8_RAT Protein Wdfy3 OS =Rattus norvegicus GN = Wdfy3 PE = 2 1 1 0.5 391732.8 6.34 0 0.189 1.07299 0.893658 0.723103 0.141773 1.56643 0.144155 1.12829 0.648608 SV = 1 D3ZBS6_RAT Protein RGD1559864 OS = Rattus norvegicus 4 3 8.0 45094.09 5.54 0 0.596 0.987942 0.913951 1.01355 0.953444 0.72235 0.327367 0.837321 0.460424 GN = RGD1559864 PE = 2 SV = 1 ETFB_RAT Electron transfer flavoprotein subunit beta OS = Rattus 11 5 25.1 27687.1 7.61 0 0.076 1.0274 0.986226 1.13837 0.530723 0.790787 0.443205 0.974136 0.900436 norvegicus GN = Etfb PE = 2 SV = 3 TBB2B_RAT Tubulin beta-2B chain OS = Rattus norvegicus GN = Tubb2b 118 21 48.3 49952.54 4.78 0 0.406 0.986484 0.910128 1.28026 0.202963 1.2238 0.607066 1.46741 0.09297 PE = 1 SV = 1 D4AB81_RAT Uncharacterized protein OS = Rattus norvegicus PE = 2 2 2 1.3 184570.7 6.15 0 0.304 1.11554 0.808533 1.03408 0.879301 1.0832 0.899736 1.08104 0.775557 SV = 1 KAT3_RAT Kynurenine–oxoglutarate transaminase 3 OS = Rattus 3 1 2.9 51043.51 8.61 0 0.139 1.07003 0.899625 1.11956 0.58835 0.852099 0.564416 0.90177 0.653167 norvegicus GN = Ccbl2 PE = 2 SV = 1 O89035_RAT Mitochondrial dicarboxylate carrier OS = Rattus norvegicus 3 2 9.1 31454.33 9.42 0 0.091 0.816913 0.500722 1.29112 0.185969 1.04469 0.984342 1.00165 0.998538 GN = Slc25a10 PE = 2 SV = 1 TRAP1_RAT Heat shock protein 75 kDa, mitochondrial OS = Rattus 6 3 5.8 80460.21 6.56 0 0.355 0.992872 0.926887 1.11405 0.605781 0.761612 0.391201 0.935174 0.764413 norvegicus GN = Trap1 PE = 1 SV = 1 EIF3A_RAT Eukaryotic translation initiation factor 3 subunit A OS = Rattus 1 1 0.6 163193.9 6.38 0 1.464 0.998218 0.940937 0.982182 0.921789 0.910267 0.692427 0.848073 0.490213 norvegicus GN = Eif3a PE = 2 SV = 2 D3ZPG5_RAT Ubiquitin carboxyl-terminal hydrolase OS = Rattus norvegicus 2 1 3.7 58205.83 8.84 0 0.374 0.917614 0.733474 0.921966 0.676796 1.0146 0.94308 0.919186 0.710393 GN = Usp30 PE = 3 SV = 1 D3ZU08_RAT Protein Napg OS = Rattus norvegicus GN = Napg PE = 4 14 8 23.1 34658.83 5.32 0 0.549 0.959656 0.840268 1.10897 0.622034 1.1849 0.684119 1.36459 0.190611 SV = 1 220–292 (2015) 298 Neuroscience / al. et Han X. F1LMV9_RAT Coronin (Fragment) OS = Rattus norvegicus GN = Coro2b 4 3 8.1 54983.68 8.23 0 0.381 0.953642 0.82476 0.975981 0.89578 0.91505 0.703423 0.87762 0.577132 PE = 2 SV = 1 SPG7_RAT Paraplegin OS = Rattus norvegicus GN = Spg7 PE = 2 5 5 8.7 82121.87 9.15 2 0.198 0.963852 0.851126 1.08494 0.701334 1.23968 0.576762 1.29668 0.287518 SV = 1 RASK_RAT GTPase KRas OS = Rattus norvegicus GN = Kras PE = 1 5 5 30.2 21655.59 6.33 0 0.433 0.836541 0.542871 0.562235 0.020312 1.03047 0.982389 0.98128 0.925824 SV = 3 F1LP30_RAT Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial 2 2 4.2 79294.77 6.66 0 0.287 0.796585 0.458971 0.895776 0.578594 1.02022 0.95699 0.86952 0.552599 OS = Rattus norvegicus GN = Mccc1 PE = 2 SV = 1 G3V8G4_RAT Brevican core protein OS = Rattus norvegicus GN = Bcan 9 4 6.1 96000.21 4.86 0 0.421 0.977613 0.886925 0.602959 0.03529 1.31998 0.435454 0.879463 0.582785 PE = 4 SV = 1 Rattus norvegicus GN = Pygb PE = 3 17 11 16.5 96736.83 6.31 0 0.332 0.993787 0.92929 1.06292 0.777 1.03758 1 1.07495 0.792446 G3V6Y6_RAT PhosphorylaseSV = 1 OS = ACSL1_RAT Long-chain-fatty-acid–CoA ligase 1 OS = Rattus norvegicus 4 4 8.4 78177.8 6.6 1 0.08 1.12706 0.785829 1.1375 0.533348 0.774101 0.412994 0.91278 0.689132 GN = Acsl1 PE = 1 SV = 1 B2GV15_RAT Dihydrolipoamide branched chain transacylase E2 1 1 2.7 53272.86 8.57 0 0.157 0.985951 0.908733 0.9218 0.676152 1.05512 0.96137 0.697228 0.171979 OS = Rattus norvegicus GN = Dbt PE = 2 SV = 1 Q5U2X8_RAT Acyl-CoA thioesterase 9 OS = Rattus norvegicus GN = Acot9 11 7 13.7 50442.94 8.8 0 0.28 0.984001 0.903624 0.902729 0.604009 1.09215 0.880206 1.05952 0.835654 PE = 2 SV = 1 THEM4_RAT Acyl-coenzyme A thioesterase THEM4 OS = Rattus 2 1 7.8 26089.02 9.11 0 0.282 0.986063 0.909026 1.106 0.63163 0.641633 0.218615 0.84059 0.469372 norvegicus GN = Them4 PE = 2 SV = 1 SCN3B_RAT Sodium channel subunit beta-3 OS = Rattus norvegicus 1 1 4.9 30307.24 4.98 0 0.19 0.906416 0.705784 1.07151 0.747172 1.07586 0.915805 1.05304 0.853968 GN = Scn3b PE = 2 SV = 1 Q6DUV1_RAT Protein kinase C epsilon OS = Rattus norvegicus GN = Prkce 4 4 7.1 83574.68 6.62 0 0.44 0.908984 0.712103 0.800078 0.288296 0.71815 0.320964 0.889583 0.614278 PE = 2 SV = 1 SIR5_RAT NAD-dependent protein deacylase sirtuin-5, mitochondrial 5 4 10.3 34097.94 9.08 0 0.266 1.06446 0.910903 0.998535 0.990713 1.1575 0.740512 1.1133 0.687989 OS = Rattus norvegicus GN = Sirt5 PE = 2 SV = 1 G3V8V3_RAT Phosphorylase OS = Rattus norvegicus GN = Pygm PE = 3 13 8 11.4 97287.19 6.65 0 0.394 0.967087 0.859516 1.16847 0.444871 1.28588 0.492897 1.4244 0.127343 SV = 1 D3ZYH3_RAT Protein Nudt10 OS = Rattus norvegicus GN = Nudt10 1 1 8.5 18592.78 5.54 0 0.754 0.936725 0.781516 0.928034 0.70044 0.760167 0.388726 0.75958 0.277263 PE = 3 SV = 1 RPN2_RAT Dolichyl-diphosphooligosaccharide–protein 1 1 3.7 69122.12 5.57 0 0.092 1.0402 0.96015 0.941257 0.752948 0.93208 0.74307 1.08853 0.754921 glycosyltransferase subunit 2 (Fragment) OS = Rattus norvegicus GN = Rpn2 PE = 4 SV = 1 AP2A2_RAT AP-2 complex subunit alpha-2 OS = Rattus norvegicus 10 7 10.1 104043.3 6.51 0 0.093 1.06616 0.907462 1.42584 0.052842 0.793022 0.447345 1.04344 0.881254 GN = Ap2a2 PE = 1 SV = 3 MMSA_RAT Methylmalonate-semialdehyde dehydrogenase [acylating], 4 4 8.0 57806.97 8.47 1 0.048 1.07042 0.898849 1.24783 0.260404 1.00734 0.925152 1.1414 0.614954 mitochondrial OS = Rattus norvegicus GN = Aldh6a1 PE = 1 SV = 1 LONM_RAT Lon protease homolog, mitochondrial OS = Rattus norvegicus 4 3 4.6 105791.3 6.17 0 0.287 0.915612 0.728496 1.06015 0.786679 1.13044 0.797598 1.26616 0.340376 261 GN = Lonp1 PE = 2 SV = 1 (continued on next page) 6 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 262

Q6AZ44_RAT Acyl-CoA thioesterase 8 OS = Rattus norvegicus GN = Acot8 1 1 2.8 35988.77 7.26 0 0.262 1.04008 0.960397 1.26306 0.232163 1.02065 0.958058 1.3779 0.174846 PE = 2 SV = 1 NSMA_RAT Sphingomyelin phosphodiesterase 2 OS =Rattus norvegicus 1 1 2.6 47644.17 6.61 2 0.135 0.920388 0.740388 0.820388 0.339888 0.964115 0.819447 0.861888 0.529959 GN = Smpd2 PE = 1 SV = 1 RAC1_RAT Ras-related C3 botulinum toxin substrate 1 OS =Rattus 14 6 33.3 21449.86 8.77 0 0.101 0.916707 0.731217 0.76876 0.219597 1.18533 0.683249 1.04968 0.863488 norvegicusGN = Rac1 PE = 1 SV = 1 G3V936_RAT Citrate synthase OS =Rattus norvegicus GN = Cs PE = 3 41 9 15.2 51830.11 8.58 0 0.176 0.919336 0.737762 1.00534 0.983269 1.13901 0.779392 1.12044 0.669116 SV = 1 LGUL_RAT Lactoylglutathione lyase OS =Rattus norvegicus GN = Glo1 5 2 9.8 20819.37 5.12 0 0.552 1.0544 0.93129 1.27463 0.212211 0.896291 0.660671 1.12009 0.670022 PE = 1 SV = 3 DYN1_RAT Isoform 4 of Dynamin-1 OS =Rattus norvegicus GN = Dnm1 29 17 22.4 96268.73 6.44 0 0.526 0.962608 0.847904 1.09581 0.665003 0.969923 0.833505 1.09285 0.743091 GBB5_RAT Guanine nucleotide-binding protein subunit beta-5 2 2 7.9 38731.22 5.67 0 0.251 0.975116 0.88041 0.642816 0.058212 1.1105 0.840393 0.715879 0.199736 OSRattus = norvegicus GN = Gnb5 PE = 2 SV = 1 SEP11_RAT Septin-11 OS =Rattus norvegicus GN = Sept11 PE = 1 12 6 16.9 49694.07 6.24 0 0.697 1.08367 0.87213 0.959178 0.825936 1.15592 0.74382 1.11021 0.696211 SV = 1 D3ZJ86_RAT Sodium/hydrogen exchanger OS =Rattus norvegicus 3 2 2.7 78011.09 5.92 0 0.273 0.896372 0.681278 1.04776 0.830397 1.05216 0.967891 1.20587 0.461881 GN = Slc9a6 PE = 2 SV = 1 G3V6R5_RAT Sulfite oxidase OS =Rattus norvegicus GN = Suox PE = 4 4 3 7.5 60805.1 6.32 0 0.406 0.933526 0.773411 1.03628 0.871401 1.35816 0.375979 1.03175 0.914625 SV = 1 D4AB17_RAT Protein Pfas OS =Rattus norvegicus GN = Pfas PE = 4 1 1 0.8 136893 5.45 0 0.188 0.936416 0.780733 0.948844 0.783621 1.13017 0.798182 1.1284 0.648315 SV = 1 GRIK5_RAT Glutamate receptor ionotropic, kainate 5 OS =Rattus 1 1 1.8 109274.6 8.54 3 0.13 0.958498 0.837277 1.08637 0.696491 1.1928 0.668162 1.64212 0.020852 norvegicusGN = Grik5 PE = 1 SV = 1 B2B9B0_RAT Eph receptor B2 OS =Rattus norvegicus GN = Ephb2 3 2 2.7 109883.9 5.49 1 0.199 0.944075 0.800231 0.807777 0.307196 1.56886 0.142323 1.07095 0.803581 PE = 2 SV = 1 RL27_RAT 60S ribosomal protein L27 OS =Rattus norvegicus 1 1 8.1 15797.53 10.56 0 0.644 0.831154 0.531129 1.11317 0.608567 1.34555 0.395049 1.50913 0.067166 GN = Rpl27 PE = 2 SV = 2 DC1L1_RAT Cytoplasmic dynein 1 light intermediate chain 1 OS =Rattus 3 3 8.2 56791.76 6.13 0 0.395 0.922848 0.746536 1.01163 0.960437 0.505178 0.098089 0.641915 0.106588 norvegicusGN = Dync1li1 PE = 1 SV = 1 REEP5_RAT Receptor expression-enhancing protein 5 OS =Rattus 1 1 5.8 21430.77 8.26 2 0.118 0.874364 0.628767 0.903948 0.608516 0.980059 0.858161 0.820623 0.416237 norvegicusGN = Reep5 PE = 1 SV = 1 FAAA_RAT Fumarylacetoacetase OS = Rattus norvegicus GN = Fah 1 1 5.0 45975.02 6.67 0 0.185 0.830484 0.529678 1.35622 0.105419 0.982215 0.863422 1.26781 0.337374 PE = 1 SV = 1 DGKB_RAT Diacylglycerol kinase beta OS =Rattus norvegicus 2 1 2.1 90287.03 8.3 0 0.448 1.17094 0.70114 1.16038 0.467156 0.821102 0.5012 0.841831 0.472795 GN = Dgkb PE = 2 SV = 1 D4A3Z3_RAT Protein Tbc1d24 OS =Rattus norvegicus GN = Tbc1d24 1 1 2.0 63409.21 7.48 0 0.143 0.893039 0.673217 0.885934 0.543504 1.07478 0.918177 0.927033 0.736744 PE = 4 SV = 1 D3ZDX7_RAT Protein Mrpl48 (Fragment) OS =Rattus norvegicus 1 1 5.7 24000.53 9.52 0 0.297 0.920219 0.739965 0.772657 0.227441 0.613558 0.187688 0.596862 0.069433 GN = Mrpl48 PE = 2 SV = 1 F1LUW9_RAT Tubulin gamma chain (Fragment) OS =Rattus norvegicus 1 1 2.4 50938.94 5.75 0 0.441 1.28772 0.495271 0.941267 0.752988 2.15517 0.002026 2.56536 1.67E 08 GN = LOC688197 PE = 3 SV = 1 USO1_RAT General vesicular transport factor p115 OSRattus = 1 1 1.2 107161.2 4.87 0 0.35 0.902696 0.696672 0.964111 0.846324 0.941675 0.76572 0.906537 0.668647 norvegicusGN = Uso1 PE = 1 SV = 1 K6PL_RAT 6-phosphofructokinase, liver type OS =Rattus norvegicus 8 6 9.9 85337.9 7.06 0 0.087 0.977545 0.886747 0.970732 0.873849 1.03514 0.993949 1.37038 0.183628 GN = Pfkl PE = 2 SV = 3 Q5RKJ9_RAT RAB10, member RAS oncogene family OS =Rattus 16 4 21.5 22540.68 8.58 0 0.33 0.862773 0.601829 0.811853 0.317525 1.26605 0.528066 0.987844 0.949219 norvegicusGN = Rab10 PE = 2 SV = 1 NEUL_RAT Neurolysin, mitochondrial OS =Rattus norvegicus GN = Nln 1 1 1.7 80253.05 6.04 0 0.363 0.959732 0.840464 0.949952 0.78813 0.879387 0.623066 0.970932 0.889083 PE = 1 SV = 1 CPPED_RAT Calcineurin-like phosphoesterase domain-containing protein 1 1 1 5.1 35260.25 5.4 0 0.391 1.39709 0.336444 1.23781 0.280227 0.689659 0.279696 0.688545 0.160086 OSRattus = norvegicus GN = Cpped1 PE = 2 SV = 1 HS105_RAT Heat shock protein 105 kDa OS =Rattus norvegicus 7 5 5.0 96417.46 5.4 0 0.548 0.857157 0.588964 0.933015 0.720068 1.35303 0.383664 1.44873 0.106854 GN = Hsph1 PE = 1 SV = 1 B2RYG2_RAT Pck2 protein (Fragment) OS =Rattus norvegicus GN = Pck2 2 2 2.9 73271.15 8.29 0 0.264 0.930439 0.765611 0.980725 0.915671 1.12038 0.819138 0.985664 0.941445 PE = 2 SV = 1 F1LMR7_RAT Dipeptidyl aminopeptidase-like protein 6 OS =Rattus 8 5 6.4 97251.64 5.95 0 0.457 0.979821 0.892691 0.77213 0.226368 1.00363 0.916001 0.858329 0.519565 norvegicusGN = Dpp6 PE = 2 SV = 1 CBPE_RAT Carboxypeptidase E OS =Rattus norvegicus GN = Cpe 4 3 8.8 53308.31 5.07 0 0.422 0.895583 0.679367 1.03826 0.864276 0.771279 0.408007 0.901353 0.651821 PE = 1 SV = 1 G3V9Z3_RAT Amine oxidase [flavin-containing] A OS = Rattus norvegicus 21 8 18.4 59520.23 8.12 0 0.213 0.932521 0.770869 1.16884 0.443877 0.9443 0.771952 1.3411 0.220975 GN = Maoa PE = 4 SV = 1 PGRC1_RAT Membrane-associated progesterone receptor component 1 8 4 26.7 21597.79 4.45 1 0.598 0.975255 0.88077 1.19673 0.372031 0.967655 0.828008 1.30578 0.272881 OS = Rattus norvegicus GN = Pgrmc1 PE = 1 SV = 3 PP2BA_RAT Serine/threonine-protein phosphatase OS = Rattus 15 10 23.0 58529.98 5.58 0 0.318 0.904459 0.700984 0.970149 0.871419 1.06965 0.929424 1.30923 0.267473 norvegicus GN = Ppp3ca PE = 2 SV = 1 D4ACU6_RAT Protein Gpr123 OS = Rattus norvegicus GN = Gpr123 1 1 1.7 59169.13 6.8 0 0.1 1.00114 0.948626 0.680228 0.089865 1.2748 0.512389 0.817518 0.408305 PE = 2 SV = 1 RALB_RAT Ras-related protein Ral-B OS = Rattus norvegicus GN = Ralb 2 2 9.7 23317.21 6.24 0 0.584 0.966261 0.857374 0.9866 0.940372 1.09505 0.873904 1.03497 0.905422 PE = 2 SV = 1 DPYL1_RAT Dihydropyrimidinase-related protein 1 OS = Rattus norvegicus 15 7 12.5 74248 6.34 0 0.35 0.886651 0.657873 0.960285 0.830502 1.35385 0.38243 1.32384 0.245384 GN = Crmp1 PE = 2 SV = 1 KPYM_RAT Pyruvate kinase isozymes M1/M2 OS = Rattus norvegicus 28 15 32.4 57817.17 6.63 0 0.093 0.925064 0.752089 0.945579 0.770377 1.11611 0.828311 1.23462 0.401146 GN = Pkm PE = 1 SV = 3 Q3B7V5_RAT Protein Rab2b OS = Rattus norvegicus GN = Rab2b PE = 2 20 6 29.8 24084.99 6.31 0 0.355 0.945209 0.803129 0.96534 0.851422 0.967898 0.828598 0.961885 0.857151 SV = 1 STXB1_RAT Isoform 2 of Syntaxin-binding protein 1 OS = Rattus 50 19 32.8 68735.18 6.32 0 0.414 0.910006 0.714621 0.779666 0.242045 0.844292 0.54814 0.622505 0.089001 norvegicus GN = Stxbp1 AMPD2_RAT AMP deaminase 2 OS = Rattus norvegicus GN = Ampd2 2 2 2.7 94785.98 6.06 0 0.462 0.891399 0.669265 0.889121 0.554751 1.03951 0.995738 0.890122 0.615977 PE = 2 SV = 2 220–292 (2015) 298 Neuroscience / al. et Han X. NRX3A_RAT Isoform 8 of Neurexin-3 OS = Rattus norvegicus GN = Nrxn3 9 6 5.8 170247.7 6.08 0 0.325 0.911834 0.719137 0.76388 0.210049 1.07625 0.91495 0.887028 0.606258 QCR2_RAT Cytochrome b-c1 complex subunit 2, mitochondrial 61 15 36.7 48395.57 9.16 0 0.067 0.912213 0.720072 1.05203 0.815272 1.0719 0.924479 1.28502 0.307022 OS = Rattus norvegicus GN = Uqcrc2 PE = 1 SV = 2 CH60_RAT 60 kDa heat shock protein, mitochondrial OS = Rattus 46 20 29.7 60954.79 5.91 0 0.085 0.951953 0.820416 1.26426 0.230038 1.09461 0.874854 1.27873 0.317898 norvegicus GN = Hspd1 PE = 1 SV = 1 GDIA_RAT Rab GDP dissociation inhibitor alpha OS = Rattus norvegicus 13 8 21.5 50536.08 5 0 0.303 0.841474 0.553734 1.359 0.102728 0.594425 0.168543 1.00469 0.992416 GN = Gdi1 PE = 1 SV = 1 D3ZHB3_RAT 40S ribosomal protein S12 OS = Rattus norvegicus 5 3 29.9 15219.67 8.81 0 0.159 0.878208 0.637813 1.03038 0.892601 0.9122 0.696863 0.803112 0.372698 GN = LOC100360573 PE = 3 SV = 1 1 1 12.9 13730.3 6.29 0 0.502 0.865579 0.608301 0.714084 0.129279 0.921747 0.718926 0.683328 0.153246 TIM16_RAT Mitochondrial import inner membraneGN = translocase Magmas-ps1 subunit PE = 3 TIM16SV = OS 1 = Rattus norvegicus D3ZH36_RAT Protein Elfn2 OS = Rattus norvegicus GN = Elfn2-ps1 1 1 1.6 89829.92 7.11 0 0.282 0.848722 0.569888 0.997737 0.987342 0.700292 0.294655 0.712854 0.195024 PE = 4 SV = 1 B0BN52_RAT Protein Mtch2 OS = Rattus norvegicus GN = Mtch2 PE = 2 14 4 15.7 32244.4 8.87 0 0.293 1.08609 0.867265 1.18076 0.412232 1.00724 0.924902 1.54286 0.050899 SV = 1 NRP2_RAT Neuropilin-2 OS = Rattus norvegicus GN = Nrp2 PE = 2 2 1 1.1 102603.3 5.29 0 0.472 1.03045 0.980008 0.842854 0.403438 0.779831 0.423228 0.817988 0.4095 SV = 1 Q6GMM8_RAT Long-chain fatty acid transport protein 1 OS = Rattus 6 5 10.5 71346.29 8.77 1 0.015 0.98219 0.898885 0.988504 0.948393 0.918643 0.711725 1.05331 0.853221 norvegicus GN = Slc27a1 PE = 2 SV = 1 D3ZFQ8_RAT Cytochrome c-1 (Predicted), isoform CRA_c OS = Rattus 36 6 25.2 35434.43 9.33 0 0.115 0.958259 0.836659 0.875813 0.508559 0.8516 0.563369 0.871218 0.557699 norvegicus GN = Cyc1 PE = 4 SV = 1 D3ZL50_RAT Protein Ttc37 OS = Rattus norvegicus GN = Ttc37 PE = 4 1 1 0.7 175157.5 6.52 0 0.251 1.04226 0.95596 1.12359 0.575782 0.604529 0.178462 0.70771 0.1872 SV = 1 F1LU71_RAT Protein Auh (Fragment) OS = Rattus norvegicus GN = Auh 18 9 24.6 33138.25 9.49 0 0.056 0.975277 0.88083 1.54146 0.013786 1.08623 0.893129 1.50442 0.069745 PE = 3 SV = 1 E9PTI1_RAT Protein Atp6v1h OS = Rattus norvegicus GN = Atp6v1h 3 3 8.5 55868.47 6.18 0 0.368 0.863176 0.602755 0.922485 0.678805 1.25716 0.544252 1.30489 0.27429 PE = 4 SV = 1 D3ZV92_RAT Protein Epha4 OS = Rattus norvegicus GN = Epha4 PE = 2 5 3 4.0 104007.2 6.11 0 0.269 0.899184 0.688107 0.787021 0.258068 1.46185 0.241326 1.03286 0.911463 SV = 1 F1LM31_RAT Uncharacterized protein (Fragment) OS = Rattus norvegicus 1 1 2.5 53310.83 5.85 0 0.226 0.854411 0.582722 1.20887 0.34314 0.86809 0.598465 1.33487 0.229566 PE = 2 SV = 1 B1WBX6_RAT Smap2 protein OS = Rattus norvegicus GN = Smap2 1 1 3.0 46493.16 9.01 0 0.426 1.06102 0.917874 1.17874 0.417501 0.680813 0.267652 0.882768 0.59299 PE = 2 SV = 1 CYTC_RAT Cystatin-C OS = Rattus norvegicus GN = Cst3 PE = 1 3 3 27.1 15436.55 9.35 0 0.27 1.04891 0.942439 1.00993 0.966583 1.04906 0.974706 1.03854 0.895222 SV = 2 TCPE_RAT T-complex protein 1 subunit epsilon OS = Rattus norvegicus 9 6 10.0 59536.14 5.51 0 0.17 0.908716 0.711443 0.811909 0.317669 0.987552 0.876477 0.92232 0.720877 GN = Cct5 PE = 1 SV = 1 PP2AB_RAT Serine/threonine-protein phosphatase 2A catalytic subunit 7 4 15.5 35574.71 5.21 0 0.446 0.87321 0.626063 1.08038 0.716792 1.09415 0.875851 1.27906 0.317311 263 beta isoform OS = Rattus norvegicus GN = Ppp2cb PE = 1 SV = 1 (continued on next page) 6 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 264

MYL6_RAT Myosin light polypeptide 6 OS = Rattus norvegicus 3 2 18.5 16974.98 4.46 0 0.406 0.862101 0.600282 0.687342 0.097224 1.14172 0.77365 0.844826 0.481108 GN = Myl6 PE = 1 SV = 3 NMT1_RAT Glycylpeptide N-tetradecanoyltransferase 1 OS =Rattus 1 1 2.2 56859.74 8.04 0 0.507 1.02573 0.989625 0.811769 0.317311 0.618657 0.193051 0.749368 0.257531 norvegicusGN=Nmt1PE=2SV=1 RAB21_RAT Ras-related protein Rab-21 OS =Rattus norvegicus 2 2 9.9 24163.11 8.11 0 0.343 1.06748 0.904784 1.02458 0.913507 1.43515 0.272234 1.43284 0.119914 GN = Rab21 PE = 2 SV = 1 F1LP05_RAT ATP synthase subunit alpha OS =Rattus norvegicus 174 32 51.2 59811.98 9.29 0 0.096 0.933751 0.773979 1.08241 0.709874 0.942985 0.768828 1.04003 0.890954 GN = Atp5a1 PE = 2 SV = 1 KCMA1_RAT Isoform 4 of Calcium-activated potassium channel subunit 2 1 0.8 138386.1 6.98 0 0.077 0.909744 0.713976 0.755553 0.194462 0.861202 0.583685 0.717528 0.20234 alpha-1 OS =Rattus norvegicus GN = Kcnma1 Q3ZB97_RAT Adaptor-related protein complex 2, beta 1 subunit, isoform 16 11 10.8 105690.6 5.19 0 0.088 0.945684 0.804341 0.795054 0.276393 1.02564 0.970399 0.937847 0.773565 CRA_b OS =Rattus norvegicus GN = Ap2b1 PE = 2 SV = 1 D3ZW49_RAT Protein Tmem9b OS =Rattus norvegicus GN = Tmem9b 1 1 7.0 22639.25 8.51 0 0.014 0.968925 0.864292 0.680851 0.090491 0.789617 0.441046 0.622483 0.088982 PE = 4 SV = 1 DHSA_RAT Succinate dehydrogenase [ubiquinone] flavoprotein subunit, 24 13 22.9 71614.43 6.75 0 0.254 0.912922 0.721827 0.981447 0.918702 0.955183 0.797945 0.955936 0.836277 mitochondrial OS =Rattus norvegicus GN = Sdha PE = 1 SV = 1 PIPNA_RAT Phosphatidylinositol transfer protein alpha isoform 3 2 9.2 31907.05 5.97 0 0.739 0.935141 0.7775 0.855931 0.443501 0.779861 0.423282 0.796644 0.357356 OSRattus = norvegicus GN = Pitpna PE = 1 SV = 2 PCSK1_RAT ProSAAS OS =Rattus norvegicus GN = Pcsk1n PE = 1 6 2 9.2 27414.05 5.68 0 0.256 1.01072 0.973849 1.25431 0.248111 0.725726 0.332576 1.31585 0.257294 SV = 1 K6PF_RAT 6-phosphofructokinase, muscle type OS =Rattus norvegicus 15 8 15.5 85558.99 8.23 0 0.191 0.896757 0.682212 0.978569 0.906622 0.712184 0.312008 0.878232 0.579006 GN = Pfkm PE = 2 SV = 3 LGI1_RAT Leucine-rich glioma-inactivated protein 1 OS =Rattus 7 6 11.0 63727.2 8.26 0 0.18 0.911467 0.718227 0.829722 0.365468 1.37071 0.35759 1.4198 0.131537 norvegicusGN = Lgi1 PE = 1 SV = 1 D3ZRN5_RAT Protein Trove2 OS =Rattus norvegicus GN = Trove2 1 1 3.4 60042.01 8.3 0 0.166 0.621385 0.186961 0.753231 0.19027 1.62782 0.103098 1.20329 0.467567 PE = 4 SV = 1 TRFE_RAT Serotransferrin OS =Rattus norvegicus GN = Tf PE = 1 6 6 8.6 76394.38 7.14 0 0.252 0.883905 0.65132 1.04783 0.830149 1.14716 0.762182 1.36235 0.193374 SV = 3 G3V734_RAT 2,4-dienoyl CoA reductase 1, mitochondrial, isoform CRA_a 3 2 9.6 36132.31 9.08 0 0.005 0.908374 0.710599 1.34163 0.120508 1.07943 0.907979 0.705019 0.183201 OSRattus = norvegicus GN = Decr1 PE = 4 SV = 1 D4ADE8_RAT Protein Ddx3x OS =Rattus norvegicus GN = Ddx3x PE = 3 5 3 7.1 73144.6 6.73 0 0.487 0.754316 0.378722 1.29562 0.17924 0.612325 0.186407 0.665481 0.131522 SV = 1 GRPE1_RAT GrpE protein homolog 1, mitochondrial OS =Rattus 2 1 7.8 24296.74 8.57 0 0.511 0.869246 0.616809 1.03127 0.889376 0.955356 0.798361 1.12425 0.659128 norvegicusGN = Grpel1 PE = 1 SV = 2 CDV3_RAT Protein CDV3 homolog OS =Rattus norvegicus GN = Cdv3 2 1 12.7 24309.83 5.7 0 1.117 1.40856 0.321933 1.2034 0.355979 1.81599 0.031582 1.40605 0.144722 PE = 2 SV = 1 MOG_RAT Myelin-oligodendrocyte glycoprotein OS =Rattus norvegicus 19 8 33.5 27881.21 8.61 2 0.096 0.938577 0.786221 0.682138 0.091795 0.92447 0.725262 0.733899 0.229534 GN = Mog PE = 1 SV = 1 F1LTJ9_RAT Protein LOC100364190 (Fragment) OS = Rattus norvegicus 2 2 4.1 59184.63 6.21 0 0.492 0.905547 0.703652 1.05389 0.808685 0.795985 0.452868 0.869437 0.552348 GN = LOC100364190 PE = 2 SV = 1 KCC2D_RAT Isoform Delta 3 of Calcium/calmodulin-dependent protein 17 7 15.3 57708.48 7.61 0 0.4 0.982516 0.899739 1.22507 0.30689 0.949376 0.784046 1.32261 0.247183 kinase type II subunit delta OS =Rattus norvegicus GN = Camk2d D3ZD09_RAT Cytochrome c oxidase subunit 6B1 OS =Rattus norvegicus 9 3 37.2 10071.35 8.96 0 0.764 0.922031 0.744492 1.39114 0.075377 1.17722 0.699765 1.87299 0.001666 GN = Cox6b1 PE = 4 SV = 1 D4A197_RAT Methylmalonyl CoA epimerase (Predicted), isoform CRA_d 2 1 7.3 18815.55 8.95 0 0.083 0.814298 0.49524 1.15925 0.470296 0.696028 0.288592 0.979213 0.91847 OSRattus = norvegicus GN = Mcee PE = 4 SV = 1 Q6JBI6_RAT LMO7b OS =Rattus norvegicus GN = Lmo7 PE = 2 1 1 1.3 156646.7 5.9 0 0.953 1.34747 0.403983 0.972369 0.880676 1.01793 0.951324 0.763299 0.284699 SV = 1 Q4FZZ4_RAT Protein LOC100365902 OS =Rattus norvegicus 40 16 32.1 43215.19 8.49 0 0.287 0.950106 0.815673 1.26037 0.236984 0.921228 0.717721 1.17261 0.538089 GN = LOC100365902 PE = 2 SV = 1 Q5XIJ3_RAT Isocitrate dehydrogenase 3 (NAD), gamma OS =Rattus 14 8 24.2 42849.99 9.17 0 0.087 0.949293 0.813587 1.25021 0.255845 0.956548 0.80122 1.26675 0.339295 norvegicusGN = Idh3g PE = 2 SV = 1 C1QBP_RAT Complement component 1 Q subcomponent-binding protein, 1 1 2.2 30996.55 4.77 0 0.441 0.959203 0.839097 1.12276 0.578353 0.982424 0.863933 1.03402 0.908133 mitochondrial OS =Rattus norvegicus GN = C1qbp PE = 1 SV = 2 F1MA38_RAT Calnexin OS = Rattus norvegicus GN = Canx PE = 2 6 3 7.4 67413.51 4.6 0 0.781 1.23357 0.586644 1.18928 0.390481 0.486163 0.086662 0.806608 0.381156 SV = 1 ABI1_RAT Abl interactor 1 OS = Rattus norvegicus GN = Abi1 PE = 2 2 2 5.3 51704.14 6.57 0 0.679 0.790503 0.446868 1.00682 0.977875 0.806961 0.473657 0.727556 0.218704 SV = 3 FAS_RAT Fatty acid synthase OS = Rattus norvegicus GN = Fasn 5 5 2.6 272646.7 5.96 0 0.063 0.777051 0.420757 0.960553 0.831608 1.20276 0.648278 1.18918 0.49935 PE = 1 SV = 3 D3ZWW5_RAT Protein Slc30a9 OS = Rattus norvegicus GN = Slc30a9 2 2 3.9 62683.57 8.72 0 0.12 0.87735 0.63579 1.15693 0.476827 0.909963 0.691731 1.16996 0.544413 PE = 4 SV = 1 ZNT3_RAT Zinc transporter 3 OS = Rattus norvegicus GN = Slc30a3 3 3 10.6 41897.94 6.83 6 0.218 0.908095 0.709912 0.795653 0.277796 1.01501 0.944106 1.11175 0.692111 PE = 2 SV = 1 PDIA3_RAT Protein disulfide-isomerase A3 OS = Rattus norvegicus 8 5 12.1 56622.69 5.88 0 0.455 0.919153 0.737306 1.0639 0.773563 1.012 0.936647 1.33042 0.23586 GN = Pdia3 PE = 1 SV = 2 CDC42_RAT Cell division control protein 42 homolog OS = Rattus 3 2 11.0 21258.36 6.16 0 0.157 1.14491 0.75101 0.708992 0.122614 1.07478 0.918178 1.08987 0.751244 norvegicus GN = Cdc42 PE = 1 SV = 2 DLG2_RAT Isoform 2 of Disks large homolog 2 OS = Rattus norvegicus 11 9 12.3 95584.02 5.86 0 0.463 0.933897 0.77435 0.71573 0.131495 0.853899 0.568203 0.620033 0.08694 GN = Dlg2 SCOT1_RAT Succinyl-CoA:3-ketoacid coenzyme A transferase 1, 8 4 5.4 56203.22 8.7 0 0.115 0.895617 0.679449 0.830929 0.368862 0.896306 0.660704 0.850132 0.496033 mitochondrial OS = Rattus norvegicus GN = Oxct1 PE = 1 SV = 1 ACADS_RAT Short-chain specific acyl-CoA dehydrogenase, mitochondrial 3 1 2.2 44764.87 8.47 0 0.146 1.00937 0.970302 1.07983 0.718642 1.00511 0.919654 1.35731 0.199676 220–292 (2015) 298 Neuroscience / al. et Han X. OS = Rattus norvegicus GN = Acads PE = 1 SV = 2 D4A807_RAT Protein Selm OS = Rattus norvegicus GN = Selm PE = 4 2 1 9.7 16312.74 6.73 0 0.235 0.750918 0.37267 1.11324 0.608341 0.693387 0.284881 0.935129 0.764258 SV = 1 TCPR1_RAT Tectonin beta-propeller repeat-containing protein 1 1 1 1.1 130185.3 6.03 0 0.497 0.822638 0.512835 0.837051 0.386377 0.867032 0.596183 0.958311 0.844594 OS = Rattus norvegicus GN = Tecpr1 PE = 2 SV = 1 CACP_RAT Carnitine O-acetyltransferase OS = Rattus norvegicus 3 3 4.5 70799.93 8.73 0 0.25 0.927863 0.759123 1.32287 0.142316 1.38581 0.336213 1.51897 0.062029 GN = Crat PE = 1 SV = 1 RAP2B_RAT Ras-related protein Rap-2b OS = Rattus norvegicus 8 4 26.8 20504.14 4.73 0 0.202 0.835872 0.541405 1.02046 0.928417 0.995616 0.896266 0.909498 0.678332 GN = Rap2b PE = 2 SV = 1 DPYL3_RAT Isoform 2 of Dihydropyrimidinase-related protein 3 5 3 4.7 73898.48 6.03 0 0.398 0.873177 0.625986 0.930215 0.709011 0.966463 0.825123 0.937743 0.77321 OS = Rattus norvegicus GN = Dpysl3Rattus norvegicus 6 3 34.0 11481.56 5.42 0 1.017 0.862132 0.600354 0.942891 0.759525 1.02933 0.979549 1.14499 0.605868 CYB5_RAT D4A1G4_RATGN = Cyb5a Cytochrome PE = 2 SV = b5 1 OS = D3Z994_RAT Protein Tbc1d22a OS = Rattus norvegicus GN = Tbc1d22a 1 1 1.8 50791.98 6.19 0 0.511 1.15239 0.736563 0.922203 0.677712 1.09512 0.873745 1.00776 0.983562 PE = 4 SV = 1 D4A1U9_RAT Leukocyte surface antigen CD47 OS = Rattus norvegicus 10 4 6.9 34944.29 8.78 0 0.594 0.945951 0.805025 0.815134 0.326004 1.15848 0.738474 1.22266 0.425801 GN = Cd47 PE = 2 SV = 1 TCPA_RAT T-complex protein 1 subunit alpha OS = Rattus norvegicus 7 6 12.8 60358.97 5.86 0 0.018 0.949643 0.814483 0.740341 0.168204 1.15846 0.738508 1.03931 0.893012 GN = Tcp1 PE = 1 SV = 1 CLAP2_RAT CLIP-associating protein 2 OS = Rattus norvegicus 3 3 2.9 140792.4 8.84 0 0.45 0.945704 0.804393 0.864991 0.47254 0.92835 0.734325 0.916844 0.702593 GN = Clasp2 PE = 2 SV = 1 E41L1_RAT Isoform L of Band 4.1-like protein 1 OS = Rattus norvegicus 5 4 3.4 171009 5.23 0 0.799 0.885855 0.655972 0.76267 0.20773 0.745685 0.364445 0.598645 0.070669 GN = Epb41l1 RB11A_RAT Ras-related protein Rab-11A OS = Rattus norvegicus 1 1 5.1 24393.23 6.12 0 0.421 1.28085 0.50643 1.07126 0.748046 1.6087 0.114749 2.09811 7.60E05 GN = Rab11a PE = 1 SV = 3 D3ZQ57_RAT Protein Plxnb2 OS = Rattus norvegicus GN = Plxnb2 3 3 3.1 154410.7 5.73 0 0.366 0.949909 0.815166 0.95428 0.805811 0.770052 0.40585 0.739166 0.238812 PE = 2 SV = 1 ATP5L_RAT ATP synthase subunit g, mitochondrial OS = Rattus 6 4 35.0 11433.31 9.57 0 0.243 0.975774 0.882125 1.05774 0.795136 0.857791 0.576428 1.01351 0.967026 norvegicus GN = Atp5l PE = 1 SV = 2 RS20_RAT 40S ribosomal protein S20 OS = Rattus norvegicus 3 3 22.7 13372.56 9.95 0 0.396 0.897872 0.684917 0.767006 0.21613 1.01966 0.955609 0.971113 0.889722 GN = Rps20 PE = 3 SV = 1 TPIS_RAT Triosephosphate isomerase OS = Rattus norvegicus 29 11 56.6 26848.61 6.89 0 0.1 0.884622 0.653031 1.03377 0.880401 0.791628 0.44476 1.06182 0.829185 GN = Tpi1 PE = 1 SV = 2 Q5XIM0_RAT BCS1-like (Yeast) OS = Rattus norvegicus GN = Bcs1l 3 3 7.7 47392.62 8.3 0 0.2 1.06067 0.91858 1.17811 0.419161 0.526502 0.1123 1.02883 0.923014 PE = 2 SV = 1 SYPH_RAT Synaptophysin (Fragment) OS = Rattus norvegicus 10 3 9.6 33949.13 4.83 0 0.045 0.882774 0.648631 0.78631 0.256489 1.01563 0.945629 0.910204 0.680651 GN = Syp PE = 4 SV = 1 B5DFI9_RAT Pdk3 protein OS = Rattus norvegicus GN = Pdk3 PE = 2 3 3 11.1 47943.47 8.88 0 0.419 0.853426 0.580492 1.00861 0.971381 0.748121 0.368462 0.967239 0.876021 SV = 1 265 NIT2_RAT Omega-amidase NIT2 OS = Rattus norvegicus GN = Nit2 2 2 10.5 30700.63 6.9 0 0.285 0.804942 0.475895 0.654689 0.067061 0.851148 0.562421 0.710931 0.192072 PE = 1 SV = 1 (continued on next page) 6 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 266

ECHM_RAT Enoyl-CoA hydratase, mitochondrial OS = Rattus norvegicus 6 6 22.4 31516.07 8.4 0 0.104 1.03964 0.961293 1.0105 0.964528 0.758126 0.385245 1.08498 0.764682 GN = Echs1 PE = 1 SV = 1 F1LTW5_RAT Protein Tanc2 (Fragment) OS =Rattus norvegicus 1 1 0.9 139003.7 7.26 0 0.198 0.735704 0.34631 0.946616 0.774577 0.787773 0.437656 0.848649 0.491837 GN = Tanc2 PE = 2 SV = 1 Q8SEZ1_RAT NADH-ubiquinone oxidoreductase chain 3 OS =Rattus 1 1 13.0 13086.43 4.5 3 0.792 0.986444 0.910023 0.859376 0.454422 1.02512 0.969117 0.734963 0.231387 norvegicusGN = Mt-nd3 PE = 3 SV = 1 Q499R7_RAT Ppa1 protein (Fragment) OS = Rattus norvegicus 1 1 3.3 37676.39 6.41 0 0.561 0.947245 0.808337 1.73415 0.000836 1.04099 0.992476 1.34575 0.214697 GN = Ppa1 PE = 2 SV = 1 D3ZQE0_RAT Sodium/potassium-transporting ATPase subunit beta-2 7 4 11.4 33167.4 6.66 0 0.381 0.94463 0.801648 0.713937 0.129084 1.07809 0.910915 0.902043 0.65405 OSRattus = norvegicus GN = Atp1b2 PE = 2 SV = 1 F1LN61_RAT Uncharacterized protein (Fragment) OS =Rattus norvegicus 8 7 20.1 36825.25 7.24 0 0.349 0.795506 0.45681 1.18365 0.404784 1.18736 0.67915 1.49684 0.07407 PE = 2 SV = 1 S12A5_RAT Isoform 2 of Solute carrier family 12 member 5 OS =Rattus 16 8 7.0 123562.1 5.93 0 0.005 0.905359 0.703192 0.887676 0.549638 0.873313 0.609784 0.714248 0.197185 norvegicusGN = Slc12a5 D3ZHI9_RAT Protein Ppp2r5e (Fragment) OS =Rattus norvegicus 1 1 2.1 50065.58 5.52 0 0.181 0.846549 0.565023 1.0829 0.708212 0.852598 0.565464 1.09271 0.743471 GN = Ppp2r5e PE = 2 SV = 1 D4A4Q4_RAT Protein LOC100365923 OS =Rattus norvegicus 5 4 24.0 17037.46 9.41 0 0.217 0.852814 0.579106 0.931187 0.71284 1.03284 0.988256 1.01947 0.949881 GN = Ociad2 PE = 4 SV = 1 BAIP2_RAT Isoform 2 of Brain-specific angiogenesis inhibitor 1-associated 12 6 16.3 57541.27 8.97 0 0.615 0.86636 0.61011 1.14833 0.501431 0.924398 0.725095 1.01933 0.950294 protein 2 OS =Rattus norvegicus GN = Baiap2 F8WFF9_RAT Leucine-rich repeat-containing protein 57 (Fragment) 1 1 2.8 36397.71 9.45 0 0.218 0.826518 0.521128 0.995316 0.977125 1.02811 0.976536 0.999905 0.992305 OSRattus = norvegicus GN = Lrrc57 PE = 4 SV = 1 HCD2_RAT 3-hydroxyacyl-CoA dehydrogenase type-2 OS =Rattus 6 3 14.6 27245.25 8.91 0 0.243 1.00234 0.951785 1.12444 0.573146 0.953866 0.794787 1.35498 0.202645 norvegicusGN = Hsd17b10 PE = 1 SV = 3 ATX10_RAT Ataxin-10 OS = Rattus norvegicus GN = Atxn10 PE = 1 1 1 3.0 53726.24 5.02 0 0.142 0.826838 0.521817 0.858789 0.452548 0.875172 0.613836 0.888853 0.611983 SV = 1 TAGL3_RAT Transgelin-3 OS =Rattus norvegicus GN = Tagln3 PE = 1 4 3 21.1 22500.46 6.84 0 0.58 0.96592 0.856489 0.979139 0.909012 1.12532 0.808544 1.27996 0.315743 SV = 2 Q63629_RAT Centaurin alpha OS =Rattus norvegicus GN = Adap1 2 2 6.0 48133.15 8.89 0 0.624 0.925553 0.753316 1.0294 0.896118 0.889308 0.645025 0.975985 0.906997 PE = 2 SV = 1 G3V6G7_RAT Polyribonucleotide nucleotidyltransferase 1 OS =Rattus 1 1 1.2 85896.92 8.42 0 0.144 0.862292 0.600721 0.845124 0.41023 0.989205 0.880528 0.859954 0.524298 norvegicusGN = Pnpt1 PE = 4 SV = 1 CD59_RAT CD59 glycoprotein OS =Rattus norvegicus GN = Cd59 3 2 16.7 13790.15 8.9 2 0.342 0.949183 0.813304 0.853564 0.436085 1.11912 0.821839 1.11245 0.690251 PE = 1 SV = 2 D3ZUY8_RAT Adaptor protein complex AP-2, alpha 1 subunit (Predicted) 14 9 8.8 107673.8 6.66 0 0.078 0.879864 0.641728 0.985207 0.934511 0.88843 0.64307 1.04898 0.865483 OS =Rattus norvegicus GN = Ap2a1 PE = 4 SV = 1 B5DEL8_RAT NADH dehydrogenase (Ubiquinone) Fe-S protein 5 11 6 50.0 12699.63 9.1 0 0.9 0.877619 0.636424 1.26723 0.224819 0.873836 0.610923 0.936961 0.770529 OSRattus = norvegicus GN = LOC100361505 PE = 4 SV = 1 F1LX07_RAT Protein Slc25a12 OS =Rattus norvegicus GN = Slc25a12 42 7 37.2 25737.49 9.56 0 0.026 0.823503 0.514678 1.00152 0.99714 0.971038 0.836209 1.06359 0.824207 PE = 3 SV = 1 RAP1B_RAT Ras-related protein Rap-1b OS =Rattus norvegicus 6 4 25.5 20797.53 5.65 0 0.375 0.902609 0.696459 0.900554 0.596006 1.15737 0.740787 1.23658 0.397194 GN = Rap1b PE = 2 SV = 2 CXA1_RAT Gap junction alpha-1 protein OS =Rattus norvegicus 23 4 13.1 43030.92 8.97 0 0.22 0.820781 0.508889 0.630573 0.050126 0.770195 0.406102 0.5946 0.067891 GN = Gja1 PE = 1 SV = 2 RAP1A_RAT Ras-related protein Rap-1A OS =Rattus norvegicus 5 3 18.5 20986.96 6.39 0 0.375 0.871181 0.621318 0.937467 0.737767 0.947442 0.779432 1.04958 0.863781 GN = Rap1a PE = 1 SV = 1 THY1_RAT Thy-1 membrane glycoprotein OS =Rattus norvegicus 12 5 21.7 18171.96 9.42 0 0.019 0.866988 0.611564 0.880914 0.526025 1.15077 0.754603 0.999887 0.992242 GN = Thy1 PE = 1 SV = 1 Q9QXU3_RAT Sodium channel, voltage-gated, type I, beta, isoform CRA_b 2 2 11.7 31062.94 6.16 1 0.369 0.845261 0.562148 0.656256 0.068307 0.793689 0.448585 0.573111 0.054604 OS =Rattus norvegicus GN = Scn1b PE = 2 SV = 1 F1LNF7_RAT Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial 33 12 28.1 39582.23 6.46 0 0.068 0.904473 0.701021 0.909553 0.629428 0.87885 0.621888 1.06161 0.829784 OSRattus = norvegicus GN = Idh3a PE = 2 SV = 1 CX6A1_RAT Cytochrome c oxidase subunit 6A1, mitochondrial 1 1 14.4 12300.9 9.3 0 0.338 0.941496 0.79365 0.866785 0.478414 0.965372 0.822485 0.974517 0.901788 OSRattus = norvegicus GN = Cox6a1 PE = 1 SV = 2 NPTX1_RAT Neuronal pentraxin-1 OS =Rattus norvegicus GN = Nptx1 5 4 12.5 47215.85 6.29 0 0.414 0.971065 0.869856 0.955395 0.810382 0.696307 0.288987 0.876061 0.572371 PE = 1 SV = 1 DHSD_RAT Succinate dehydrogenase [ubiquinone] cytochrome b small 1 1 5.0 16975.55 9.42 0 0.389 1.58703 0.14812 0.752646 0.189224 1.10369 0.855139 1.11261 0.689823 subunit, mitochondrial OS =Rattus norvegicus GN = Sdhd PE = 2 SV = 1 Q6IN22_RAT Cathepsin B OS = Rattus norvegicus GN = Ctsb PE = 2 5 3 11.2 37543.74 5.47 0 -0.345 0.887111 0.658974 1.30062 0.171975 0.868423 0.599184 1.20618 0.461194 SV = 1 F1LZ51_RAT Protein RGD1565653 (Fragment) OS = Rattus norvegicus 1 1 21.2 13101.77 6.15 0 0.517 0.75431 0.378711 1.22285 0.311691 0.955492 0.798686 1.44059 0.113396 GN = RGD1565653 PE = 4 SV = 1 EFTU_RAT Elongation factor Tu, mitochondrial OS = Rattus norvegicus 33 13 31.9 49521.81 7.23 0 0.179 0.909824 0.714174 0.841373 0.399039 0.813787 0.486848 0.902396 0.655192 GN = Tufm PE = 1 SV = 1 FABP5_RAT Fatty acid-binding protein, epidermal OS = Rattus norvegicus 2 2 21.5 15059.24 6.73 0 0.367 0.84552 0.562724 1.08154 0.712847 0.82118 0.501354 1.07919 0.780661 GN = Fabp5 PE = 1 SV = 3 PDIA1_RAT Protein disulfide-isomerase OS = Rattus norvegicus 7 5 11.0 56950.63 4.82 0 0.382 0.830424 0.529549 0.882343 0.530969 1.18228 0.689436 1.17102 0.541893 GN = P4hb PE = 1 SV = 2 VDAC1_RAT Voltage-dependent anion-selective channel protein 1 54 18 63.6 30755.12 8.62 0 0.423 0.82663 0.52137 0.847714 0.418067 1.02061 0.957962 1.06702 0.814588 OS = Rattus norvegicus GN = Vdac1 PE = 1 SV = 4 VPS29_RAT Vacuolar protein sorting-associated protein 29 OS = Rattus 2 1 5.5 20468.41 6.29 0 0.007 1.01151 0.975947 0.951382 0.793958 0.938414 0.758 1.15974 0.56919 norvegicus GN = Vps29 PE = 1 SV = 2 Q6IE71_RAT Ubiquitin specific protease 11 OS = Rattus norvegicus 1 1 1.4 80107.59 5.02 0 0.658 2.02832 0.010083 0.872821 0.498459 1.21163 0.630758 2.31926 1.98E06 GN = Usp11 PE = 2 SV = 1 TXTP_RAT Tricarboxylate transport protein, mitochondrial OS = Rattus 3 2 7.1 33834.97 9.88 0 0.069 0.926083 0.754647 1.12281 0.578197 0.99091 0.884709 1.25483 0.361491 norvegicus GN = Slc25a1 PE = 1 SV = 1 D4AAB3_RAT Protein Tmem88b OS = Rattus norvegicus GN = Tmem88b 1 1 6.1 18052.96 8.64 0 0.216 0.82277 0.513116 0.943781 0.763114 0.95713 0.80262 1.10825 0.70145 PE = 4 SV = 1 220–292 (2015) 298 Neuroscience / al. et Han X. G3V9L3_RAT Protein Dusp3 OS = Rattus norvegicus GN = Dusp3 PE = 4 1 1 6.2 23115.04 5.79 0 0.223 0.790993 0.447838 0.821722 0.34347 0.702083 0.297227 0.661939 0.127509 SV = 1 LRC59_RAT Leucine-rich repeat-containing protein 59 OS = Rattus 2 2 7.2 34868.9 9.57 1 0.781 1.05651 0.92702 1.39564 0.072074 0.818909 0.496873 1.03198 0.913981 norvegicus GN = Lrrc59 PE = 1 SV = 1 D3ZAN3_RAT Protein Ganab OS = Rattus norvegicus GN = Ganab 12 8 8.7 106902.8 5.69 0 0.337 0.885281 0.654601 0.952965 0.800427 0.814912 0.489041 1.00206 1 PE = 2 SV = 1 G3P_RAT Glyceraldehyde-3-phosphate dehydrogenase OS = Rattus 93 14 39.9 35827.59 8.14 0 0.089 0.850172 0.573147 0.913792 0.645445 0.975218 0.846364 1.19996 0.474953 norvegicus GN = Gapdh PE = 1 SV = 3 CNDP2_RAT Cytosolic non-specific dipeptidase OS = Rattus norvegicus 1 1 2.5 52692.54 5.43 0 0.294 0.8736 0.626975 0.766958 0.216035 0.870649 0.603998 0.793124 0.349179 GN = Cndp2 PE = 1 SV = 1 0.344 0.87489 0.630002 1.32657 0.137786 1.10681 0.848375 1.69051 0.012942 Q4QQV0_RAT Protein Tubb6 OS = Rattus norvegicus GN = Tubb6 PE = 2 56 11 25.1 50058.83 4.8 0 PP2BB_RATSV =Serine/threonine-protein 1 phosphatase 2B catalytic subunit 9 6 13.3 59112.74 5.6 0 0.295 0.884982 0.653887 1.02618 0.907747 0.977277 0.851378 0.989627 0.955581 beta isoform OS = Rattus norvegicus GN = Ppp3cb PE = 2 SV = 1 MPRD_RAT Cation-dependent mannose-6-phosphate receptor 2 2 12.6 31095.03 5.25 1 0.16 1.1855 0.673795 1.13906 0.528692 1.40431 0.311168 0.863713 0.535329 OS = Rattus norvegicus GN = M6pr PE = 2 SV = 1 1433E_RAT 14-3-3 protein epsilon OS = Rattus norvegicus GN = Ywhae 28 10 38.4 29173.58 4.63 0 0.54 0.909003 0.712149 1.03832 0.864078 1.02622 0.971854 1.21842 0.434756 PE = 1 SV = 1 GSTM1_RAT Glutathione S-transferase Mu 1 OS = Rattus norvegicus 8 5 23.5 28398.69 8.21 0 0.299 0.814095 0.494816 0.966479 0.856148 1.09373 0.87676 1.16128 0.565418 GN = Gstm1 PE = 2 SV = 1 B1WC64_RAT Cyp46a1 protein OS = Rattus norvegicus GN = Cyp46a1 2 2 4.4 56699.31 9.16 0 0.201 0.906357 0.705641 1.28937 0.188633 0.986327 0.873479 1.12652 0.653196 PE = 2 SV = 1 G6PI_RAT Glucose-6-phosphate isomerase OS = Rattus norvegicus 14 6 9.5 62826.24 7.38 0 0.285 0.812681 0.491868 1.0159 0.944948 0.658833 0.239283 1.04921 0.864831 GN = Gpi PE = 1 SV = 1 D3ZVQ0_RAT Ubiquitin carboxyl-terminal hydrolase OS = Rattus 2 2 2.3 95778.06 4.89 0 0.436 0.839305 0.548944 0.912276 0.639699 0.876159 0.615993 1.00742 0.984559 norvegicus GN = Usp5 PE = 3 SV = 1 SSDH_RAT Succinate-semialdehyde dehydrogenase, mitochondrial 18 10 21.2 56130.7 8.35 0 0.036 0.863916 0.604461 0.984372 0.930999 0.963316 0.817518 1.09509 0.736975 OS = Rattus norvegicus GN = Aldh5a1 PE = 1 SV = 2 LPHN1_RAT Latrophilin-1 OS = Rattus norvegicus GN = Lphn1 PE = 1 3 2 1.6 166613.2 6.21 8 0.226 0.882121 0.647078 1.17362 0.43104 1.08129 0.903916 1.67451 0.0152 SV = 1 D4A719_RAT Protein Snx12 OS = Rattus norvegicus GN = Snx12 PE = 2 1 1 6.5 19807.47 8.58 0 0.564 0.99772 0.939626 1.42312 0.054376 0.739373 0.354167 1.21041 0.451944 SV = 1 F1LQX0_RAT Uncharacterized protein (Fragment) OS = Rattus norvegicus 5 4 15.8 38180.87 7.67 0 0.316 0.918505 0.735691 1.44371 0.04363 0.652693 0.231752 1.23616 0.398048 PE = 2 SV = 1 O70511_RAT 270 kDa ankyrin G isoform (Fragment) OS = Rattus 33 18 6.9 284455.3 7.94 0 0.395 0.923755 0.748809 0.882271 0.53072 0.804437 0.468832 0.840329 0.468654 norvegicus GN = Ank3 PE = 2 SV = 2 Q5BJX2_RAT Pdhx protein (Fragment) OS = Rattus norvegicus 10 5 16.1 40889.73 8.83 0 0.26 0.964233 0.852113 0.870627 0.491123 1.16043 0.734412 1.17217 0.539132 GN = Pdhx PE = 2 SV = 1 267 (continued on next page) 6 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 268

SLK_RAT STE20-like serine/threonine-protein kinase OS = Rattus 1 1 1.2 137886.7 4.96 0 1.008 0.872209 0.623719 0.695656 0.106426 1.49947 0.202109 1.19864 0.477905 norvegicusGN = Slk PE = 1 SV = 1 Q35737_RAT NADH-ubiquinone oxidoreductase chain 4 OS =Rattus 3 2 5.2 51764.25 9.45 0 0.792 1.07945 0.880621 0.991366 0.960458 1.20511 0.643621 1.39024 0.161108 norvegicusGN = Mt-nd4 PE = 2 SV = 1 HS90A_RAT Heat shock protein HSP 90-alpha OS = Rattus norvegicus 27 16 21.6 84813.92 4.93 0 0.745 0.857205 0.589075 0.950571 0.790652 0.946767 0.777823 1.20637 0.460765 GN = Hsp90aa1 PE = 1 SV = 3 SCN2B_RAT Sodium channel subunit beta-2 OS =Rattus norvegicus 2 2 13.5 24144.33 6.12 0 0.27 0.844123 0.559613 0.828875 0.363099 0.713938 0.314624 0.655945 0.120937 GN = Scn2b PE = 1 SV = 1 RGS6_RAT Regulator of G-protein signaling 6 (Fragment) OS =Rattus 1 1 18.2 7530.29 4.92 0 0.648 1.02882 0.98333 0.993122 0.967866 0.808269 0.476171 0.908654 0.675566 norvegicusGN = Rgs6 PE = 2 SV = 1 Q68FQ9_RAT LanC lantibiotic synthetase component C-like 2 (Bacterial) 5 4 11.1 50968.05 7.19 0 0.314 0.806266 0.478608 0.989817 0.953929 0.836154 0.531422 0.851673 0.500412 OSRattus = norvegicus GN = Lancl2 PE = 2 SV = 1 Q71UZ2_RAT Sarco/endoplasmic reticulum Ca2+-ATPase (Fragment) 20 13 13.6 95254.46 5.45 8 0.11 0.874445 0.628958 0.936483 0.733844 0.76466 0.396455 0.852855 0.503786 OSRattus = norvegicus GN = Atp2a2 PE = 2 SV = 1 EF1G_RAT Elongation factor 1-gamma OS = Rattus norvegicus 4 4 12.4 50060.15 6.31 0 0.485 0.835755 0.541149 0.860896 0.459287 0.957319 0.803073 1.0087 0.98086 GN = Eef1g PE = 1 SV = 3 VDAC2_RAT Voltage-dependent anion-selective channel protein 2 33 12 46.1 31745.47 7.44 0 0.221 0.859304 0.593868 0.837652 0.388122 0.904762 0.67985 0.884598 0.598673 OSRattus = norvegicus GN = Vdac2 PE = 1 SV = 2 D3ZS58_RAT NADH dehydrogenase (Ubiquinone) 1 alpha subcomplex, 2 10 4 36.1 10844.46 9.75 0 0.301 0.862507 0.601215 1.01808 0.937039 1.00928 0.929926 1.23251 0.405448 (Predicted) OS =Rattus norvegicus GN = Ndufa2 PE = 4 SV = 1 G3V7S2_RAT Neurofilament 3, medium OS =Rattus norvegicus 15 9 12.0 95706.91 4.77 0 1.124 0.805278 0.476583 0.790954 0.266933 0.993045 0.88995 0.962815 0.860423 GN = Nefm PE = 3 SV = 1 ECHA_RAT Trifunctional enzyme subunit alpha, mitochondrial 5 4 6.6 82663.94 9.16 0 0.081 0.868067 0.614068 1.167 0.448882 0.689674 0.279717 1.1802 0.520168 OSRattus = norvegicus GN = Hadha PE = 1 SV = 2 SV2A_RAT Synaptic vesicle glycoprotein 2A OS =Rattus norvegicus 16 7 11.1 82660.35 5.38 12 0.022 0.903279 0.698097 0.80491 0.300062 0.928558 0.73481 0.93576 0.766418 GN = Sv2a PE = 1 SV = 2 NDRG1_RAT Protein NDRG1 OS =Rattus norvegicus GN = Ndrg1 3 1 4.1 42954.21 5.77 0 0.303 0.779252 0.424968 0.752624 0.189184 0.888112 0.642362 0.963695 0.86352 PE = 1 SV = 1 D3ZXQ2_RAT Uncharacterized protein OS =Rattus norvegicus PE = 4 1 1 1.2 137023.7 9.09 0 0.528 0.979463 0.891755 0.831369 0.370105 1.2863 0.492165 1.34075 0.221446 SV = 1 B6DYP8_RAT Glutathione S-transferase OS =Rattus norvegicus 3 2 10.4 25319.09 8.78 0 0.324 1.05248 0.9352 1.05274 0.812772 0.994403 0.893283 1.16561 0.554896 GN = Gsta1 PE = 2 SV = 1 ATP5J_RAT ATP synthase-coupling factor 6, mitochondrial OS =Rattus 14 4 22.2 12494.27 9.43 0 0.546 0.932151 0.769933 0.796538 0.279875 0.730919 0.340688 0.7115 0.192943 norvegicusGN = Atp5j PE = 1 SV = 1 SNAA_RAT Alpha-soluble NSF attachment protein OS =Rattus 16 10 40.7 33192.31 5.3 0 0.355 0.865905 0.609057 1.04853 0.827656 0.833459 0.525945 0.999496 0.990843 norvegicusGN = Napa PE = 1 SV = 2 NRX2A_RAT Isoform 4a of Neurexin-2 OS =Rattus norvegicus 2 2 1.4 184299.3 5.63 0 0.369 0.919972 0.739349 0.824993 0.352362 1.14371 0.769458 1.19772 0.479975 GN = Nrxn2 CSKP_RAT Peripheral plasma membrane protein CASK OS =Rattus 5 5 7.1 102112.4 5.93 0 0.405 0.83954 0.549464 0.775771 0.23385 0.974652 0.844989 0.759958 0.278013 norvegicusGN = Cask PE = 2 SV = 1 D3ZWC6_RAT Protein Sntb1 OS =Rattus norvegicus GN = Sntb1 PE = 4 1 1 1.7 58291.77 8.51 0 0.268 0.83434 0.538059 1.05542 0.803299 1.05297 0.966106 1.26647 0.339813 SV = 1 G3V7Q6_RAT Proteasome subunit beta type OS =Rattus norvegicus 2 2 10.7 28559.08 6.52 0 0.114 0.892503 0.671924 0.902597 0.603522 0.900534 0.670251 0.982938 0.931729 GN = Psmb5 PE = 3 SV = 1 D3ZEG8_RAT Protein RGD1309188 OS =Rattus norvegicus 3 2 12.4 29872.79 8.23 0 0.214 0.831855 0.532649 0.961151 0.834077 1.13545 0.786953 1.24627 0.377975 GN = RGD1309188 PE = 4 SV = 1 F1M4V6_RAT Kalirin (Fragment) OS =Rattus norvegicus GN = Kalrn 3 3 2.0 186960.6 5.68 0 0.55 0.886497 0.657505 1.03781 0.865917 0.979594 0.857025 1.10041 0.722558 PE = 2 SV = 1 Q5XI77_RAT Annexin OS =Rattus norvegicus GN = Anxa11 PE = 2 2 2 5.4 54159.87 7.53 0 0.511 0.800224 0.466298 0.846617 0.414738 0.860885 0.583008 0.900894 0.65034 SV = 1 F1M779_RAT Clathrin heavy chain 1 OS =Rattus norvegicus GN = Cltc 57 34 24.7 191557.4 5.48 0 0.241 0.888028 0.66117 1.0846 0.702467 0.869726 0.602001 1.20264 0.469002 PE = 2 SV = 1 B4F762_RAT Fanconi anemia group C protein homolog OS =Rattus 1 1 1.3 63619.06 5.71 0 0.016 0.736847 0.348248 1.18243 0.407925 0.772548 0.410246 1.43124 0.121295 norvegicusGN = Fancc PE = 2 SV = 1 GTDC2_RAT Glycosyltransferase-like domain-containing protein 2 1 1 2.9 66716.35 8.74 0 0.11 0.880691 0.643686 0.828466 0.361958 0.702262 0.297484 0.908293 0.674386 OSRattus = norvegicus GN = Gtdc2 PE = 2 SV = 1 D3ZDH8_RAT Platelet glycoprotein Ib beta chain OS =Rattus norvegicus 20 11 28.3 43891.81 6.21 0 0.584 0.857791 0.59041 0.882519 0.531582 0.996179 0.89765 1.08948 0.752298 GN = Gp1bb PE = 3 SV = 1 GLNA_RAT Glutamine synthetase OS = Rattus norvegicus GN = Glul 20 12 33.2 42267.34 6.64 0 0.595 0.859685 0.59474 0.748973 0.182757 0.924357 0.725 0.845255 0.482306 PE = 1 SV = 3 B0K026_RAT Letmd1 protein OS = Rattus norvegicus GN = Letmd1 3 2 6.2 43120.76 10.68 0 0.351 0.703739 0.294904 1.04509 0.839915 0.873291 0.609737 1.28929 0.299774 PE = 2 SV = 1 PRRT2_RAT Proline-rich transmembrane protein 2 OS = Rattus 2 2 7.0 35820.21 4.58 0 0.588 0.930636 0.76611 0.766507 0.215151 1.04292 0.988233 0.86923 0.551729 norvegicus GN = Prrt2 PE = 1 SV = 1 B2GV57_RAT Protein Cars2 OS = Rattus norvegicus GN = Cars2 PE = 2 1 1 6.7 29107.09 9.05 0 0.1 0.955979 0.830779 1.00633 0.979684 0.704138 0.300195 0.907959 0.673293 SV = 1 Q6AXY8_RAT Dehydrogenase/reductase (SDR family) member 1 1 1 3.2 34014.88 8.5 0 0.025 0.969438 0.865626 0.844886 0.409517 1.10679 0.84841 1.15159 0.589327 OS = Rattus norvegicus GN = Dhrs1 PE = 2 SV = 1 APEX1_RAT DNA-(apurinic or apyrimidinic site) lyase OS = Rattus 1 1 4.7 35538.05 8.04 0 0.59 0.778091 0.422743 0.754884 0.193247 0.682285 0.269631 0.612127 0.080604 norvegicus GN = Apex1 PE = 1 SV = 2 D3ZUF9_RAT Protein Pitrm1 OS = Rattus norvegicus GN = Pitrm1 PE = 2 2 2 2.3 113059.6 6.67 0 0.456 0.865217 0.607466 1.07988 0.718485 1.01081 0.933723 1.43872 0.114938 SV = 1 CA2D1_RAT Voltage-dependent calcium channel subunit alpha-2/delta-1 6 3 3.5 113659.1 5.16 0 0.395 0.799079 0.463987 0.751428 0.187061 0.842557 0.544554 0.804866 0.376928 OS = Rattus norvegicus GN = Cacna2d1 PE = 2 SV = 1 F1LZW6_RAT Protein Slc25a13 (Fragment) OS = Rattus norvegicus 5 4 7.7 74381.91 8.86 0 0.022 0.853661 0.581022 0.930538 0.710281 1.01184 0.936249 1.22518 0.42054 GN = Slc25a13 PE = 3 SV = 1 MSRB2_RAT Methionine-R-sulfoxide reductase B2, mitochondrial 1 1 11.5 19072.69 9.19 0 0.532 0.828817 0.526077 0.880794 0.52561 1.06154 0.947245 1.10125 0.720284 OS = Rattus norvegicus GN = Msrb2 PE = 2 SV = 1 220–292 (2015) 298 Neuroscience / al. et Han X. D4A6U1_RAT Protein Adam11 OS = Rattus norvegicus GN = Adam11 4 3 6.6 84870.3 7.08 0 0.427 0.744788 0.361902 0.996766 0.983246 1.15692 0.741713 1.13462 0.632246 PE = 2 SV = 1 F1LX73_RAT Protein Nbea OS = Rattus norvegicus GN = Nbea PE = 4 2 2 0.9 307688.2 5.84 0 0.337 0.841711 0.55426 0.936889 0.735461 0.900161 0.669407 0.904732 0.662769 SV = 1 TPPC4_RAT Trafficking protein particle complex subunit 4 OS = Rattus 1 1 7.3 24358.68 5.84 0 0.046 0.806515 0.479118 0.967852 0.861854 0.601056 0.175005 0.726558 0.217034 norvegicus GN = Trappc4 PE = 2 SV = 1 DNJA2_RAT DnaJ homolog subfamily A member 2 OS = Rattus 3 2 5.6 45765.11 6.06 0 0.695 0.416241 0.045752 0.830187 0.366774 0.570725 0.14691 0.511518 0.027949 norvegicus GN = Dnaja2 PE = 2 SV = 1 G3V985_RAT Protein Sco1 OS = Rattus norvegicus GN = Sco1 PE = 4 4 3 10.2 31768.24 8.89 0 0.454 0.895435 0.679008 0.902831 0.604386 1.01702 0.949069 1.18959 0.498397 SV = 1 Rattus norvegicus GN = Coro1a PE = 1 2 2 5.9 51064.7 6.05 0 0.275 0.854836 0.583687 0.832143 0.372297 0.916122 0.705897 0.882423 0.591921 COR1A_RAT Coronin-1ASV = 3 OS = G3V980_RAT Protein Rap2a OS = Rattus norvegicus GN = Rap2a 4 2 14.8 20642.26 4.73 0 0.178 0.745498 0.363139 0.815324 0.326501 0.989351 0.880885 0.889403 0.613713 PE = 4 SV = 1 YIPF5_RAT Protein YIPF5 OS = Rattus norvegicus GN = Yipf5 PE = 2 1 1 3.5 27902.84 4.2 1 0.379 0.841216 0.553164 1.31579 0.151302 0.89431 0.656216 1.34633 0.213934 SV = 1 F1M5N4_RAT Malic enzyme (Fragment) OS = Rattus norvegicus 15 8 16.3 60834.62 6.05 0 0.13 0.772203 0.411572 1.15331 0.487113 1.10368 0.855165 1.55027 0.047809 GN = Me3 PE = 2 SV = 1 D3ZX82_RAT Protein Cyfip2 OS = Rattus norvegicus GN = Cyfip2 PE = 2 9 4 5.3 111789.1 8.21 0 0.162 0.851219 0.575504 1.0336 0.881013 0.956236 0.800473 0.973433 0.897942 SV = 1 ERP29_RAT Endoplasmic reticulum resident protein 29 OS = Rattus 2 2 8.5 28574.47 6.23 0 0.266 0.828151 0.524641 1.17607 0.424518 1.43813 0.268652 1.80709 0.003659 norvegicus GN = Erp29 PE = 1 SV = 2 GSTK1_RAT Glutathione S-transferase kappa 1 OS = Rattus norvegicus 2 1 7.1 25492.69 9.13 0 0.116 0.955722 0.830117 1.1858 0.399285 0.574814 0.150482 0.995738 0.977409 GN = Gstk1 PE = 1 SV = 3 NDUA9_RAT NADH dehydrogenase [ubiquinone] 1 alpha subcomplex 14 8 18.6 42558.67 9.83 0 0.091 0.828403 0.525183 0.980784 0.915917 0.88844 0.64309 1.13327 0.635714 subunit 9, mitochondrial OS = Rattus norvegicus GN = Ndufa9 PE = 1 SV = 2 D3Z955_RAT Protein Pgm2l1 OS = Rattus norvegicus GN = Pgm2l1 3 3 5.5 70233.66 6.09 0 0.301 1.14163 0.757366 1.40012 0.068903 0.696466 0.289212 1.04028 0.890249 PE = 4 SV = 1 F1LV42_RAT Uncharacterized protein (Fragment) OS = Rattus norvegicus 11 8 4.1 215355.6 8.8 0 0.562 0.835565 0.540733 1.07199 0.745533 0.881462 0.627632 0.98406 0.935726 PE = 2 SV = 1 KPCA_RAT Protein kinase C alpha type OS = Rattus norvegicus 5 5 9.8 76791.12 6.61 0 0.479 0.794451 0.454705 0.865322 0.47362 0.811159 0.481747 0.863868 0.535786 GN = Prkca PE = 1 SV = 3 Q5D009_RAT Scamp1 protein (Fragment) OS = Rattus norvegicus 1 1 4.2 29761.16 8.97 4 0.189 0.666022 0.241162 0.929742 0.707147 0.893427 0.654236 0.909609 0.678699 GN = Scamp1 PE = 2 SV = 1 RINI_RAT Ribonuclease inhibitor OS = Rattus norvegicus GN = Rnh1 1 1 3.3 49973.97 4.67 0 0.024 0.674509 0.252608 0.972778 0.882385 0.676231 0.261555 0.7293 0.221644 PE = 1 SV = 2 Q7TMZ5_RAT ADP-ribosylation factor-like 6 interacting protein 1 1 1 4.9 23450.65 9.38 0 0.204 0.83998 0.550433 1.04517 0.839619 0.847967 0.555773 1.03502 0.905282 OS = Rattus norvegicus GN = Arl6ip1 PE = 2 SV = 1 269 Q5FVT5_RAT Pyruvate dehydrogenase kinase, isozyme 1 OS = Rattus 2 2 5.1 49094.48 8.09 0 0.326 0.687385 0.270689 1.10161 0.645914 0.954909 0.797287 1.22266 0.425805 norvegicus GN = Pdk1 PE = 2 SV = 1 (continued on next page) 7 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 270

GBRL2_RAT Gamma-aminobutyric acid receptor-associated protein-like 2 2 2 17.1 13666.68 7.81 0 0.316 0.827794 0.523872 0.798912 0.285502 0.959027 0.80718 0.852172 0.501837 OS = Rattus norvegicus GN = Gabarapl2 PE = 3 SV = 1 D3ZJD3_RAT Protein RGD1565183 OS =Rattus norvegicus 2 2 10.2 15720.34 11.92 0 0.693 0.909015 0.712178 0.909517 0.629294 0.936264 0.752921 0.975125 0.903945 GN = RGD1565183 PE = 4 SV = 1 NPM_RAT Nucleophosmin OS =Rattus norvegicus GN = Npm1 1 1 4.9 29524.38 4.45 0 0.912 0.784956 0.435992 0.6458 0.06034 0.724433 0.330575 0.573258 0.054687 PE = 2 SV = 1 AATC_RAT Aspartate aminotransferase, cytoplasmic OS =Rattus 10 6 17.0 46428.17 6.73 0 0.305 0.819838 0.506891 0.929055 0.704446 1.15163 0.752784 1.6187 0.026007 norvegicusGN = Got1 PE = 1 SV = 3 Q6V9V9_RAT Protein Stk25 OS =Rattus norvegicus GN = Stk25 PE = 2 2 2 5.6 48157.16 6.33 0 0.538 0.940587 0.791334 0.947439 0.777913 1.32843 0.421847 1.48648 0.080327 SV = 1 Q4V8H5_RAT Aspartyl aminopeptidase OS =Rattus norvegicus 2 2 5.3 52554.63 6.82 0 0.152 0.923218 0.747463 1.12006 0.586794 0.913707 0.700331 1.03436 0.907174 GN = Dnpep PE = 2 SV = 1 Q9Z1X8_RAT Neural F box protein NFB42 OS =Rattus norvegicus 1 1 7.4 33699.54 4.3 0 0.663 1.03598 0.968752 1.03798 0.865293 0.808302 0.476234 1.01798 0.954168 GN = Fbxo2 PE = 2 SV = 1 SFXN3_RAT Sideroflexin-3 OS =Rattus norvegicus GN = Sfxn3 PE = 2 5 3 13.9 31668.71 9.71 0 0.119 0.775033 0.41692 0.756175 0.195595 0.853744 0.567876 0.788121 0.337758 SV = 1 CAP2_RAT Adenylyl cyclase-associated protein 2 OS = Rattus 5 4 13.4 52911.71 6.69 0 0.413 0.771448 0.410151 0.925287 0.689699 0.989481 0.881206 1.07391 0.795343 norvegicusGN = Cap2 PE = 2 SV = 1 D3ZQ02_RAT Protein Wdr37 OS =Rattus norvegicus GN = Wdr37 1 1 2.0 48891.51 6.67 0 0.373 0.934544 0.775987 0.934294 0.725137 0.773351 0.411665 0.927042 0.736776 PE = 2 SV = 1 SEPT3_RAT Neuronal-specific septin-3 OS =Rattus norvegicus 13 6 16.2 40597.33 6.74 0 0.492 0.779674 0.425777 0.909023 0.627438 0.971429 0.837156 1.02647 0.929787 GN = Sept3 PE = 1 SV = 2 HXK1_RAT Hexokinase-1 OS =Rattus norvegicus GN = Hk1 PE = 1 72 27 27.9 102406.9 6.29 0 0.198 0.816146 0.499113 0.971785 0.878242 1.02189 0.961128 1.41425 0.136747 SV = 4 Q66HF3_RAT Electron transfer flavoprotein-ubiquinone oxidoreductase, 7 7 16.2 68163.27 7.33 0 0.31 0.791299 0.448443 1.01331 0.954328 1.05198 0.968266 1.10437 0.711859 mitochondrial OS =Rattus norvegicus GN = Etfdh PE = 2 SV = 1 D3ZJR1_RAT Protein Eps15l1 (Fragment) OS =Rattus norvegicus 1 1 1.2 99113.2 4.88 0 0.119 0.963653 0.850611 1.05714 0.797248 1.00539 0.920346 1.18342 0.51265 GN = Eps15l1 PE = 2 SV = 1 GBRB2_RAT Gamma-aminobutyric acid receptor subunit beta-2 3 3 7.8 54632.84 9.35 4 0.068 0.989524 0.9181 0.563934 0.020803 0.572114 0.148116 0.483 0.02003 OS =Rattus norvegicus GN = Gabrb2 PE = 1 SV = 1 GBRB3_RAT Gamma-aminobutyric acid receptor subunit beta-3 5 4 11.6 54165.03 9.19 4 0.09 1.01713 0.990749 0.83447 0.37893 0.617133 0.191436 0.71093 0.192071 OSRattus = norvegicus GN = Gabrb3 PE = 1 SV = 1 A4_RAT Amyloid beta A4 protein OS =Rattus norvegicus GN = App 3 3 4.2 86703.2 4.73 1 0.546 0.865215 0.607461 1.1416 0.52114 0.927828 0.733103 1.11944 0.671734 PE = 1 SV = 2 D3ZAI6_RAT Protein Nt5dc3 OS =Rattus norvegicus GN = Nt5dc3 6 4 8.4 63123.72 8.74 0 0.358 0.805198 0.476419 1.001 0.999048 0.821114 0.501224 1.0385 0.895337 PE = 3 SV = 1 A1L1L9_RAT Protein RGD1563224 OS =Rattus norvegicus 7 3 16.8 24662.53 6.96 0 0.119 0.792677 0.451174 1.18341 0.405393 0.83694 0.533026 0.994449 0.972805 GN = RGD1563224 PE = 2 SV = 1 D4ADW6_RAT Protein Ktn1 OS =Rattus norvegicus GN = Ktn1 PE = 2 1 1 1.1 145586.8 5.87 0 0.845 1.06509 0.909628 1.42773 0.051797 0.822411 0.503792 1.06638 0.816367 SV = 1 DLDH_RAT Dihydrolipoyl dehydrogenase, mitochondrial OS =Rattus 17 11 20.6 54037.46 7.96 0 0.01 0.814606 0.495885 0.854523 0.43908 0.722889 0.328196 0.955637 0.835227 norvegicusGN = Dld PE = 1 SV = 1 RAB35_RAT Ras-related protein Rab-35 OS =Rattus norvegicus 8 4 23.9 23024.96 8.53 0 0.473 0.865972 0.60921 0.983205 0.92609 1.51847 0.184171 1.35665 0.200511 GN = Rab35 PE = 2 SV = 1 G3V6P7_RAT Myosin, heavy polypeptide 9, non-muscle OS =Rattus 7 6 3.8 226410.6 5.54 0 0.84 0.797651 0.46111 0.946062 0.772333 0.760278 0.388915 0.793343 0.349682 norvegicusGN = Myh9 PE = 4 SV = 1 Q6P9Y4_RAT ADP/ATP translocase 1 OS =Rattus norvegicus 71 15 32.2 32903.92 9.76 4 0.056 0.804763 0.475529 0.908046 0.623776 0.983997 0.867778 1.0321 0.913627 GN = Slc25a4 PE = 2 SV = 1 G3V6H9_RAT Nucleosome assembly protein 1-like 1 OS = Rattus 3 1 2.6 45372.63 4.36 0 0.956 0.793195 0.452202 0.926743 0.695381 0.797763 0.456201 0.870652 0.555995 norvegicusGN = Nap1l1 PE = 3 SV = 1 Q3B8N9_RAT Biphenyl hydrolase-like (Serine hydrolase) OS =Rattus 5 3 16.2 32822.46 8.94 0 0.258 1.08364 0.8722 1.23357 0.288923 0.655522 0.235201 1.22044 0.430477 norvegicusGN = Bphl PE = 2 SV = 1 B2RYN6_RAT Protein Ap1g1 OS =Rattus norvegicus GN = Ap1g1 PE = 2 1 1 1.2 91720.87 6.36 0 0.126 0.877326 0.635733 0.983698 0.928164 0.871541 0.605933 1.01571 0.9607 SV = 1 HBA_RAT Hemoglobin subunit alpha-1/2 OS =Rattus norvegicus 79 10 60.6 15328.35 7.81 0 0.115 0.834101 0.537536 1.68349 0.001873 0.861644 0.584628 2.13924 4.04E 05 GN = Hba1 PE = 1 SV = 3 MDHM_RAT Malate dehydrogenase, mitochondrial OSRattus = 108 19 57.7 35683.15 8.93 0 0.119 0.802726 0.471373 1.13907 0.528651 1.02813 0.976591 1.48366 0.082107 norvegicusGN = Mdh2 PE = 1 SV = 2 D4A0F5_RAT Septin-7 OS = Rattus norvegicus GN = Sept7 PE = 2 21 9 23.5 48627.19 8.76 0 0.783 0.828419 0.525219 0.938329 0.741213 0.992621 0.888908 1.07672 0.787515 SV = 1 B0BN30_RAT Mtch1 protein OS = Rattus norvegicus GN = Mtch1 PE = 2 7 3 9.8 41591.89 9.4 2 0.094 0.913734 0.723837 0.935914 0.731578 0.987568 0.876517 1.06938 0.80799 SV = 1 D4A5W8_RAT Protein Pgs1 OS = Rattus norvegicus GN = Pgs1 PE = 4 2 2 4.3 62469.26 9 0 0.123 0.795486 0.456771 0.976368 0.897398 0.878206 0.620473 0.977486 0.912332 SV = 1 Q5RKG9_RAT Eukaryotic translation initiation factor 4B OS = Rattus 2 1 1.6 69063.29 5.59 0 1.585 0.684792 0.266978 0.735568 0.160541 1.15615 0.743337 1.04218 0.88484 norvegicus GN = Eif4b PE = 2 SV = 1 MPPA_RAT Mitochondrial-processing peptidase subunit alpha 1 1 2.1 58606.91 8.29 0 0.193 0.975558 0.881561 0.892259 0.565933 0.864368 0.590457 1.12618 0.654086 OS = Rattus norvegicus GN = Pmpca PE = 1 SV = 1 Q68FU2_RAT Phosphoserine aminotransferase 1 OS = Rattus norvegicus 3 3 10.8 40626.38 7.57 0 0.001 0.807695 0.481545 0.889388 0.555699 0.769396 0.4047 1.00551 0.990043 GN = Psat1 PE = 2 SV = 1 WDR1_RAT WD repeat-containing protein 1 OS = Rattus norvegicus 9 7 11.6 66180.66 6.15 0 0.265 0.789091 0.444086 0.86413 0.469737 1.28971 0.486246 1.37491 0.178303 GN = Wdr1 PE = 1 SV = 3 UBE2N_RAT Ubiquitin-conjugating enzyme E2 N OS = Rattus norvegicus 3 2 11.2 17123.59 6.13 0 0.272 0.774612 0.416122 0.772653 0.227432 1.33986 0.403838 1.25909 0.353463 GN = Ube2n PE = 1 SV = 1 MSRA_RAT Mitochondrial peptide methionine sulfoxide reductase 1 1 4.7 25850.95 8.21 0 0.454 0.880597 0.643464 1.01688 0.941368 0.830325 0.51961 1.03186 0.914325 OS = Rattus norvegicus GN = Msra PE = 1 SV = 1 NDUS1_RAT NADH-ubiquinone oxidoreductase 75 kDa subunit, 40 17 27.9 79411.47 5.65 0 0.101 0.823606 0.514898 1.09733 0.659978 0.876583 0.616919 1.08311 0.769824 mitochondrial OS = Rattus norvegicus GN = Ndufs1 PE = 1 220–292 (2015) 298 Neuroscience / al. et Han X. SV = 1 D3ZE15_RAT RCG38845, isoform CRA_b OS = Rattus norvegicus 15 9 47.2 16776.35 9.47 0 0.437 0.733854 0.343188 0.808524 0.309072 0.764159 0.395588 0.840991 0.470477 GN = LOC100911483 PE = 4 SV = 1 SODM_RAT Superoxide dismutase [Mn], mitochondrial OS = Rattus 10 5 28.4 24673.75 8.96 0 0.422 0.761792 0.392252 1.14061 0.524055 1.1162 0.828118 1.92243 0.000892 norvegicus GN = Sod2 PE = 1 SV = 2 G3V8H3_RAT Glutathione S-transferase Yb-3 OS = Rattus norvegicus 5 3 8.7 25617.25 6.13 0 0.398 0.832062 0.533099 0.949513 0.786343 0.883791 0.632774 1.03968 0.891967 GN = Gstm3 PE = 3 SV = 1 AL1B1_RAT Aldehyde dehydrogenase X, mitochondrial OS = Rattus 12 6 17.9 57624.14 6.62 0 0.248 0.907063 0.707376 1.11556 0.600973 0.825432 0.5098 1.11127 0.693398 norvegicus GN = Aldh1b1 PE = 1 SV = 1 B5DFN2_RAT Adenosylhomocysteinase OS = Rattus norvegicus 6 5 11.3 58908.89 7.02 0 0.26 0.743862 0.360293 0.818653 0.335262 0.818767 0.496593 0.838365 0.463273 GN = Ahcyl1 PE = 2 SV = 1 8 3 9.6 47356.6 5.61 0 0.267 0.805655 0.477354 1.06384 0.773799 1.11312 0.834755 1.19369 0.489057 ARP3_RAT Actin-relatedPE = 1 SV = protein 1 3 OS = Rattus norvegicus GN = Actr3 MRCKB_RAT Serine/threonine-protein kinase MRCK beta OS = Rattus 1 1 0.9 194885.5 6.05 0 0.572 0.914535 0.725824 0.77776 0.23801 0.864647 0.591055 0.870746 0.556277 norvegicus GN = Cdc42bpb PE = 1 SV = 1 D3ZXT1_RAT Leucine rich repeat containing 4C (Predicted), isoform CRA_a 1 1 1.4 71990.93 6.7 0 0.116 0.634438 0.201786 1.04212 0.850494 0.975642 0.847396 1.14137 0.615016 OS = Rattus norvegicus GN = Lrrc4c PE = 4 SV = 1 MTOR_RAT Serine/threonine-protein kinase mTOR OS = Rattus 2 2 0.6 288791.2 6.73 0 0.191 0.835607 0.540825 1.19482 0.376702 0.971526 0.837393 1.23802 0.394308 norvegicus GN = Mtor PE = 1 SV = 1 NMDZ1_RAT Glutamate receptor ionotropic, NMDA 1 OS = Rattus 3 2 3.2 105507.7 8.99 3 0.27 0.758585 0.386411 0.81388 0.322748 0.997543 0.901003 1.08062 0.776717 norvegicus GN = Grin1 PE = 1 SV = 1 RL23_RAT 60S ribosomal protein L23 OS = Rattus norvegicus 1 1 5.7 14865.28 10.51 0 0.194 0.840155 0.550819 0.809539 0.311633 1.12629 0.806477 1.07177 0.801286 GN = Rpl23 PE = 2 SV = 1 AT5F1_RAT ATP synthase subunit b, mitochondrial OS = Rattus 23 8 23.8 28868.45 9.39 0 0.137 0.760896 0.390614 1.0999 0.651526 0.834683 0.528428 1.53762 0.053187 norvegicus GN = Atp5f1 PE = 1 SV = 1 WDR7_RAT Isoform 2 of WD repeat-containing protein 7 OS = Rattus 6 3 2.5 160191.7 6.57 0 0.091 0.911093 0.717305 1.44879 0.041275 0.637335 0.213657 0.984874 0.938627 norvegicus GN = Wdr7 PTPRS_RAT Isoform 2 of Receptor-type tyrosine-protein phosphatase S 6 4 4.1 207076.1 6.92 0 0.351 0.819094 0.505319 0.879878 0.522452 0.674546 0.259337 0.862672 0.532262 OS = Rattus norvegicus GN = Ptprs GELS_RAT Gelsolin OS = Rattus norvegicus GN = Gsn PE = 4 SV = 1 5 3 4.5 86285.01 5.9 0 0.454 0.788199 0.442333 0.906926 0.619591 0.748352 0.368844 0.865175 0.539652 COMT_RAT Isoform 2 of Catechol O-methyltransferase OS = Rattus 3 2 15.8 24747.16 5.11 0 0.241 0.830074 0.52879 0.973229 0.884268 0.746963 0.366549 1.09579 0.735066 norvegicus GN = Comt AK1A1_RAT Alcohol dehydrogenase [NADP(+)] OS = Rattus norvegicus 4 4 17.9 36505.43 6.84 0 0.289 0.620723 0.18623 0.777546 0.23756 0.949965 0.785452 1.07346 0.796585 GN = Akr1a1 PE = 1 SV = 2 KAD3_RAT GTP:AMP phosphotransferase, mitochondrial OS = Rattus 1 1 4.4 25438.03 8.89 0 0.327 0.701577 0.291623 1.07895 0.721659 0.960926 0.811753 1.0367 0.900472 norvegicus GN = Ak3 PE = 2 SV = 2 SYVC_RAT Valine–tRNA ligase OS = Rattus norvegicus GN = Vars 4 3 3.2 140366.7 7.54 0 0.305 0.941755 0.794311 0.681334 0.090979 0.75328 0.377059 0.985897 0.942273 PE = 2 SV = 2

PDK2_RAT [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, 5 3 10.3 46105.15 6.13 0 0.256 0.861107 0.597998 1.00456 0.986106 0.883345 0.631787 1.06168 0.82958 271 mitochondrial OS = Rattus norvegicus GN = Pdk2 PE = 1 SV = 1 (continued on next page) 7 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 272

ABHGA_RAT Abhydrolase domain-containing protein 16A OS = Rattus 4 4 8.8 63037.39 8.5 2 0.191 1.20439 0.638928 0.982588 0.923496 0.887397 0.64077 1.43789 0.115635 norvegicusGN = Abhd16a PE = 2 SV = 1 Q6P7S6_RAT Clusterin OS =Rattus norvegicus GN = Clu PE = 2 SV = 1 1 1 2.2 51463.85 5.53 0 0.54 0.754831 0.379646 1.15908 0.47078 1.11136 0.83855 1.30806 0.2693 ECHB_RAT Trifunctional enzyme subunit beta, mitochondrial 6 4 8.0 51413.9 9.5 0 0.073 0.823365 0.514383 1.063 0.776704 0.866445 0.594919 1.01988 0.948711 OSRattus = norvegicus GN = Hadhb PE = 1 SV = 1 GUAA_RAT GMP synthase [glutamine-hydrolyzing] OS =Rattus 1 1 1.6 76756.55 6.21 0 0.175 0.869687 0.617834 1.31422 0.153344 0.770382 0.406431 1.24941 0.371886 norvegicusGN=GmpsPE=1SV=1 ARBK1_RAT Beta-adrenergic receptor kinase 1 OS =Rattus norvegicus 1 1 2.3 79783.92 6.54 0 0.464 0.745675 0.363448 1.18409 0.403657 0.874434 0.612226 1.33825 0.224879 GN = Adrbk1 PE = 2 SV = 1 GPX1_RAT Glutathione peroxidase 1 OS =Rattus norvegicus 1 1 6.0 22154.99 7.7 0 0.315 0.893576 0.674514 1.42816 0.05156 0.802977 0.466051 1.5525 0.046909 GN = Gpx1 PE = 1 SV = 4 APOD_RAT Apolipoprotein D OS =Rattus norvegicus GN = Apod 1 1 8.5 21634.61 4.93 0 0.138 0.876015 0.632645 1.03064 0.891662 0.619456 0.193901 0.827132 0.433155 PE = 1 SV = 1 Q5U1Z9_RAT Metaxin 2 OS =Rattus norvegicus GN = Mtx2 PE = 2 3 2 7.6 29717.85 5.23 0 0.167 0.806716 0.479531 0.959815 0.828565 1.14371 0.769456 1.265 0.3425 SV = 1 D4A746_RAT GDP-mannose pyrophosphorylase B (Predicted), isoform 1 1 2.2 39902.06 6.27 0 0.056 0.803562 0.473076 1.00159 0.996891 0.973259 0.841603 1.22274 0.425642 CRA_a OS =Rattus norvegicus GN = Gmppb PE = 4 SV = 1 THIO_RAT Thioredoxin OS =Rattus norvegicus GN = Txn PE = 1 3 3 31.4 11673.36 4.8 0 0.006 0.826394 0.520864 0.865009 0.472599 1.04019 0.994243 0.996079 0.978628 SV = 2 Q6QI09_RAT ATP synthase gamma chain OS = Rattus norvegicus 34 13 18.3 67719.85 8.03 0 0.231 0.777928 0.422431 1.05197 0.81549 0.815307 0.489811 1.18936 0.498931 GN = Taf3 PE = 2 SV = 1 ES1_RAT ES1 protein homolog, mitochondrial OS =Rattus norvegicus 12 6 30.1 28172.23 9.11 0 0.067 0.832342 0.533708 1.06995 0.752569 0.789935 0.441632 1.10933 0.698563 PE = 1 SV = 2 Q6AYS2_RAT RCG24191 OS =Rattus norvegicus GN = Sfxn1 PE = 2 7 5 13.0 35587.88 9.22 2 0.016 0.855036 0.58414 0.887629 0.549472 0.688645 0.278297 1.08739 0.758045 SV = 1 KAP3_RAT cAMP-dependent protein kinase type II-beta regulatory 9 6 21.9 46122.44 4.9 0 0.39 0.792076 0.449982 0.780507 0.243842 0.750603 0.372582 0.79566 0.355059 subunit OS =Rattus norvegicus GN = Prkar2b PE = 1 SV = 3 PRDX5_RAT Peroxiredoxin-5, mitochondrial OS =Rattus norvegicus 15 9 45.5 22178.44 8.94 0 0.179 0.869 0.616237 1.40329 0.066725 0.84489 0.549379 1.49855 0.073074 GN = Prdx5 PE = 1 SV = 1 IP3KA_RAT Inositol-trisphosphate 3-kinase A OS = Rattus norvegicus 5 3 8.7 50870.04 7.65 0 0.543 0.799794 0.46543 0.818549 0.334984 1.37554 0.350659 1.16817 0.548718 GN = Itpka PE = 1 SV = 3 D3ZWA8_RAT Protein Appl1 OS =Rattus norvegicus GN = Appl1 PE = 4 2 2 3.1 79363.19 5.24 0 0.579 0.799953 0.46575 1.05426 0.807404 0.655469 0.235137 0.82959 0.439647 SV = 1 B2RZ72_RAT Actin related protein 2/3 complex, subunit 4 (Predicted), 3 3 17.3 19666.8 8.53 0 0.133 0.740665 0.354772 0.67851 0.088156 1.73237 0.055017 1.50525 0.069288 isoform CRA_a OS =Rattus norvegicus GN = Arpc4 PE = 2 SV = 1 Q3MHS9_RAT Chaperonin containing Tcp1, subunit 6A (Zeta 1) 8 6 11.7 58016.61 6.63 0 0.095 0.78155 0.42939 0.823224 0.347534 1.28195 0.499773 1.13111 0.641287 OSRattus = norvegicus GN = Cct6a PE = 2 SV = 1 BACH_RAT Cytosolic acyl coenzyme A thioester hydrolase OS =Rattus 5 5 13.2 39055.46 8.38 0 0.36 0.899724 0.689422 1.63505 0.003863 0.964722 0.820913 1.31529 0.258151 norvegicusGN = Acot7 PE = 2 SV = 1 AMPL_RAT Cytosol aminopeptidase OS =Rattus norvegicus 4 4 8.7 56149.5 6.78 0 0.167 0.80474 0.475481 0.980631 0.915277 0.991937 0.887229 1.42427 0.127457 GN = Lap3 PE = 1 SV = 1 ABCB7_RAT ATP-binding cassette sub-family B member 7, mitochondrial 3 3 4.5 82556.85 9.35 5 0.015 0.75541 0.380685 1.15684 0.477072 0.817636 0.494372 1.24399 0.382443 OSRattus = norvegicus GN = Abcb7 PE = 2 SV = 1 F1M6P0_RAT Enolase (Fragment) OS =Rattus norvegicus PE = 3 SV = 1 12 6 18.2 39842.65 5.06 0 0.21 0.727537 0.332663 0.924678 0.687324 0.933763 0.747027 1.00226 0.999408 G3V9U2_RAT 3-ketoacyl-CoA thiolase, mitochondrial OS =Rattus 4 3 5.0 41884.52 8.37 0 0.043 0.756912 0.383387 1.63863 0.003668 0.734117 0.345747 1.04095 0.888328 norvegicusGN = Acaa2 PE = 3 SV = 1 A1AT_RAT Alpha-1-antiproteinase OS =Rattus norvegicus 2 2 4.1 46135.27 5.7 0 0.158 0.754496 0.379045 1.35396 0.107653 0.987337 0.875951 1.68155 0.014167 GN = Serpina1 PE = 1 SV = 2 RAB18_RAT Ras-related protein Rab-18 OS =Rattus norvegicus 2 1 5.3 22975.82 5.11 0 0.308 0.621006 0.186543 0.807599 0.306748 1.17444 0.705467 1.40043 0.150397 GN = Rab18 PE = 2 SV = 1 VAPA_RAT Vesicle-associated membrane protein-associated protein A 4 2 13.3 27840.93 8.58 1 0.396 0.897794 0.684728 1.02065 0.927741 0.622983 0.197687 0.818808 0.411588 OSRattus = norvegicus GN = Vapa PE = 1 SV = 3 GDIR1_RAT Rho GDP-dissociation inhibitor 1 OS =Rattus norvegicus 4 3 22.1 23407.13 5.12 0 0.73 0.815806 0.498398 0.791948 0.269206 0.590168 0.164491 0.586462 0.062576 GN = Arhgdia PE = 1 SV = 1 LASP1_RAT LIM and SH3 domain protein 1 OS =Rattus norvegicus 2 1 2.7 29970.08 6.61 0 1.035 0.792827 0.451473 0.848309 0.419878 0.88916 0.644696 0.970889 0.888928 GN = Lasp1 PE = 1 SV = 1 RNF34_RAT E3 ubiquitin-protein ligase RNF34 OS =Rattus norvegicus 1 1 3.4 42680.31 4.73 0 0.583 0.85673 0.587991 0.728396 0.149526 1.42294 0.287225 1.04269 0.88339 GN = Rnf34 PE = 1 SV = 1 D3ZRT6_RAT Protein Plekha7 OS = Rattus norvegicus GN = Plekha7 1 1 1.0 117018.8 8.97 0 0.999 0.642338 0.211165 0.673361 0.083193 0.744134 0.361903 0.649239 0.113901 PE = 2 SV = 1 B0BMV5_RAT RAB8B, member RAS oncogene family OS = Rattus 10 4 21.3 23602.83 9.15 0 0.372 0.737138 0.348743 0.852526 0.432854 1.17501 0.704297 1.09389 0.740265 norvegicus GN = Rab8b PE = 2 SV = 1 FAHD2_RAT Fumarylacetoacetate hydrolase domain-containing protein 2 7 5 21.7 34580.89 8.63 0 0.039 0.765555 0.399171 1.04161 0.852303 0.761865 0.391636 1.01572 0.960662 OS = Rattus norvegicus GN = Fahd2 PE = 1 SV = 1 GTPB1_RAT GTP-binding protein 1 OS = Rattus norvegicus 2 1 1.8 72017.42 8.33 0 0.286 0.584189 0.149143 0.886243 0.544592 0.533913 0.117604 0.599119 0.071 GN = Gtpbp1 PE = 2 SV = 1 VPS45_RAT Vacuolar protein sorting-associated protein 45 OS = Rattus 1 1 2.5 64892.84 8.42 0 0.298 0.854499 0.582922 2.10693 4.70E07 0.518289 0.106646 1.97707 0.000432 norvegicus GN = Vps45 PE = 2 SV = 1 LAC2_RAT Ig lambda-2 chain C region OS = Rattus norvegicus PE = 2 1 1 15.4 11317.51 5.76 0 0.442 0.858564 0.592176 1.0286 0.899012 1.33062 0.418363 1.6864 0.013492 SV = 1 DRS7B_RAT Isoform 2 of Dehydrogenase/reductase SDR family member 1 1 4.1 34397.52 9.49 0 0.094 0.989527 0.918106 0.804655 0.299434 0.711727 0.311329 0.727356 0.218368 7B OS = Rattus norvegicus GN = Dhrs7b GRM2_RAT Metabotropic glutamate receptor 2 OS = Rattus norvegicus 3 2 3.1 95772.8 8.11 7 0.08 0.743367 0.359435 0.83879 0.391441 0.931781 0.742369 0.788873 0.33946 GN = Grm2 PE = 1 SV = 1 GPDM_RAT Glycerol-3-phosphate dehydrogenase, mitochondrial 15 11 16.9 80971.85 6.18 1 0.195 0.766096 0.40017 1.0726 0.743436 0.863429 0.588445 1.13485 0.631659 OS = Rattus norvegicus GN = Gpd2 PE = 1 SV = 1 D3ZRJ0_RAT AarF domain containing kinase 1 (Predicted) OS = Rattus 1 1 1.5 51710.15 8.5 0 0.055 1.14766 0.745691 0.912939 0.64221 1.01178 0.936118 1.06722 0.814021 norvegicus GN = Adck1 PE = 4 SV = 1 220–292 (2015) 298 Neuroscience / al. et Han X. D4A4A9_RAT Protein Mrpl19 OS = Rattus norvegicus GN = Mrpl19 1 1 3.4 33632.53 9.42 0 0.566 0.894537 0.676836 1.04379 0.844513 1.24702 0.562989 1.94049 0.000705 PE = 4 SV = 1 EF1A1_RAT Elongation factor 1-alpha 1 OS = Rattus norvegicus 13 6 12.8 50113.26 9.1 0 0.252 0.855718 0.58569 1.22702 0.302711 0.805451 0.470767 1.39555 0.155452 GN = Eef1a1 PE = 1 SV = 1 D4AC23_RAT Protein Cct7 OS = Rattus norvegicus GN = Cct7 PE = 3 5 4 8.1 59657.56 8.21 0 0.087 0.820378 0.508036 0.792898 0.271392 0.95494 0.797362 0.822111 0.420069 SV = 1 F1LSM5_RAT Nck-associated protein 1 OS = Rattus norvegicus 4 4 4.1 121235 6.22 0 0.095 0.790184 0.44624 0.828922 0.36323 0.774734 0.414118 0.853789 0.506461 GN = Nckap1 PE = 2 SV = 1 Q45QL6_RAT Guanine nucleotide binding protein beta 2 (Fragment) 39 9 31.0 35003.07 5.91 0 0.186 0.718087 0.317311 0.757998 0.198947 0.985546 0.871567 1.07097 0.803528 OS = Rattus norvegicus GN = Gnb2 PE = 2 SV = 1 9 7 13.9 57805.14 7.3 0 0.475 0.71814 0.317396 0.77548 0.233246 0.777948 0.419849 0.863696 0.53528 ANS1B_RAT Isoform 3 of Ankyrin repeat andRattus sterile norvegicus alpha motifGN domain- = Anks1b HCDH_RATcontaining Hydroxyacyl-coenzyme protein 1B OS A= dehydrogenase, mitochondrial 2 2 5.7 34447.41 8.83 0 0.142 0.829555 0.527669 0.903174 0.605653 0.971367 0.837007 1.11032 0.69591 OS = Rattus norvegicus GN = Hadh PE = 2 SV = 1 CSN2_RAT COP9 signalosome complex subunit 2 OS = Rattus 3 3 7.7 51596.1 5.36 0 0.635 0.764322 0.396895 1.03697 0.868926 0.847894 0.555621 1.08345 0.768877 norvegicus GN = Cops2 PE = 2 SV = 1 TM9S2_RAT Transmembrane 9 superfamily member 2 OS = Rattus 2 2 3.3 75551.49 7.22 0 0.267 0.780368 0.427112 1.04248 0.849185 0.806971 0.473678 1.03593 0.902677 norvegicus GN = Tm9sf2 PE = 2 SV = 1 D3ZUP5_RAT Protein Brk1 OS = Rattus norvegicus GN = Brk1 PE = 4 1 1 10.7 8760.82 5.35 0 0.581 0.764106 0.396497 0.837703 0.388271 0.964296 0.819885 1.04509 0.876547 SV = 1 F1M3T0_RAT ARF GTPase-activating protein GIT1 (Fragment) 3 3 4.2 82487.69 6.28 0 0.592 0.797487 0.460781 1.0105 0.964532 0.951635 0.789446 1.25868 0.354237 OS = Rattus norvegicus GN = Git1 PE = 2 SV = 1 KKCC2_RAT Calcium/calmodulin-dependent protein kinase kinase 2 1 1 1.8 66490.29 6.11 0 0.34 0.845783 0.56331 1.02536 0.910702 0.854335 0.569121 1.14709 0.600576 OS = Rattus norvegicus GN = Camkk2 PE = 2 SV = 1 TEN2_RAT Teneurin-2 OS = Rattus norvegicus GN = Tenm2 PE = 1 1 1 0.3 307470.6 6.28 1 0.382 1.30035 0.475096 0.718292 0.134998 1.11908 0.821923 1.27402 0.326205 SV = 2 D3ZT90_RAT Glutaryl-Coenzyme A dehydrogenase (Predicted) 3 3 10.3 49712.7 8.95 0 0.193 0.715157 0.312647 1.14006 0.525708 0.993712 0.891588 1.30706 0.27087 OS = Rattus norvegicus GN = Gcdh PE = 3 SV = 1 D4A3N4_RAT Protein Adcy1 OS = Rattus norvegicus GN = Adcy1 PE = 3 1 1 1.3 123398.4 8.8 0 0.105 1.14477 0.751266 1.10666 0.629498 0.967954 0.828733 1.28505 0.306971 SV = 1 PUR9_RAT Bifunctional purine biosynthesis protein PURH OS = Rattus 1 1 2.2 64207.66 6.69 0 0.064 0.769044 0.40565 1.67596 0.002102 0.776368 0.417025 1.78684 0.00461 norvegicus GN = Atic PE = 1 SV = 2 NCEH1_RAT Neutral cholesterol ester hydrolase 1 OS = Rattus 3 3 9.3 45821.25 6.56 1 0.007 0.851235 0.57554 1.28784 0.190993 0.886887 0.639637 1.55566 0.045661 norvegicus GN = Nceh1 PE = 2 SV = 1 EF2_RAT Elongation factor 2 OS = Rattus norvegicus GN = Eef2 5 4 6.2 95282.97 6.41 0 0.206 0.748959 0.369207 0.828095 0.360926 0.879499 0.623313 0.942902 0.790962 PE = 1 SV = 4 Q45QL2_RAT Guanine nucleotide binding protein beta 4 (Fragment) 24 5 20.3 34383.41 6.24 0 0.145 0.70249 0.293005 0.746008 0.177656 0.864518 0.590778 0.960171 0.851125 OS = Rattus norvegicus GN = Gnb4 PE = 2 SV = 1 SYGP1_RAT Ras GTPase-activating protein SynGAP OS = Rattus 24 12 12.2 144720.4 9.18 0 0.596 0.736711 0.348017 0.887864 0.550301 0.729726 0.338813 0.760647 0.279383 273 norvegicus GN = Syngap1 PE = 1 SV = 2 (continued on next page) 7 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 274 Q5XI17_RAT Protein Tarsl2 OS = Rattus norvegicus GN = Tarsl2 PE = 2 2 2 2.5 64118.31 7.89 0 0.657 0.797054 0.459912 2.3531 7.30E 10 0.568823 0.14527 1.94015 0.000708 SV = 1 Q32PX6_RAT Protein Rhog OSRattus = norvegicus GN = Rhog PE = 2 5 3 20.9 21308.27 8.41 0 0.213 0.753586 0.377417 1.0684 0.757942 0.922927 0.72167 0.936932 0.770429 SV = 1 LDHA_RAT L-lactate dehydrogenase A chain OS =Rattus norvegicus 4 4 9.0 36450.08 8.45 0 0.064 0.831309 0.531465 0.765673 0.213522 0.908404 0.688161 0.961306 0.855113 GN = Ldha PE = 1 SV = 1 F1LW77_RAT Protein Rab33b (Fragment) OS = Rattus norvegicus 4 2 10.6 29518.68 8.94 0 0.232 0.760353 0.389624 0.684167 0.093882 0.986254 0.873299 0.900798 0.650029 GN = Rab33b PE = 3 SV = 1 RAB14_RAT Ras-related protein Rab-14 OS =Rattus norvegicus 9 5 27.4 23926.7 5.85 0 0.411 0.72226 0.324032 0.740665 0.168735 0.661776 0.242954 0.609786 0.078801 GN = Rab14 PE = 1 SV = 3 FAHD1_RAT Acylpyruvase FAHD1, mitochondrial OS =Rattus norvegicus 1 1 6.3 24480.13 7.61 0 0.128 0.940351 0.790735 0.946912 0.775777 0.75066 0.372677 0.868922 0.550807 GN = Fahd1 PE = 2 SV = 1 AOFB_RAT Amine oxidase [flavin-containing] B OS =Rattus norvegicus 19 9 21.0 58458.06 8.47 0 0.166 0.783345 0.432861 1.18288 0.406763 0.735864 0.348531 1.20481 0.464194 GN = Maob PE = 1 SV = 3 CLCN7_RAT H(+)/Cl(-) exchange transporter 7 OS =Rattus norvegicus 1 1 2.1 88729.95 6.82 11 0.218 0.878186 0.637763 0.809234 0.310861 1.11526 0.83013 1.41398 0.137001 GN = Clcn7 PE = 2 SV = 1 RAB3C_RAT Ras-related protein Rab-3C OS = Rattus norvegicus 19 6 35.2 25871.82 5.1 0 0.523 0.678539 0.258175 0.799369 0.286594 1.00733 0.925111 1.01236 0.970324 GN = Rab3c PE = 1 SV = 1 PAK1_RAT Serine/threonine-protein kinase PAK 1 OS =Rattus 3 3 7.9 60577.13 5.63 0 0.607 0.831819 0.532571 0.994366 0.973117 0.882527 0.62998 1.16972 0.545009 norvegicusGN = Pak1 PE = 1 SV = 3 RTN1_RAT Reticulon-1 OS =Rattus norvegicus GN = Rtn1 PE = 2 5 3 6.6 83000.85 4.53 2 0.377 0.833346 0.535891 1.09954 0.652685 1.03067 0.982879 1.16726 0.550916 SV = 1 FA98A_RAT Protein FAM98A OS =Rattus norvegicus GN = Fam98a 1 1 2.3 55069.78 9.06 0 0.737 1.03447 0.971814 1.44897 0.041197 0.743926 0.361563 1.41456 0.136451 PE = 2 SV = 1 B2RYT5_RAT Cox7a2l protein OS =Rattus norvegicus GN = Cox7a2l 6 4 46.0 12650.61 9.78 1 0.22 0.900965 0.692445 0.982871 0.924685 0.701616 0.296554 1.07474 0.793009 PE = 4 SV = 1 Q7TP54_RAT Ab2-162 OS =Rattus norvegicus GN = Fam65b PE = 2 3 2 1.8 144707.1 5.31 0 0.409 0.652044 0.223114 0.913534 0.644467 0.910654 0.693315 1.04031 0.890156 SV = 1 RS15A_RAT 40S ribosomal protein S15a OS =Rattus norvegicus 1 1 6.9 14839.34 10.14 0 0.12 0.723927 0.326742 1.29683 0.177465 0.8087 0.477 1.49021 0.078027 GN = Rps15a PE = 1 SV = 2 ENPL_RAT Endoplasmin OS =Rattus norvegicus GN = Hsp90b1 11 8 10.6 92769.86 4.72 0 0.732 0.743735 0.360073 1.09606 0.664154 0.859151 0.579317 1.2196 0.432263 PE = 1 SV = 2 Q9JMA8_RAT Exostoses (Multiple)-like 3, isoform CRA_a OS =Rattus 1 1 1.0 104442.6 6.07 1 0.212 0.911548 0.718428 1.17884 0.417245 0.714865 0.316012 1.06776 0.812512 norvegicusGN = Extl3 PE = 2 SV = 1 Q9QZX1_RAT Nucleolin-related protein NRP OS =Rattus norvegicus 1 1 1.1 77438.3 4.59 0 1.143 0.774155 0.415256 0.975121 0.892179 0.89131 0.649496 1.18838 0.501175 GN = Norp PE = 2 SV = 1 MPPB_RAT Mitochondrial-processing peptidase subunit beta 1 1 2.0 54264.59 6.26 0 0.164 0.731599 0.339406 1.12994 0.55621 0.674328 0.259052 0.882396 0.591837 OSRattus = norvegicus GN = Pmpcb PE = 1 SV = 3 G3V7X2_RAT Secretogranin 2, isoform CRA_a OS =Rattus norvegicus 1 1 2.1 71000.39 4.71 0 0.949 0.799837 0.465516 1.07697 0.728425 0.783913 0.430608 1.32635 0.241721 GN = Scg2 PE = 4 SV = 1 TBA8_RAT Tubulin alpha-8 chain OS =Rattus norvegicus GN = Tuba8 32 11 25.4 50036.93 4.98 0 0.209 0.794342 0.454487 1.10079 0.648584 0.820558 0.500125 1.34612 0.214203 PE = 2 SV = 1 SC31A_RAT Protein transport protein Sec31A OS =Rattus norvegicus 1 1 1.1 133432.2 6.26 0 0.398 0.749685 0.370489 0.799289 0.286404 1.33112 0.417574 1.03284 0.911515 GN = Sec31a PE = 4 SV = 1 ACADL_RAT Long-chain specific acyl-CoA dehydrogenase, mitochondrial 4 3 7.4 47872.31 7.63 0 0.223 0.783268 0.432712 1.20786 0.345494 0.86837 0.599069 1.60344 0.029929 OSRattus = norvegicus GN = Acadl PE = 1 SV = 1 TXD12_RAT Thioredoxin domain-containing protein 12 OS =Rattus 1 1 8.8 19018.36 5.25 0 0.314 0.93053 0.765841 0.82396 0.349537 0.781089 0.425495 0.928911 0.743098 norvegicusGN = Txndc12 PE = 2 SV = 2 NDUF4_RAT NADH dehydrogenase [ubiquinone] 1 alpha subcomplex 2 2 12.1 20157.92 8.98 0 0.735 0.674969 0.253239 0.906068 0.616389 0.871012 0.604785 1.08629 0.761077 assembly factor 4 OS =Rattus norvegicus GN = Ndufaf4 PE = 1 SV = 1 F1LQ63_RAT Tenascin-R OS =Rattus norvegicus GN = Tnr PE = 2 19 9 9.7 149518.6 4.82 0 0.337 0.728442 0.334157 0.837878 0.388779 0.876966 0.617757 0.958467 0.845144 SV = 1 KCNA2_RAT Potassium voltage-gated channel subfamily A member 2 4 3 11.6 56700.13 4.77 5 0.035 0.754947 0.379854 1.10925 0.621137 0.561742 0.139289 0.774375 0.307636 OSRattus = norvegicus GN = Kcna2 PE = 1 SV = 1 Q4G079_RAT Protein Aimp1 OS =Rattus norvegicus GN = Aimp1 PE = 2 2 2 10.5 34573.52 8.52 0 0.48 0.711495 0.306881 1.09725 0.660244 0.769924 0.405627 1.13461 0.63227 SV = 1 CAND1_RAT Cullin-associated NEDD8-dissociated protein 1 OS =Rattus 3 3 2.4 136360.2 5.52 0 0.019 0.721973 0.323567 0.889142 0.554825 0.842944 0.545353 0.992156 0.964611 norvegicusGN = Cand1 PE = 1 SV = 1 ECSIT_RAT Evolutionarily conserved signaling intermediate in Toll 1 1 1.6 49619.09 5.99 0 0.468 0.858138 0.591204 0.93149 0.714036 0.999176 0.905023 1.41975 0.131587 pathway, mitochondrial OS =Rattus norvegicus GN = Ecsit PE = 2 SV = 1 F1LVC6_RAT Glutathione S-transferase OS = Rattus norvegicus 1 1 6.3 23008.62 5.86 0 0.06 0.766647 0.401191 1.09644 0.662918 0.766086 0.398927 1.13191 0.639221 GN = LOC100365881 PE = 2 SV = 1 PHOCN_RAT MOB-like protein phocein OS = Rattus norvegicus 1 1 6.7 26032.16 5.5 0 0.492 0.691278 0.276325 0.908605 0.625872 0.483825 0.085335 0.594726 0.067977 GN = Mob4 PE = 1 SV = 1 B2RZA9_RAT Protein Ube2l3 OS = Rattus norvegicus GN = Ube2l3 1 1 5.9 17818.23 7.64 0 0.75 0.85477 0.583537 0.984197 0.93026 0.655008 0.234572 0.901387 0.651929 PE = 2 SV = 1 B0BNB9_RAT HtrA serine peptidase 2 OS = Rattus norvegicus GN = Htra2 3 2 5.9 49093.73 9.51 1 0.018 0.740614 0.354684 1.01261 0.956857 1.17597 0.70233 1.44599 0.109016 PE = 2 SV = 1 D3ZUL1_RAT Protein Ccdc124 OS = Rattus norvegicus GN = Ccdc124 1 1 10.1 25317.48 9.62 0 1.3 1.05278 0.93459 0.450722 0.003607 0.535045 0.118431 0.286192 0.001338 PE = 4 SV = 1 VATC1_RAT V-type proton ATPase subunit C 1 OS = Rattus norvegicus 9 5 9.2 43900.02 7.02 0 0.305 0.75157 0.373826 1.02043 0.928536 0.646186 0.223957 1.01348 0.967106 GN = Atp6v1c1 PE = 2 SV = 1 O88565_RAT Protein Rab5a OS = Rattus norvegicus GN = Rab5a 7 4 25.1 23614.37 8.32 0 0.42 0.809164 0.484574 0.971227 0.875913 0.783503 0.429864 1.1718 0.540033 PE = 2 SV = 1 D3ZGN0_RAT Protein Tbc1d4 OS = Rattus norvegicus GN = Tbc1d4 1 1 0.6 147898.2 8.17 0 0.503 0.913012 0.72205 0.908196 0.624337 0.981798 0.862404 1.24856 0.373535 PE = 2 SV = 1 PYRD_RAT Dihydroorotate dehydrogenase (quinone), mitochondrial 1 1 3.8 42662.39 9.45 1 0.147 0.795556 0.45691 1.03742 0.867302 0.786329 0.435012 1.12572 0.655276 OS = Rattus norvegicus GN = Dhodh PE = 1 SV = 1 EHD1_RAT EH domain-containing protein 1 OS = Rattus norvegicus 2 2 3.8 60602.06 6.35 0 0.363 0.872307 0.623949 1.2677 0.224013 0.62797 0.203135 0.747454 0.253943 GN = Ehd1 PE = 1 SV = 1 220–292 (2015) 298 Neuroscience / al. et Han X. SHLB2_RAT Endophilin-B2 OS = Rattus norvegicus GN = Sh3glb2 5 3 9.3 44447.85 5.62 0 0.416 0.77451 0.415927 1.28768 0.191238 0.533233 0.117109 0.987567 0.94823 PE = 2 SV = 1 KCAB2_RAT Voltage-gated potassium channel subunit beta-2 13 5 13.6 41020.81 9.11 0 0.269 0.704729 0.296416 0.984188 0.930225 0.799826 0.460083 1.02702 0.928187 OS = Rattus norvegicus GN = Kcnab2 PE = 1 SV = 1 F1LNE8_RAT Gamma-aminobutyric acid receptor subunit alpha-2 2 2 5.8 51121.41 9.21 0 0.11 0.756562 0.382755 0.852035 0.431331 0.824569 0.508079 0.925656 0.732097 OS = Rattus norvegicus GN = Gabra2 PE = 2 SV = 1 D3ZLT1_RAT NADH dehydrogenase (Ubiquinone) 1 beta subcomplex, 7 6 3 23.4 16567.79 8.69 0 1.102 0.765723 0.399481 0.990995 0.958894 0.775937 0.416257 1.09639 0.733459 (Predicted) OS = Rattus norvegicus GN = Ndufb7 PE = 4 SV = 1 CD9_RAT CD9 antigen OS = Rattus norvegicus GN = Cd9 PE = 1 5 2 10.2 25214.65 6.93 4 0.537 0.790075 0.446024 0.584648 0.027671 0.710093 0.30891 0.663898 0.129717 SV = 2 Rattus 6 4 12.4 43025.58 5.32 0 0.402 0.805667 0.477378 0.808521 0.309064 0.79256 0.446487 1.05242 0.855723 SIR2_RAT NAD-dependentnorvegicus GN protein = Sirt2 deacetylase PE = 2 SV sirtuin-2 = 1 OS = IQEC3_RAT IQ motif and SEC7 domain-containing protein 3 OS = Rattus 2 2 1.5 129016.6 5.84 0 0.406 1.03795 0.964738 1.16513 0.45399 1.02796 0.976157 1.35434 0.203464 norvegicus GN = Iqsec3 PE = 1 SV = 1 ADT2_RAT ADP/ATP translocase 2 OS = Rattus norvegicus 54 15 34.6 32900.87 9.74 2 0.021 0.680165 0.260445 0.915657 0.652545 0.84809 0.556029 1.06093 0.8317 GN = Slc25a5 PE = 1 SV = 3 D4A0A1_RAT Protein LOC100363805 OS = Rattus norvegicus 3 2 2.3 103024.8 5.83 0 0.83 0.719692 0.319885 1.11553 0.601076 0.770261 0.406217 1.01096 0.974355 GN = Soga3 PE = 4 SV = 1 TOMT_RAT Transmembrane O-methyltransferase OS = Rattus 2 1 3.5 28863.43 9.03 0 0.112 1.02485 0.991415 1.24094 0.273931 0.648514 0.226724 0.576568 0.056582 norvegicus GN = Tomt PE = 2 SV = 1 D3ZF13_RAT Acyl carrier protein OS = Rattus norvegicus 1 1 5.8 17514.29 4.93 0 0.038 0.66145 0.235149 1.09853 0.656021 0.777438 0.418936 1.14512 0.605523 GN = LOC683884 PE = 3 SV = 1 DHPR_RAT Dihydropteridine reductase OS = Rattus norvegicus 10 4 27.0 25551.92 7.67 0 0.034 0.731987 0.340055 0.885269 0.541174 0.674635 0.259454 0.958692 0.845931 GN = Qdpr PE = 1 SV = 1 DDX1_RAT ATP-dependent RNA helicase DDX1 OS = Rattus 2 1 2.4 82496.19 6.8 0 0.399 0.656479 0.228732 0.773331 0.228817 0.791603 0.444714 0.664574 0.130485 norvegicus GN = Ddx1 PE = 2 SV = 1 ST4A1_RAT Sulfotransferase 4A1 OS = Rattus norvegicus GN = Sult4a1 1 1 2.8 33053.48 5.32 0 0.338 0.648441 0.218624 0.864518 0.470998 0.754212 0.378625 1.00354 0.995741 PE = 2 SV = 1 D3ZAN1_RAT Type I inositol 3,4-bisphosphate 4-phosphatase OS = Rattus 1 1 1.0 104475.5 6.89 0 0.302 1.03917 0.962261 1.41103 0.061659 0.798728 0.458015 1.6799 0.014404 norvegicus GN = Inpp4a PE = 2 SV = 1 C9WPN7_RAT Eif2s3y (Fragment) OS = Rattus norvegicus GN = Eif2s3y 1 1 5.9 29589.08 7.2 0 0.056 0.660908 0.234443 0.699922 0.111409 1.06049 0.949554 1.20688 0.459662 PE = 2 SV = 1 NUDT9_RAT ADP-ribose pyrophosphatase, mitochondrial OS = Rattus 1 1 3.4 38561.71 6.61 0 0.635 0.621058 0.186599 0.857304 0.447836 0.840006 0.539303 1.09448 0.738641 norvegicus GN = Nudt9 PE = 2 SV = 1 FUT8_RAT Alpha-(1,6)-fucosyltransferase OS = Rattus norvegicus 1 1 2.4 66483.87 7.13 1 0.557 0.722619 0.324614 1.00863 0.971327 0.772391 0.409968 0.994199 0.971909 GN = Fut8 PE = 2 SV = 1 PLD3_RAT Phospholipase D3 OS = Rattus norvegicus GN = Pld3 1 1 2.5 54398.5 6.07 1 0.153 0.727927 0.333306 1.49217 0.0252 0.84073 0.540791 1.20776 0.457731 PE = 2 SV = 1 275 (continued on next page) 7 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 276

Q6P503_RAT ATPase, H+ transporting, V1 subunit D, isoform CRA_c 6 3 8.9 28308.58 9.44 0 0.453 0.717316 0.31608 1.12855 0.56046 0.953418 0.793713 1.12529 0.656403 OS = Rattus norvegicus GN = Atp6v1d PE = 2 SV = 1 RAB3A_RAT Ras-related protein Rab-3A OS =Rattus norvegicus 28 9 47.3 24969.6 4.85 0 0.49 0.742253 0.357508 0.835992 0.38331 0.733141 0.344199 0.904732 0.662769 GN = Rab3a PE = 1 SV = 1 G3V624_RAT Coronin OS =Rattus norvegicus GN = Coro1c PE = 3 1 1 2.1 53177.34 6.65 0 0.346 0.569411 0.135854 0.735563 0.160533 1.01997 0.956377 1.17418 0.534346 SV = 1 Q4V8H2_RAT SEC3-like 1 (S. cerevisiae) OS =Rattus norvegicus 1 1 1.3 76670.18 5.51 0 0.407 1.1952 0.655788 0.96368 0.844538 1.09325 0.877823 1.15216 0.58791 GN = Sec3l1 PE = 2 SV = 1 RL14_RAT 60S ribosomal protein L14 OS =Rattus norvegicus 3 2 12.2 23338.54 11.11 0 0.492 0.755608 0.381041 0.989274 0.951638 0.841183 0.541722 1.1443 0.607589 GN = Rpl14 PE = 1 SV = 3 JPH2_RAT Junctophilin-2 OS =Rattus norvegicus GN = Jph2 PE = 2 1 1 1.3 74257.62 8.43 1 0.791 0.662461 0.236469 0.806309 0.303529 0.939489 0.760541 1.0909 0.748416 SV = 1 Q499T3_RAT Sirpa protein OS =Rattus norvegicus GN = Sirpa PE = 2 13 3 6.8 56117.62 7.16 0 0.396 0.700789 0.290432 0.854689 0.4396 0.874691 0.612787 1.08613 0.761511 SV = 1 F1LUM5_RAT Protein Tubal3 (Fragment) OS =Rattus norvegicus 10 6 9.7 49891.37 5.47 0 0.118 0.769252 0.406039 1.41522 0.059047 0.657918 0.23815 1.44166 0.112518 GN = Tubal3 PE = 3 SV = 1 HBB2_RAT Hemoglobin subunit beta-2 OS =Rattus norvegicus PE = 1 33 10 74.2 15982.24 8.91 0 0.003 0.761825 0.392311 1.9311 2.26E 05 0.785523 0.433539 2.69229 1.05E 09 SV = 2 MYPR_RAT Myelin proteolipid protein OSRattus = norvegicus 50 7 24.6 30076.85 8.71 1 0.55 0.690373 0.275009 0.591181 0.030209 1.04038 0.993824 0.92671 0.735654 GN = Plp1 PE = 1 SV = 2 D4A2Z6_RAT Protein Sec63 OS =Rattus norvegicus GN = Sec63 PE = 2 1 1 1.2 87715.71 5.3 0 0.666 0.865589 0.608326 0.95327 0.801673 1.37343 0.35367 1.46022 0.098133 SV = 1 D3ZX01_RAT Protein Rps4y2 OS =Rattus norvegicus GN = Rps4y2 1 1 4.2 29197.86 10.28 0 0.317 0.888324 0.661879 1.00292 0.992042 0.915452 0.70435 1.08278 0.770724 PE = 4 SV = 1 HBB1_RAT Hemoglobin subunit beta-1 OS =Rattus norvegicus 35 10 75.5 15979.19 7.87 0 0.042 0.758063 0.385467 1.72359 0.000993 0.807122 0.473967 2.24838 6.82E 06 GN = Hbb PE = 1 SV = 3 D3ZRH1_RAT Protein Oxa1l OSRattus = norvegicus GN = Oxa1l PE = 3 1 1 2.1 48022.64 9.76 0 0.034 0.966595 0.85824 0.969021 0.866718 0.856627 0.573963 1.39452 0.156545 SV = 1 HPCA_RAT Neuron-specific calcium-binding protein hippocalcin 6 3 12.4 22427.16 4.87 0 0.56 0.69395 0.280241 1.19066 0.387019 0.894987 0.657736 1.04423 0.879007 OS =Rattus norvegicus GN = Hpca PE = 1 SV = 2 EXOC8_RAT Exocyst complex component 8 OS =Rattus norvegicus 1 1 2.0 81042.33 5.3 0 0.392 0.586052 0.150886 1.17647 0.423479 0.62568 0.200619 1.09338 0.741643 GN = Exoc8 PE = 1 SV = 1 Q62669_RAT Protein Hbb-b1 OS =Rattus norvegicus GN = Hbb-b1 18 5 32.0 16022.32 7.93 0 0.001 0.757825 0.385037 2.13809 2.22E 07 0.826309 0.51155 3.08147 6.06E 14 PE = 3 SV = 1 OS9_RAT Protein OS-9 OSRattus = norvegicus GN = Os9 PE = 1 1 1 1.5 75364.03 4.77 1 0.885 0.576102 0.141752 1.00909 0.969639 0.745199 0.363647 0.908435 0.674849 SV = 1 D3ZVI9_RAT Parkinson disease 7 domain containing 1 (Predicted), isoform 1 1 9.1 23263.18 6.36 0 0.156 0.83545 0.540482 1.07325 0.741193 0.655056 0.234631 1.21645 0.438945 CRA_a OS =Rattus norvegicus GN = Pddc1 PE = 4 SV = 1 D3ZRC4_RAT Similar to intracellular membrane-associated calcium- 1 1 2.3 87959.96 9.19 0 0.453 0.525464 0.1017 0.501816 0.008284 0.795555 0.452064 0.715128 0.198558 independent phospholipase A2 gamma (Predicted), isoform CRA_b OS =Rattus norvegicus GN = Pnpla8 PE = 4 SV = 1 FSCN1_RAT Fascin OS =Rattus norvegicus GN = Fscn1 PE = 1 4 2 5.3 54490.36 6.29 0 0.424 0.782534 0.431291 0.812466 0.319098 0.999656 0.906203 0.989093 0.953676 SV = 2 D3ZDP2_RAT Protein Ict1 OS =Rattus norvegicus GN = Ict1 PE = 4 2 2 14.6 23469.74 10.2 0 0.677 0.539539 0.111802 0.644248 0.059226 1.04924 0.974314 0.935117 0.76422 SV = 1 CPLX1_RAT Complexin-1 (Fragment) OS =Rattus norvegicus 6 4 42.1 15143.98 5.02 0 1.22 0.81331 0.493178 0.834272 0.378363 0.715729 0.317311 0.612421 0.080833 GN = Cplx1 PE = 4 SV = 1 F1LRZ7_RAT Neurofilament heavy polypeptide OS =Rattus norvegicus 13 7 7.1 114410.5 5.71 0 1.029 0.662558 0.236597 0.71802 0.134623 0.903203 0.676304 1.00507 0.991319 GN = Nefh PE = 2 SV = 1 D3ZCI5_RAT Protein Stxbp6 OS =Rattus norvegicus GN = Stxbp6 1 1 6.3 21695.47 9.34 0 0.555 0.699235 0.288095 0.797143 0.2813 0.750781 0.372878 0.801124 0.36794 PE = 4 SV = 1 DYN3_RAT Dynamin-3 OS =Rattus norvegicus GN = Dnm3 PE = 2 10 5 6.5 97894.97 8.19 0 0.466 0.756667 0.382946 0.93299 0.719969 0.562833 0.140197 0.813846 0.399041 SV = 1 DCTN2_RAT Dynactin subunit 2 OS =Rattus norvegicus GN = Dctn2 2 1 2.2 44147.36 5.14 0 0.499 0.909429 0.713199 1.10944 0.620509 0.757989 0.385012 1.21313 0.446072 PE = 1 SV = 1 ABCB8_RAT ATP-binding cassette sub-family B member 8, mitochondrial 4 4 8.5 77769.52 9.61 4 0.149 0.60997 0.174669 0.95535 0.810195 0.730169 0.33951 1.20073 0.47324 OSRattus = norvegicus GN = Abcb8 PE = 2 SV = 1 NDUS4_RAT NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, 8 3 18.3 19740.41 10.14 0 0.545 0.648629 0.218855 0.934727 0.726857 0.743034 0.360106 1.00808 0.982642 mitochondrial OS = Rattus norvegicus GN = Ndufs4 PE = 1 SV = 1 Q6TXF3_RAT Acyl-CoA-binding protein OS = Rattus norvegicus GN = Dbi 3 1 2.7 66448.74 8.94 0 0.576 0.718914 0.318635 0.942264 0.756998 0.359947 0.035254 0.642727 0.10738 PE = 2 SV = 1 FKBP4_RAT Peptidyl-prolyl cis-trans isomerase FKBP4 OS = Rattus 1 1 3.3 51505.68 5.46 0 0.557 0.746036 0.364079 0.8405 0.396462 0.772939 0.410937 1.04579 0.874548 norvegicus GN = Fkbp4 PE = 4 SV = 1 HPT_RAT Haptoglobin OS = Rattus norvegicus GN = Hp PE = 1 1 1 2.0 38562.75 6.1 0 0.257 0.82602 0.52006 1.19066 0.38701 0.783353 0.429591 1.38409 0.167846 SV = 3 RAB3D_RAT GTP-binding protein Rab-3D OS = Rattus norvegicus 13 4 21.5 24289.94 4.75 0 0.363 0.680241 0.260551 0.79552 0.277483 0.838832 0.536894 0.991753 0.963172 GN = Rab3d PE = 1 SV = 2 SCN8A_RAT Sodium channel protein type 8 subunit alpha (Fragment) 2 2 1.5 211394.1 5.93 0 0.055 1.66086 0.102111 1.39243 0.074419 0.683838 0.271729 0.813095 0.397162 OS = Rattus norvegicus GN = Scn8a PE = 2 SV = 1 Q5XI34_RAT Protein Ppp2r1a OS = Rattus norvegicus GN = Ppp2r1a 6 4 7.1 65321.88 5 0 0.075 0.685092 0.267407 0.960344 0.830748 0.782268 0.427625 1.09448 0.738644 PE = 2 SV = 1 B0BN02_RAT Mtx1 protein OS = Rattus norvegicus GN = Mtx1 PE = 2 2 2 4.2 48443.08 9.58 1 0.448 0.734648 0.344525 1.10817 0.62462 0.682103 0.269386 0.989952 0.956744 SV = 1 FRS1L_RAT DOMON domain-containing protein FRRS1L OS = Rattus 5 3 13.7 32456.22 5.22 0 0.287 0.622417 0.188102 0.683095 0.092774 1.05466 0.962381 0.925394 0.731213 norvegicus GN = Frrs1l PE = 1 SV = 1 CAP1_RAT Adenylyl cyclase-associated protein 1 OS = Rattus 3 3 6.8 51588.29 7.16 0 0.352 0.657606 0.230176 0.840079 0.395223 0.838932 0.537099 1.18542 0.508002 220–292 (2015) 298 Neuroscience / al. et Han X. norvegicus GN = Cap1 PE = 1 SV = 3 F8WFS9_RAT Beta-adducin OS = Rattus norvegicus GN = Add2 PE = 4 4 4 6.2 80575.72 5.7 0 0.687 0.702503 0.293025 0.836624 0.385138 0.686822 0.275794 0.928393 0.741345 SV = 1 Q5RK08_RAT Glioblastoma amplified sequence OS = Rattus norvegicus 3 3 10.3 32941.35 9.4 0 -0.561 0.704193 0.295597 1.00449 0.986353 0.646312 0.224105 1.12692 0.652171 GN = Gbas PE = 2 SV = 1 LIS1_RAT Platelet-activating factor acetylhydrolase IB subunit alpha 2 1 7.5 31753.75 6.99 0 0.281 0.603304 0.167776 0.354242 0.000623 0.364179 0.036413 0.308192 0.001877 (Fragment) OS = Rattus norvegicus GN = Pafah1b1 PE = 2 SV = 1 B4F774_RAT Protein Gdap1l1 OS = Rattus norvegicus GN = Gdap1l1 5 3 11.0 35114.04 6.33 0 0.281 0.651236 0.222101 0.858698 0.452259 0.449544 0.067692 0.617432 0.084812 PE = 2 SV = 1 SCMC2_RAT Calcium-binding mitochondrial carrier protein SCaMC-2 1 1 1.7 54179.2 8.84 0 0.117 0.604154 0.168643 1.08394 0.70471 0.754429 0.37899 1.27673 0.3214 OS = Rattus norvegicus GN = Slc25a25GN = Wfs1 PE = PE 2 = SV 2 = SV 1 = 1 3 3 3.9 100531.6 8.24 9 0.032 0.670964 0.247782 0.952228 0.797415 0.527123 0.112738 0.872844 0.562604 Q9JLT5_RATLYPA2_RAT WFS1 Acyl-protein OS = Rattus thioesterase norvegicus 2 OS = Rattus norvegicus 1 1 7.8 24806.75 6.74 0 0.135 0.459292 0.063541 1.37735 0.086278 0.490575 0.089213 0.674662 0.14238 GN = Lypla2 PE = 1 SV = 1 D3ZJH5_RAT Protein RGD1562409 OS = Rattus norvegicus 1 1 4.9 29970.14 10.48 0 0.532 0.608517 0.173148 0.790086 0.264958 0.810045 0.479592 1.12871 0.647503 GN = RGD1562409 PE = 4 SV = 1 PEA15_RAT Astrocytic phosphoprotein PEA-15 OS = Rattus norvegicus 2 1 9.2 15039.91 4.93 0 0.644 0.870675 0.620137 2.78542 4.34E16 0.32032 0.025844 1.18851 0.500887 GN = Pea15 PE = 1 SV = 1 VP33A_RAT Vacuolar protein sorting-associated protein 33A OS = Rattus 2 2 1.7 67512.95 6.6 0 0.248 1.06115 0.917606 0.982771 0.924265 0.696676 0.289509 1.19494 0.486226 norvegicus GN = Vps33a PE = 1 SV = 1 D3ZQD3_RAT Oxoglutarate dehydrogenase-like (Predicted), isoform CRA_a 11 9 9.8 116710.7 6.41 0 0.325 0.618948 0.184284 0.912306 0.639812 0.691109 0.281706 0.836182 0.45733 OS = Rattus norvegicus GN = Ogdhl PE = 4 SV = 1 Q45QM4_RAT Guanine nucleotide binding protein alpha q subunit 13 5 20.0 38282.95 5.46 0 0.577 0.62346 0.189261 0.893721 0.571181 1.24258 0.571297 1.77656 0.005174 (Fragment) OS = Rattus norvegicus GN = Gnaq PE = 2 SV = 1 RYR2_RAT Isoform 2 of Ryanodine receptor 2 OS = Rattus norvegicus 4 4 1.0 562334 5.73 0 0.31 0.607308 0.171891 0.652511 0.06536 0.610977 0.185015 0.675786 0.143754 GN = Ryr2 ETFA_RAT Electron transfer flavoprotein subunit alpha, mitochondrial 2 1 3.0 34950.94 8.62 0 0.131 0.685673 0.268236 0.90843 0.625214 0.598436 0.17243 0.787168 0.335611 OS = Rattus norvegicus GN = Etfa PE = 1 SV = 4 RASN_RAT GTPase NRas OS = Rattus norvegicus GN = Nras PE = 1 3 3 21.7 21242.97 5.02 0 0.317 0.570909 0.137158 0.650484 0.063808 0.557459 0.135764 0.598085 0.070278 SV = 1 RASH_RAT Protein Hras (Fragment) OS = Rattus norvegicus GN = Hras 5 5 24.5 26185.42 7.71 0 0.424 0.649964 0.220514 0.672876 0.082737 0.646842 0.224734 0.761843 0.281772 PE = 4 SV = 1 DNJC5_RAT DnaJ homolog subfamily C member 5 OS = Rattus 7 2 7.6 22100.52 4.93 0 0.483 0.717899 0.31701 0.884598 0.538824 0.72452 0.330709 0.936534 0.769065 norvegicus GN = Dnajc5 PE = 1 SV = 1 DLGP1_RAT Disks large-associated protein 1 OS = Rattus norvegicus 2 2 3.1 109262.6 6.75 0 0.771 0.654838 0.226642 0.73292 0.156404 0.798436 0.457466 0.98192 0.928105 GN = Dlgap1 PE = 2 SV = 1

B2GV92_RAT Ptges3 protein OS = Rattus norvegicus GN = Ptges3 2 1 10.6 18721.22 4.36 0 1.047 0.691474 0.276612 0.751967 0.188016 0.622262 0.19691 0.533186 0.035649 277 PE = 2 SV = 1 (continued on next page) 7 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 278

SEPT8_RAT Septin-8 OS = Rattus norvegicus GN = Sept8 PE = 1 10 4 11.8 51251.47 5.74 0 0.679 0.724125 0.327065 0.785387 0.254448 1.15578 0.744093 1.37647 0.17649 SV = 1 GTR8_RAT Solute carrier family 2, facilitated glucose transporter member 1 1 2.5 51458.41 8.56 12 0.679 0.843115 0.557372 1.12181 0.581305 0.606092 0.180035 0.894228 0.628981 8OS=Rattus norvegicus GN = Slc2a8 PE = 1 SV = 1 MK01_RAT Mitogen-activated protein kinase 1 OS = Rattus norvegicus 7 7 20.1 41178.01 6.5 0 0.289 0.673937 0.251825 0.900405 0.595461 0.672887 0.257167 1.10558 0.7086 GN = Mapk1 PE = 4 SV = 1 Q45QK2_RAT Guanine nucleotide-binding protein subunit gamma 1 1 43.9 4346.96 6.13 0 0.12 0.531481 0.105926 1.0501 0.822102 0.441993 0.06424 0.797647 0.359709 (Fragment) OS =Rattus norvegicus GN = Gng10 PE = 2 SV = 1 ACY1A_RAT Aminoacylase-1A OS =Rattus norvegicus GN = Acy1a 1 1 2.0 45803.53 6.03 0 0.292 0.518411 0.096919 0.94589 0.771638 0.731247 0.341205 1.08262 0.77119 PE = 1 SV = 1 DLG1_RAT Disks large homolog 1 OS =Rattus norvegicus GN = Dlg1 5 5 5.9 102788 5.67 0 0.551 0.659598 0.232743 0.69192 0.102208 0.706833 0.304119 0.694563 0.16826 PE = 2 SV = 1 D4AB01_RAT Histidine triad nucleotide binding protein 2 (Predicted), 5 1 9.2 17379.92 9.46 0 0.02 0.729129 0.335296 0.757914 0.198793 1.12223 0.815172 1.10558 0.708624 isoform CRA_a OS =Rattus norvegicus GN = Hint2 PE = 4 SV = 1 Q5FVS1_RAT Ferritin (Fragment) OS =Rattus norvegicus GN = Fth1 4 3 14.1 26624.57 6.27 0 0.712 0.627018 0.193256 0.832876 0.374378 0.703969 0.299951 1.0883 0.755541 PE = 2 SV = 1 B2CZC8_RAT Glutamate receptor, metabotropic 5, isoform CRA_a 2 2 1.6 131884 8.07 6 0.107 1.01531 0.985972 1.90447 3.85E 05 0.831261 0.521499 1.38223 0.169928 OSRattus = norvegicus GN = Grm5 PE = 2 SV = 1 MPRIP_RAT Myosin phosphatase Rho-interacting protein OSRattus = 1 1 1.5 118134.1 6.05 0 0.941 0.520921 0.098599 0.564996 0.021115 0.702252 0.297469 0.48112 0.019585 norvegicusGN = Mprip PE = 2 SV = 1 Q5XI86_RAT Peptidyl-tRNA hydrolase 2 OS =Rattus norvegicus 1 1 8.3 19529.44 6.95 0 0.043 0.578987 0.144356 0.83143 0.370277 0.392995 0.045204 0.653078 0.117888 GN = Ptrh2 PE = 1 SV = 1 AIP_RAT AH receptor-interacting protein OS =Rattus norvegicus 1 1 4.6 37598.49 6.08 0 0.527 0.629349 0.195906 0.703732 0.116013 1.18789 0.678075 1.3816 0.170631 GN = Aip PE = 1 SV = 1 D3ZLK9_RAT ATP-dependent (S)-NAD(P)H-hydrate dehydratase 2 2 7.3 34961.73 8.11 0 0.028 0.60986 0.174554 1.11879 0.590782 0.542419 0.12393 1.06414 0.822653 OSRattus = norvegicus GN = Carkd PE = 3 SV = 1 OST48_RAT Dolichyl-diphosphooligosaccharide–protein 2 2 3.9 48895.09 5.62 2 0.003 0.626162 0.19229 1.16103 0.465326 0.811495 0.482396 1.45324 0.10336 glycosyltransferase 48 kDa subunit OS = Rattus norvegicus GN = Ddost PE = 2 SV = 1 THRB_RAT Prothrombin OS =Rattus norvegicus GN = F2 PE = 1 1 1 1.9 70411.04 6.28 0 0.54 0.71562 0.313381 3.04131 1.48E 20 2.88079 3.58E-07 14.2467 0 SV = 1 S4A4_RAT Isoform 2 of Electrogenic sodium bicarbonate cotransporter 15 5 5.7 116040.2 6.44 0 0.006 0.638323 0.206359 0.676671 0.086357 0.623266 0.197994 0.712432 0.194374 OSRattus = norvegicus GN = Slc4a4 IDHP_RAT Isocitrate dehydrogenase [NADP], mitochondrial 2 1 2.9 50966.71 8.88 0 0.408 0.562136 0.129657 0.601789 0.034754 0.969398 0.83223 0.957331 0.841162 OSRattus = norvegicus GN = Idh2 PE = 1 SV = 2 NUCB1_RAT Nucleobindin-1 OS =Rattus norvegicus GN = Nucb1 2 1 3.5 44373.13 5.09 0 1.031 0.478595 0.0732 0.737266 0.163237 0.638465 0.214952 0.816312 0.405249 PE = 4 SV = 1 D4A1C0_RAT Protein Cnnm1 OS =Rattus norvegicus GN = Cnnm1 2 1 1.1 103683 6.1 0 0.203 0.790632 0.447125 0.961706 0.836373 0.62046 0.194973 0.792874 0.3486 PE = 4 SV = 1 Q5BJU0_RAT Protein Rras2 (Fragment) OS =Rattus norvegicus 2 2 17.9 20388.88 5.33 0 0.672 0.790424 0.446713 0.848391 0.420127 0.735887 0.348568 0.902467 0.65542 GN = Rras2 PE = 2 SV = 1 F1LNW6_RAT Protein Ly6h (Fragment) OS =Rattus norvegicus 2 2 11.3 16834.43 8.68 0 0.246 0.688752 0.272659 0.668657 0.078859 0.663227 0.244778 0.702661 0.179748 GN = Ly6h PE = 2 SV = 1 D4A315_RAT Protein LOC680058 OS = Rattus norvegicus 3 2 11.5 17668.48 8.8 0 0.09 0.681697 0.262596 1.03692 0.869108 1.13923 0.778919 1.80333 0.00382 GN = LOC680058 PE = 4 SV = 1 F1M9V7_RAT Protein Npepps OS =Rattus norvegicus GN = Npepps 8 5 6.5 103343.2 5.53 0 0.199 0.562195 0.129706 0.893617 0.570807 0.810775 0.481003 0.791205 0.344768 PE = 2 SV = 1 H1UBM5_RAT Copine 6 protein OS =Rattus norvegicus GN = Cpne6 1 1 1.8 61188.6 5.5 0 0.304 0.671477 0.248477 1.54918 0.01249 0.774382 0.413493 1.7816 0.00489 PE = 2 SV = 1 RS27A_RAT Ubiquitin-40S ribosomal protein S27a OS =Rattus 13 6 46.8 17950.69 9.68 0 0.858 0.59449 0.158978 0.990021 0.95479 0.595094 0.169188 0.958207 0.844232 norvegicusGN = Rps27a PE = 1 SV = 2 CAH2_RAT Carbonic anhydrase 2 OS =Rattus norvegicus GN = Ca2 5 4 23.9 29113.45 6.89 0 0.526 0.656812 0.229159 0.83633 0.384288 0.605875 0.179816 1.23758 0.395191 PE = 1 SV = 2 B1WC61_RAT Acad9 protein OS =Rattus norvegicus GN = Acad9 PE = 2 6 5 8.0 68842.46 7.59 0 0.052 0.522388 0.099592 0.812732 0.319783 0.818978 0.49701 0.995195 0.975471 SV = 1 D3ZX38_RAT Prefoldin 1 (Predicted) OS =Rattus norvegicus GN = Pfdn1 1 1 8.2 14255.36 6.32 0 0.642 0.677156 0.256256 0.855317 0.441569 0.556331 0.134847 0.757291 0.272752 PE = 4 SV = 1 D4A772_RAT Protein Dtna OS =Rattus norvegicus GN = Dtna PE = 2 1 1 1.2 84168.5 6.45 0 0.506 0.787341 0.44065 0.884468 0.538371 0.663636 0.245293 0.938339 0.775254 SV = 1 GNAZ_RAT Guanine nucleotide-binding protein G(z) subunit alpha 7 4 14.9 40879.23 7.53 0 0.376 0.643399 0.212448 0.937056 0.736129 0.709172 0.307551 1.02641 0.929941 OS = Rattus norvegicus GN = Gnaz PE = 2 SV = 3 F1LM82_RAT Heterogeneous nuclear ribonucleoproteins A2/B1 (Fragment) 1 1 4.8 33778.61 9.16 0 0.91 0.858461 0.59194 1.624 0.004529 0.353287 0.033493 1.08984 0.751311 OS = Rattus norvegicus GN = Hnrnpa2b1 PE = 2 SV = 1 DYL1_RAT Dynein light chain 1, cytoplasmic OS = Rattus norvegicus 4 2 20.2 10365.77 6.89 0 0.448 0.59511 0.159584 0.758276 0.199463 0.779089 0.421894 0.956897 0.839641 GN = Dynll1 PE = 1 SV = 1 DYL2_RAT Dynein light chain 2, cytoplasmic OS = Rattus norvegicus 5 3 21.4 10349.73 6.81 0 0.456 0.619621 0.18502 0.830055 0.366403 0.736506 0.349559 1.06141 0.83033 GN = Dynll2 PE = 1 SV = 1 D3ZG43_RAT NADH dehydrogenase (Ubiquinone) Fe-S protein 3 7 6 15.2 30226.07 7.06 0 0.325 0.648918 0.219214 1.36226 0.099632 0.4353 0.061303 0.981837 0.927808 (Predicted), isoform CRA_c OS = Rattus norvegicus GN = Ndufs3 PE = 3 SV = 1 D4A3V2_RAT NADH dehydrogenase (Ubiquinone) 1 alpha subcomplex, 6 12 5 37.7 15223.58 10.15 0 0.54 0.624699 0.190646 1.26792 0.223632 0.701703 0.296679 1.35445 0.203322 (B14) (Predicted) OS = Rattus norvegicus GN = Ndufa6 PE = 4 SV = 1 LDHB_RAT L-lactate dehydrogenase B chain OS = Rattus norvegicus 10 8 20.7 36611.95 5.7 0 0.039 0.61726 0.182447 0.719296 0.136391 0.724024 0.329944 0.802682 0.371665 GN = Ldhb PE = 1 SV = 2 CSK21_RAT Casein kinase II subunit alpha OS = Rattus norvegicus 3 2 8.4 45072.94 7.29 0 0.452 0.560992 0.128702 1.28725 0.1919 0.434173 0.060819 1.13476 0.631901 GN = Csnk2a1 PE = 1 SV = 2 CYC_RAT Cytochrome c, somatic OS = Rattus norvegicus GN = Cycs 25 6 41.0 11605.31 9.61 0 0.757 0.631494 0.198369 1.30667 0.16349 0.720896 0.325142 1.53847 0.052809 PE = 1 SV = 2 220–292 (2015) 298 Neuroscience / al. et Han X. KCNA1_RAT Potassium voltage-gated channel subfamily A member 1 7 4 9.7 56378.75 5.04 4 0.067 0.626478 0.192646 0.900394 0.59542 0.653326 0.232521 0.918921 0.709508 OS = Rattus norvegicus GN = Kcna1 PE = 1 SV = 1 CALM_RAT Calmodulin OS = Rattus norvegicus GN = Calm1 PE = 1 12 6 32.2 16837.42 4.09 0 0.654 0.547091 0.117539 0.816822 0.330423 0.521163 0.108598 0.812106 0.394696 SV = 2 TIM9_RAT Mitochondrial import inner membrane translocase subunit 4 2 34.8 10375.83 6.71 0 0.582 0.593623 0.158131 0.884565 0.538709 0.575472 0.151063 0.865221 0.539787 Tim9 OS = Rattus norvegicus GN = Timm9 PE = 1 SV = 3 PI4KA_RAT Protein Pi4ka OS = Rattus norvegicus GN = Pi4ka PE = 2 2 2 1.0 231941.6 6.57 0 0.149 0.571896 0.138021 1.16621 0.451036 0.91031 0.692526 1.39165 0.159596 SV = 1 GSTM4_RAT Glutathione S-transferase Yb-3 OS = Rattus norvegicus 8 5 21.6 25680.4 6.84 0 0.399 0.57198 0.138096 0.90767 0.622371 0.699905 0.294101 1.01452 0.964125 GN = Gstm3 PE = 1 SV = 2 ATPK_RAT ATP synthase subunit f, mitochondrial OS = Rattus 1 1 14.8 10452.24 10.05 0 0.348 0.656617 0.228909 1.81412 0.000212 0.562779 0.140152 1.759 0.006284 norvegicus GN = Atp5j2 PE = 1 SV =GN 1 = Scai PE = 4 1 1 1.7 66647.21 6.7 0 0.451 0.726288 0.330606 1.05589 0.801644 0.524553 0.110938 0.877494 0.576748 F1M3P6_RAT ProteinSV = Scai1 OS = Rattus norvegicus GRM3_RAT Metabotropic glutamate receptor 3 OS = Rattus norvegicus 2 1 1.3 96502.6 8.16 6 0.016 0.545992 0.11669 0.863325 0.467122 0.580108 0.155206 0.852776 0.503562 GN = Grm3 PE = 3 SV = 1 ENPP6_RAT Ectonucleotide pyrophosphatase/phosphodiesterase family 2 1 2.3 50700.76 6.47 0 0.188 0.575202 0.140948 1.02766 0.902402 0.653268 0.23245 1.06337 0.824832 member 6 OS = Rattus norvegicus GN = Enpp6 PE = 2 SV = 1 F1LNT1_RAT Inositol 1,4,5-trisphosphate receptor type 1 OS = Rattus 3 3 1.6 310776.1 5.75 0 0.304 0.668794 0.244859 1.00455 0.986137 0.718673 0.321757 1.13636 0.627782 norvegicus GN = Itpr1 PE = 2 SV = 1 D4A441_RAT Uncharacterized protein OS = Rattus norvegicus PE = 4 10 3 9.3 37455.38 9.51 0 0.624808 0.190768 1.00313 0.991298 0.71731 0.319693 1.22262 0.42589 SV = 1 RL10_RAT 60S ribosomal protein L10 OS = Rattus norvegicus 3 2 10.3 24603.64 10.11 0 0.553 0.579803 0.145099 1.3234 0.141667 0.492198 0.090166 0.828408 0.43652 GN = Rpl10 PE = 1 SV = 3 PROF2_RAT Profilin-2 OS = Rattus norvegicus GN = Pfn2 PE = 1 8 5 28.6 15001.98 6.55 0 0.046 0.642651 0.211543 0.893578 0.570668 0.94407 0.771405 1.20816 0.456862 SV = 3 Q45QK6_RAT Guanine nucleotide-binding protein subunit gamma 15 2 62.8 5667.56 5.66 0 0.069 0.60734 0.171924 0.862772 0.465331 0.539399 0.121655 0.838529 0.463719 (Fragment) OS = Rattus norvegicus GN = Gng2 PE = 2 SV = 1 D3ZFY8_RAT Protein Tmem189 OS = Rattus norvegicus GN = Tmem189 2 1 6.8 16354.56 7.75 0 0.47 0.629351 0.195909 0.909335 0.628609 0.794517 0.450127 1.10463 0.711172 PE = 2 SV = 1 D3ZP34_RAT Protein Daam2 OS = Rattus norvegicus GN = Daam2 2 2 2.4 127330.5 6.19 0 0.495 0.948021 0.810325 1.01688 0.941378 0.706213 0.303213 0.962702 0.860024 PE = 4 SV = 1 PLMN_RAT Plasminogen OS = Rattus norvegicus GN = Plg PE = 2 1 1 1.1 90534.82 6.79 0 0.697 0.394336 0.038445 1.52146 0.017706 0.769194 0.404347 1.87659 0.001594 SV = 2 Q331S7_RAT Protein Dbndd2 OS = Rattus norvegicus GN = Dbndd2 1 1 12.0 17186.39 4.13 0 0.789 0.51788 0.096566 0.637467 0.054555 1.79916 0.035449 1.42996 0.122411 PE = 2 SV = 1

F1LQ75_RAT Protein Myo1g (Fragment) OS = Rattus norvegicus 1 1 1.3 117219.6 8.79 0 0.441 0.527874 0.103376 0.775734 0.233773 0.849294 0.558541 1.22961 0.411375 279 GN = Myo1g PE = 2 SV = 1 (continued on next page) 8 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 280 D3ZTN1_RAT Protein Tesc OS = Rattus norvegicus GN = Tesc PE = 4 1 1 7.5 24599.42 4.89 0 0.514 0.796221 0.458242 0.809394 0.311267 0.417347 0.053969 0.766892 0.29201 SV = 1 Q5U2P5_RAT Protein C2cd2l OS =Rattus norvegicus GN = C2cd2l 1 1 3.0 60529.46 6.45 1 0.436 0.834436 0.538267 0.825995 0.355114 0.437774 0.062375 0.791527 0.345506 PE = 2 SV = 1 RS13_RAT 40S ribosomal protein S13 OS =Rattus norvegicus 1 1 8.6 17222.08 10.53 0 0.454 0.483423 0.075795 0.891385 0.562808 0.53697 0.119848 0.943753 0.793899 GN = Rps13 PE = 1 SV = 2 F1M6C4_RAT Protein Arl15 (Fragment) OS =Rattus norvegicus 1 1 6.4 20942.69 5.84 0 0.279 0.624595 0.19053 0.987049 0.942266 0.735826 0.348471 1.38555 0.16623 GN = Arl15 PE = 4 SV = 1 B4F7C8_RAT Agpat5 protein OS =Rattus norvegicus GN = Agpat5 3 2 5.9 41530.99 9.47 1 0.154 0.395696 0.038868 0.817397 0.331939 0.981678 0.862111 0.870023 0.554108 PE = 2 SV = 1 ASGL1_RAT Isoaspartyl peptidase/L-asparaginase OS =Rattus 1 1 3.0 34410.03 8.04 0 0.095 0.616593 0.181725 1.07912 0.721067 0.512122 0.10255 0.927772 0.739242 norvegicusGN = Asrgl1 PE = 1 SV = 1 S100B_RAT Protein S100-B OS =Rattus norvegicus GN = S100b 1 1 16.3 10743.94 4.52 0 0.517 0.835142 0.539809 1.17921 0.416269 0.775317 0.415153 1.16621 0.553462 PE = 1 SV = 2 B0BNJ4_RAT Ethylmalonic encephalopathy 1 OS =Rattus norvegicus 3 2 13.4 27676.38 6.58 0 0.102 0.661053 0.234632 1.09327 0.673415 1.15112 0.753868 1.51999 0.061515 GN = Ethe1 PE = 2 SV = 1 KAD4_RAT Adenylate kinase isoenzyme 4, mitochondrial OS =Rattus 5 3 15.3 25202.61 7.8 0 0.318 0.55161 0.121082 0.739874 0.167443 1.00608 0.922025 1.08047 0.777121 norvegicusGN = Ak4 PE = 2 SV = 1 D3ZVW0_RAT Uncharacterized protein OS =Rattus norvegicus PE = 4 1 1 9.6 12794.62 8.93 0 0.23 0.526 0.102071 0.516408 0.010376 0.750585 0.372552 0.750655 0.259963 SV = 1 Q5U3Z7_RAT Serine hydroxymethyltransferase OS =Rattus norvegicus 2 2 4.4 55764.07 8.46 0 0.265 0.688204 0.271868 0.831942 0.371725 0.579454 0.154617 0.891014 0.618793 GN = Shmt2 PE = 2 SV = 1 ACBD6_RAT Acyl-CoA-binding domain-containing protein 6 OS =Rattus 1 1 3.6 30810.1 4.93 0 0.475 0.470641 0.069084 1.54067 0.013925 0.379079 0.040758 0.808311 0.385319 norvegicusGN = Acbd6 PE = 2 SV = 1 O70371_RAT Annexin (Fragment) OS =Rattus norvegicus GN = Anxa5 2 1 3.6 33965.11 4.99 0 0.322 0.594442 0.15893 0.582626 0.026924 0.672321 0.256429 0.726113 0.216292 PE = 2 SV = 1 A1L1J8_RAT Protein Rab5b OS =Rattus norvegicus GN = Rab5b 6 4 24.2 23674.5 8.29 0 0.39 0.554657 0.123517 0.745304 0.176462 0.59692 0.170953 0.791 0.3443 PE = 2 SV = 1 D4A786_RAT Protein LOC100364994 OS =Rattus norvegicus 4 2 27.6 6381.45 9.84 0 0.047 0.554392 0.123304 1.13631 0.536895 0.4303 0.059182 0.866496 0.543572 GN = LOC100362685 PE = 4 SV = 1 GBRA1_RAT Gamma-aminobutyric acid receptor subunit alpha-1 2 2 7.3 51753.08 9.34 4 0.234 0.55198 0.121375 0.729659 0.151423 0.606689 0.180638 0.616114 0.08375 OS =Rattus norvegicus GN = Gabra1 PE = 1 SV = 1 ACACA_RAT Acetyl-CoA carboxylase 1 OS =Rattus norvegicus 2 2 1.1 269874.1 6.03 0 0.236 0.66473 0.239451 0.900714 0.596593 0.488021 0.087729 0.743489 0.246623 GN = Acaca PE = 2 SV = 1 SYT1_RAT Synaptotagmin-1 OS =Rattus norvegicus GN = Syt1 19 13 26.6 47398.4 8.57 0 0.416 0.554625 0.123491 0.763698 0.209699 0.622957 0.19766 0.875118 0.569501 PE = 1 SV = 3 B5DFH0_RAT Downstream of Stk11 OS =Rattus norvegicus GN = Dos 1 1 2.3 45732.7 6.32 1 0.804 0.725602 0.329481 0.841352 0.398977 0.736058 0.348842 1.16387 0.559111 PE = 2 SV = 1 FUMH_RAT Fumarate hydratase, mitochondrial OS =Rattus norvegicus 6 4 8.7 54463.27 9.06 0 0.09 0.564674 0.131793 0.99233 0.964525 0.946753 0.77779 1.34954 0.209683 GN=FhPE=1SV=1 SPRY4_RAT SPRY domain-containing protein 4 OS =Rattus norvegicus 1 1 4.8 23249.38 9.39 0 0.233 0.631728 0.19864 0.666721 0.07713 1.00775 0.926154 1.40526 0.14551 GN = Spryd4 PE = 2 SV = 1 D3Z9I6_RAT Heterogeneous nuclear ribonucleoproteins 1 1 3.8 42435.16 5.24 0 0.446545 0.05776 1.4339 0.048503 0.440684 0.063656 1.13761 0.62459 methyltransferase-like 2 (S. cerevisiae), isoform CRA_b OSRattus = norvegicus GN = LOC100361025 PE = 4 SV = 1 KIF5A_RAT Kinesin heavy chain isoform 5A OS = Rattus norvegicus 1 1 1.2 116914.2 5.56 0 0.752 0.598834 0.163269 0.819985 0.338808 0.592435 0.16664 0.828242 0.43608 GN = Kif5a PE = 1 SV = 1 D3Z9Z0_RAT Protein Ank1 OS =Rattus norvegicus GN = Ank1 PE = 2 17 9 5.2 206716.5 6.1 0 0.376 0.575941 0.141608 0.850406 0.426302 0.710439 0.309421 0.954085 0.829802 SV = 1 GTR3_RAT Solute carrier family 2, facilitated glucose transporter member 1 1 1.8 53580.24 4.95 6 0.63 0.700305 0.289703 0.78685 0.257688 0.703609 0.299429 0.709716 0.190223 3OS=Rattus norvegicus GN = Slc2a3 PE = 1 SV = 1 F1M1J2_RAT Protein Neb (Fragment) OS = Rattus norvegicus GN = Neb 2 2 0.5 425878.9 9.13 0 0.816 0.515531 0.095018 0.920688 0.671853 0.635438 0.211494 1.00897 0.980095 PE = 2 SV = 1 TALDO_RAT Transaldolase OS =Rattus norvegicus GN = Taldo1 1 1 2.7 37459.64 6.57 0 0.275 0.571018 0.137253 1.02027 0.929108 0.715935 0.31762 1.3288 0.238176 PE = 1 SV = 2 LIN7C_RAT Protein lin-7 homolog C OS =Rattus norvegicus GN = Lin7c 4 2 11.7 21833.72 8.52 0 0.447 0.530699 0.105369 0.789032 0.262576 1.12023 0.819458 1.04965 0.863588 PE = 1 SV = 1 D3ZXF9_RAT Protein Mrpl12 OS =Rattus norvegicus GN = Mrpl12 1 1 4.0 29441.09 9.7 0 0.162 0.608301 0.172923 1.05322 0.811054 0.460091 0.072769 0.817777 0.408962 PE = 4 SV = 1 GNA11_RAT Guanine nucleotide-binding protein subunit alpha-11 9 2 5.0 42025.66 5.91 0 0.351 0.557125 0.125517 0.873073 0.499306 0.995737 0.896562 1.63897 0.021489 OSRattus = norvegicus GN = Gna11 PE = 2 SV = 1 TOM70_RAT Mitochondrial import receptor subunit TOM70 OS = Rattus 15 11 16.4 67444.26 7.44 0 0.498 0.525561 0.101767 0.953603 0.803038 0.606454 0.1804 0.967852 0.878187 norvegicus GN = Tomm70a PE = 1 SV = 1 CATD_RAT Cathepsin D OS = Rattus norvegicus GN = Ctsd PE = 1 5 3 9.8 44680.18 6.66 1 0.008 0.634634 0.202014 1.20136 0.360829 0.657579 0.237732 1.30685 0.271188 SV = 1 SV2B_RAT Synaptic vesicle glycoprotein 2B OS = Rattus norvegicus 7 4 5.1 77459.52 5.4 12 0.079 0.590104 0.154731 0.772392 0.226901 0.81009 0.47968 1.11694 0.678347 GN = Sv2b PE = 4 SV = 1 PRDX2_RAT Peroxiredoxin-2 OS = Rattus norvegicus GN = Prdx2 8 4 22.2 21783.41 5.34 0 0.164 0.487014 0.077773 0.845237 0.410571 0.783997 0.43076 1.08146 0.774378 PE = 1 SV = 3 Q4QQV4_RAT Dead end homolog 1 (Zebrafish) OS = Rattus norvegicus 2 2 4.9 57359.55 5.86 0 0.309 0.416308 0.045775 0.851497 0.429668 0.402199 0.048365 0.66055 0.125962 GN = Hars PE = 2 SV = 1 M0R6L3_RAT Uncharacterized protein OS = Rattus norvegicus 1 1 6.2 17163.85 10.6 0 1.135 0.9525 0.821821 1.16312 0.459548 0.570062 0.146336 1.47088 0.090553 GN = LOC100910721 PE = 3 SV = 1 MLEC_RAT Malectin OS = Rattus norvegicus GN = Mlec PE = 2 2 2 6.9 32417.71 5.38 1 0.22 0.529393 0.104444 0.771275 0.224636 0.697752 0.291034 0.976337 0.908248 SV = 1 GFAP_RAT Glial fibrillary acidic protein OS = Rattus norvegicus 23 11 24.8 49489.18 5.72 0 0.827 0.502006 0.086491 0.744642 0.175342 0.681655 0.268782 0.838217 0.462868 GN = Gfap PE = 3 SV = 1 ADA17_RAT Disintegrin and metalloproteinase domain-containing protein 1 1 1.2 73637.38 5.89 1 0.532 0.509367 0.091052 0.894981 0.575723 0.46593 0.07571 0.61715 0.084584 17 OS = Rattus norvegicus GN = Adam17 PE = 2 SV = 1 D4A7Y1_RAT Aggrecan core protein OS = Rattus norvegicus GN = Acan 2 2 1.0 223896 4.16 0 0.377 0.506556 0.089288 0.553736 0.018006 0.580784 0.155817 0.553109 0.044258 PE = 2 SV = 1 220–292 (2015) 298 Neuroscience / al. et Han X. D3ZIE9_RAT Protein Aldh18a1 OS = Rattus norvegicus GN = Aldh18a1 1 1 1.4 87328.41 7.2 0 0.09 0.633584 0.20079 0.737252 0.163214 0.511914 0.102413 0.772214 0.303067 PE = 4 SV = 1 PHYIP_RAT Phytanoyl-CoA hydroxylase-interacting protein OS = Rattus 2 2 6.4 37554.15 6.53 0 0.382 0.523745 0.100517 0.619142 0.043448 0.656172 0.235998 0.844948 0.481449 norvegicus GN = Phyhip PE = 2 SV = 1 D3ZUZ4_RAT Protein Fam20b OS = Rattus norvegicus GN = Fam20b 1 1 2.9 46568.11 6.47 0 0.219 0.524147 0.100793 0.802337 0.293756 0.708256 0.306203 1.13107 0.641392 PE = 4 SV = 1 RAB15_RAT Ras-related protein Rab-15 OS = Rattus norvegicus 6 2 9.9 24283.15 5.36 0 0.534 0.576707 0.142295 0.805527 0.301588 1.20478 0.644256 2.17955 2.13E05 GN = Rab15 PE = 2 SV = 1 PPID_RAT Peptidyl-prolyl cis-trans isomerase D OS = Rattus 2 2 4.9 40765.22 6.73 0 0.421 0.41661 0.045884 0.851746 0.430437 0.636291 0.212464 0.86062 0.526243 norvegicus GN = Ppid PE = 1 SV = 3 2 2 14.4 23890.31 9.03 0 0.407 0.578019 0.143478 0.839137 0.392456 0.595871 0.169937 0.81554 0.403298 Q5U1W6_RAT ProteinSV = 1 Apool OS = Rattus norvegicus GN = Apool PE = 2 SGTA_RAT Small glutamine-rich tetratricopeptide repeat-containing 1 1 4.1 34284.92 5.05 0 0.5 0.486695 0.077596 1.01776 0.938199 0.713581 0.314091 1.54994 0.047941 protein alpha OS = Rattus norvegicus GN = Sgta PE = 2 SV = 1 OCAD1_RAT OCIA domain-containing protein 1 OS = Rattus norvegicus 1 1 3.2 27658.77 6.97 0 0.753 0.572082 0.138185 0.938663 0.742549 0.555162 0.133902 0.98551 0.940894 GN = Ociad1 PE = 2 SV = 1 BPNT1_RAT 3’(2’),5’-bisphosphate nucleotidase 1 (Fragment) 2 1 6.0 28968.76 5.59 0 0.052 0.720132 0.320593 1.04534 0.838999 0.355432 0.034052 0.645983 0.110602 OS = Rattus norvegicus GN = Bpnt1 PE = 2 SV = 1 SAP_RAT Sulfated glycoprotein 1 OS = Rattus norvegicus GN = Psap 6 3 5.8 61123.4 5.13 0 0.034 0.526148 0.102174 1.06383 0.773811 0.574728 0.150407 1.15111 0.590516 PE = 1 SV = 1 ARPC2_RAT Actin related protein 2/3 complex, subunit 2 (Predicted), 4 4 10.0 34346.63 6.84 0 0.44 0.499616 0.085051 0.766597 0.215326 0.684022 0.271979 0.945878 0.801251 isoform CRA_a OS = Rattus norvegicus GN = Arpc2 PE = 4 SV = 1 MFR1L_RAT Mitochondrial fission regulator 1-like OS = Rattus norvegicus 2 1 4.2 31729.8 5.77 0 0.289 0.503946 0.087675 0.948447 0.782007 0.422642 0.056052 0.827728 0.434724 GN = Mtfr1l PE = 2 SV = 1 Q6P9W6_RAT Rab3b protein OS = Rattus norvegicus GN = Rab3b PE = 2 10 3 14.9 25913.9 5.03 0 0.346 0.532013 0.106305 0.678564 0.08821 0.694299 0.286159 0.885759 0.60229 SV = 1 LPHN3_RAT Isoform 4 of Latrophilin-3 OS = Rattus norvegicus 1 1 0.7 144890.6 7.32 0 0.199 0.665002 0.239811 0.896943 0.582825 0.670561 0.254144 1.0824 0.771773 GN = Lphn3 F1LZ53_RAT Protein Exoc6b (Fragment) OS = Rattus norvegicus 1 1 15.0 9470.79 9.61 0 0.483 0.984861 0.905878 0.737812 0.16411 0.562374 0.139815 0.693617 0.166955 GN = Exoc6b PE = 4 SV = 1 PITM1_RAT Membrane-associated phosphatidylinositol transfer protein 1 3 2 2.6 134982.4 5.64 0 0.306 0.647866 0.217913 0.876333 0.510328 0.616964 0.191257 1.3493 0.209998 OS = Rattus norvegicus GN = Pitpnm1 PE = 2 SV = 1 GLSK_RAT Glutaminase kidney isoform, mitochondrial OS = Rattus 21 12 23.2 74022.9 8.06 0 0.29 0.51301 0.09338 0.791389 0.267926 0.564937 0.141964 0.899846 0.646963 norvegicus GN = Gls PE = 1 SV = 2 PCCB_RAT Propionyl-CoA carboxylase beta chain, mitochondrial 4 2 4.6 54981.3 8.26 0 0.022 0.553039 0.122219 0.827511 0.359304 0.502927 0.096676 0.915344 0.697613 OS = Rattus norvegicus GN = Pccb PE = 2 SV = 1 C9WPN2_RAT DEAD (Asp-Glu-Ala-Asp) box polypeptide 3 Y-linked 4 3 6.8 73005.64 6.67 0 0.666 0.396328 0.039065 0.766073 0.214301 0.608784 0.182766 1.10313 0.715195 281 OS = Rattus norvegicus GN = Ddx3y PE = 2 SV = 1 (continued on next page) 8 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 282

PAFA2_RAT Platelet-activating factor acetylhydrolase 2, cytoplasmic 1 1 2.6 43491.42 6.23 0 0.074 1.01355 0.981305 1.33921 0.123158 0.715999 0.317717 0.575948 0.056223 OS = Rattus norvegicus GN = Pafah2 PE = 1 SV = 2 F1LP82_RAT Ras-related protein Rab-2A OS =Rattus norvegicus 26 7 36.8 23517.23 6.08 0 0.46 0.479803 0.073842 0.673094 0.082942 0.781519 0.426271 1.29679 0.287331 GN = Rab2a PE = 2 SV = 1 Q924Y3_RAT Claudin 11 (Fragment) OS =Rattus norvegicus 4 2 14.4 12040.45 8.62 4 0.777 0.468573 0.068045 0.331074 0.000394 0.508366 0.100117 0.377782 0.005154 GN = Cldn11 PE = 2 SV = 1 G3V7I0_RAT Peroxiredoxin 3 OS = Rattus norvegicus GN = Prdx3 4 3 12.8 28299.03 7.14 0 0.03 0.410954 0.043888 0.831115 0.369387 0.864756 0.591289 1.24765 0.375297 PE = 4 SV = 1 D3ZT36_RAT Protein Adam23 OS =Rattus norvegicus GN = Adam23 4 3 6.0 91608.62 6.95 0 0.469 0.431641 0.051561 0.50061 0.008129 0.620363 0.19487 0.846185 0.484907 PE = 2 SV = 1 Q566E4_RAT Heterogeneous nuclear ribonucleoprotein R OS =Rattus 1 1 1.7 70873.17 8.23 0 0.934 0.415975 0.045656 0.649557 0.063109 0.406139 0.049773 0.69643 0.170858 norvegicusGN = Hnrnpr PE = 2 SV = 1 D3ZYM7_RAT Protein LOC100363003 OS =Rattus norvegicus 1 1 7.7 10816.37 10.06 0 0.664 0.501281 0.086052 1.03917 0.861048 0.543687 0.124896 1.21552 0.440942 GN = Lyrm4 PE = 4 SV = 1 Q99PW9_RAT Huntingtin interacting protein 1 related (Fragment) 1 1 0.7 120570.3 6.12 0 0.561 0.567451 0.134161 0.772592 0.227307 0.402423 0.048444 0.515183 0.029141 OSRattus = norvegicus GN = Hip1r PE = 2 SV = 1 MK10_RAT Mitogen-activated protein kinase 10 OS =Rattus norvegicus 1 1 3.2 52529.78 6.37 0 0.294 0.423933 0.048581 0.874218 0.503163 0.479742 0.083056 0.664381 0.130266 GN = Mapk10 PE = 1 SV = 2 O35357_RAT Guanine nucleotide-binding protein subunit gamma 3 1 47.2 3992.52 5.56 0 0.103 0.421709 0.047748 0.48117 0.005968 0.597945 0.171951 0.600611 0.072051 (Fragment) OS =Rattus norvegicus GN = Gng4 PE = 2 SV = 1 VDAC3_RAT Isoform 2 of Voltage-dependent anion-selective channel 27 13 44.7 30928.66 8.91 0 0.289 0.50663 0.089334 0.911423 0.636474 0.556573 0.135044 1.06081 0.83203 protein 3 OS =Rattus norvegicus GN = Vdac3 R4RL2_RAT Reticulon-4 receptor-like 2 OS =Rattus norvegicus 1 1 1.9 46183.08 7.59 0 0.204 0.580583 0.145812 0.82318 0.347417 0.554828 0.133633 0.960006 0.850544 GN = Rtn4rl2 PE = 2 SV = 1 KCNC2_RAT Potassium voltage-gated channel subfamily C member 2 1 1 1.1 70189.87 7.83 6 0.099 0.516757 0.095823 0.656828 0.068767 0.59837 0.172366 0.79674 0.357581 OSRattus = norvegicus GN = Kcnc2 PE = 1 SV = 1 NEB1_RAT Neurabin-1 OS =Rattus norvegicus GN = Ppp1r9a PE = 1 1 1 0.9 122733.9 5.05 0 1.011 0.509173 0.09093 1.0122 0.958346 0.446729 0.066388 0.799854 0.36492 SV = 1 Q6P9U5_RAT Ribosomal protein L9 OS =Rattus norvegicus GN = Rpl9 1 1 5.2 21921.19 10 0 0.37 0.474198 0.0709 0.881134 0.526785 0.519207 0.107266 1.14939 0.594806 PE = 2 SV = 1 B5DEP0_RAT Dguok protein OS =Rattus norvegicus GN = Dguok PE = 2 1 1 4.4 21469.18 5.65 0 0.436 0.533351 0.107267 1.02475 0.912913 0.513674 0.103569 1.05805 0.839803 SV = 1 MOSC2_RAT MOSC domain-containing protein 2, mitochondrial 3 2 4.1 38248.09 8.95 1 0.21 0.581289 0.146459 0.964422 0.847615 0.62255 0.19722 1.33867 0.2243 OSRattus = norvegicus GN = Marc2 PE = 2 SV = 1 PSA6_RAT Proteasome subunit alpha type-6 OS =Rattus norvegicus 1 1 3.7 27399.16 6.35 0 0.178 0.589247 0.153912 0.924496 0.686618 0.767756 0.401833 1.53888 0.052628 GN = Psma6 PE = 1 SV = 1 LRRT1_RAT Leucine-rich repeat transmembrane neuronal protein 1 1 1 1.5 58731.07 6.65 0 0.021 0.513686 0.093817 0.79079 0.26656 0.474997 0.08047 1.0031 0.997007 OSRattus = norvegicus GN = Lrrtm1 PE = 3 SV = 1 A1L1L6_RAT Mitochondrial Rho GTPase OS =Rattus norvegicus 5 5 8.0 80693.78 6.57 1 0.276 0.435214 0.052994 0.863621 0.468083 0.819039 0.497129 1.07499 0.792317 GN = Rhot1 PE = 2 SV = 1 RLA2_RAT 60S acidic ribosomal protein P2 OS =Rattus norvegicus 2 2 20.9 11691.82 4.44 0 0.263 0.411142 0.043954 0.769667 0.221405 0.356717 0.03439 0.687402 0.158568 GN = Rplp2 PE = 1 SV = 2 G3V7L6_RAT 26S protease regulatory subunit 7 OS =Rattus norvegicus 1 1 3.2 48633.3 5.71 0 0.416 0.45868 0.063253 0.79538 0.277156 0.527315 0.112873 0.931713 0.752611 GN = Psmc2 PE = 3 SV = 1 D3ZZ32_RAT Prolyl endopeptidase-like OS =Rattus norvegicus 1 1 1.2 83338.33 5.84 0 0.467 0.368104 0.031023 0.754226 0.192058 0.332795 0.028539 0.662629 0.128283 GN = Prepl PE = 2 SV = 1 Q4G022_RAT Asna1 protein (Fragment) OS =Rattus norvegicus 3 1 2.7 36946.44 5.02 0 0.111 0.50337 0.087322 0.869083 0.485992 0.294263 0.020915 0.731683 0.225709 GN = Asna1 PE = 2 SV = 1 RL10A_RAT 60S ribosomal protein L10a OS =Rattus norvegicus 2 2 13.4 24831.02 9.94 0 0.408 0.45774 0.062813 0.89879 0.589551 0.691838 0.282719 1.32138 0.249002 GN = Rpl10a PE = 1 SV = 2 IVD_RAT Isovaleryl-CoA dehydrogenase, mitochondrial OS =Rattus 4 3 10.4 46434.95 8.03 0 0.113 0.444727 0.056972 0.996148 0.980638 0.589234 0.163612 1.46927 0.091672 norvegicusGN = Ivd PE = 1 SV = 2 LACB2_RAT Beta-lactamase-like protein 2 OS =Rattus norvegicus 1 1 3.8 32483.76 5.9 0 0.315 0.625434 0.19147 1.0098 0.96706 0.652646 0.231696 1.10083 0.721425 GN = Lactb2 PE = 2 SV = 1 F1LSL8_RAT Protein Sptbn4 OS =Rattus norvegicus GN = Sptbn4 3 3 1.4 288312 5.73 0 0.593 0.35701 0.028275 0.551284 0.017384 0.550461 0.130153 0.628846 0.094469 PE = 2 SV = 1 F1LUA1_RAT Protein Eea1 (Fragment) OS =Rattus norvegicus 1 1 1.4 97195.36 5.29 0 1.01 0.635947 0.203553 0.879547 0.521313 0.508506 0.100207 1.25729 0.35684 GN = Eea1 PE = 2 SV = 1 B1WBY5_RAT DnaJ (Hsp40) homolog, subfamily C, member 11 2 2 5.4 63204.32 8.5 0 0.403 0.809432 0.485128 0.814454 0.324236 1.15405 0.747725 1.43403 0.118896 OS = Rattus norvegicus GN = Dnajc11 PE = 2 SV = 1 F1LN88_RAT Aldehyde dehydrogenase, mitochondrial OS = Rattus 7 5 9.3 56310.47 6.99 0 0.14 0.461481 0.064581 0.924136 0.685216 0.425625 0.057254 1.20217 0.470032 norvegicus GN = Aldh2 PE = 2 SV = 1 PRDX6_RAT Peroxiredoxin-6 OS = Rattus norvegicus GN = Prdx6 3 3 16.5 24818.28 5.64 0 0.215 0.469145 0.068331 1.62084 0.004737 0.643402 0.220679 0.729614 0.222177 PE = 1 SV = 3 NCPR_RAT NADPH–cytochrome P450 reductase OS = Rattus 1 1 1.3 76961.98 5.3 1 0.433 0.415112 0.045348 1.24565 0.264638 0.495034 0.091852 1.56531 0.042018 norvegicus GN = Por PE = 1 SV = 3 CREL1_RAT Cysteine-rich with EGF-like domain protein 1 OS = Rattus 2 1 2.6 45696.47 4.94 2 0.214 0.974729 0.879401 0.912639 0.641074 0.893367 0.654101 0.918798 0.709099 norvegicus GN = Creld1 PE = 2 SV = 1 F210A_RAT Protein FAM210A OS = Rattus norvegicus GN = Fam210a 1 1 5.5 31473.98 9.82 1 0.541 0.51702 0.095997 1.10246 0.64314 0.492495 0.090341 1.21841 0.434781 PE = 2 SV = 1 GLRX2_RAT Glutaredoxin-2, mitochondrial OS = Rattus norvegicus 1 1 7.6 17274.67 9.69 0 0.232 0.490234 0.079583 0.889123 0.554757 0.811993 0.483363 2.04215 0.000174 GN = Glrx2 PE = 2 SV = 2 B5DEP1_RAT Pdcd6 protein OS = Rattus norvegicus GN = Pdcd6 PE = 2 1 1 5.8 21700.03 5.36 0 0.435 0.529339 0.104406 0.679117 0.088757 0.550719 0.130357 1.05076 0.860442 SV = 1 G3V7J7_RAT Eukaryotic translation initiation factor 5A2 (Predicted) 2 1 7.8 16793.04 5.38 0 0.351 0.605136 0.169649 0.490147 0.006892 0.386981 0.043235 0.637147 0.102031 OS = Rattus norvegicus GN = Eif5a2 PE = 4 SV = 1 VATF_RAT V-type proton ATPase subunit F OS = Rattus norvegicus 1 1 6.7 13370.11 5.52 0 0.258 0.559931 0.127822 0.672554 0.082436 0.417466 0.054015 0.712015 0.193732 GN = Atp6v1f PE = 1 SV = 1 220–292 (2015) 298 Neuroscience / al. et Han X. D4ABK1_RAT Protein Syngr3 OS = Rattus norvegicus GN = Syngr3 1 1 9.6 21369.36 9.4 0 0.464 0.388065 0.036545 0.434951 0.002752 0.261073 0.015838 0.323844 0.002374 PE = 4 SV = 1 D3ZP44_RAT Protein Slitrk6 OS = Rattus norvegicus GN = Slitrk6 PE = 4 1 1 1.2 94661.24 6.04 0 0.173 0.504559 0.088052 0.963055 0.841953 0.294368 0.020933 0.671419 0.138468 SV = 1 B0BNK1_RAT Protein Rab5c OS = Rattus norvegicus GN = Rab5c PE = 2 5 3 15.1 25178.31 8.24 0 0.309 0.352696 0.027264 0.59191 0.030503 0.770283 0.406256 1.27747 0.320094 SV = 1 ACLY_RAT ATP-citrate synthase OS = Rattus norvegicus GN = Acly 2 2 1.7 120634.6 6.96 0 0.098 0.492757 0.081024 1.18493 0.401492 0.488245 0.087859 1.1413 0.615198 PE = 1 SV = 1 TCTP_RAT Translationally-controlled tumor protein OS = Rattus 2 1 8.1 19461.97 4.76 0 0.361 0.409175 0.043276 0.674126 0.083916 0.283538 0.019138 0.588159 0.063655 GBB3_RAT Guaninenorvegicus nucleotide-bindingGN = Tpt1 PE = protein 1 SV =G(I)/G(S)/G(T) 1 subunit 9 3 8.5 37179.75 5.51 0 0.077 0.342908 0.025087 0.587079 0.028593 0.538834 0.121232 0.785498 0.331869 beta-3 OS = Rattus norvegicus GN = Gnb3 PE = 1 SV = 1 Q6P7A8_RAT SPARC-like 1 (Hevin) OS = Rattus norvegicus 2 2 4.3 70610.9 4.56 0 1.061 0.981203 0.896304 1.58288 0.008015 0.464977 0.075224 1.1957 0.484514 GN = Sparcl1 PE = 2 SV = 1 AMPH_RAT Amphiphysin OS = Rattus norvegicus GN = Amph PE = 1 1 1 1.6 74876.95 4.57 0 0.678 0.319219 0.02043 0.620549 0.044227 0.325115 0.026853 0.596624 0.069269 SV = 1 SYDC_RAT Aspartate–tRNA ligase, cytoplasmic OS = Rattus norvegicus 1 1 2.0 57125.57 6.02 0 0.395 0.379367 0.034044 0.333851 0.000417 1.09073 0.883304 1.16494 0.556522 GN = Dars PE = 2 SV = 1 D4A164_RAT Protein Nebl OS = Rattus norvegicus GN = Nebl PE = 4 2 2 1.8 116172.6 8.19 0 1.026 0.38609 0.035964 0.3806 0.001032 0.941996 0.766481 0.876767 0.574525 SV = 1 D4A376_RAT Ras-related protein Rab-12 OS = Rattus norvegicus 2 2 21.4 16143.51 9.86 0 0.477 0.632731 0.1998 0.488488 0.006712 0.502376 0.096333 0.469181 0.016954 GN = Rab12 PE = 2 SV = 1 AP2S1_RAT AP-2 complex subunit sigma OS = Rattus norvegicus 1 1 5.6 17017.5 5.82 0 0.052 0.338802 0.024219 0.519931 0.010947 0.406995 0.050084 0.592541 0.066513 GN = Ap2s1 PE = 2 SV = 1 DLRB1_RAT Dynein light chain roadblock-type 1 (Fragment) OS = Rattus 1 1 20.4 11956.74 9.35 0 0.392 0.786587 0.439173 0.994384 0.97319 0.210357 0.010164 0.921888 0.719428 norvegicus GN = Dynlrb1 PE = 4 SV = 1 CNRP1_RAT CB1 cannabinoid receptor-interacting protein 1 OS = Rattus 3 2 15.9 18987.71 9.45 0 0.341 0.373902 0.032548 0.633966 0.052267 0.386928 0.043218 0.912202 0.687225 norvegicus GN = Cnrip1 PE = 2 SV = 1 F1LN92_RAT Protein Afg3l2 OS = Rattus norvegicus GN = Afg3l2 PE = 2 6 4 5.5 89350.45 8.77 0 0.359 0.439416 0.054722 0.867479 0.480694 0.457607 0.071546 0.592553 0.06652 SV = 1 Q7TP78_RAT Aa2-258 OS = Rattus norvegicus GN = Ndufa8 PE = 2 5 4 20.1 21966.06 8.39 0 0.581 0.348857 0.026392 0.825086 0.352616 0.358642 0.034903 1.01713 0.956601 SV = 1 NMDE1_RAT Glutamate receptor ionotropic, NMDA 2A OS = Rattus 2 2 2.0 165466.7 6.59 4 0.403 0.345537 0.025656 0.598308 0.033202 0.523543 0.110236 0.764273 0.286668 norvegicus GN = Grin2a PE = 1 SV = 2 PPIB_RAT Peptidyl-prolyl cis-trans isomerase B OS = Rattus norvegicus 6 4 19.0 23802.3 9.5 1 0.202 0.338857 0.024231 0.608568 0.037956 0.368401 0.037602 1.10276 0.716197 GN = Ppib PE = 2 SV = 3 VP33B_RAT Vacuolar protein sorting-associated protein 33B OS = Rattus 1 1 1.5 70692.66 6.43 0 0.244 0.483251 0.075701 0.880798 0.525624 0.405824 0.049659 1.08929 0.75283 norvegicus GN = Vps33b PE = 2 SV = 1 G3V8C3_RAT Vimentin OS = Rattus norvegicus GN = Vim PE = 3 3 2 3.4 53700.03 5.06 0 0.839 0.33738 0.023925 0.5967 0.032505 0.32481 0.026787 0.67227 0.139486 283 SV = 1 (continued on next page) 8 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 284

SYTM_RAT Threonine–tRNA ligase, mitochondrial OS = Rattus 2 2 3.2 81542.13 8.24 0 0.318 0.266841 0.012721 1.69424 0.001585 0.324403 0.026701 1.74609 0.007231 norvegicusGN = Tars2 PE = 2 SV = 1 ANXA6_RAT Annexin A6 OS =Rattus norvegicus GN = Anxa6 PE = 1 2 2 2.2 75753.3 5.39 0 0.432 0.236683 0.009565 0.862219 0.463545 0.312902 0.024348 1.07717 0.786269 SV = 2 CX7A2_RAT Cytochrome c oxidase subunit 7A2, mitochondrial 9 2 18.1 9352.87 10.28 1 0.258 0.308413 0.018569 0.634825 0.052821 0.205817 0.009757 0.550054 0.042834 OSRattus = norvegicus GN = Cox7a2 PE = 1 SV = 1 Q4V8I9_RAT Protein Ugp2 (Fragment) OS =Rattus norvegicus 2 2 5.4 56220.79 7.8 0 0.289 0.924983 0.751887 0.87877 0.518648 0.653286 0.232472 1.07042 0.805067 GN = Ugp2 PE = 2 SV = 1 PP1A_RAT Serine/threonine-protein phosphatase PP1-alpha catalytic 6 4 13.3 37511.67 5.94 0 0.301 0.329001 0.022253 0.688096 0.098031 0.543782 0.124969 0.702694 0.179797 subunit OS =Rattus norvegicus GN = Ppp1ca PE = 1 SV = 1 SYRC_RAT Arginine–tRNA ligase, cytoplasmic OS =Rattus norvegicus 1 1 1.5 75809.54 6.65 0 0.336 0.606814 0.171379 0.945604 0.770479 0.326968 0.027251 1.05016 0.862141 GN = Rars PE = 1 SV = 2 RM37_RAT 39S ribosomal protein L37, mitochondrial OS =Rattus 1 1 2.1 48365.34 9.08 0 0.326 0.394579 0.03852 0.956365 0.814364 0.406934 0.050061 1.60725 0.028905 norvegicusGN = Mrpl37 PE = 2 SV = 1 D3Z912_RAT Uncharacterized protein OS =Rattus norvegicus PE = 4 2 2 8.5 38831.88 6.99 0 0.368 0.324958 0.021483 0.52217 0.011324 0.446988 0.066507 1.38428 0.167637 SV = 1 NLTP_RAT Non-specific lipid-transfer protein OS =Rattus norvegicus 2 2 2.6 58812.68 6.62 0 0.222 0.272637 0.013424 0.70968 0.123499 0.296006 0.021217 0.831101 0.443664 GN = Scp2 PE = 1 SV = 3 OTUB1_RAT Ubiquitin thioesterase OTUB1 OS =Rattus norvegicus 5 3 7.8 31269.66 4.85 0 0.553 0.405167 0.041923 0.77562 0.233535 0.388892 0.043853 0.922038 0.719933 GN = Otub1 PE = 1 SV = 1 F1M027_RAT Chn3 OS =Rattus norvegicus GN = Chn3 PE = 2 SV = 1 1 1 4.0 46401.41 6 0 0.466 1.47602 0.244925 0.645228 0.059927 0.273119 0.017539 0.311065 0.00196 SYJ2B_RAT Synaptojanin-2-binding protein OS =Rattus norvegicus 2 1 8.3 15824.72 6.27 1 0.137 0.299718 0.017181 0.776883 0.23617 0.237574 0.012932 0.738629 0.237854 GN = Synj2bp PE = 1 SV = 2 TMEDA_RAT Transmembrane emp24 domain-containing protein 10 2 2 7.8 24857.45 6.01 2 0.127 0.412416 0.044397 1.04983 0.823046 0.685581 0.274098 1.81596 0.003301 OSRattus = norvegicus GN = Tmed10 PE = 1 SV = 2 DCAKD_RAT Dephospho-CoA kinase domain-containing protein 1 1 5.4 27351.8 9.7 1 0.113 0.261169 0.012065 1.47373 0.031216 0.224625 0.011541 1.43698 0.116392 OSRattus = norvegicus GN = Dcakd PE = 2 SV = 1 SAC1_RAT Phosphatidylinositide phosphatase SAC1 OS =Rattus 1 1 1.4 67038.14 6.83 2 0.136 0.216878 0.007893 0.700124 0.111649 0.195124 0.008857 0.566685 0.05108 norvegicusGN = Sacm1l PE = 1 SV = 1 Q6PCT9_RAT Proteasome (Prosome, macropain) 26S subunit, non- 2 1 2.3 45597.94 5.38 0 0.365 0.711698 0.3072 0.867127 0.479535 0.503909 0.09729 0.945187 0.798859 ATPase, 6 OS =Rattus norvegicus GN = Psmd6 PE = 2 SV = 1 B2RYF6_RAT Cleft lip and palate associated transmembrane protein 1 2 1 2.4 75275.63 5.65 5 0.159 0.255814 0.011474 0.475471 0.005441 0.307059 0.023222 0.357511 0.003876 OSRattus = norvegicus GN = Clptm1 PE = 2 SV = 1 B2GUZ9_RAT Fam49b protein OS =Rattus norvegicus GN = Fam49b 1 1 5.6 36775.57 5.76 0 0.384 0.387602 0.036408 1.07154 0.747081 0.169865 0.007017 0.979417 0.919196 PE = 2 SV = 1 PRDX4_RAT Peroxiredoxin-4 OS =Rattus norvegicus GN = Prdx4 3 2 9.9 31007.08 6.18 0 0.249 0.313034 0.019346 0.857395 0.448122 0.271538 0.017307 1.00367 0.995354 PE = 2 SV = 1 D4A1W2_RAT Uncharacterized protein OS =Rattus norvegicus PE = 2 1 1 1.4 47712.98 7.96 0 0.783 0.230451 0.009008 0.788523 0.261431 0.213777 0.01048 0.870947 0.556883 SV = 1 D3ZBB7_RAT Ubiquitin carboxyl-terminal hydrolase OS =Rattus 1 1 0.8 161919.3 5.95 0 0.5 0.309157 0.018692 0.313375 0.000275 0.209405 0.010077 0.739074 0.238649 norvegicusGN = Usp32 PE = 3 SV = 1 BI2L1_RAT Brain-specific angiogenesis inhibitor 1-associated protein 2- 1 1 1.7 57467.76 8.95 0 0.627 0.496984 0.083487 0.605733 0.036587 0.92838 0.734395 1.92957 0.000813 like protein 1 OS =Rattus norvegicus GN = Baiap2l1 PE = 2 SV = 1 2ABA_RAT Serine/threonine-protein phosphatase 2A 55 kDa regulatory 1 1 2.5 51677.47 5.82 0 0.611 0.469163 0.06834 0.419957 0.002116 0.11035 0.003965 0.323227 0.002353 subunit B alpha isoform OS =Rattus norvegicus GN = Ppp2r2a PE = 2 SV = 1 Appendix Table 3a. Differentially expressed membrane proteins (74 proteins) identified from the susceptible and unsusceptible groups through iTRAQ-based quantitative proteomics. MW, molecular weight; pI, isoelectric point; TMDs, transmembrane domains; GRAVY, grand average hydropathicity

Accession Protein name Gene Unique % MW (Da) pI TMDs GRAVY Susceptible 113/115 Susceptible 116/118 Unsusceptible 114/ Unsusceptible 117/118 Membrane Synaptic localization number name peptides Sequence 115 localization coverage Ratio p-Value Ratio p-Value Ratio p-value Ratio p-Value Presynaptic Presynaptic Synaptic Postsynaptic proteins active zone vesicles density

CX6C2_RAT Cytochrome c oxidase subunit 6C- Cox6c2 2 27.6 8454.83 10.07 1 0.108 1.7896 0.049595 1.94724 0.012 Membrane 2 p DNJA2_RAT DnaJ homolog subfamily A Dnaja2 2 5.6 45765.11 6.06 0 0.695 0.416241 0.045752 0.570725 0.14691 0.83019 0.366774 0.511518 0.027949 Membrane member 2 TMEDA_RAT Transmembrane emp24 domain- Tmed10 2 7.8 24857.45 6.01 2 0.127 0.412416 0.044397 0.685581 0.274098 Membrane containing protein 10 p G3V7Y3_RAT ATP synthase subunit delta, Atp5d 3 16.7 17562.79 5.16 0 0.211 1.81525 0.042467 2.16807 0.001796 Membrane mitochondrial pp p UN13A_RAT Isoform 3 of Protein unc-13 Unc13a 2 1.8 194360.9 5.15 0 0.554 1.81562 0.042369 2.07493 0.004173 Membrane homolog A p CNKR2_RAT Connector enhancer of kinase Cnksr2 2 2.8 109695.9 6.09 0 0.728 1.82396 0.040251 1.49871 0.202854 Membrane suppressor of ras 2 SC11A_RAT Signal peptidase complex catalytic Sec11a 2 10.6 20598.99 9.15 2 0.119 1.8394 0.036565 1.33804 0.40668 Membrane subunit SEC11A p

D3ZT16_RAT Protein Map6d1 Map6d1 2 15.7 20412.55 9.94 0 0.516 1.84475 0.035356 1.67856 0.076706 Membrane 220–292 (2015) 298 Neuroscience / al. et Han X. pp PACN1_RAT Protein kinase C and casein Pacsin1 7 21.5 50448.57 5.15 0 1.02 1.8529 0.033581 1.24948 0.558424 Membrane kinase substrate in neurons protein 1 p Q99P36_RAT Protein Syt7 Syt7 2 6.9 58160.81 9.35 0 0.532 1.86126 0.031841 1.46107 0.242198 Membrane p LRRC7_RAT Isoform 5 of Leucine-rich repeat- Lrrc7 6 6.4 158648.5 6.01 0 0.647 1.8738 0.029374 1.37116 0.356938 Membrane containing protein 7 pp F1LSL8_RAT Protein Sptbn4 Sptbn4 3 1.4 288312 5.73 0 0.593 0.35701 0.028275 0.550461 0.130153 0.55128 0.017384 0.628846 0.094469 Membrane p B5DEG8_RAT LOC685144 protein Sec24c 2 3.3 118522.8 6.71 0 0.228 1.88383 0.027522 1.74991 0.049162 Membrane p B0BNK1_RAT Protein Rab5c Rab5c 3 15.1 25178.31 8.24 0 0.309 0.352696 0.027264 0.770283 0.406256 Membrane p p Q7TP78_RATNMDE1_RAT Aa2-258 Glutamate receptor ionotropic, Ndufa8Grin2a 4 2 20.1 2.0 21966.06 165466.7 8.39 6.59 0 40.5810.403 0.348857 0.345537 0.026392 0.025656 0.358642 0.523543 0.034903 0.110236 0.59831 0.033202 0.764273 0.286668 Membrane Membrane NMDA 2A pp CADH2_RAT Cadherin-2 Cdh2 3 5.6 99685.04 4.61 1 0.347 1.90336 0.024202 1.60723 0.115683 Membrane p G3V8C3_RAT Vimentin Vim 2 3.4 53700.03 5.06 0 0.839 0.33738 0.023925 0.32481 0.026787 0.5967 0.032505 0.67227 0.139486 Membrane p PP1A_RAT Serine/threonine-protein Ppp1ca 4 13.3 37511.67 5.94 0 0.301 0.329001 0.022253 0.543782 0.124969 Membrane phosphatase PP1-alpha catalytic subunit p CX7A2_RAT Cytochrome c oxidase subunit Cox7a2 2 18.1 9352.87 10.28 0 0.258 0.308413 0.018569 0.205817 0.009757 0.63483 0.052821 0.550054 0.042834 Membrane 7A2, mitochondrial p G3V8K2_RAT Guanine nucleotide-binding Gng3 2 32.0 8304.69 7.65 0 0.121 1.96822 0.015541 1.50322 0.198474 Membrane protein subunit gamma pp D3ZMM4_RAT ERC protein 2 Erc2 4 6.5 98023.61 6.41 0 0.949 1.97706 0.014603 1.26531 0.52941 Membrane SYTM_RAT Threonine–tRNA ligase, Tars2 2 3.2 81542.13 8.24 0 0.318 0.266841 0.012721 0.324403 0.026701 1.69424 0.001585 1.74609 0.007231 Membrane mitochondrial pp p ANXA6_RAT Annexin A6 Anxa6 2 2.2 75753.3 5.39 0 0.432 0.236683 0.009565 0.312902 0.024348 Membrane p Q76LU9_RAT Glutathione peroxidase Gpx4 2 13.0 29111.31 10.31 0 0.875 2.07201 0.007263 1.97087 0.009955 Membrane pppp VAMP2_RAT Vesicle-associated membrane Vamp2 3 35.3 12690.64 7.84 1 0.004 2.18637 0.002916 1.47564 0.226375 Membrane protein 2 p DLGP2_RAT Disks large-associated protein 2 Dlgap2 2 2.8 118977.2 6.3 0 0.868 2.28604 0.001234 1.33779 0.407061 Membrane SKP1_RAT S-phase kinase-associated protein Skp1 2 11.0 18671.82 4.4 0 0.716 2.32185 0.000892 1.99347 0.008296 Membrane 1 p B1VKB4_RAT Synaptopodin Synpo 3 7.6 96717.32 9.69 0 0.711 3.47943 3.43E10 3.96524 6.21E16 2.04391 2.02E06 1.49719 0.073864 Membrane DGLA_RAT Sn1-specific diacylglycerol lipase Dagla 2 3.5 115300.1 6 5 0.077 3.60509 4.14E11 1.26976 0.521404 Membrane alpha p M2OM_RAT Mitochondrial 2- Slc25a11 2 8.0 34132.51 9.89 0 0.101 1.42587 0.300805 1.74927 0.049367 Membrane oxoglutarate/malate carrier protein GPM6B_RAT Neuronal membrane glycoprotein Gpm6b 3 8.5 36196.32 5.76 4 0.548 1.37206 0.369551 1.75041 0.049004 Membrane M6-b p NEUG_RAT Neurogranin Nrgn 3 26.9 7496.25 6.53 0 0.612 1.58853 0.147048 1.76185 0.045485 Membrane p D4A5X7_RAT Ganglioside-induced Gdap1 5 14.0 41216.11 8.86 2 0.394 1.28879 0.493531 1.76401 0.044843 Membrane differentiation-associated-protein 1 (Predicted) 0.266 1.69747 0.083952 1.79993 0.035264 Membrane DNM1L_RAT Isoform 5 of Dynamin-1-like Dnm1l 4 7.1 82538.89 6.51 0 FKB1A_RAT Peptidyl-prolylprotein cis-trans isomerase Fkbp1a 2 15.7 11922.49 7.89 0 0.38 1.41737 0.311065 1.82527 0.029609 Membrane FKBP1A p KCC2B_RAT Calcium/calmodulin-dependent Camk2b 15 31.9 60401.11 6.73 0 0.353 1.73409 0.068502 1.83977 0.026737 1.34355 0.118429 1.56141 0.043456 Membrane protein kinase type II subunit beta

p 285 D3ZQL7_RAT Protein Tppp Tppp 3 15.6 23546.3 9.45 0 0.748 1.75205 0.061826 1.84113 0.02648 Membrane (continued on next page) 8 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. p 286 A9UMV9_RAT Ndufa7 protein Ndufa7 8 52.7 12500.31 10.48 0 0.662 1.66864 0.098011 1.84332 0.026072 Membrane ppp RTN3_RAT Reticulon-3 Rtn3 6 10.6 101515.7 5 3 0.409 1.56595 0.163808 1.89721 0.017599 Membrane NB5R3_RAT Isoform 2 of NADH-cytochrome b5 Cyb5r3 2 9.5 34865.15 8.56 0 0.213 1.24571 0.565506 1.92744 0.013993 Membrane reductase 3 pppp VATE1_RAT V-type proton ATPase subunit E 1 Atp6v1e1 7 22.6 26128.12 8.44 0 0.49 1.56403 0.165295 1.94464 0.012247 1.61803 0.00493 1.96348 0.000519 Membrane p G3V6T1_RAT Protein Copa Copa 2 2.4 138358.3 7.69 0 0.279 1.6798 0.092359 2.06645 0.004493 Membrane p G3V728_RAT 4-nitrophenylphosphatase domain Nipsnap1 5 17.6 33345.9 9.44 0 0.596 1.63347 0.117636 2.07727 0.004089 Membrane and non-neuronal SNAP25-like protein homolog 1 (C. elegans), isoform CRA_b NCKX2_RAT Sodium/potassium/calcium Slc24a2 2 3.4 74655.81 5.93 11 0.209 1.62693 0.1216 2.10525 0.003193 Membrane exchanger 2 p Q91ZE7_RAT Band 3 anion exchange protein Slc4a1 3 4.8 94311.68 5.83 10 0.327 1.43918 0.28521 2.38937 0.000189 2.31773 1.99E09 3.28321 1.79E 16 Membrane DHSB_RAT Succinate dehydrogenase Sdhb 5 18.1 31829.64 8.96 0 0.37 1.41043 0.319598 2.72809 3.03E 06 1.66788 0.002377 3.20927 1.61E 15 Membrane [ubiquinone] iron-sulfur subunit, mitochondrial CP4F4_RAT Cytochrome P450 4F4 Cyp4f4 2 4.0 60822.84 7.24 2 0.147 1.30014 0.475429 4.32687 1.05E 19 1.88387 5.76E 05 1.47305 0.089076 Membrane p PPIB_RAT Peptidyl-prolyl cis-trans isomerase Ppib 4 19.0 23802.3 9.5 1 0.202 0.338857 0.024231 0.368401 0.037602 Membrane B pp ODP2_RAT Dihydrolipoyllysine-residue Dlat 12 18.8 67165.04 8.76 0 0.017 1.43714 0.046849 1.46697 0.093277 Membrane acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial ppp SC6A1_RAT Sodium- and chloride-dependent Slc6a1 2 8.4 67000.71 8.25 12 0.468 0.61128 0.039304 0.688171 0.159588 Membrane GABA transporter 1 p CD9_RAT CD9 antigen Cd9 2 10.2 25214.65 6.93 4 0.537 0.58465 0.027671 0.663898 0.129717 Membrane Q56A26_RAT Protein Opalin Opalin 2 21.8 15672.53 4.98 1 0.376 1.49147 0.025409 1.5213 0.060862 Membrane GBRB2_RAT Gamma-aminobutyric acid Gabrb2 3 7.8 54632.84 9.35 4 0.068 0.56393 0.020803 0.483 0.02003 Membrane receptor subunit beta-2 p F1LUE2_RAT Calcium/calmodulin-dependent Camk2g 8 16.7 53592.45 7.39 0 0.42 1.51285 0.019673 1.7957 0.004169 Membrane protein kinase type II subunit gamma (Fragment) p KAD1_RAT Adenylate kinase isoenzyme 1 Ak1 5 32.0 21583.52 7.66 0 0.43 1.51853 0.018355 2.14985 3.42E 05 Membrane D4A7Y1_RAT Aggrecan core protein Acan 2 1.0 223896 4.16 0 0.377 0.55374 0.018006 0.553109 0.044258 Membrane Q76GL9_RAT Protein Slc1a4 (Fragment) Slc1a4 3 6.6 56137.88 6.38 10 0.529 0.55061 0.017218 0.618312 0.085527 Membrane Q06QG6_RAT NADH-ubiquinone oxidoreductase Mt-nd5 3 7.9 68587.28 9.34 15 0.621 1.54435 0.013287 1.39349 0.157635 Membrane chain 5 pp PRDX1_RAT Peroxiredoxin-1 Prdx1 8 34.7 22109.14 8.27 0 0.222 1.57432 0.008989 1.2538 0.363457 Membrane p D4A376_RAT Ras-related protein Rab-12 Rab12 2 21.4 16143.51 9.86 0 0.477 0.48849 0.006712 0.469181 0.016954 Membrane Q924Y3_RAT Claudin 11 (Fragment) Cldn11 2 14.4 12040.45 8.62 1 0.777 0.33107 0.000394 0.377782 0.005154 Membrane p B2CZC8_RAT Glutamate receptor, metabotropic Grm5 2 1.6 131884 8.07 6 0.107 1.90447 3.85E 05 1.38223 0.169928 Membrane 5, isoform CRA_a PPT1_RAT Palmitoyl-protein thioesterase 1 Ppt1 2 11.8 31531.1 6.72 0 0.146 1.90674 3.68E 05 1.54995 0.047937 Membrane (Fragment) pp p ATP5H_RAT ATP synthase subunit d, Atp5h 8 44.7 18763.21 6.16 0 0.702 1.90881 3.53E 05 1.92459 0.000867 Membrane mitochondrial pppp VATB2_RAT V-type proton ATPase subunit B, Atp6v1b2 13 29.9 56550.16 5.57 0 0.176 1.31607 0.150929 1.54945 0.048142 Membrane brain isoform NCEH1_RAT Neutral cholesterol ester Nceh1 3 9.3 45821.25 6.56 1 0.007 1.28784 0.190993 1.55566 0.045661 Membrane hydrolase 1 pp CNTP1_RAT Contactin-associated protein 1 Cntnap1 2 3.1 149647.2 6.44 0 0.306 0.69692 0.107888 0.519136 0.030475 Membrane (Fragment) ACADL_RAT Long-chain specific acyl-CoA Acadl 3 7.4 47872.31 7.63 0 0.223 1.20786 0.345494 1.60344 0.029929 Membrane dehydrogenase, mitochondrial p ADDG_RAT Isoform 1 of Gamma-adducin Add3 2 4.8 75360.54 5.75 0 0.543 0.70252 0.114534 0.51055 0.027642 Membrane A1AT_RAT Alpha-1-antiproteinase Serpina1 2 4.1 46135.27 5.7 0 0.158 1.35396 0.107653 1.68155 0.014167 Membrane p D3ZRF5_RAT Protein Slc25a22 Slc25a22 10 34.1 34661.99 9.26 2 0.179 1.29793 0.175852 1.71517 0.010043 Membrane p AATM_RAT Aspartate aminotransferase, Got2 17 38.8 47313.74 9.13 0 0.23 1.22532 0.306347 1.76443 0.00592 Membrane mitochondrial p D3ZD09_RAT Cytochrome c oxidase subunit 6B1 Cox6b1 3 37.2 10071.35 8.96 0 0.764 1.39114 0.075377 1.87299 0.001666 Membrane Appendix Table 3b. Differentially expressed nonmembrane proteins (35 proteins) identified from the susceptible and unsusceptible groups through iTRAQ-based quantitative proteomics

Accession Protein name Gene Unique % MW (Da) pI TMDs GRAVY Susceptible 113/115 Susceptible 116/118 Unsusceptible 114/115 Unsusceptible 117/118 Membrane number name peptides Sequence localization coverage Ratio p-Value Ratio p-Value Ratio p-Value Ratio p-Value

PPID_RAT Peptidyl-prolyl Ppid 2 4.9 40765.22 6.73 0 0.421 0.41661 0.045884 0.636291 0.212464 Nonmembrane cis-trans isomerase D Q4QQV4_RAT Dead end Hars 2 4.9 57359.55 5.86 0 0.309 0.416308 0.0457753 0.402199 0.0483645 Nonmembrane homolog 1 (Zebrafish) RLA2_RAT 60S acidic Rplp2 2 20.9 11691.82 4.44 0 0.263 0.411142 0.0439535 0.356717 0.0343902 Nonmembrane ribosomal protein P2 OTUB1_RAT Ubiquitin Otub1 3 7.8 31269.66 4.85 0 0.553 0.405167 0.0419231 0.388892 0.0438526 Nonmembrane thioesterase OTUB1 C9WPN2_RAT DEAD (Asp- Ddx3y 3 6.8 73005.64 6.67 0 0.666 0.396328 0.0390653 0.608784 0.182766 Nonmembrane

Glu-Ala-Asp) 220–292 (2015) 298 Neuroscience / al. et Han X. box polypeptide 3 Y-linked SCPDL_RAT Saccharopine Sccpdh 2 9.9 35411.12 8.09 0 0.12 1.85696 0.0327266 1.55531 0.152779 Nonmembrane dehydrogenase- like oxidoreductase GBB3_RAT Guanine Gnb3 3 8.5 37179.75 5.51 0 0.077 0.342908 0.0250867 0.538834 0.121232 0.587079 0.028593 0.785498 0.331869 Nonmembrane nucleotide- binding protein G(I)/G(S)/G(T) subunit beta-3 PRDX4_RAT Peroxiredoxin-4 Prdx4 2 9.9 31007.08 6.18 0 0.249 0.313034 0.0193455 0.271538 0.0173069 Nonmembrane NLTP_RAT Non-specific Scp2 2 2.6 58812.68 6.62 0 0.222 0.272637 0.0134236 0.296006 0.0212171 Nonmembrane lipid-transfer protein STMN1_RAT Stathmin Stmn1 2 16.1 17288.28 5.76 0 1.313 2.00308 0.0121239 1.91688 0.0151699 Nonmembrane ARP2_RAT Actin-related Actr2 3 15.7 32490.99 6.15 0 0.123 2.04618 0.00882984 1.79542 0.036362 Nonmembrane protein 2 B2RZ27_RAT Protein Sh3bgrl3 2 29.0 10476.63 5.02 0 0.522 2.12015 0.00499369 2.37561 0.00021979 Nonmembrane Sh3bgrl3 Q5XFV9_RAT Rps16 protein Rps16 2 13.2 17899.83 10.21 0 0.342 3.11855 8.48E08 2.41858 0.00013685 Nonmembrane (Fragment) PTMS_RAT Parathymosin Ptms 2 22.6 11558.77 4.15 0 2.047 1.4956 0.22523 1.85037 0.0247932 Nonmembrane NDRG2_RATCYLD_RAT ProteinUbiquitin NDRG2Cyld Ndrg2 23 13.2 2.9 106711.4 40778.74 5.445.16 0 0.2720.354 1.344791.7638 0.4078490.0577538 1.858572.0484 0.005246390.023374 Nonmembrane carboxyl- terminal hydrolase CYLD B2GUZ3_RAT Mthfd1l protein Mthfd1l 2 2.6 105840.9 7.29 0 0.092 1.67336 0.0955869 2.27685 0.00062077 Nonmembrane ARPC5_RAT Actin-related Arpc5 2 21.2 16320.23 5.47 0 0.404 1.43661 0.0471138 1.43573 0.117448 Nonmembrane protein 2/3 complex subunit 5 A1I3_RAT Alpha-1- A1i3 2 2.2 163771.4 5.7 0 0.216 1.44416 0.0434176 1.56611 0.0417258 Nonmembrane inhibitor 3 D4A7L4_RAT NADH Ndufb11 2 25.8 17633.8 5.17 0 0.436 0.593568 0.0311841 0.729673 0.222277 Nonmembrane dehydrogenase (Ubiquinone) 1 beta 287 subcomplex, 11 (Predicted) (continued on next page) 8 .Hne l ersine28(05 220–292 (2015) 298 Neuroscience / al. et Han X. 288 D3ZJH9_RAT Malic enzyme Me2 2 4.3 65350.91 7.87 0 0.148 1.47671 0.0301663 1.20207 0.470262 Nonmembrane F1LU71_RAT Protein Auh Auh 9 24.6 33138.25 9.49 0 0.056 1.54146 0.0137857 1.50442 0.0697445 Nonmembrane (Fragment) BACH_RAT Cytosolic acyl Acot7 5 13.2 39055.46 8.38 0 0.36 1.63505 0.00386339 1.31529 0.258151 Nonmembrane coenzyme A thioester hydrolase HBA_RAT Hemoglobin Hba1 10 60.6 15328.35 7.81 0 0.115 1.68349 0.00187259 2.13924 4.04E 05 Nonmembrane subunit alpha-1/ 2 HBB1_RAT Hemoglobin Hbb 10 75.5 15979.19 7.87 0 0.042 1.72359 0.0009935 2.24838 6.82E 06 Nonmembrane subunit beta-1 HBB2_RAT Hemoglobin N/A 10 74.2 15982.24 8.91 0 0.003 1.9311 2.26E 05 2.69229 1.05E 09 Nonmembrane subunit beta-2 Q62669_RAT Protein Hbb-b1 Hbb-b1 5 32.0 16022.32 7.93 0 0.001 2.13809 2.22E07 3.08147 6.06E 14 Nonmembrane Q5XI17_RAT Protein Tarsl2 Tarsl2 2 2.5 64118.31 7.89 0 0.657 2.3531 7.30E 10 1.94015 0.000707803 Nonmembrane B4F7C2_RAT RCG45085 Tubb4 19 48.7 49585.25 4.78 0 0.321 1.30015 0.172646 1.54997 0.0479303 Nonmembrane TBB3_RAT Tubulin beta-3 Tubb3 18 39.1 50418.13 4.82 0 0.371 1.25815 0.241011 1.59416 0.0325559 Nonmembrane chain 1433T_RAT 14-3-3 protein Ywhaq 7 24.9 27777.97 4.69 0 0.512 1.2445 0.266892 1.66904 0.016048 Nonmembrane theta Q4QQV0_RAT Protein Tubb6 Tubb6 11 25.1 50058.83 4.8 0 0.344 1.32657 0.137786 1.69051 0.0129423 Nonmembrane STIP1_RAT Stress-induced- Stip1 3 5.2 62569.41 6.4 0 0.945 1.2081 0.344935 1.74467 0.00734337 Nonmembrane phosphoprotein 1 F1LM47_RAT Protein Sucla2 Sucla2 12 23.3 47286.13 6.08 0 0.026 1.35867 0.103039 1.80977 0.00354687 Nonmembrane (Fragment) PPIA_RAT Peptidyl-prolyl Ppia 12 65.9 17874.13 8.34 0 0.326 1.2499 0.256441 1.82094 0.00311451 Nonmembrane cis-trans isomerase A

Appendix Table 3b. Differentially expressed proteins without known localization (4 proteins) from the susceptible and unsusceptible groups through iTRAQ-based quantitative proteomics

Accession Protein name Gene Unique % Sequence MW (Da) pI TMDs GRAVY Susceptible 113/115 Susceptible 116/118 Membrane number name peptides coverage localization Ratio p-Value Ratio p-Value

CNRP1_RAT CB1 cannabinoid receptor- Cnrip1 2 15.9 18987.71 9.45 0 0.341 0.373902 0.0325476 0.386928 0.0432178 Unknown interacting protein 1 F1M5F9_RAT Protein Efr3b (Fragment) Efr3b 2 3.8 87513.01 6.39 0 0.175 1.95817 0.0166728 1.28001 0.503185 Unknown D3ZII1_RAT Protein Rftn2 Rftn2 2 8.5 54746.58 5.25 0 0.552 2.32033 0.00090478 1.59251 0.125398 Unknown IMPCT_RAT Protein IMPACT Impact 2 7.6 35994.52 5.07 0 0.593 2.35611 0.000649819 1.82125 0.0304501 Unknown X. Han et al. / Neuroscience 298 (2015) 220–292 289

Appendix Table 4. Summative description of the research literature and studies regarding the associations between the differentially expressed PSD- related proteins and mental disorders

Gene name Related to depression Related to other mental disorders

Dnaja2 Schizophrenia (Rippey et al., 2013; Martin et al., 2014) Atp5d Schizophrenia (Martin et al., 2014), Alzheimer’s disease (Ding et al., 2014; Suszynska-Zajczyk et al., 2014) Unc13a Schizophrenia (Focking et al., 2014), amyotrophic lateral sclerosis (Diekstra et al., 2012; Su et al., 2014) Cnksr2 Intellectual, attention, and language deficits (Vaags et al., 2014) Pacsin1 Huntington’s disease (Caron et al., 2013; Marco et al., 2013) Sptbn4 Alzheimer’s disease (Sanchez-Mut et al., 2013) Sec24c Prefrontal cortex of patients with major depression and Alzheimer’s disease (Morgan et al., 2007) bipolar disorder (Lee et al., 2011) Grin2a Brain tissue of post-stroke depression rat model (Zhao Schizophrenia (Tang et al., 2006; Wright et al., 2013; et al., 2013), frontal cortex and hippocampus of Barkus et al., 2014), Huntington’s disease (Saft et al., 2011), unpredictable chronic mild stress rat model (Lou et al., bipolar disorder (Itokawa et al., 2003), anxiety (Park et al., 2010) 2013) Cdh2 Anxiety (Danglot et al., 2012), Alzheimer’s disease (Ando et al., 2011), Huntington’s disease (Reis et al., 2011) Ppp1ca Alzheimer’s disease (Kakiya et al., 2012; Banzhaf- Strathmann et al., 2014) Gng3 Seizures (Schwindinger et al., 2004) Gpx4 Huntington’s disease (Cong et al., 2012), Alzheimer’s disease (Yoo et al., 2010) Vamp2 Frontal cortex of major depressive patients treated with Alzheimer’s disease (Chen et al., 2008; Shi et al., 2012; fluvoxamine (Saito et al., 2006), frontal cortex and Koldamova et al., 2014), anxiety (Valdez et al., 2007) hippocampus of electroconvulsive therapy rat model (Elfving et al., 2008) Dlgap2 Prefrontal cortex of patients with major depression and Schizophrenia (Li et al., 2014), autism (Chien et al., 2013; bipolar disorder (Lee et al., 2011) Jiang-Xie et al., 2014) Synpo Postmortem hippocampus CA3 of depression patients Schizophrenia (Focking et al., 2014), anxiety (Soetanto (Soetanto et al., 2010) et al., 2010) Slc25a11 Schizophrenia (Focking et al., 2014) Nrgn Schizophrenia (Thong et al., 2013; Walton et al., 2013), anxiety (Miyakawa et al., 2001; Wilcoxon et al., 2007) Dnm1l Alzheimer’s disease (Gan et al., 2014), Huntington’s disease (Guo et al., 2013) Lrrc7 Schizophrenia (Carlisle et al., 2011), autism (Carlisle et al., 2011) Camk2b Postmortem frontal cerebral cortex tissues from severe Schizophrenia (Novak et al., 2006; Focking et al., 2014), depression patients (Novak et al., 2006), lateral habenula of anxiety (Choi et al., 2011) animal models of depression (Li et al., 2013) Tppp Saliva of maltreated children with depression (Weder et al., Alzheimer’s disease (Olah et al., 2011), autism (Iurov et al., 2014) 2010) Rtn3 Alzheimer’s disease (Masliah et al., 2010; Araki et al., 2013) Atp6v1e1 Hippocampus of social defeat rat model (Carboni et al., 2006), anterior cingulate cortex of patients with major depression (Beasley et al., 2006), synaptosomes of prefrontal/frontal cortex and hippocampus of learned helplessness rat model (Mallei et al., 2011) Slc4a1 Hippocampus of mice treated with paroxetine (Sillaber et al., 2008) Camk2g Schizophrenia (Focking et al., 2014) Ak1 Synaptosomes of prefrontal/frontal cortex and hippocampus Alzheimer’s disease (Park et al., 2012), Huntington’s of learned helplessness rat model (Mallei et al., 2011) disease (Brackenridge et al., 1978) Prdx1 Alzheimer’s disease (Cumming et al., 2007), Huntington’s disease (Pitts et al., 2012), schizophrenia (Focking et al., 2014) Grm5 Locus coeruleus of postmortem patients with major Alzheimer’s disease (Hamilton et al., 2014), schizophrenia depressive disorder (Chandley et al., 2014), brain molecular (Turlington et al., 2014; Yu et al., 2014), Huntington’s imaging of sleep-deprived human with depression (Hefti disease (Doria et al., 2013), anxiety (Felts et al., 2013; et al., 2013), antidepressant administrated mice (Pomierny- Kumar et al., 2013) Chamiolo et al., 2010), hippocampus of rat injected with corticosterone (Iyo et al., 2010)

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Atp5h Alzheimer’s disease (Boada et al., 2014) Atp6v1b2 Blood of major depressive disorder patients (Shyn et al., Schizophrenia (Ji et al., 2009), Alzheimer’s disease (Coffey 2011) et al., 2014) Cntnap1 Alzheimer’s disease (Fan et al., 2013) Slc25a22 Seizures (Mastrangelo and Leuzzi, 2012; Poduri et al., 2013) Got2 Schizophrenia (Tsai et al., 2007; Wesseling et al., 2013), anxiety (Owada et al., 2006) Vim Monocyte of depressed patients (Cervera Enguix et al., Alzheimer’s disease (Kamphuis et al., 2012; Shan et al., 1995), hippocampus of mice treated with paroxetine 2012), anxiety (Lalonde and Strazielle, 2003) (Sillaber et al., 2008), embryonic stem cell-derived neural cells exposed to antidepressant paroxetine (McHugh et al., 2008)

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