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Pharmaceutical Sciences Faculty Publications Department of Pharmaceutical Sciences
6-2004
Analysis of the Human Serum Proteome
King C. Chan
David A. Lucas
Denise Hise
Carl F. Schaefer
Zhen Xiao
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This Article is brought to you for free and open access by DigitalCommons@Cedarville, a service of the Centennial Library. It has been accepted for inclusion in Pharmaceutical Sciences Faculty Publications by an authorized administrator of DigitalCommons@Cedarville. For more information, please contact [email protected]. Authors King C. Chan, David A. Lucas, Denise Hise, Carl F. Schaefer, Zhen Xiao, George M. Janini, Kenneth H. Buetow, Haleem J. Issaq, Timothy D. Veenstra, and Thomas P. Conrads Clinical Proteomics Journal Copyright ©Humana Press Inc. All rights of any nature whatsoever are reserved. ISSN 1542-6416/04/01:101–225/$25.00 Serum/Plasma Proteome
Analysis of the Human Serum Proteome King C. Chan,1,† David A. Lucas,1,† Denise Hise,2 Carl F. Schaefer,2 Zhen Xiao,1 George M. Janini,1 Kenneth H. Buetow,2 Haleem J. Issaq,1 Timothy D.Veenstra,1 and Thomas P. Conrads1,*
1Laboratory of Proteomics and Analytical Technologies, National Cancer Institute at Frederick, SAIC-Frederick, Inc, PO Box B, Frederick, MD 21702 2Center for Bioinformatics, National Cancer Institute, Bethesda, MD 20892 †These authors contributed equally to this work.
each of which was analyzed by microcapillary Abstract reversed-phase liquid chromatography coupled Changes in serum proteins that signal online with MS/MS analysis. histopathological states, such as cancer, are useful This investigation resulted in the identifica- diagnostic and prognostic biomarkers. Unfortu- tion of 1444 unique proteins in serum. Proteins nately, the large dynamic concentration range from all functional classes, cellular localization, of proteins in serum makes it a challenging and abundance levels were identified. proteome to effectively characterize. Typically, This study illustrates that a majority of lower methods to deplete highly abundant proteins abundance proteins identified in serum are pre- to decrease this dynamic protein concentra- sent as secreted or shed species by cells as a result tion range are employed, yet such depletion of signalling, necrosis, apoptosis, and hemolysis. results in removal of important low abundant These findings show that the protein content of proteins. serum is quite reflective of the overall profile of Amulti-dimensional peptide separation strat- the human organism and a conventional multi- egy utilizing conventional separation techniques dimensional fractionation strategy combined with combined with tandem mass spectrometry MS/MS is entirely capable of characterizing a sig- (MS/MS) was employed for a proteome analysis nificant fraction of the serum proteome. We have of human serum. Serum proteins were digested constructed a publicly available human serum with trypsin and resolved into 20 fractions by proteomic database (http://bpp.nci.nih.gov) to ampholyte-free liquid phase isoelectric focusing. provide a reference resource to facilitate future These 20 peptide fractions were further fraction- investigations of the vast archive of pathophysio- ated by strong cation-exchange chromatography, logical content in serum.
*Author to whom all correspondence and reprint requests should be addressed: E-mail: [email protected]
101 102 ______Chan et al.
Key Words: Serum; proteomics; mass spectrome- to correlate data obtained from tandem MS try; multi-dimensional separation; isoelectric (MS/MS) measurements for protein identifi- focusing; biomarker. cation. Because a potential archive of patho- Introduction physiological information is endowed to serum from its constant perfusion of tissues, Amajor trend underlying current biological particular focus has been given to developing research is the development and application methods to allow its facile investigation by of analytical methods capable of making proteomic technologies. Serum is a rather global measurements of entire biological sys- unique biological sample in that no specific tems. These advances have created unique cellular genomic expression per se contributes opportunities in the field of medicine, where to its protein content, but rather it may be the results from gene expression studies are hypothesized that the protein content is con- expected to help identify cellular alterations tributed by the summation of all cellular associated with disease diagnosis, etiology, genomic expression in the organism. It is progression, outcome, and response to ther- therefore clear that the collection of histo- apy. A major goal is to obtain a greater under- pathological information in serum is com- standing of the function of proteins in a prised not only of the expected circulatory cellular context, as well as their more con- proteins such as immunoglobulins, but also of ventionally delineated individual molecular peptides and proteins that are secreted into function. This global view promises to provide the blood and shed species from diseased, a greater understanding of the cellular responses dying, or dead cells (2). to events such as cell division, differentiation, The importance of characterizing the protein respiration, hormonal signalling, and changes content of serum is underscored by the fact in homeostasis. The impetus for conducting that subtle changes of low abundance proteins global measurements of biological systems is have been shown to indicate development of to establish new diagnostic approaches and different disease states such as ovarian (3,4), therapeutic targets for a host of maladies, breast, (5) and prostate (6,7) cancer. Despite including infectious diseases, behavioral dis- decades of research, however, only a few hun- orders, developmental defects, neurodegener- dred proteins have been identified from either ative diseases, aging, and cancer. serum or plasma (8,9). Unfortunately, the large Whereas the availability of complete genome dynamic concentration range of proteins in sequences opens the door to important biologi- serum renders this proteome cumbersome to cal advances, much of the detailed under- effectively characterize. Most serum proteome standing of cellular systems and the roles of studies have therefore removed high abun- its constituents will, by necessity, be based dance proteins, such as albumin or immuno- upon proteomics, which has classically been globulins, prior to analysis. It is plausible that defined as the study of the entire complement depletion of highly abundant proteins from of proteins, and their modifications, expressed serum may in fact result in concomitant deple- by a cell. Typically, proteomic investigations tion of the histopathological archive of poten- are conducted using mass spectrometry (MS) tially important peptides and proteins that as the core analytical technique for protein may be present at low abundance. Hence, the identification and relative quantitation (1). multi-dimensional chromatographic-MS/MS Current MS-based proteomic measurements method we have utilized in the present work rely heavily on databases of predicted proteins does not rely on the depletion of any highly generated from genome sequence information abundant proteins.
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While the importance of studying the serum were identified, demonstrating the ability to proteome is clear, its composition and com- conduct investigations of human serum using plexity make it one of the most challenging conventional proteomic technologies. proteome samples to characterize. Serum is composed of a wide variety of biomolecules Materials ranging from large molecules such as pro- 1. Pooled standard human serum, NH4HCO3, teins and lipids, to small metabolites such as NaHCO2, urea, formic acid, trifluoroacetic peptides, amino acids, and electrolytes. Twenty- acid (TFA), and dithiothreitol (DTT) were two proteins, such as albumin, immunoglobu- purchased from Sigma (St. Louis, MO). lins, haptoglobin, transferrin, and lipoproteins, 2. Porcine sequencing grade modified trypsin account for 99% of the protein mass of serum was purchased from Promega (Madison, WI). (2). It is estimated that as many as 10,000 unique 3. High performance liquid chromatography proteins are present within the human serum (HPLC) grade acetonitrile was obtained proteome that span a dynamic range of concen- from EMD Chemicals Inc. (Gibbstown, NJ). tration estimated to be greater than 109 (2). This 4. All buffers and reagents were used as sup- dynamic range of protein concentration is the plied from the manufacturer and prepared primary factor that makes global characteriza- in double distilled water using a NANOP- tion of the serum proteome so challenging and ure Diamond water system (Barnstead International, Dubuque, IA). necessitates effective fractionation methods capable of separating high abundance proteins Methods from low abundance species prior to MS or MS/MS analyses. Serum Tryptic Digestion The most extensive characterization and Two hundred microliters of a pooled stan- cataloging of serum proteins to date is that dard human serum (approx 15 mg total pro- reported by Adkins et al., in which 490 pro- tein, Sigma) was diluted 1:1 (v/v) with 100 mM teins were identified (8). Because the presence NH4HCO3, pH 8.2, and boiled for 5 min. of high abundant proteins, such as albumin Trypsin (Promega) was added to the denatured and immunoglobulins, in serum pose a seri- serum at a protein to enzyme ratio of 50 1 ous problem for MS analysis, a common strat- (w/w). Trypsin digestion was carried out at egy is to deplete these proteins using affinity 37°C overnight. The digest was supplemented based methods as in the study by Adkins et with the same amount of trypsin the following al. (8). It has been proposed, however, that day and incubated for an additional 5 h. The such a depletion may also result in the loss of entire digestion process was completed in 20 h. pathophysiologically important low abundant proteins (10). Liquid-Phase Isoelectric Focusing Here we show that a multidimensional pep- The serum tryptic digest was fractionated tide separation strategy utilizing conventional using a preparative-scale isoelectric focusing separation techniques combined with tandem (IEF) device (Rotofor, Bio-Rad, Hercules, CA). mass spectrometry is capable of providing The focusing cell, which is divided into 20 broad-scale identification of proteins in human chambers by permeable membranes, was serum without the need for prior depletion of assembled, filled with 2M urea, 2 mM DTT highly abundant proteins. Our investigation and pre-run for 5 min at a constant power of resulted in the identification of 1444 proteins 5 W to remove any residual ionic contaminants in serum. Proteins from all functional classes, from the system. The tryptically digested cellular localization, and abundance levels serum sample was diluted to a total of 15 mL
Volume 1, 2004 ______Clinical Proteomics 104 ______Chan et al. in 2M urea, 2 mM DTT and loaded onto the tion was lyophilized and reconstituted in 20 µL focusing cell followed by a focusing step sepa- of 0.1% formic acid prior to µRPLC-MS/MS. rating the entire peptide mixture into 20 frac- tions. The peptides in the different chambers, Microcapillary LC-MS/MS Analysis approx 625 µL each, were aspirated simultane- Microcapillary RPLC was performed using ously with vacuum into separate test tubes. The an Agilent 1100 capillary LC system (Agilent apparatus was kept at 10°C using a circulating Technologies, Palo Alto, CA) coupled online to refrigerated water bath. The focusing was con- an ion trap (IT) mass spectrometer (LCQ ducted at 10 W for 2 h. Formation of a pH gra- DecaXP, ThermoElectron, San Jose, CA) with dient was confirmed by measuring the pH of the nanoelectrospray interface supplied by the each fraction using pH indicator paper. manufacturer. Microcapillary RPLC separa- The IEF peptide fractions were desalted to tions of each sample were performed using remove urea by solid phase extraction (SPE) 75 µm id × 360 µm od × 10 cm long fused using C-18-bonded cartridges (Extract-Clean silica capillary columns (Polymicro Technolo- Columns, Alltech, Deerfield, IL). Each car- gies, Phoenix, AZ) that were slurry packed in tridge was equilibrated with 2 bed volumes of house with 3 µm, 300 Å pore size C-18 silica- methanol and washed with 2 volumes of 0.1% bonded stationary phase (Vydac, Hysperia, (v/v) trifluoroacetic acid (TFA). The peptide CA). After injecting 7 µLof sample, the fractions were applied to the columns and the column was washed for 20 min with 98% sol- cartridge was washed with 2 volumes of 0.1% vent A (0.1% formic acid in water, v/v) and (v/v) TFA. Peptides were eluted with 4 mL of peptides were eluted using a linear gradient acetonitrile: H2O TFA (80 19.9 0.1, v/v/v). of 2% solvent B (0.1% formic acid in 100% ace- The eluent was initially concentrated to 1 mL tonitrile, v/v) to 85% solvent B in 160 min at a by evaporation under argon atmosphere at constant flow rate of 0.5 µL/min. 37°C and to 300 µL by vacuum centrifugation. The IT mass spectrometer was operated in a The peptide fractions were stored at 4°C prior data dependent mode in which each full MS to microcapillary reversed-phase liquid chro- scan was followed by three MS/MS scans motography (µRPLC)-MS/MS analysis. where the three most abundant peptide molec- ular ions were dynamically selected from the Strong Cation Exchange Fractionation prior scan for collision-induced dissociation Typically, 250 µL of each Rotofor fraction (CID) using a normalized collision energy of were injected onto a strong cation exchange 38%. Dynamic exclusion was utilized to pre- liquid chromatography (SCXLC) column (Poly- vent redundant acquisition of peptides previ- sulfoethyl A, PolyLC Inc., Columbia, MD). An ously selected for MS/MS. The temperature of ammonium formate/acetonitrile multistep gra- the heated capillary and electrospray voltage dient was used to elute the peptides from the were 180°C and 1.5 kV, respectively. column at a flow rate of 1 mL/min: 2% solvent B for 2 min, followed by 30% B in 50 min, then Bioinformatic Analysis 100% B in 28 min and maintained at 100% B for Tandem MS spectra from the µRPLC-MS/ 16 min. Solvent A was 20% acetonitrile, and sol- MS analyses were searched against the Expert vent B was 20% acetonitrile, 0.5M ammonium Protein Analysis System’s human prote- formate, pH 3.0. Six fractions from the SCXLC omic database (http://www.expasy.org) with column were collected between minutes 10 and SEQUEST operating on an 18 node Beowulf 51. The last (seventh) fraction was collected cluster (ThermoElectron). For a peptide to be between minutes 52 and 76. Each SCXLC frac- considered legitimately identified, it had to
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Table 1 SEQUEST Filter Criteria for Peptide Identification
Charge Statea Xcorrb Proteolytic Constraint +1 ≥ 1.9 Fully Tryptic +1 ≥ 2.1 Fully chymotryptic and/or elastic +1 ≥ 2.2 Partially tryptic, chymotryptic, and/or elastic +1 ≥ 2.2 No protease constraint +2 ≥ 2.2 Fully Tryptic +2 ≥ 2.2 Fully chymotryptic and/or elastic +2 ≥ 2.4 Partially tryptic, chymotryptic, and/or elastic +2 ≥ 3.0 No protease constraint +3 ≥ 3.5 Fully Tryptic +3 ≥ 3.5 Fully chymotryptic and/or elastic +3 ≥ 3.75 Partially tryptic, chymotryptic, and/or elastic +3 ≥ 3.75 No protease constraint aCharge state of the peptide molecular ion chosen for tandem MS. bSEQUEST cross correlation score. achieve stringent charge state and proteolytic separation/fractionation step prior to MS cleavage-dependent cross correlation (Xcorr) analysis to enable identification of greater scores similar to those previously reported numbers of proteins. (8,11) (Table 1) and a minimum delta correla- The presence of high abundant proteins, tion (DelCN) of 0.08. such as albumin and immunoglobulins, in serum pose a serious analytical challenge for Results MS-based proteomic analysis. A common One of the primary focuses in the field of strategy employed in serum proteomic inves- proteomics is to develop technologies to effi- tigations is depletion of the highly abundant ciently interrogate the pathophysiological state proteins using affinity based methods. How- of an organism through the analysis of serum. ever, such depletion strategies likely result in A number of technologies have been devel- loss of physiologically important low abun- oped toward achieving this goal and range dant proteins. The objective of this study was from those designed to recognize a diagnostic to determine if a three-dimensional fractiona- proteomic pattern (3,5–7) (without the need to tion based on liquid phase peptide IEF in the identify any of the components contributing first dimension, strong cation exchange in to the diagnostic pattern) to those that iden- the second dimension, and hydrophobicity tify a unique biomarker for a specific disease in the third dimension prior to MS would state (12). Disease biomarker identification is allow for the identification of lower abun- generally accomplished using one of two dance proteins in serum in the presence of the strategies: resolution of serum by two dimen- more common highly abundant proteins. sional-polyacrylamide gel electrophoresis (2D- PAGE) followed by MS analysis of the stained Serum Proteome Analysis protein spots, or multi-dimensional liquid The experimental procedure employed in chromatographic/electrophoretic separation this study (Fig. 1) utilized a tryptic digestate coupled with MS analysis. Both of these of 200 µL of a standard pooled human serum approaches rely heavily on a high-resolution sample (approx 15 mg) that was fractionated
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Fig. 1. Flowchart of the experimental strategy employed for the global analysis of the human serum proteome. Tw o hundred microliters of pooled human serum was digested with trypsin.The serum digestate was subjected to ampholyte-free IEF from which 20 fractions were collected. Each IEF fraction was further fractionated by SCX into seven fractions that were each analyzed by µLC-MS/MS. by liquid phase isoelectric focusing (IEF). by µRPLC coupled online to a conventional Typically, preparative liquid phase IEF is IT-MS for peptide identification by MS/MS. employed for separating or fractionating pro- Bioinformatic analysis of the MS/MS spectra teins, not peptides. In the separation of pro- from the 20 IEF serum peptide fractions resulted teins by IEF, the pH gradient is generated in the identification of 957 unique peptides cor- using ampholytes that must be removed prior responding to 473 proteins. In addition, the to additional downstream separations and/or remaining aliquots of each of the 20 IEF frac- MS analysis (13). Arising from the amphoteric tions were further resolved by SCXLC into 7 nature of complex peptide mixtures, it is pos- fractions. Each of the 140 IEF-SCXLC serum sible to exploit peptide “auto focusing” for pH peptide fractions was analyzed by µRPLC- gradient generation in liquid phase IEF, MS/MS. Analysis of the set of MS/MS spectra enabling the separation of peptide mixtures obtained from the 140 IEF/SCX/µRPLC frac- without the use of ampholytes. The potential tions resulted in the identification of 2071 sample loss during the necessary ampholyte unique peptides corresponding to 1143 proteins. removal prior to subsequent separations or When combined, the µRPLC-MS/MS analyses MS analysis is also eliminated. Twenty IEF of the 20 IEF and the 140 IEF-SCXLC serum fractions were collected with measured pH peptide fractions resulted in the total identifica- values ranging from 3.0 to 10.0 (data not tion of 2646 unique peptides corresponding to shown), indicating that the peptides had suc- 1444 unique proteins from the human serum cessfully autofocused. A small aliquot of each proteome (Table 1, Supplemental). of the 20 IEF fractions was desalted by solid We sought to estimate the confidence inter- phase extraction, concentrated and analyzed val of our bioinformatic results by searching the
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MS/MS spectra of selected µRPLC-MS/MS monly associated with serum, such as coagu- analyses agains a proteomic database derived lation and complement factors, transport and from Archea that possesses 12,038 “non-human” binding proteins, cytokines, growth factors, protein sequences. The number of peptides and hormones. Quite remarkably, we find a identified from the MS/MS spectra of the number of proteins not commonly associated human-derived serum peptides when searched with serum, for example, intracellular and against this Archea database should give a rea- membrane associated proteins make up 39.6% sonable measure of the false positive rate inher- and 32.1% of the identified proteins, respec- ent in the data. We found the overall confidence tively. Indeed, such proteins as transcription interval of our analysis to be >90% using the factors, nuclear proteins, channels, and recep- present SEQUEST filtering criteria. For exam- tors were identified, substantiating the notion ple, 624 identified human peptides were identi- that serum possesses an archive of potentially fied from one particularly rich µRPLC-MS/MS pathophysiological information arising from run. When this same µRPLC-MS/MS run was the fact that cellular proteins and peptides may searched against the Archea database, only 60 be released into the bloodstream during necro- peptides were identified, giving a confidence sis, apoptosis, and hemolysis (2,8). interval in the identifications when the data is Detection and Identification searched against the appropriate human of Low Abundant Proteins database of approx 90% of this specific run. Serum contains thousands of proteins and Recent reports estimate that the dynamic peptides such as the common highly abundant concentration range separating the lowest proteins (such as albumin and immunoglobu- abundant proteins (e.g., hormones and cyto- lins) to the extremely low abundant proteins kines) from the most abundant proteins (e.g., that are present in a large dynamic concentra- albumin) in human serum to be more than tion range (2). Indeed a single protein, albumin, nine orders of magnitude (2). Hence, if the comprises greater than 50% of the protein con- average concentration of serum albumin is tent (Fig. 2). A total of ten proteins constitute greater than 50 mg/mL, analytical technolo- approx 90% of the protein content of serum gies must be able to detect proteins present at and the remaining approx 9% is primarily or below the pg/mL level to enable compre- made up of only twelve different proteins. hensive proteomic measurements. Indeed, this Hence, it is potentially only the remaining low concentration is a level at which many approx 1% of the protein content of serum that key proteins currently utilized as disease indi- is important to characterize in the search for cators are present, such as prostate-specific potential biomarkers of disease states. antigen (PSA) (14) and cancer antigen 125 (CA 125) (15) for prostate and ovarian cancer, The Nature of the Human Serum respectively. Inspection of the proteins identi- Proteome fied in our study demonstrates that the use of To identify biomarkers in serum, any given a conventional multi-dimensional separation list of identified proteins must be reflective of strategy coupled with conventional MS detec- the organism as a whole and not just contain tion successfully enables identification of pro- the expected circulatory proteins. The proteins teins that span this dynamic concentration we have identified arise from a wide range of range. For example, we confidently identified functional classes (Fig. 3). As anticipated all of interferon γ (<10 pg/mL) (2) and amyloid A4 the 22 highest abundant proteins, as illustrated (>10 ng/mL) (16) (Fig. 4), proteins known in Fig. 2, were identified as were proteins com- to be present in serum at low abundance,
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Fig. 2. Pie chart representing the relative contribution of proteins within the blood proteome. Twenty-two proteins constitute approx 99% of the protein content.
Fig. 3. Pie charts illustrating the classification of the proteins identified in human serum according to the three organizing principles of the gene ontology consortium (http://www.geneontology.org). (A) Cellular compart- ment, (B) biological process, and (C) molecular function.
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Volume 1, 2004 ______Clinical Proteomics 110 ______Chan et al. without the need to deplete highly abundant level lies within the samples being assayed. proteins, such as albumin, the various immu- For true utility, a biomarker should be noglobulins, and apolipoprotein, all of which assayable through protein-rich and readily are present at well above the mg/mL level. obtainable biofluids, such as plasma or serum. Unfortunately, these samples are made up of A Serum Proteome Database a myriad of different biological molecules The development of new technologies including proteins, peptides, carbohydrates, promises new biomarker discoveries to aid in small molecules, and lipids that are present at the diagnosis and prognosis of diseases. It is extreme dynamic ranges of concentration. A likely that the most successful strategies for second level of complexity arises from the biomarker discovery will employ methods that organism itself with respect to the particular allow parallel characterization of proteins. disease state. In the case of identifying a Because serum possesses such a rich archive of serum biomarker for the presence of cancer for potential histopathological information as example, such a biomarker is being used to demonstrated in this work, there exists great indicate a malignancy within a patient that potential and benefit to “mine” serum for dis- may comprise less than 0.1% of the body ease-specific biomarkers. To increase the suc- mass. In essence the search is on for analytical cess rate at which novel and more effective “needles in the haystack.” A clear need exists ensembles of biomarkers may be enumerated for a more complete understanding of the from serum requires the ability to comprehen- matrix protein background of the “haystack” sively characterize such analytically challeng- of serum and for public dissemination of such ing samples, as no targeted methods exist for information as updatable databases of pro- their discovery. We have produced a bench- teins, interpreted MS/MS spectra, and even mark serum proteome database (http://bpp. raw MS data, as in the case of the publicly nci.nih.gov) that represents a three-fold increase available database constructed from the pre- in the number of proteins identified to date sent work (http://bpp.nih.nci.gov). that will serve as a web-accessible resource Although serum is one of the most analyti- to aid in serum biomarker investigations. In cally challenging proteome samples to charac- the future, this database will be sequentially terize, the ability to do so promises rich updated and annotated as new proteins and information regarding the histopathological their function are discovered. Presently, this ref- state of a patient and its analysis using pro- erence resource should contribute substantially teomic techniques is being heavily relied upon to the advancement of our understanding of for the discovery of reliable disease biomark- the human serum proteome, to comparative ers. Fortunately, our study illustrates that a biology, and to the isolation of human disease majority of lower abundance proteins identi- biomarkers, particularly those underlying com- fied in serum are present as secreted or shed plex disease states such as cancer. species likely by cells as a result of signalling, necrosis, apoptosis and hemolysis. Taken Conclusions together, these findings show that the protein A major thrust in proteomics aims at identi- content of serum is quite reflective of the over- fication of biomarkers useful for early disease all profile of the human organism and that diagnosis, disease progression, or response to conventional multi-dimensional fractionation therapy. This task is obviously laborious as strategies combined with conventional MS there are several levels of complexity that are analysis are entirely capable of characterizing counter to biomarker discovery. One such a significant fraction of the serum proteome.
Clinical Proteomics ______Volume 1, 2004 Fig. 4. Ion-trap MS/MS for the identification of human serum peptides. Shown for illustration are two peptides at m/z 421.8 (A) and 940.8 (B) that were selected for MS/MS and dissociated using collision-induced disso- ciation in the ion-trap MS.The resulting fragment ions detected in the MS/MS spectra unambiguously identify these peptides as N.LKKYFNAG.H (A) and R.GPGGVWAAK.L (B) that arise from serum amyloid A4 and interferon-γ,respectively. Supplementary Table 1 Proteins/Peptides Identified From Human Serum
Swiss-Prot Peptide Charge Protein Peptidea Accessionb Countc Xcorrd Statee
ABC transporter ABCA6 L.GNSPVLLLDEPS.T Q8N139 1 2.644 2 Abnormal spindles R.EKLNLKKKTDLSIFRT.P Q8IZT6 1 2.4331 2 ABP125 I.DASQTEFEKNVWS.F Q9UM06 1 2.4392 2 Absent in melanoma 1 protein I.YSKLKPNLVLDIKGGTQ.Y Q9Y4K1 1 2.486 2 Acetylcholine receptor protein, β chain I.DGPNRAVALLPEL.R P11230 1 2.6529 2 Acetyl-CoA carboxylase 2 (EC 6.4.1.2) (ACC-β) V.SIQCADHLEDEALVPIL.R O00763 1 2.2843 2 V.EVAVPADPANL.D O00763 1 2.2644 2 112 Acidic leucine-rich nuclear phosphoprotein 32 family member D.EEEEGEEE.D P39687 1 2.224 1 Acidic leucine-rich nuclear phosphoprotein 32 family member E.EFDEEDDEDEDV.E Q92688 1 2.9979 2 Actin-related protein Arp11 V.KEFAKYDVDPQK.W Q9C0K3 1 2.441 2 Activating signal cointegrator 1 (ASC-1) L.MSGVENSGKVDISTKDLLPHQELRIKSG.L Q15650 1 2.9918 2 Acyl-coenzyme A oxidase 1, peroxisomal (EC 1.3.3.6) L.FSEKLLKIQDKA.I Q15067 1 2.537 2 AD036 P.ESLKIQFENVYNT.F Q9H2L6 1 2.7828 1 ADAM 12 L.VTILCLLAAG.F O43184 1 2.5405 2 ADAM 21 H.DFFIYSQ.S Q9UKJ8 1 2.3327 1 ADAMTS-10 R.DVEQYVLAIMNIVAKL.F Q9H324 1 2.8216 2 ADAMTS-9 S.FSGETDDDNYLALSSSK.G Q9P2N4 3 2.4151 2 Adapter-related protein complex 1 β 1 subunit G.SYVAPKAVWLPAMKAKGL.E Q10567 1 2.8714 2 Adapter-related protein complex 1 γ 1 subunit L.DSCEPEFKADCAS.G O43747 1 2.6335 2 Adapter-related protein complex 3 β 2 subunit S.IQPPVGELMAPVFMSE.N Q13367 1 2.3839 1 Adenomatous polyposis coli protein (APC protein) E.CISSAMPKKKKPSR.L P25054 1 2.9705 2 Adenylate cyclase type I (EC 4.6.1.1) (Fragment) -.MAGAPRGGGGGGGGAGEPGGAER.A Q8NFM5 1 2.7466 2 Adenylate cyclase type III (EC 4.6.1.1) Q.QENLMLSILPK.H O60266 1 2.276 1 Adhesion regulating molecule 1 A.LTGPGLASLLGSSGPPGSSS.S Q16186 1 2.9009 2 Adlican L.VEPEVTSTPLEEVVD.D Q9NR99 6 2.6423 2 F.LKTKDDAINGD.K Q9NR99 3 2.631 2 Q.LVCMARNEGGEAR.L Q9NR99 1 2.6167 2
113 AF-4 protein (Proto-oncogene AF4) (FEL protein) Y.RQQTFEKTDLKVPA.K P51825 1 2.5416 2 Afamin (α-albumin) (α-Alb) K.SDVGFLPPFPTLD.P P43652 1 2.2582 1 K.LPNNVLQEK.I P43652 1 2.7702 2 K.DMVEYK.D P43652 1 2.0797 1 R.ESLLNHFLYEVAR.R P43652 3 2.4602 2 R.DADPDTFFAK.F P43652 1 2.2087 2 Aggrecan core protein A.EVSGESSRAEIGSSLPSGA.Y P16112 1 2.9114 2 A-kinase anchor protein 11 V.EGLGQDGKTL.L Q9UKA4 1 3.3994 2 A-kinase anchor protein 9 (Protein kinase A anchoring protein K.SLKQEKEQVSLRCRELE.I Q99996 1 2.8081 2 M.KLEFGEENLPKE.E Q99996 3 3.3013 1 Aldehyde dehydrogenase 1A1 C.PFGGFKMSGNGREL.G P00352 1 2.3626 1 ALMS1 protein A.SVQVLITGDENLS.D Q8TCU4 1 2.463 2 (continued) Supplementary Table 1 (continued)
Swiss-Prot Peptide Charge Protein Peptidea Accessionb Countc Xcorrd Statee
α-(1,3)-fucosyltransferase N.GSRFPDSTGTPAHSIPLILL.W P51993 1 2.4898 2 α-1-acid glycoprotein 1 (AGP 1) K.NWGLSVYADKPETTK.E P02763 2 4.6259 2 K.TEDTIFLR.E P02763 5 2.975 2 G.LSVYADKPETTK.E P02763 2 2.916 2 K.WFYIASAFR.N P02763 1 3.1987 2 K.SDVVYTDWKK.D P02763 2 2.547 2 K.SDVVYTDWK.K P02763 4 3.02 2 R.YVGGQEHFAHLLILR.D P02763 1 4.1392 2 α-1-acid glycoprotein 2 (AGP 2) R.SDVMYTDWK.K P19652 1 2.6156 2 W.GLSFYADKPETTK.E P19652 1 2.9649 2 α-1-antichymotrypsin (ACT)
114 K.AVLDVFEEGTEASAATAVK.I P01011 2 5.7892 2 G.SEAFATDFQDSAAAK.K P01011 1 3.0441 2 K.MEEVEAMLLPETLK.R P01011 2 2.2959 2 K.ADLSGITGAR.N P01011 6 2.6098 2 K.LINDYVK.N P01011 2 2.6841 2 K.ITLLSALVETR.T P01011 2 2.7783 2 R.LYGSEAFATDFQDSAAAK.K P01011 13 4.3353 2 R.EIGELYLPK.F P01011 5 2.202 2 R.NLAVSQVVHK.A P01011 12 2.9613 2 P.NSPLDEENLTQENQDR.G P01011 4 3.838 2 α-1-antitrypsin (α-1 protease inhibitor) K.LYHSEAFTVNFGDTEEAKK.Q P01009 6 5.1736 2 L.SGVTEEAPLK.L P01009 14 3.307 2 K.FNKPFVFLMIEQNTK.S P01009 4 4.6986 2 K.LYHSEAFTVNFG.D P01009 1 2.6451 2 F.HVDQVTTVK.V P01009 1 2.9002 2 K.QINDYVEK.G P01009 1 2.3965 2 K.TDTSHHDQDHPTFNK.I P01009 23 3.6922 3 K.DTEEEDFHVD.Q P01009 1 2.4445 2 G.VTEEAPLK.L P01009 1 2.5992 1 D.FHVDQVTTVK.V P01009 2 2.5239 2 K.WERPFEVK.D P01009 7 2.2646 2 K.DTEEEDFHVDQVTTVK.V P01009 23 3.6016 2 D.LSGVTEEAPLK.L P01009 6 2.4237 2 K.VFSNGADLSGVTEEAPLK.L P01009 42 5.0453 2 A.TAIFFLPDEGK.L P01009 5 2.4793 2 L.ENELTHDIITK.F P01009 4 2.4688 2 K.FLENEDRR.S P01009 10 2.5207 2 K.SVLGQLGITK.V P01009 28 2.2582 2 H.LENELTHDIITK.F P01009 3 3.9513 2 K.SPLFMGK.V P01009 11 1.9787 1 K.AVLTIDEK.G P01009 30 2.0124 1 E.NELTHDIITK.F P01009 6 2.8188 2 K.FLEDVKK.L P01009 12 2.602 2 K.FLENEDR.R P01009 5 2.2743 2 K.ELDRDTVFALVNYIFFK.G P01009 1 3.6105 2 G.LFLSEGLK.L P01009 1 2.4399 2 K.LQHLENELTHD.I P01009 9 3.3513 2 F.TVNFGDTEEAK.K P01009 6 2.8353 2 K.LQHLENELTHDIITK.F P01009 94 3.831 3 115 F.TVNFGDTEEAKK.Q P01009 28 2.8769 2 K.LSITGTYDLK.S P01009 56 2.6557 2 K.LQHLENELTH.D P01009 1 2.9785 2 K.KQINDYVEK.G P01009 4 3.1848 2 K.ITPNLAEFAFSLYR.Q P01009 3 2.2774 1 F.SNGADLSGVTEEAPLK.L P01009 6 2.4139 2 G.ADLSGVTEEAPLK.L P01009 15 3.5818 2 A.DLSGVTEEAPLK.L P01009 6 2.829 2 L.TTGNGLFLSEGLK.L P01009 2 2.6057 2 K.GKWERPFEVK.D P01009 7 3.1221 2 K.LSSWVLLMK.Y P01009 2 2.7493 2 R.SASLHLPK.L P01009 38 2.5588 2 N.LAEFAFSLYR.Q P01009 1 2.5092 2 N.GADLSGVTEEAPLK.L P01009 9 3.5966 2 S.NGADLSGVTEEAPLK.L P01009 4 2.6898 2 R.TLNQPDSQLQLTTGNGLFLSEGLK.L P01009 15 4.5806 2 T.VNFGDTEEAKK.Q P01009 2 2.4483 2 Q.HLENELTHDIITK.F P01009 1 3.935 2 Q.INDYVEK.G P01009 2 2.7765 2 (continued) e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table .REKLLQR.L Q92186 4 2.9102 2 .VQIKAELTPKDNIYTSEVVSQRG.L Q8IZJ3 3 3.1897 2 .TPGAAANLELIFVGPQHAGNYR.C.AEGVTVQIKAE.L P04217 23.HGPGLIYR.Q 5.0976 Q8IZJ3 3 1 3.01 2 P02765 10 2.4429 2 .MGVVSLGSPSGEVSHPR.K P02765 1 3.6727 2 K.LPPNVVEESAR.AK.HYDGSYSTFGER.YK.VDLSFSPSQSLPASHAH.LK.YGAATFTR.TK.DTVIKPLLVEPEG.LL.SFSPSQSLPASHAH.LD.SLVFVQTDK.S P01023 P01023 P01023 P01023 101 8 P01023 P01023 32 P01023 2.2359 3.2719 1 3.2648 1 13 2 2 2 2.5304 1 2.5569 2.2899 2 2 2 2.4615 2 K.HQFLLTGDTQGR.YA.PEFSPEPESGR.AK.LLELTGPK.SK.NGVAQEPVHLDSPAIK.HE.TLPAPEFSPEPESGR.AL.SDETLPAPEFSPEPESGR.AP R.SWVPHTFESELSD.PP T K.PALNLIYK.PW P04217K.HTLNQIDEVK.V P04217G.SPSGEVSHPR.K P04217K.FSVVYAK.C P04217 P04217G.VVSLGSPSGEVSHPR.K 27 P04217F 4M.GVVSLGSPSGEVSHPR.K 1R.HTFMGVVSLGSPSGEVSHPR.K P04217 1 3.5625P 1 13R.AQLVPLPPSTYVEFTVSGTDCVAK.E 4.0614 2.4665 2 3.9795 2.9326 2 1 2.4429 2 2 2 Q9Y274 2 3.6388 P02765 2 P02765 P02765 P02765 P02765 1 P02765 P02765 42 2.9461 3 2 1 1 1 3.5955 2 5 3.2757 5.5066 2.7098 2.6556 2.962 2 2 2.5008 3 2 2 2 2 -2-M) -1-B glycoprotein) α α -2 macroglobulin family protein VIP family protein -2 macroglobulin 2,3-sialyltransferase ST3GAL VI -2,8-sialyltransferase 8B (EC 2.4.99.-) (ST8Sia II) (Fetuin-A) -2-HS-glycoprotein ( -2-macroglobulin -1B-glycoprotein ( -1B-glycoprotein α α α α α Proteinα Peptide
116 (continued) .SSTQDTVVALHALSK.Y.FVELTMPYSVIR.G P01023 12 3.7274 P01023 2 2 2.4262 2 A.SPAFLAVPVEK.EK.SIYKPGQTVK.FL.PPNVVEESAR.AK.DTVIKPLLVEPEGLEK.EH.PFTVEEFVLPK.FK.DMYSFLEDMGLK.AK.YDVENCLANK.VA.SVSGKPQYMVLVPSLLHTETTEK.GK.ATVLNYLPK.CK.TAQEGDHGSHVYTK.AF G.TVVELTGR.QG.FSSTQDTVVALHALSK.YK.GHFSISIPVK.SK.FEVQVTVPK.IK.NEDSLVFVQTDK.SK.DNSVHWERPQKPK.A P01023 P01023F P01023 P01023K.SLNEEAVKK.D P01023K.MVSGFIPLKPTVK.MK.LHTEAQIQEEGTVVELTGR.Q P01023 10 P01023M.VLVPSLLHTETTEK.G 30 1K.QFSFPLSSEPFQGSYK.V P01023 4 P01023K.MVSGFIPLKPTV.K 4 3.7168K.VDLSFSPSQSLPASH.A 16 4.1965 4.4279 P01023 1K.DNSVHWER.P P01023 2.2077K.VYDYYETDEFAIAEYNAPCSK.D 2 3.1942 6D.TVVALHALSK.Y 2 3 3 3.7441K.FQVDNNNR.L 3.146 2 P01023K.PLLVEPEGLEK.E 17 2 L.EASPAFLAVPVEK.E 2.1307 1 P01023 2 P01023 P01023 3.7946K.PQYMVLVPSLLHTETTEK.G P01023 2 P01023K.ALLAYAFALAGNQDK.R 2.2869 1 K.AAQVTIQSSGTFSSK.F 2 3.9512 2 K.AIGYLNTGYQR.Q P01023 33 49 P01023 4R.TGTHGLLVK.Q 2 P01023 4R.SLFTDLEAENDVLHCVAFAVPK.S 2 P01023 2.9096 2 P01023R.SSGSLLNNAIK.G 3.0319 3.1756 23 3.3328 P01023 P01023 2 2.4979 4 3.6176 4 2 5 2 2 1 3.3094 2 P01023 2 2.6727 2 1 P01023 P01023 2.7605 4.0516 2 3.3003 P01023 P01023 P01023 2 P01023 2 2.8676 P01023 2 2.8228 5 P01023 2 6 4 2 2 2 1 6 P01023 2 2.6082 3 2.5027 4.4423 P01023 8 2 2.4831 3.1655 2.3542 P01023 4.4268 2 3 33 3.7014 3.0378 2 2 2 2 11 2 2.5474 18 2 2.5347 2 2.5526 2 2
117 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table HVEEPHTETVR.KSMDENFHPLNELIPLVYIQDPK.G P01023 P01023 2 1 3.3294 2.5361 2 2 VIKPLLVEPEGLEK.E P01023 1 3.2207 2 .MVLVPSLLHTETTEK.G P01023 1 2.4408 2 .PNVVEESAR.A.GTSNHLLL.A P01023 4 2.3505 1 O14686 1 2.5903 2 R.AVDQSVLLMKPDAELSASSVYNLLPEK.DQ.FSFPLSSEPFQGSYK.VR.TEVSSNHVLIYLDK.VS.STQDTVVALHALSK.YN.GITYTPVSSTNEK.DR.VVSMDENFHPLNELIPLVYIQDPK.GR.SLFTDLEAENDVLH.CR.SASNMAIVDVK.M P01023R.VTAAPQSVCALR.AT. R.VGFYESDVMGR.GR.TEHPFTVEEFVLPK.FR.LVHVEEPHTETVR.K 3R.KDTVIKPLLVEPEGLEK.ER.LLIYAVLPTGDVIGDSAK.Y P01023V. P01023 3.8699P P01023R.LVHVEEPHTETV.R P01023V. 2 R.IAQWQSFQLEGGLK.Q 4 P01023R.NALFCLESAWK.T 1 P01023R.NQGNTWLTAFVLK.T 1Y 1 3.2632 P01023R.HNVYINGITYTPVSSTNEK.D P01023 3.1744 5R.QTVSWAVTPK.S 4.3545Q.DTVVALHALSK.Y 1 2 2.7694 P01023 P01023R.QGIPFFGQVR.L 2 P01023 P01023 P01023 7 3.2414 2 7L.DTTVPLLVLIEAAKN.G 2 3.4195 2 29S.DISNPTAHENYEKNNVMLQW.- 26 3.1983 7 18 2 20 2.2157P P01023N.EEMPLLPPPEE.S 2 P01023 3.4185 4.1984 2 2.9462 2.6208 3.0381 P01023 P01023 P01023 2 3 2 2 2 2 7 18 2 3 P01023 3.1365 P01023 P47710 2.7785 Q9UI47 P01023 3.5073 2 3.3135 2.4561 2 2 4 2 1 2 1 1 1 2.6846 2.989 2.4844 O14686 3.128 2.549 2 2 2 2 2 5 2.4816 1 -catenin-like protein VR22 -catenin-like protein -s1 casein [Contains: Casoxin D] Protein Peptide α α ALR
118 (continued) .YLNGNYLIIF.V Q969I6 2 2.5468 2 .EAQCGLVLNGQGGVIRRG.G Q8IWX0 1 2.4971 2 .WLTNQGNYKLLVTMED.W Q9UKU9 1 2.418 2 .GPVDEETFLK.A Q9GZV1 1 2.8445 2 .DVNQLQNTTIKR.I P22966 1 2.8034 2 W K.EDSCSGSDAGSAAGST.YA.EVEVTDEAAGGEVNESVE.AD.KFRGVEFVCCPLA.EI.RKQLEVLVSPTCSCK.QY Q8TDM9 Q02410 1 3 P05067 Q9Y451 2.8712 2.4854 2 3 2 1 2.913 3.2163 2 L.LRELQRLAAADGA.VF K.ALQDQLVLVAAK.LK.QPFVQGLALYTPVVLPR.SK.DPTFIPAPIQAK.TR.LQAILGVPWK.DR.SLDFTELDVAAEK.IQ.ECKTVQETRGTFYTTR.QT K.LPGIVAEGR.D Q9BZZ0K.SKLPGIVAEGR.DR.DDLYVSDAFHK.AV P01019 1 P01019L.GPVTQEFWDNLEK.EK.LHELQEK.LK.LLDNWDSVTSTFSK.L P01019 2.2504 3K.VSFLSALEEYTK.K P01019 P01019 Q12955 1K.PALEDLR.Q 2 3.5813 7 2.5331 1 5 1 2 2 2.2056 P01008 P01008 2.359 3.2971 2.7253 P01008 2 2 2 2 P02647 4 3 8 P02647 P02647 2.2544 P02647 2.6239 6 2.633 81 2 2 P02647 2 3.5104 73 2 3.778 1 3.8248 3 2.2824 2 2 1 1.9462 1 A4 protein-binding family A family A4 protein-binding member 1 (APP) (ABPP) A4 protein β β Amino acid transporter hNAT3 Amino acid transporter hNAT3 cancer 1 Amplified in breast Amyloid Amyloid associated shutoff proliferative prostate Androgen-induced 2 (Angiopoietin-like 2) protein Angiopoietin-related Angiopoietin-related protein 5 protein Angiopoietin-related Angiotensin-converting enzyme, testis-specific isoform Angiotensin I (Ang I) Angiotensinogen [Contains: Ankyrin 3 (ANK-3) (Ankyrin G) 2 (Skeletal muscle ankyrin) domain protein Ankyrin repeat (PRO0309) (ATIII) Antithrombin-III AP-2-like protein A-I Apolipoprotein (Apo-AI)
119 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table .TQEFWDNLEK.E P02647 1 2.2243 1 .VSQFEGSALGK.Q P02647 1 3.2428 2 .HLAPYSDELR.Q P02647 8 2.8164 2 D.YVSQFEGSALGK.QK.AKPALEDLR.QK.LREQLGPVTQEFWDNLEK.EG.PVTQEFWDNLEK.EK.VSFLSALEEYTKK.LL.PVLESFK.VK.ATEHLSTLSEK.AL.DNWDSVTSTFSK.LA.PYSDELR.QK.VQPYLDDFQK.KK.DLATVYVDVLK.DD.NWDSVTSTFSK.LL.LDNWDSVTSTFSK.LR.AELQEGAR.QQ.GLLPVLESFK.V P02647Q.PYLDDFQK.K P02647Y T P02647N.WDSVTSTFSK.L P02647 2V P02647 3R.THLAPYSDE.LR.LAEYHAK.AR.QGLLPVLESFK.V 26 3.4443 P02647 11 P02647Q.DEPPQSPWDR.V 2.922 P02647 1R.EQLGPVTQEFWDNLEK.E 2 R.AHVDALR.T P02647 2.3827 P02647 3.4813R.THLAPYSDELR.Q P02647 2 63R.DYVSQFEGSALGK.Q P02647 P02647 4 2.9771 2R.DYVSQFEG.S 2 2 R.VKDLATVYVDVLK.D 3.2899 2 18 2 P02647 3.503 1 P02647K.SPELQAEAK.S 2.4006 3 1K.SKEQLTPLIK.K P02647 2 K.VKSPELQAEAK.S 2.0188 2.2466 2 2 2.3052 P02647 1 2.4802 2.8585 4 1 2 1 5 P02647 P02647 2 2 P02647 2.7327 2.4088 P02647 1 P02647 2.2534 2 2 20 1 P02647 P02647 13 2.521 P02647 1 1 P02647 1 3.1572 2.529 2 P02647 2.3848 91 94 2.2094 2.4812 2 2 14 2 P02652 2 P02652 P02652 2 2.6133 2.8903 2 1 1.9003 2.5871 2 2 56 58 11 1 2.3581 2 2.2975 1 3.1895 2.706 2 2 2 Protein Peptide A-II (Apo-AII) (ApoA-II) Apolipoprotein
120 (continued) .IEDVNKFLDMLIKKLKSFD.Y P04114 1 2.7093 2 S.KEQLTPLIK.KK.LVPFATELHER.LK.LGEVNTYAGDLQK.KK.SVSLPSLDPASAK.IK.FPEVDVLTK.YK.MGLAFESTK.SK.ALVEQGFTVPEIK.TK.GNVATEISTER.DK.SVSDGIAALDLNAVANK.IF K.TGLKEFLK.TK.LTISEQNIQR.AK.TEVIPPLIENR.QL.SGGNTLHLVSTTK.TK.HINIDQFVR.KA.GKLKQHIEAIDVR.V P02652 P06727K.SVGFHLPSR.E P06727K.VLVDHFGYTK.DG.GNTLHLVSTTK.T P04114K.FSVPAGIVIPSFQALTAR.FK.EVYGFNPEGK.A 1 2 1 P04114K.IISDYHQQFR.Y P04114 P04114K.SPAFTDLHLR.Y P04114K.FVTQAEGAK.Q 1 P04114 2.5479 2.3551K.GFEPTLEALFGK.Q 2.4198K.ATFQTPDFIVPLTDLR.I 18 3 1K.YSQPEDSLIPFFEITVPESQLTVSQFTLPK.S 2 2 2.3814 1 2 K.ATGVLYDYVNK.Y P04114 5 P04114K.IEGNLIFDPNNYLPK.E P04114 P04114 2.4942 4.2328K.LLSGGNTLHLVSTTK.T 2 2.3459 P04114R.TSSFALNLPTLPEVK.F 2.3956R.VIGNMGQTMEQLTPELK.S 3.1074 P04114 2 2 2 R.TGISPLALIK.G P04114 1 1 2 2R.SEILAHWSPAK.L 4 P04114 P04114 2 P04114R.VPSYTLILPSLELPVLHVPR.N P04114 1R.LPYTIITTPPLKD.F 2.3911 1 2.5093 2.9646 P04114 2.2401 3 6 9 P04114 2.7493 2 2 2 1 P04114 2 2.4716 2 P04114 P04114 P04114 2.3473 2 2 2.8297 2.621 2 3.0624 2.5701 P04114 1 P04114 2 15 P04114 2 2 P04114 2 2 2.0261 4 2 2 P04114 2.3364 P04114 3.5189 2 1 3.6204 4 10 2.6842 2.2888 2 2 2 3 P04114 P04114 2 2 3.4729 1 2.6852 4.307 7 P04114 3.3675 2.3633 2 2 6 2 4 5.4198 2 2 1 3 2.3031 3.2666 2.6241 2 2 2 Apolipoprotein A-IV Apolipoprotein (Apo-AIV) B-100 (Apo B-100) Apolipoprotein
121 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table PESQLTVSQFTLPK.S P04114 1 2.7832 1 .EALFQLWTAEPLDQAAA.S Q9HAU8 1 2.2979 2 R.LPYTIITTPPLK.DV. R.KGNVATEISTER.DR.ITENDIQIALDDAK.IG.TPDVSSALDK.LK.LKEFGNTLEDK.AK.TAAQNLYEK.TK.DALSSVQESQVAQQAR.GR.GWVTDGFSSLK.DK.VLNQELR.AK.NILTSNNIDVK.KR.NPNLPPETVDSLK.N P04114A.KVEQAVETEPEPELR.Q P04114K.SELEEQLTPVAEETR.A P04114A.AVIGIIVPIVVIALLCMS.G 13 P02654 P02654R.VQQNVPSGTDTGDPQSK.P 8 2R.VTEPISAESGEQVER.V P02656 3.8202R.NEADELRK.A P02655 3.8081 2.9551G.SGGQAERTIAGTTRAVSR.G 2 6 2 P02656 2K.WIYHLTEGSTDLR.T 2 2 1 2.6324 3.1292L.LQDLLLGLQFRAELGLQGCLGRGAGM.H P05090 P05090 P05090 P02649 3.9693 9L.HGQPVSFLLK.E 2 P02649 2 2.4772 Q99876 2 V 1 3 O14791 2.4324 2 1 2 1 2 O14791 1 Q9Y5L6 2.8552 3.0569 O95236 2.2702 2.4094 1 2.8404 2 2 2.8511 O14791 2 2 2 1 2.8038 2 1 O95445 2 2 2.7808 3.0424 2 2.7241 1 2 2 P05089 2 2.551 3.5798 2 2 2 2.6211 2 Protein C-I (Apo-CI) Apolipoprotein C-II (Apo-CII) Apolipoprotein C-III (Apo-CIII) Apolipoprotein D (Apo-D) (ApoD) Apolipoprotein Peptide E (Apo-E) Apolipoprotein 2 906 E receptor Apolipoprotein L-I) L1 (Apolipoprotein Apolipoprotein L-III) (ApoL-III) L3 (Apolipoprotein Apolipoprotein M (Apo-M) (ApoM) (G3a) (HSPC336) Apolipoprotein APR-5 (Fragment) protein Apoptosis related arginase) 1 (EC 3.5.3.1) (Liver-type Arginase aminopeptidase-like 1 Arginyl
122 (continued) .NARSFTAGREHGPR.C Q9H4T6 1 2.4344 2 .HHHVPNATLESSAGA.E.IEAEHTLRELDALDAN.D Q99758 Q08211 1 2.3863 2 2 2.4785 2 .IFAAAQMIGWYDPK.V P54136 1 2.6361 2 .VTSSVSDPGVGSI.S Q8WWM7 1 2.6951 2 T A.AETASLEEQLQ.GI.RSNVYVDVKPL.SR.EGATANVSEGEKK.TS.EIPKLPAVSLLIGGVWF.NP D.FKGSSDDEEESR.LR.NNVKVWFNNKGWH.AV S.FSESRADEVAPAK.K Q15041V Q9NR48 Q9NR48 Q9UHB3K.KVEFVLK.Q 1L.AAHQIHQGLQASSAK.E 1 1 2H.LLNAFTVTVPK.D 2.8104 O95477 Q96QE3A.SRDAGAREQQDALVLYQQ.D 2.3294 2.4186 2.436 2 L.RAEIENLHRTFGQFL.E 2 2 1 1W 1 P53396L.MKVHLKFEINAYDPAI.V 2.4684 2.2257A.VVFIPCGHLVT.C 1 O60474 2 N.LEKEKEDVPVEMSNGEPVCHYF.E 1 Q9H1S5 O75882 2.4802 Q9NZQ7 1 2 1 Q9NU64 1 2.535 1 2.9715 Q9NR09 2.5028 Q9H301 1 2 2.7083 2 2 1 2.7546 2 Q96P09 1 2 2.3275 3.2829 1 2 2 2.5654 2 TP(GTP)-binding protein A, member 1 TP-binding cassette, sub-family A, member 3 TP-binding cassette, sub-family (pro-S-)-lyase) TP-citrate synthase (EC 2.3.3.8) (ATP-citrate TP-dependent RNAA helicase (Nuclear DNA helicase II) Arginyl-tRNA synthetase (EC 6.1.1.19) (Arginine—tRNA ligase) (Aip-1) ARL-6 interacting protein-1 ASH1 3 (Fragment) Aspartyl protease domain protein Ataxin-2 related A A A A A Attractin (Mahogany homolog) (DPPT-L) B cell RAG associated protein B7-H1 (PD-1-ligand) (Similar to membrane protein) BA110H4.2 MOG) glycoprotein, BA145L22.1.2 (Myelin/oligodendrocyte (Fragment) BA93B14.2 (Novel protein) Baculoviral IAP 6 protein repeat-containing Baculoviral IAP 8 protein repeat-containing BAF180
123 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table PRDMEKEKTMLVLALLLAKKVASHTP.S P55957 1 4.032 3 .KTEMVTISDASQRTEIS.T.VNLSVHGPPTVSVLP.E O43491 1 P98160 3.273 4 2 2.7867 2 .QPSYDIDNFD.I P54132 1 2.2413 1 .AGILENGAVR.Y P02749 3 2.5211 2 V L.SHRAGSPALPKGDPLLGDCRS.PV K.ETGVEKAGSVLVQAGPWVG.YA.ASDDDDDDV.VR.RSGIRRTWGNENY.VK.ATVVYQGER.VK.FICPLTGLWPINTLK.C Q9BZE3F K.WSPELPVCAPIICPPPSIPTFATLR.VR.VCPFAGILENGAVR.Y 1 P43320 2.4621 1 2 P08588 Q9BYG0 P02749 2.5157 P02749 2 P02749 1 1 3 P02749 1 2.5016 2.1109 2.8171 4 2 1 1 4.2545 2 2.4423 2 3.4264 2 2 R.KLLKFILQ.HL.RGDVFQKFIESDK.FY. P25098 Q8NHY0 1 1 2.4102 3.2741 2 2 T Q.FQACIMKMVCGK.AH.YLLEYKKGDGIALLSEE.RI.GCKVLSFIR.LA.EGKAEEKEGE.K P03999 Q9P0V3 1 1 P32247 P80723 3.0467 2.5039 2 2 7 5 2.864 2.8084 2 2 -acetylglucosaminyltransferase 5 -acetylgalactosaminyltransferase N N crystallin B2 (BP) -1 adrenergic receptor -1 adrenergic 1,3- H) (Apo-H) I (Apolipoprotein -2-glycoprotein -4- -adrenergic receptor kinase 1 (EC 2.7.1.126) receptor -adrenergic Protein 4.1) protein 2 (Generally expressed Band 4.1-like protein BarH-like 1 homeobox protein Basement membrane-specific heparan sulfate proteoglycan β β β β Peptide β β BH3 interacting domain death agonist (BID) Bloom’s syndrome protein (EC 3.6.1.-) (RecQ protein-like 3) (EC 3.6.1.-) (RecQ protein-like protein Bloom’s syndrome pigment) Blue-sensitive opsin (Blue cone photoreceptor BOG25 subtype-3 (BRS-3) Bombesin receptor 1 (BASP1 protein) Brain acid soluble protein
124 (continued) YLSLR.E O60241 1 2.4837 2 L RY .VVTIQYRLGIWGFFSTGDEHGRGN.W.LEAPSGALSLLDLFSTLCNDLVN.S Q8TDZ9 Q9UK28 1 1 2.4089 2 2.5122 2 .IKTDITE.T O14789 2 2.5388 1 .DKPIVKKSIDE.L O94833 2 2.3235 1 S.GFAISGFNVNHLDIA.PC.LKEEVEKRKKF.KA.KDLFEIRTIKE.VY A.SGYLTDENEVGFR.GS.VTDSENTNQREAASHGF.GS.LKAAVGGQ.VS.GAEVTRTAGGAVEPGAGLLSGAEVTRTAGGAV.ES.KLQTRKMKGLKK.R Q9P2U7G.EKVSEIPLTR.D Q14127A.QEMSECNSNKE.N Q92560 1L.NEVSSALLELVPWRARE.G Q9BX63P 1 2.6642 P51587 1 P51587A.LYFLFCLPGFLFQ.F 2 2.8363 1 3.1534 1 P51587 2 1 2.9589 2 Q9H7B2 2.5041 2 2.8909 1 2 Q9UIF9 O94833 1 2 O95696 2.3265 3.0236 1 1 1 1 Q15800 2 2.9498 2.4983 2.7016 1 2 2 2 2.4194 2 K.GYILVGQAK.LK.LNNGEITQHR.KR.GSSVIHCDADSK.WR.KPELVNGR.L P04003 P04003 P04003 P04003 1 4 1 2.4154 2 2.3276 3.1372 2 2 2 2.3665 2 V V I.VILLAIVVLYV.AY. P55289 6 2.3064 1 chain (C4bp) α Brain-specific Na-dependent inorganic phosphate Brain-specific Na-dependent inorganic 1 (BRCA1 associated protein-1) BRCA1 associated protein BACH1 BRCA1-binding helicase-like protein BRDT cancer type 2 susceptibility protein Breast antigen (Fragment) carcinoma-associated Breast 1 Brix domain containing protein adjacent to zinc finger domain 2A Bromodomain 1 (BR140-like protein) protein Bromodomain-containing Bullous pemphigoid antigen 1, isoforms 6/9/10 oxidase (EC 1.-.-.-) C-4 methyl sterol C4b-binding protein Brain carboxylesterase hBr2 protein Brain specific membrane-anchored Brain-cadherin (BR-cadherin) (Cadherin-12) Brain-specific angiogenesis inhibitor 2
125 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table β KNIKTVMKAF.E Q9NQ18 4 2.1034 1 .AIVTVDDCDQGANGDIASLSIVAGDL.L Q14517 1 3.2841 2 .SIHLETCDGA.V Q9H4D0 2 2.4341 2 .TIRRKMEQMREEKEL.V Q9Y2L9 1 2.8398 1 L.ILLNMYASILLL.AR.FNEKHDFIALEIVDE.QK.IQDINDNEPK.FH.SPVVHVQANSPEGLK.VH.EMVASVDVSIQVK.DY G.ERYRLGGGNVDLESQAE.G P21730 Q9NYQ6 Q14517 3 2 Q9ULB5 Q14517 Q9HAT3 3.3684 2.2779 2 1 2 2 2 2 2.7667 2.282 2.4434 3.4537 2 2 2 2 E.SSDSANTTIEDEDAKAPR.VN.CMRTMGYMPTEMELIEL.SK.YISQFKNPLIM.LF L.TSLKKETSPAESKDWE.QK.ESEMDWDDSALTITVNPMEKHE.GP Q13554K.LIKKEFIETGK.V Q9NZU7L.KGQDEDQVHSVPIAQM.GF. 1 1A.VVGENGLAVIGV.F Q9H4D0 P98194 2.4545L.ESLMLRS.S Q96L12 3.8169N.HPIMKTGEPHCPGDEDETF.K 2 1 3 1 1 3.8028 Q9UL03 2.7841 2.5547 Q92887 3 2 2 1 O75976 9 P35218 2.8302 2.4517 2 1 1 O75976 2 3.0889 2.4335 1 2 2 2.7435 2 12.2 subunit (Fragment) α Protein (C5a-R) C5a anaphylatoxin chemotactic receptor 1 Cadherin EGF LAG seven-pass G-type receptor Cadherin-7 homolog tumor suppressor Cadherin-related Calcium channel kinase type II Calcium/calmodulin-dependent protein Peptide Calcium-binding protein CaBP1 (Calbrain) Calcium-binding protein type 2C, member 1 (EC) ATPase Calcium-transporting 1 (Fragment) Calponin homology domain containing protein 2) 3 (Calreticulin Calreticulin Calsyntenin-2 anion transporter 1 Canalicular multispecific organic DICE1 protein Candidate tumor suppressor 1 (Fragment) complex interacting protein CAP-binding protein mitochondrial (EC 4.2.1.1) Carbonic anhydrase VA, Carboxypeptidase D (EC 3.4.17.-) (gp180)
126 (continued) YEGTNEDELTF.K Q9Y5K6 2 2.8094 2 ASSSKCGKDKTK.S P11717 4 3.2816 2 F AHVHPRTQVPVAGT.L O43246 1 2.7712 2 A .SDVRVSPAAPERQ.E P43121 1 2.923 2 K.LSNNALSGLPQGVFGK.LR.LFQPLTHLK.TA.KPPGTPPSLGASPAK.PL.IALLLEAQATVDIKD.SL.DVSESGVLMRRR.PF. V. P22792 Q8WXD9 1 P22792 Q8WXE0 1 3.1996 Q9BXL6 1 1 2 2.4718 2.2958 2.7645 3 2 2 2 2.5863 2 L.FKLFKDLGCL.SK.TNLLQTVGSLEVLIL.SF. Q99467 P32248 2 1 2.774 2.3545 2 1 L.NMPLTRLNQPLQQS.RG.TPSGILYEPPAEK.EA.QYQFTDSETDVE.GQ.FPAQVTDVSENAKDPI.RL.KAEFGLLQ.RD.FCSTNVINKIILQSEGL.RV A.WGLADVRELHPGLLAH.R Q15429D.RNLARALSTDCTPSGDLSPLSREPPPSP.MA.SSPRVVGDARARALCADM.K O43866 1 Q9BZ29 Q8IWQ7 1 2.8726 1 1 Q9UEP1 Q99490 2 2.9673 Q8WYA0 2.9172 Q96P50 2.606 1 2 1 Q99490 4 2 2 3.0582 1 3.2548 2.9411 1 2 2 2.5926 2 2.8958 2 2 β ) (CT-2) ) (CT-2) α 5 (Cnt-b5) 1 β γ Carboxypeptidase N 83 kDa chain 1 Cask-interacting protein KIAA1139) 2 (Hypothetical protein Cask-interacting protein 14 domain protein Caspase recruitment (CAT4) (CAT-4) Cationic amino acid transporter-4 Cation-independent mannose-6-phosphate receptor C-C chemokine receptor type 7 (C-C CKR-7) C-C chemokine receptor antigen 64) CD180 antigen (Lymphocyte (Cas ligand with multiple SH3) CD2-associated protein CD46 CD5 antigen-like (SP- Cdc42 guanine nucleotide exchange factor zizimin 1 kinase CDC42-binding protein CDV-1R Cell cycle checkpoint protein MUC18 Cell surface glycoprotein Centaurin Centaurin
127 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table I.SSRNINDHH.SQ.EKIQELKANE.HK.AERGSHQGKKSGTSSKLSVKDFEQ.TK.MYYSAVDPTK.DK.ERGPEEEHLGILGPVIWAEVGDTIR.VK.DIFTGLIGPMK.IL.GPQLHADVGDK.VK.EVGPTNADPVCLAK.MK.ALYLQYTDETFR.TK.VNKDDEEFIESNK.MK.DVDKEFYLFPTVFDENESLLLEDNIR.M Q8WY20K.VDKDNEDFQESNR.MK.NNEGTYYSPNYNPQS.RK.GAYPLSIEPIGVR.F P00450K.LISVDTEHSNIYLQNGPDR.I Q03188 1R.TTIEKPVWLGFLGPIIK.A Q02224R.GPEEEHLGILGPVIWAEVGDTIR.VR.SVPPSASHVAPTETFTYEWTVPK.E 2.4347 1R.DTANLFPQTSLTLH.M P00450 1R.MFTTAPDQVDKED.E P00450 2R.GVYSSDVFDIFPGTYQTLEMFPR.T 2 P00450R.MFTTAPDQVDKEDEDFQESNK.M 4.6581 P00450 P00450R.EYTDASFTNR.K 2.4284R.KAEEEHLGILGPQLHADVGDK.V 2.5254 1 P00450 5 3 P00450Q.SEDSTFYLGER.T 2 R.IYHSHIDAPK.D P00450 2 19 P00450 1 1 P00450 P00450 4.1304K.ARPELEE.L 2.5961 P00450 44 1 P00450 P00450 3.4912L.IIILAIMIYKKSATDVF.E 2.2282 2 2.6795 2 1 1 P00450 3 3 P00450 4.2563 2 3.1961 2 6 2 P00450 26 3 3.1031 P00450 P00450 2.4743 2 2 5.6504 3.1481 4 2.4653 7 2 3.1325 2 3.2893 2 2 2 2 1 1 3.4632 P00450 2 2 4.0216 2.8672 P00450 2 3.7408 2.4251 P00450 2 2 Q8WUD6 3 3 2 1 Q96GC5 8 2.306 1 2.9725 1 2 2.7255 2.5755 2 2 2.6653 2 1 Protein autoantigen C) C (CENP-C) (Centromere protein Centromere E (CENP-E protein) protein Centromeric 350 protein Centrosome-associated (EC 1.16.3.1) (Ferroxidase) Ceruloplasmin Peptide protein CGI-118 Cholinephosphotransferase 1
128 (continued) WLWPLPKLALLPLLWV.L O60624 1 2.4653 2 .TPSQRCGGGLPGV.K Q96GW7 1 2.6023 2 .LLESQAALAV.L Q9UHF4 26 3.2839 2 V L.LLLGLLLLGSRPAR.GI.RNHFSVPLSVYEG.DK.QVNIYRLVTKGTVEEEIIERA.KR.AILEKNFSFLTKGANQHNMPN.LE.EEAAARRARSFAQDA.RG.FPAPSQSSTSDEEPGA.YC.SKMSSIVDR.DA.FKNDISFWKKK.K Q9H2X0 O14647F. Q8TD26 Q96RL7T 1 1G.YFEELILLLE.A 3 1 Q96DT5K.TLLSNLEEAKK.K 2.4964K.FMETVAEK.A 2.558 Q9P2M7D.PITVTVPVEVSR.K 2.4874 2 2.5277K.TLLSNLEEAK.K 1K.LFDSDPITVTVPVEVSR.K 2 2 R.KTLLSNLEEAK.K 2 5R.VTTVASHTSDSDVPSGVTEVVVK.LR.ASSIIDELFQDR.F O15516 2.5977 Q96KA5R.IDSLLENDR.Q 2.9358 2 K.MAESGYDIALLK.L 1 2 3S.FTEMEKNNLLLK.W 2.4089 P53675 2.4677 P10909 P10909 P10909 2 P10909 2 P10909 2 P10909 11 11 P10909 2 6 2 2.625 P10909 3.634 2.8565 6 P10909 4.7358 P03951 1 2.4485 1 2.1842 2 2 P05160 2.4298 1 2 2 1 3.3445 3 1 2 2.5528 2 1 2.5579 2.6059 2 2.5062 2 2 2 Chondroitin sulfate proteoglycan BEHAB/brevican sulfate proteoglycan Chondroitin Chordin protein) (Chorea-acanthocytosis Chorein 2 (CHD-2) protein Chromodomain-helicase-DNA-binding 5 (CHD-5) protein Chromodomain-helicase-DNA-binding Ciliary dynein heavy chain 11 Cingulin (hCLOCK) locomoter output cycles kaput protein Circadian CRR9p protein related Cisplatin resistance (CRL1 protein) Class I cytokine receptor ZCYTOR7 Class II cytokine receptor Clathrin heavy chain 2 (CLH-22) Clusterin Coagulation factor XI (EC 3.4.21.27) Coagulation factor XIII (B chain)
129 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table ALLTHGQEEGQVEGQDEDIPPITCVQN.G P02452 1 3.0983 2 GLPGPPGPSAVGK.P Q03692 1 2.4213 2 .GGRGALGPGGPLGHPGEKGEKGNSVFI.L P53420 3 2.8053 2 .GPPGKDGLPGPPG.D Q14993 1 2.3793 1 G.DMDLEPLFYLQQL.VR.FDHVITNMNNNYEPR.SK.TNQVNSGGVLLR.LR.FNAVLTNPQGDYDTSTGK.FK.VLNYVDWIK.KK.LFGEVTSPLFPK.PK.EDTPNSVWEPAK.AR.HAFILQDTK.AR.HAIILLTDGK.S Q9UKZ7K.TIYTPGSTVLYR.I P02746I.PPADLSDQVPDTESETR.II.PIVTSPYQIHFTK.T P02747K.GYTQQLAFR.Q 2 P02747 2 4 2.4156 3.5548 P00736 2 P00736 2 P09871 4.1056 3 2.2661 2 1 1 P06681 P01024 3 2 P06681 P01024 2.3732 2.9637 P01024 2.8012 1 2 2 1 2 P01024 11 2 2.7998 5 2.6694 3.287 2.3738 12 2 2 2 2.7953 2 2.2316 2 2 P K.GPQGDDGPKGNPGP.V P13942 1 2.6128 2 P G.EKGAKGEAGAEG.P P12107 4 3.0303 2 P. G.FQGLPGPAGPPGEAGKPGEQGV.PT. P02452 1 2.904 2 L.QPVVMCVMKHLPKVP.E Q8WX92 1 2.7555 2 4(IV) chain 2(XI) chain 1(XIX) chain 1(XI) chain 1(X) chain 1(I) chain α α α α α α Colon carcinoma related protein related Colon carcinoma Complement C1q subcomponent, B chain Complement C1q subcomponent, C chain Complement C1r component (EC 3.4.21.41) Complement C1s component (EC 3.4.21.42) (C1) Complement C2 (EC 3.4.21.43) (C3/C5 convertase) Complement C3 [Contains: C3a anaphylatoxin] Collagen Collagen Collagen Collagen Collagen ProteinCofactor of BRCA1 Collagen Peptide
130 (continued) K.SSLSVPYVIVPLK.TK.SGSDEVQVGQQR.TK.TGLQEVEVK.AG.SGEVVLSR.KD.VPVTVTVHDFPGK.KD.TVQSLTQGDGVAK.LK.GVFVLNK.KK.PGMPFDLMVFVTNPDGSPAYR.VG.EDTVQSLTQGDGVAK.LK.LSINTHPSQKPLSITVR.TK.AGDFLEANYMNLQR.SL.SITTDFIPSFR.LK.FYYIYNEK.GH.YLDETEQWEK.FK.IWDVVEK.AK.GQGTLSVVTMYHAK.A P01024K.AAVYHHF.I P01024L.PLSITTDFIPSFR.L P01024K.SDDKVTLEER.L P01024 P01024K.QELSEAEQATR.T P01024 19K.KQELSEAEQATR.T P01024 8K.LMNIFLK.D P01024G.NSNNYLHLSVLR.T 1 P01024G.DVPVTVTVHDFPGK.K 10 2.7553 2 P01024K.LSINTHPSQK.P P01024 3.7153 1K.AAVYHHFISDGVR.K 1 3.3407 2 K.EYVLPSFEVIVEPTEK.F 1 3.274 3.5905 2 L.PSFEVIVEPTEK.F 3 2.794K.YFKPGMPFDLMVFVTNPDGSPAYR.V 2 P01024 4 2.46 4 P01024G.TPVAQMTEDAVDAER.L 2 P01024 2 2.6133 P01024K.VQLSNDFDEYIMAIEQTIK.S 2 2.9305K.QDSLSSQNQLGVLPLSWDIPELVNMGQWK.I 1.9376 P01024 2 4.3759G.TLSVVTMYHAK.A 2 2K.VTIKPAPETEK.R P01024 2 8 1 P01024K.DYAGVFSDAGLTFTSSSGQQTAQR.A 2 1 2 P01024K.DYAGVFSDA.G P01024 P01024K.VLLDGVQNLR.A 2.4352 9 3.0788R.FYHPEKEDGK.L P01024 P01024 3.2252 P01024 P01024 2.7441 1 4 2 31 P01024 2 7 19 2.2257 P01024 2 2 P01024 P01024 2.547 11 3 2.4465 1 2 3.2001 1 P01024 P01024 3.2493 3.88 P01024 P01024 2 1 8 2 3.1498 2 8 4.0167 3.5111 1 2.7869 2 2 3.0209 5 1 2 2 P01024 3.8402 4 1 2 2 2.8204 2.2019 P01024 2 2.6527 2 5.1231 1 4.876 3.1425 2 P01024 P01024 1 2 2 P01024 22 1 2 2.5064 2 1 2.6495 6 2 2 2.2306 2.4432 2.5705 1 2 2
131 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table .GEKPNLSYIIGK.D P01024 1 2.9463 2 .PYVIVPLK.T P01024 3 2.559 1 .STVGNSNNYLHLSVLR.T P01024 3 3.8014 2 R.SGIPIVTSPYQIHFTK.TV R.LKGPLLNK.FR.APSTWLTAYVVK.VR.VPVAVQGEDTVQSLTQGDGVAK.LR.TFISPIK.CQ.PSSAFAAFVK.RR.SGIPIVTSPYQIHF.TR.LPYSVVR.NW R.EPGQDLVVLPLSITTDFIPSFR.LR.LVAYYTLIGASGQR.ER.YYTYLIMNK.GR.VVLVAVDK.G P01024R.SEFPESWLWNVEDLK.E P01024R.EVVADSVWVDVK.DR.NTLIIYLDK.VY R.SGIPIVTSPYQIH.F P01024 8 13R.IPIEDGSGEVVLSR.K P01024R.TVMVNIENPEGIPVK.QR.VELLHNPAFCSLATTK.R P01024 3.3679R.HQQTVTIPPK.S 3.8726 P01024 P01024 1R.EALKLEEK.K P01024N.SNNYLHLSVLR.T 1 2 2 R.TMQALPYSTVGNSNNYLHLSVLR.T P01024R.SNLDEDIIAEENIVSR.S 2 P01024 3.0801R.TELRPGETLNVNFLLR.M 5 1 2.3518 P01024R.SVQLTEK.R 7 2 Q.GDVPVTVTVHDFPGK.K P01024 3.5572 P01024 2 P01024 4 2.6277 3.1185 1K.YVLPNFEVK.I 2.241K.LGQYASPTAK.R 2 3K.LELSVDGAK.Q 2 2 P01024 4 3.8479 P01024K.LHLETDSLALVALGALDTALYAAGSK.S 2.2632 P01024 P01024 4 P01024 1 P01024 6 3.5286 2 2 2.4523 2.0769 4 1.9507 10 92 2 1 P01024 1 2 1 P01024 P01024 1 P01024 P01024 1 2.242 2.5193 3.8576 2.62 P01028 3.7676 P01024 3.5062 66 2 2 1 12 1 2 2 4 2 2 P01024 2.6705 2 2 4.8268 2.5302 P01028 2.689 P01028 2.5509 2 P01028 5.7793 2 2 3.4315 1 2 2 1 3 3 2 1.9184 3 2.2999 2.5413 1 2.3268 2 2 2 Protein Peptide Complement C4 [Contains: C4A anaphylatoxin]
132 (continued) G.ALSPGGVASLLR.LK.ITQVLHFTK.DK.KYVLPNFEVK.IK.ADGSYAAWLSR.DK.ITPGKPYILTVPGHLDEMQLDIQAR.YK.LNMGITDLQGLR.LK.AEFQDALEK.LK.VLQIEK.EK.VLSLAQEQVGGSPEK.LL.SVSAGSPHPAIAR.LK.PVQGVAYVR.FK.LVNGQSHISLSK.AK.EVYMPSSIFQDDFVIPDISEPGTWK.IK.VDFTLSSER.D P01028G.SEGALSPGGVASLLR.LK.DHAVDLIQK.G P01028R.EELVYELNPLDH.RR.KADGSYAAWLSR.D 1R.LTVAAPPSGGPGFLSIER.P P01028 P01028 P01028R.DFALLSLQVPLK.DR.TYNVLDMK.N 2 P01028R.LLLFSPSVVHLGVPLSVGVQLQDVPR.G 2.3723 P01028R.DFALLSLQVPLKDAK.S P01028 10 P01028R.YIYGKPVQGVAYVR.F 1 1 2.5173 2 R.VGDTLNLNLR.A P01028 4R.FGLLDEDGKK.T 2.6133 P01028R.NVNFQK.A 2 16 4 2.3694 P01028 2.3535 P01028R.EMSGSPASGIPVK.V 9R.GPEVQLVAHSPWLK.D P01028 3.7404 2 2R.TTNIQGINLLFSSR.R 2 2 3.0274 P01028 3.483R.GLQDEDGYR.M P01028 1 12 1.9015 2 R.VTASDPLDTLGSEGALSPGGVASLLR.L P01028 1 P01028 P01028R.GHLFLQTDQPIYNPGQR.V P01028 2 2.5536 3 2 R.STQDTVIALDALSAYWIASHTTEER.G 1 2.0926R.PVAFSVVPTAAAAVSLK.V 1 2.9044 P01028 2.2721 4 2 R.GSFEFPVGDAVSK.V 1 26 P01028 7 2.5801 1 2 2 K.LNLVATPLFLKPGIPYPIK.V P01028 2 3.8368 P01028 2.5931 2 3.5154 1 3.2355 3.4035 P01028 3.9674 3 P01028 2 2 P01028 2 2 2 6 2 P01028 P01028 P01028 2.3949 2 2.846 P01028 P01028 6 6 P01028 2.3154 1 3.6262 17 P01028 8 5 2 P01028 2 1 3.1882 2 3.2146 4 1 2.8166 2 P01031 3.7467 P01028 3.891 2.2813 2 2 4 2 2 3.1061 2.1602 2 2 3.6101 3 2 16 2.693 2 1 4.0718 3 2 2 4.3531 2.9325 2 2 Complement C5 [Contains: C5a anaphylatoxin]
133 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table .PLYELVK.E P10643 1 2.6771 2 .EGVKRESYSGVTLDPR.G P01031 1 2.7207 2 R.HTSLGPLEAK.RR.SDLEVAHYK.LR.LPLEYSYGEYR.DR.RPASPISTIQPK.AK.LSPIYNLVPVK.MS.PIYNLVPVK.MR.RPWNVASLIYETK.GR.DGNTLTYYR.RR.GTVIDVTDFVNWASSINDAPVLISQK.LR.AIEDYINEFSVR.KR.VVEESELAR.TD.SGGPLIVHK.RK.KDNEQHVFK.V P07357K.EELLPAQDIK.AK.VASYGVKPR.Y P07358K.VKDISEVVTPR.F P07358 P02748 7 P07360 P02748 3 2 P02748 2 3.2061 P02748 1 3.0505 P02748 2 3.2865 3.8251 4 P02748 5 2.7071 2 1 2 2 P02748 2.2413 1 2 3.335 P00751 2 P00751 2.4517 P00751 2 2 2.4076 P00751 2 P00751 2 3.1027 1 1 2 2.2974 1 2 3 6 3.1641 2.5118 2 2.3281 2 2.3782 2 3.7009 2 2 2 K.TLLPVSKPEIR.SK.KIEEIAAK.YK.IDTQDIEASHYR.GK.DSEITFIK.KK.TDAPDLPEENQAR.ER.YGMWTIK.AR.VYSLNDDLKPAK.RP R.IPLDLVPK.TK.HEGSFIQGAEK.SK.MEILHPGK.CT P01031 P01031 P01031 P01031 P01031 6 P01031 1 P01031 2 1 2.6767 2.9317 1 6 P01031 P13671 2.3406 2.3225 2 1 2 P13671 2.4918 2.9785 2 2 1 2.4396 1 2 2 2 2 2.4103 2.8464 2.5188 2 2 2 chain chain chain β γ α Complement component C8 Complement component C8 Complement component C9 Complement factor B K.EAGIPEFYDYDVALIK.L P00751 2 2.7504 2 ProteinComplement component C6 Complement component C7 Complement component C8 Peptide
134 (continued) .KGKAGAIGRAGPRGPKGVNGTPGKHGTPGKK.G Q9BXJ5 1 4.3781 3 .QTLLFERVFVNLDGCF.D Q9BXI9 1 2.316 2 K.DISEVVTPR.FK.DNEQHVFK.VK.ISVIRPSK.GK.ALFVSEEEKK.LK.VSEADSSNADWVTK.QK.QLNEINYEDHK.LQ.LNEINYEDHK.LR.LPPTTTCQQQK.ER.DAQYAPGYDK.VR.PHDFENGEYWPR.SR.GDSGGPLIVHK.RR.LEDSVTYHCSR.GR.YGLVTYATYPK.IK.EFDHNSNIR.YK.SPPEISHGVVAH.MK.SIDVACHPGYALPK.AK.SPDVINGSPISQK.I P00751K.WSSPPQCEGLPCK.S P00751 P00751K.GEWVALNPLR.K P00751K.IDVHLVPDR.K P00751 P00751K.SSNLIILEEHLK.NR.RPYFPVAVGK.Y 8 26 P00751 1R.SSQESYAHGTK.L P00751 16R.EIMENYNIALR.W P00751 P00751 1R.NTEILTGSWSDQTYPEGTQAIYK.C 2.9229 2 3.3877R.KGEWVALNPLR.K P00751 2.0972R.EYHFGQAVR.F 4 P00751 2.7728 1 2 2.4795 2 P00751 4 1 2.7017 1K.INHGILYDEEK.Y 2 13 3.4909 P08603 P08603 2 K.HGNTDSEGIVEVK.L 2.6828 P08603 2 1K.VTYTSQEDLVEK.K 2.62 3.2673 18 P08603 2 P08603 2.8478 2 H.YYQTVIFDT.E 22 2 2 3.4477 P08603 P08603 2 3 3.2602P 2 11 P08603 P08603 1 2 F 3.7585 3.3067 2 P08603 2.2884 P08603 3 4 P08603 2.3132 2 2 3.2118 14 18 P08603 2 21 2 2.9386 3.2054 2 1 P08603 1 2.7979 3.7921 Q03591 2 2 10 P05156 3.0302 2.5866 2 3 P05156 2.906 3 2 2.2205 4 2 8 2 Q9BXJ1 2 2.551 1 4.1175 4.3404 2 2.6967 1 2 2 2 2.2641 1 Complement factor H (H 1) 1 protein Complement factor H-related Complement factor I (EC 3.4.21.45) 1 protein factor-related Complement-c1q tumor necrosis 2 protein factor-related Complement-c1q tumor necrosis 6 protein factor-related Complement-c1q tumor necrosis
135 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table 3 α .VKSGSVTTKGSVCNIALR.F P82279 1 2.4323 2 .LCVSLMEPPAVLL.L P78396 1 2.4801 2 .SSDESSEEDLSAEMTEDETPK.K Q15021 1 4.1533 3 F K.SRMQLAAESLQE.AL.DSNGELLIRNAQLKHAG.RR.SPSYTNDSTATFIIDGMHCKSCVS.NK.HLVALSPK.KW G.SFGLALKVQEVPASAQNR.PK.EMYIINEGKLAVVADDG.V Q04656Y Q12860 P83436A.RAGFLDTLQTLL.E 1 3 1 2.744 Q8IZW8 3.005 3.0161 P08185 2 Q16281 2 2 1 3 1 2.2963 2.7278 P42773 1 2.4106 2 2 1 2.7742 2 A.VKAAQELQEGQ.RL.SRNNSVPNYCKN.DK.ADIYTQNFYWE.LL.EFFPKPNEFTL.EI.LNYIIPSGDLLML.SQ.LYDPDYMKVI.LH.RRMLTPAFHFNILKSYI.TG.GLWLRVEPLNVGLQ.- P35520 Q9NZV1 P05108 1 1 P11511 2.3807 Q9NYL5 1 2.7154 Q9HCS2 1 Q02928 1 2 Q9HCS2 1 2.4613 1 2 2.2896 1 2.4257 4 3.8916 2 2 2.4671 3.0699 3 1 2 -synthase (EC 4.2.1.22) β ProteinCondensin subunit 1 Conserved oligomeric Golgi complex component 7 gP135) Contactin (Glycoprotein 1 (EC 3.6.3.4) (Copper pump 1) ATPase Copper-transporting globulin (CBG) (Transcortin) Corticosteroid-binding homolog 1 protein Crumbs C-terminal tensin-like protein Cyclic-nucleotide-gated cation channel Peptide Cyclin A1 Cyclin-dependent kinase 6 inhibitor (p18-INK6) Cystathionine Cysteine-rich repeat-containing protein S52 protein Cysteine-rich repeat-containing mitochondrial (EC) P450 11A1, Cytochrome (EC 1.14.14.1) P450 19A1 (Aromatase) Cytochrome P450 39A1 (EC 1.14.13.-) - Cytochrome (EC 1.14.15.3) P450 4A11 Cytochrome P450 4F12 (EC 1.14.14.1) (CYPIVF12) Cytochrome
136 (continued) ADLIPVPLTYM.I Q9UJA2 2 3.2709 2 SPHISPFTAVNDLGHLLG.R Q9BQM4 1 2.4743 2 .FQYNFGLM.T.FFVIFIKHLIHSQIP.A Q96PD6 1 2.2373 1 Q9UJA9 1 2.5835 2 M.SSGQEYLF.RG.EGLNKTAI.GG.LWGSALGNTE.VE.NLEKYVVKDGKLPLLLSRMKEVGK.VE.QFKQLYELDGDPK.RE.DEESGMEEGDDAEDSQGESEEDR.AG.FLRRADSLVSATEM.AV P49902L.DRIMEHIKAAMEMVPVLKKADIINVV.N Q9UNU6L.FPDEVGCVDPDVC.Q Q15438 1 Q9NY61C.LLVDFLLDIVSLETYIEIQTEHL.P O75457 1L.NPSAIPDDTF.M Q99856E.LEELRAALEQGER.S 2.6414 1 1 Q9UI17 1 2.4775L.DNGELRSY.Q 2 Q96NW7F. 2.9923 2.5683 1 2 2.2107 1V 2 2 1 1 2.8137I.SLTVEYFLSEKQYDEFEIFDGPSGQSP.L Q9NTT5 2.2669 Q9NPZ7Y. 2 3.1557 2 1 2 1 Q9H430 2.4515 Q9H430 2.4438 Q9H4W3 2 1 Q9H102 2 1 1 2.7813 2.4177 1 3.8984 2 2 3 2.4766 2 E.ARFIARSLSGRL.RS.EVLKRFEEAAFTCEYK.Y P18858 P18858 1 1 2.93 2.5389 2 2 γ Cytochrome P450 8B1 (EC 1.14.-.-) (CYPVIIIB1) Cytochrome Cytohesin 1 (SEC7 homolog B2-1) A2- Cytosolic phospholipase Cytosolic purine 5’-nucleotidase (EC 3.1.3.5) of IgH transcription) (B-cell regulator Dead ringer like-1 protein (Apoptosis antagonizing transcription factor) Ded protein Densin-180 acyltransferase 2-like protein Diacylglycerol mitochondrial (EC) Dimethylglycine dehydrogenase, DJ1024N4.1 (Novel sodium:solute symporter family member) similar to C21ORF5 [KIAA0933]) DJ202D23.2 (Novel protein DJ756N5.1.1 (Continues in Em:AL133324 as dJ1161H23.3) of mouse P47) DJ776F14.1 (ORTHOLOG (Fragment) DJ842G6.1.2 (Novel protein) PC- DJ8B1.3 (Similar to plasma-cell membrane glycoprotein (Fragment) DJ947L8.1.7 (Novel CUB domain protein) DJ967N21.6 (Novel CDP-alcohol phosphatidyltransferase DNA ligase I
137 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table .GLPGGFAKRVLVTGGAGF.I O95455 1 2.4086 2 MKLDIAAVRALNLFQGSVE.D P43246 1 3.4995 2 .RKNLESRGVEVDPSL.I O60313 1 2.4064 2 .QLKGLLKKNYLN.Q P28715 1 2.5338 2 .PDADPVE.I.DKNKDENAETQFRQLVAIYEVLKDD.E Q96KC8 1 3.039 Q9H1D9 2 2 2.3972 1 D.KFVVLRQ.QE.FGEVEISSLP.DE.PLVMQLIHWF.TL.QAESVSEVVVNRVDV.AP P Y Q13472 P48380 O00411 P78527 1 5 1 1 2.448 3.0035 2.3162 2.6599 1 2 2 2 N.STYSEQDPLLK.NW L.EFQDFVNKCLIK.NG.VYPDKSVAENDENGQAE.NA.IPSPGPHSGAPPVPFRPGPLPPFPSSS.DV Q9UQ16 O75691 Q9UQ16 Q02750 1 1 1 2.5505 2.2725 1 3.1389 2 1 2.7179 2 2 R.ACSETEESNTCC.SY. Q9UHC1 1 2.4471 2 L.YMQRLGEINVI.GA.CLLFGGSR.KL.FDEEFPGGLTIRCSPGRGY.R P33991 Q8IZH2 P33992 3 1 10 2.1488 2.7869 1 2 2.4689 2 (EC 5.99.1.2) α DNA-binding protein RFX3 DNA-binding protein kinase catalytic subunit (EC 2.7.1.37) DNA-dependent protein RNADNA-directed polymerase, mitochondrial (EC) RNADNA-directed polymerases III 39 kDa polypeptide (EC) DnaJ homolog subfamily C member 1 complementing XP-G cells (Xeroderma) protein DNA-repair DRIM protein dTDP-D-glucose 4,6-dehydratase (EC 4.2.1.46) kinase 1 Dual specificity mitogen-activated protein Dynamin 3 (EC 3.6.1.50) (Dynamin, testicular) (T-dynamin) mitochondrial Dynamin-like 120 kDa protein, ProteinDNA Mlh3 (MutL protein mismatch repair homolog 3) protein DNA Msh2 protein mismatch repair Peptide DNA licensing factor MCM4 (CDC21 homolog) replication DNA licensing factor MCM5 (CDC46 homolog) replication DNA SEP1 strand-exchange protein DNA topoisomerase III
138 (continued) SQPQPANSNNGTSTATST.N Q8NDV7 1 2.4694 2 .SGRELEEKDGDVQAGAN.L O14576 1 2.7692 2 .SVNGAEVEVQ.S Q96RI7 1 2.3057 1 .ENIPGGAEEISEVLD.S P11532 1 2.4451 1 .EDLHIQE.S Q13201 1 2.7637 2 K.IGGIGTVPVGR.VT R.NRVSFLGAVTVEPPK.PF I.KELEVKQTHLEGA.LL.AAGLVACLAALGI.QK.RELPVAIKTLKVGYTE.K P04720 P10266 2 Q13201 1 P42892 2.3929 P54756 2.3795 1 2 3 1 1 2.5078 2.8259 2 2.4487 2 2 H.TVLVERSTLKEDVGDE.GL.SGSEERVQVALEELQDL.KN.PGYAGRSNLPDNLK.KA.QDFKYYDDAADE.YY A.GTTVPGQIRPTMTI.PT Q.VYARKEALKGGLEKTVSLQKDLS.EK.LSSSIQVKKTRAEGSSKIQ.A Q14204 Q14204A.STTASSSVTSASPNPLATGPL.GR.NFTLGGPSAGMTGPGAS.G Q14204 1V. 1 Q9UI46L.VSSTNLINEINGVSEKLSAT.E 1 P11532 3.0782 2.8861G.AAAGLVPGGPGFGPGVVGVPGAGVPGVGVPGA.G Q14118 1 2 2.4943L.LVSRSLGGAVGSVASGARAA.Q 2 2 Q96JC9 P15502 P11161 2 2.8685 1 P11161 4.4343 2 1 2.2736 5 1 3 O43432 1 2 2.4514 2.9085 2.2978 Q8NEX1 2 2.4338 1 2 2 1 2 2.4901 2.2572 2 2 -1) α 1 (EF-1- α Endocytosis protein HSTNB Endocytosis protein putative pol polyprotein HERV-K10 Endogenous retrovirus Endothelial cell multimerin Endothelin-converting enzyme 1 (EC 3.4.24.71) (ECE-1) Ephrin type-A 5 (EC 2.7.1.112) receptor Dynein heavy chain, cytosolic (DYHC) Dynein intermediate chain 1, axonemal Dynein intermediate chain 1, cytosolic (DH IC-1) glycoprotein) (Dystrophin-associated Dystroglycan Dystrophin EAF1 protein) 2 (EGR-2) (Krox-20 protein response Early growth EDIE protein EIF4GII Elastin (Tropoelastin) Ells2 (Fragment) Elongation factor 1-
139 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table VVVIAIVCLRK.Q P54753 1 2.662 2 WTTFMAVIVGIFMVSIIHPGSAA.Q O00341 1 3.114 2 VA L .TYRILCKRCSWEQGECVPCGSNIGYMPQQTGL.E Q15375 1 2.2024 2 .FKKGDQAYLTGDV.L O95186 2 2.3191 2 I.DTIAADESFTQGDL.GV V. Q15375 1 2.3523 2 L.AADDPEVRVLHSI.GS.CTKEPETSNKYIDAF.TS.SRVLITTDLLARGID.VD.HKQGTYGGYFR.DL.SPDVLELLAKLE.EY. G.MLAICDVAEYRK.CC.SCRESGYRASRSQR.K P20827D.MYAKVTEIWQEVMQR.R Q9NY74G.AFPIENIYSATKIGKE.S P04765 1G.RSLRPHLIPLLL.R 1 Q99613D.TRLTQHVPLLKK.T 2.3379 1 O60447 2.7888V 2 K.KLNQALLDLHALGSAR.T 1 2 3.0417 O00471Q.GKVTITVDEYSSNPTQA.F 1 Q8IWU6 2 P08294 2.6721 2.4354 1 2 O95677 1 1 2 2.8493 2.8941 O14560 2 2.5427 Q9BXW9 2 2 P02792 2 3.4668 1 Q15777 1 2 1 2.5722 2.4038 4 2 2.2528 2 2.843 2 2 ProteinEphrin type-A 7 (EC 2.7.1.112) receptor (Tyrosine- 3 (EC 2.7.1.112) Ephrin type-B receptor Peptide Ephrin-A1 protein ETAA16 Eukaryotic initiation factor 4A-I (eIF-4A-I) (eIF4A-I) Eukaryotic translation initiation factor 3 subunit 8 (eIF3 p110) EVI-5 homolog Excitatory amino acid transporter 5 Exocyst complex component Sec10 (hSec10) Extracellular sulfatase SULF-1 dismutase [Cu-Zn] Extracellular superoxide Eyes absent homolog 4 F25965_3 isoform D2 protein, Fanconi anemia complementation group Fatty acid transport protein Ferritin light chain (Ferritin L subunit) 239 (239FB) Fetal brain protein
140 (continued) K.VQHIQLLQK.NK.ESSSHHPGIAEFPS.RR.EVDLKDYEDQQK.QR.GGSTSYGTGSETESPR.N P02671 P02671 P02671 P02671 1 5 1 1 2.5937 2.4138 2.8677 2.6038 2 2 2 2 K.KIYMTCPDCPS.SK.GGETSEMYLIQPDSSVKPYR.VK.AHYGGFTVQNEANK.YK.DNENVVNEYSSELEK.HK.YQISVNK.YR.TPCTVSCNIPVVSGK.ER.EEAPSLRPAPPPISGG.GR.DNDGWLTSDPR.KK.QSGLYFIKPLK.AK.MLEEIMK.Y Q9UGM5K.YEASILTHDSSIR.YR.VELEDWNGR.T P02675R.LDGSVDFK.K 1R.YLQEIYNSNNQK.IQ.SGLYFIKPLK.A P02675 P02675G.MNPPPYSQFLSRRNEI.P 5 2.4988K.TPFVTHPGYDTG.N P02675 2 K.TYHVGEQWQK.E P02675 8 3.7406K.HYQINQQWER.T 1K.WLPSSSPVTGYR.V P02675 P02675K.EATIPGHLNSYTIK.G 2 3.6279 2K.IYLYTLNDNAR.S 1 4.558D.SPASSKPISINYR.T P02679K.LGVRPSQGGEAPR.E 2 3 P02679G.TSTSATLTGLTR.G 1 3.0189 2 2.4296 P02679R.GATYNIIVEALK.D P02679R.EESPLLIGQQSTVSDVPR.D P02679 1 2 R.DAPIVNK.V 2.0031 P02679 2.4716 2 Q9GZV9 23 P02679 2 1 2 2.706 1 2 3.5925 P02751 1 1 2.6501 P02751 2 1 2.23 2 P02751 4.3201 P02751 P02751 2.8888 2.2951 2 1 2.8861 2 P02751 2 3 2 P02751 P02751 2 1 P02751 1 2.4835 2 6 P02751 P02751 2.644 6 2 2.3483 2 6 2.3004 2.8305 2 2 1 2 P02751 2.8349 2 2 2 2.7738 3.7013 4.0035 2 2.4302 2 3 2.2258 2 1 2 2 1.9595 1 -E chain α chain [Contains: Fibrinopeptide B] chain (PRO2061) / β α γ Fibrinogen Fetuin-B (IRL685) (16G2) Fibrinogen Fibrinogen (FGF-23) factor-23 growth Fibroblast (FN) (Cold-insoluble globulin) (CIG) Fibronectin
141 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table .RSTQPQQNNEELPTY.E Q8TEN8 1 2.4103 2 .LPQPPPTTCPPGA.L Q9H7J3 1 3.1311 2 .RNAEAAHQAQLIPK.L Q8TEN7 1 2.4001 2 R.NLQPASEYTVSLVAIK.GR.ESKPLTAQQTTK.LR.SSPVVIDASTAIDAPSNLR.FR.VTWAPPPSIDLTNFLVR.YR.STTPDITGYR.IR.GDSPASSKPISINYR.TR.VPGTSTSATLTGLTR.GR.VGDTYERPK.DR.HTSVQTTSSGSGP.FR.SYTITGLQPGTDYK.IA.DFKVYTKGAGSGEL.KL.AAFLNLAMCYLKLREY.T P02751 P02751L.LLFTVITYFFVVIGIAPIFILY.E P02751 P02751G.FYIAVQEVLALEV.S 1G.AFGKVMNATAYGISK.T 3 P02751 P02751 1R.LQAVTDDHIR.M 1 P02751 3.8221 3.9583G.KLTNLEE.F P02751 P02751 P02751 3.0002 2 8 23 2.2801A.TSTAAAAPSTAPSAGSTAGDSG.A 2 P21333 1K.KTKGTKGKTK.P Q13451 2 2 Q96QA1 3.5151 2.6938 1S.PGAPGPLLPSGAGPSPRPG.A 12 5 2.2454 1T 2 2 1 1 2.8058 3.5552 2 2.8814V Q9BWW2 P36888 2.2533 2 A.WRAPEFLQTLA.I 2.7367 2 2 2.6214P Q9H7N4 2 2 2 2 P30043 1 2.4473 1 Q9H7K2 2.7227 Q13045 1 2 Q9H7N4 2.4096 2 1 2.5936 2 1 1 2.484 2 2.343 2.1376 Q8TEN7 1 1 1 3 2.6827 2 -filamin) (Filamin 1) (Endothelial actin-binding α ProteinFilamin A ( cis-trans 5 (EC 5.2.1.8) (Peptidyl-prolyl FK506-binding protein FKSG16 Peptide FKSG72 FL (EC 2.7.1.112) cytokine receptor (EC 1.5.1.30) (FR) Flavin reductase homolog Flightless-I protein (Fragment) FLJ00034 protein (Fragment) FLJ00070 protein (Fragment) FLJ00086 protein (Fragment) FLJ00155 protein (Fragment) FLJ00156 protein
142 (continued) WLPKVSLLANP.V Q14439 1 2.4889 2 .WSAWYGKCVKGKGS.L.RSSTYSLIPITVAEAGL.T.VCGVSSLGIDHTSLL.G Q8TEN5 1 Q8TEF9 2.6935 1 Q05932 2 2.5518 1 2 2.3424 2 .FHLIVSYDWLILQGPAKPVFEGDL.L Q8WXH3 1 3.7714 3 .SINCTVDEMTEA.V Q9UBS5 1 2.693 2 .TLRDEGKTIAIGKVLKLV.P P15170 1 2.4176 2 V L.RTVFGTTPLPMACPA.LV A.EAERFLL.QV R.SELMDADG.LQ.KFHLVPSINTMSGSQELQWMV.QK.MLKKLVEEATFSEILIPL.QL.KETLYKNQEKL.I Q8TEH2P G.DGYRIGFGQCAGKVLPALL.P 1Q.LKVGILHLGSRQKK.I P15407H.AVVASVPVFAVTNVADIYATST.C 2.2603V. Q92735L.EKEILEKVSSP.F 2 G.SREKSDDPR.K 1 Q13535 O43524 1F 2.5355 P16930S.FLCELSLLHTSLSA.Y Q13535 1 3 2.3667R.TFYLVAETEEDMNK.W 2 Q14439 2 2.5184S.QGDVTFAGDGQEATP.W 2.5501 1 2 Q9HD64P 2 1 2 2.3997 2.4427 1 3.2774 1 2 Q8WTQ7 2.7411 2 Q8WTQ7 2 P41002 1 Q9UQC2 1 P19526 2.4976 1 1 2.7559 2 1 2 2.4248 2.2368 3.0188 2 2 2 -L-fucosyltransferase 1 (EC 2.4.1.69) α FLJ00158 protein (Fragment) FLJ00158 protein (Fragment) FLJ00225 protein (Fragment) FLJ00238 protein FMI protein Folylpolyglutamate synthase, mitochondrial O3AForkhead box protein - antigen 1 (FRA-1) Fos-related ATR) kinase (Protein protein FRAP-related X) protein related FREB (FCRLa) (Fc receptor Fumarylacetoacetase (EC 3.7.1.2) (XAGE-1 protein) G antigen family D 2 protein receptor G protein-coupled kinase GRK7 (EC 2.7.1.-) receptor G protein-coupled 1 homolog G1 to S phase transition protein G2/mitotic-specific cyclin F KIAA0571) Gab2 (Hypothetical protein Galactoside 2- subunit 1 Gamma-aminobutyric acid type B receptor,
143 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table VNPLKMSPHSL.T P23378 1 2.4462 2 R .KAKVTGDEWGDNYF.L P13807 1 2.7616 2 .AILKLLKH.Y O75899.KDFLSVMLEK.G 1 2.4531 1 Q9Y2Q3 1 2.679 2 .FTGDAYVILK.T P06396 1 2.6815 2 .YELEPEKFQ.N P11216 1 2.284 1 P R.GLEHLRLAQYTIERYFTL.VR.CVAAVSSVPKIVDWMDN.FS.TDSPLPLEK.EK.HVVPNEVVVQR.LK.AGALNSNDAFVLK.TK.PALPAGTEDTAK.EK.TGAQELLR.VF K.DSQEEEKTEALTSAK.RK.TPSAAYLWVGTGASEAEK.T O00591R.DPDQTDGLGLSYLSSH.IN.SMVVEHPEFLK.A Q9UH48R.PNSMVVEHPEFLK.AL.QGVTLPPSAVAMLNTPDGLVQPATPA.A 1 1P 2.4493N.IVSNASCTTNCLAPLAK.V O43241 P06396 P06396 2.6477R.WLLDNVR.K 2 P06396 P06396 2 Q9NZM4P. P06396 13 2 1 P06396 P06396 4 1 3 3.7006 2.4993 3.1985 9 P06396 P06396 1 1 2.8072 2 2 2.8757 2.377 2 2.3629 2 O14556 1 2.614 1 2 2.5308 2 2 2 2 2.505 3.882 2 Q14409 2 2 2.5814 2 1 2.2752 2 T F D.LQIPPPNIPR.D P11216 1 2.5961 2 Protein subunit 2 Gamma-aminobutyric acid type B receptor, pi subunit Gamma-aminobutyric-acid receptor GCYS-20 protein Gastric cancer-related GCP170 Gelsolin , plasma (Actin-depolymerizing factor) Peptide gene 1 protein candidate region Glioma tumor suppressor Glutathione S-transferase, mitochondrial (EC 2.5.1.18) testis-specific Glyceraldehyde 3-phosphate dehydrogenase, kinase, testis specific 1 (EC 2.7.1.30) Glycerol [decarboxylating], mitochondrial Glycine dehydrogenase Glycogen [starch] synthase, muscle (EC 2.4.1.11) Glycogen [starch] Glycogen phosphorylase, brain form (EC 2.4.1.1)
144 (continued) -10 γ .PILLSLVKIFLETRKS.W.KEEKKKFDKETEKNYSLI.D Q96S52 Q96S75 2 1 3.3987 2.6956 2 2 .YGNGDDIGVFL.S Q14663 1 2.4738 2 N.ACKDALLVGV.PF K.LRTEGDGVYTLNNE.KK.DYAEVGR.V P50151 P00737 5 P00737 1 3.3705 3.3611 2 18 2 2.795 2 S.DALILAKSKGFDVFNAL.DI.EPSFGLGRIMYTVFE.HK.DQLTDLSNSLEK.CL.QELLKEK.QL.REHNSILETAL.AV R.REQLMREEAEQ.KV O60551C.PEGDIDILLDKF.H P41250L.CFPISLGSQASGGEAQIAAS.A 1R.PVGAAGGGLLGGLPR.L Q14789 2.7849I.SLFNSVSQ.W 1H.SVLESLRELQAEGSEPSV.N Q14789 Q08378 2 1 2.2917 Q14444 1 2.9274 1 1 O60383 2 3.0693 Q9H2Q8 2.2617 3 Q9C056 1 2 2 2.7813 1 O15068 2.9543 1 2 2.349 Q9UL65 2 1 2.2203 1 8 2 3.008 2.2712 2 1 I.IGGKAAPGYHMA.KA.LQLNGGQYWAVTSPER.SL.WGPMAIFLLALQR.- Q96J90 P06737 Q8NFP4 5 1 2.483 1 2.2104 2 2 2.6332 2 -tetradecanoyltransferase 2 (EC 2.3.1.97) N H-2K binding factor-2 Haptoglobin-1 Glycyl-tRNA synthetase (EC 6.1.1.14) (Glycine—tRNA ligase) Golgi autoantigen, golgin subfamily B member 1 (Giantin) Golgin-160 (Fragment) GPI transamidase component PIG-S p137 (p137GPI) protein GPI-anchored Graf2 GREB1a (Fragment) factor 9 (GDF-9) Growth/differentiation GTX Guanine exchange factor MCG7 isoform 1 big sister) Guanine nucleotide exchange factor DBS (DBL’s G(I)/G(S)/G(O) Guanine nucleotide-binding protein Glycogen phosphorylase, liver form (EC 2.4.1.1) 1 Glycogenin-interacting protein Glycosyl-phosphatidyl-inositol-MAM Glycylpeptide
145 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table K.AVGDKLPECEAVCGKPK.NK.VVLHPNYSQVDIGLIK.LK.LPECEAVCGKPK.NK.LPECEAVCGK.PG.DGVYTLNNE.KK.AVGDKLPECEAVCGK.PK.SCAVAEYGVYVK.VK.VTSIQDWVQK.TG.DGVYTLNNEK.QK.SPVGVQPILNEHTF.CK.LRTEGDGVYTLNNEK.QK.GSFPWQAK.MK.PPEIAHGYVEHSVR.Y P00737H.GYVEHSVR.YK.DIAPTLTLYVGKK.Q P00737K.NPANPVQ.RK.DIAPTLTLYVGK.KK.SPVGVQPIL.N 1 P00737K.SPVGVQPILNEH.T P00737K.YVMLPVADQDQCIR.H 4 P00737K.SPVGVQPILNEHTFCAGMSK.Y 3.5565 P00737K.SPVGVQPILNEHT.F P00737 1Q.PILNEHTFCAGMSK.Y 3.6348R.TEGDGVYTLNNEK.Q 2 1 P00737 P00737 P00737R.TEGDGVYTLNNE.K 1 P00737R.ILGGHLDAK.G 1 3 3.9034 9R.HYEGSTVPEKK.T 2.7706 P00737R.HYEGSTVPEK.K 2.1871 31 2 29R.VGYVSGWGR.N P00737 1 3.0942 4 P00737 2.6394 2 K.LRTEGDGVYTLNDK.K 1 P00737 2.2246G.DGVYTLNDKK.Q 1 2 3.8496 P00737 3.8851 P00737 1 K.LPECEADDGCPKPPEIAHGYVEHSVR.Y 2.5794 17 P00737K.AVGDKLPECEADDGCPKPPEIAHGYVEHSVR.Y P00737 2 4 P00737 2 G.DGVYTLNDK.K P00737 2 3.5875 2 1 2.5038 61 5 P00737 P00737 2.6556 3 3 9 P00737 14 2 2.5362 P00738 1 2.4193 P00737 3.6784 2 P00738 2.3159 4 2 2.9424 1 3.6468 2 87 P00737 3 P00737 2.3265 1 1 13 P00737 2 2 2.7975 P00738 3.6047 P00737 1 1 3.2547 46 4.0167 7 2 3.5205 1 P00738 37 2 5.2132 38 4 3 2 2.7723 3.1812 P00738 3 2.2078 3 2 3.2308 4.6631 2 2 2 2 2.4752 3 2 3.1704 2 Protein Peptide Haptoglobin-2
146 (continued) .GKVGAHAGEYGAEALER.M.GKVNVDEVGGEALGR.L P01922 2 4.049 3 P02023 2 4.5473 2 .PRAGKQGQHAV.S Q9NZ71 1 2.2894 1 .SDGLAHLDNLK.G P02023 1 3.0574 2 -.VLSPADKTNVK.AK.VGAHAGEYGAEALER.MG.AHAGEYGAEALER.MW K.VNVDEVGGEALGR.LK.SAVTALWGK.VG.AFSDGLAHLDNLK.G-.VHLTPEEK.SK.VVAGVANALAHK.YF K.VLGAFSDGLAHLDNLK.GR.LLVVYPWTQR.FW P01922I.LRVDPVNFK.L P01922 P01922 22 P02023 9 1 P02023 3.6518 P02023 27 P02023 2.7209 P02023 3.7523 3 P02023 2 2 2 4.0625 1 16 P02023 3 2.9683 2 3 2.4949 2.7082 4.6803 2 P02008 1 2 2.5311 2 2 2.4235 2 4 2 2.8083 2 D.GVYTLNDKK.QR.TEGDGVYTLNDK.KR.TEGDGVYTLNDKK.QK.VVLHPNYHQVDIGLIK.LR.VGYVSGWGQSDNFK.LD.DGYMICCDK.CK.DAGTIAGLNVLR.II.ISDITELAPASPMASPGG.SQ.PTLPTPPALGEVPQELQS.PS.LISIALPENK.VV P00738 P00738 P00738 P00739G.RMLWALLSGPGRRGSTR.G P00739 105 81 1 1 2.8057 7 Q9NS29 3.2237 Q00613 2.937 P11142 2.4709 Q8NG67 2 2 4.0885 2 1 2 2 5 2 1 Q9Y5R4 Q8NG67 2.2315 2.7146 3.1295 3.0924 1 2 1 1 2 2 H.GNVAEGETKPDPDVTER.CK.GGYTLVSGYPK.R 2.6693 2.4666 2 2 P02790 P02790 2 3.2595 20 2 2.7084 2 chain chain -1B-glycoprotein) β α β Hemoglobin Hemoglobin zeta chain (HBAZ) Hemopexin ( Haptoglobin-related protein protein Haptoglobin-related HDCMC04P Heat shock cognate 71 kDa protein 1 (HSF 1) Heat shock factor protein LASU1 HECT domain protein NHL Helicase-like protein homolog (EC 2.1.1.-) (M.HsaHemKP) HemK protein Hemoglobin
147 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table PQGPPKISPQGPPQSPPQS.P Q8TD91 1 3.7006 2 .QPDQNFTGLIAGVVS.I P08581 1 2.6197 2 .TSAHGNVAEGETKPD.P P02790 1 4.5025 2 .PSPVDAAFR.Q P02790 1 2.6462 1 R.PAVLDDFVSTIDLPN.YV S.HLSLISVERCV.EN.FGGGGGNFGRDGNF.GH.IDLVEGDEGR.M P14210 1 P51991 Q9UPZ3 2.81 P19367 1 3 2 2.6149 2.4266 5 2 2 3.2456 2 K.SLGPNSCSANGPGLYLIHGPNLYCYSDVEK.LK.VWVYPPEK.KK.VWVYPPEKK.EK.EVGTPHGIILDSVD.AG.HNSVFLIK.GK.EVGTPHGIILDSVDAAFICPGSSR.LD.PVRGEVPPR.Y P02790F G.NVAEGETKPDPDVTER.CK.SGAQATWTELPWPHEK.VK.NFPSPVDAAFR.QK.GDKVWVYPPEK.K 1P R.LHIMAGR.RN.VAEGETKPDPDVTER.C 2.9118R.YYCFQGNQFLR.F P02790Q.GHNSVFLIK.GR.EWFWDLATGTMK.E 2 P02790 P02790 P02790K.TLEAQLTPR.V 1K.FAFNLYR.VK.NYNLVESLK.L P02790 P02790 P02790K.YEITTIHNLFR.K 2 3 P02790 4.4389 2P. 3.4031 2 1 P02790 17 1 2.4217 P02790 2.2546 1 P02790 2 2 2.9036 2 4.8058 2.8246 5 P02790 3.0371 P02790 1 2 P02790 3 2 3 P02790 2 2.2169 2.3765 1 2 3.2258 P05546 11 2 2 1 P05546 P05546 2 P05546 2.0483 3.5206 3.2395 5 2.5141 1 2 2 2 2 4 2 2.546 2.6494 2.48 2.5139 2 1 2 2 Hepatocyte growth factor (Scatter factor) (SF) Hepatocyte growth (EC 2.7.1.112) factor receptor Hepatocyte growth 5 protein Hermansky-Pudlak syndrome A3 (hnRNP nuclear ribonucleoprotein Heterogeneous A3) Hexokinase, type I (EC 2.7.1.1) (HK I) (Brain form hexokinase) Protein Peptide inhibitor) Heparin cofactor II (HC-II) (Protease HCA2 protein Hepatocellular carcinoma-associated
148 (continued) KLWFVIRSFGVKNLQ.A P19113 4 2.9676 2 R.DEIPHNDIALLK.LS.STCALTTTLHSTPAAA.GG.FNRRFMENSSI.IV. K.ALDLINKR.RK.SGFPQVSMFFTHTFPK.-K.YKEENDDFASFR.VK.ALDLINK.RR.ADLFYDVEALDLESPK.NR.IADAHLDR.VR.KGEVLPLPEANFPSFPLPH.H Q9UKB0 Q14520A.LLTEGGAVGSEIAGGAGPGWVLPFTAGGFI.YI.GRAAGTGFTVNVA.W 1L.LGNELEPLAEDILHQ.S 1 O95263S.GSFKLNKK.A Q92504 P04196 2.4382 2.5987R.VGAGAPVYLAAVLEYLTAEILELAGNAAR.D 12 P04196 P04196 P04196 2 I.KLWKVALHFWDPPAE.E 2 P04196 1 1 2.8346 P04196 2 5 3 2.5372 P04196 2 P28001 4 2.5977 Q9UBN7 2 5.0052 2.9198 2.6832 2 1 4.1708 Q9UKV0 2 3 2 2 2 1 3 1.9613 1 2.8101 5.0718 Q02539 1 Q14493 2.3972 2 2 3.0823 2 1 1 2 2.4731 2.4426 2 2 R.YMVQRGGCVYSK.EA.LVGSPNGGSETPKSNG.GA.AAAAASGAAA.AG.GGGGGGGGGGGGGGAGAGGGSDFGCSAA.AL.DQWLRASTAGMILPKM.PE.NTTGNWLTAKSGR.K Q03828 Q96KQ7 1 P49640 2.5463 1 Q03828 1 P50219 2 2.3359 2.9071 Q9NYD6 1 1 2 2 1 2.1173 2.5005 1 2 2.7168 2 -methyltransferase, H3 lysine-9 specific 3 N HGF activator like protein (Hyaluronan binding protein 2) binding protein (Hyaluronan HGF activator like protein protein-R High mobility group cAMP-specific and IBMX-insensitive 3’,5’-cyclic High-affinity Histidine decarboxylase (EC 4.1.1.22) (HDC) rich) (Histidine-proline Histidine-rich glycoprotein Ke4 Histidine-rich membrane protein Histone deacetylase 6 (HD6) Histone deacetylase 9 (HD9) (HD7B) (HD7) Histone H1.1 Histone H2A.a (H2A/a) (H2A.2) Histone RNA hairpin-binding protein Histone-lysine Homeobox even-skipped homolog protein 1 (EVX-1) Homeobox even-skipped homolog protein 2 (EVX-2) Homeobox even-skipped homolog protein HB9 Homeobox protein Hox-C10 Homeobox protein
149 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table .VQYPDCKSSANT.N P31273 2 2.4897 2 .KAAAAAAAAAG.E P13378 1 2.4063 1 .KVTQLYK.C O95568 1 2.5526 2 V Y A.QRYDELPHYGGM.DR.HSLCLQPDSGGPPELGSSP.PQ.FKLNKYLSRPK.RS.LKTDIEE.SI.GKGKDITTKHDEVVCG.RE.EIFDDASPGKQKE.IK.KYSYIRKTRPDGNCFYR.AM.NVDHEVNLLV.E P50222 O14770G.QEDPVQREIHQDW.AL.ETSAQSEANWAAE.F 1 1E.DYQEMLQSLA.Q Q9Y648 O14730K.ISKEESKILKK.A 2.4828 2.5709R.NVPPIVFVQDK.G 2 O95349 2 Q9P0B8 2 O60264 1P 2.8032N.FEFEDLQVTFR.G 1 2.4096 1 1 Q9P0A1 2 Q9P082 2 2.4532 2.7274 O00291 3.1664 19 1 1 2 2 Q9H1J2 2.5998 1 2.7438 Q9BZ01 2 Q8N0V3 1 2.6925 1 2 2 2.5293 2 Q8IV20 2.6246 2 2.3496 1 2 2 2.6495 2 Protein Hox-C8 (Hox-3A) Homeobox protein Hox-D8 (Hox-4E) (Hox-5.4) Homeobox protein 1) protein Meis2 (Meis1-related Homeobox protein MOX-2 (Mesenchyme homeobox 2) Homeobox protein HB9 (Fragment) Homeotic protein Homer-2b nidulans sudD gene product Homolog of the aspergillus HSNF2H Peptide HSPC263 (Fragment) HSPC280 (Fragment) HSPC300 (Fragment) 1 (HIP-I) Huntingtin interacting protein HUPF2 c20orf80 Hypothetical FRG1-like protein Hypothetical p38 protein Hypothetical protein Hypothetical protein
150 (continued) YCEPSQLQEYA.K Q8IZG0 1 2.4993 2 L .YLCELGFSILTR.L Q8TCP9 1 2.4316 2 .EAEEVFVPVLNIKR.S Q8N654 2 3.0269 2 .VREPVDNLSPEERDA.R Q8ND16 1 2.6866 2 .KFAKAPFLSCILSPG.E Q8N371 1 2.5397 1 M.EPTFVQVPTLKK.PR.NDQRPSGVPDR.FK.LQETKEKVSFKK.KK.EEEEPNPNYKEVEDPQQ.ET N.KKKEEKKGK.GC.EVQLVESGGGLVQPGR.SQ.LVESGGGLVQPGR.SE.LLKGNETIARLQALA.K Q8ND61 Q8NEJ1 Q8TBY9 1 Q8TBL3 1 2.6039 2 1 Q8WU38 2.6961 2 3.3833 Q8WTQ4 2.5113 Q8WU38 2 Q8WUC8 2 4 2 1 1 4.5022 1 2.2496 2.6193 2 2.4825 1 2 2 A.GCTGGFLQA.YK.GTTVTVSSASPTSPK.VT P Q8N5K4 Q8N413 17 1 3.9123 2.2455 2 2 R.NYSVASGIQSSLDEGQSVG.FR.ATWSGAVLAGR.DY. R.VRLAEAEETAR.TS.YVLTQPPSVSVAPGQTAR.IS.YVLTQPPSVSVAPGQ.TP Q8IXU4 1 Q8IYJ6 2.7555 Q8N355 7 Q8N163 2 Q8N355 2 2.869 1 8 3.3694 2 2.0744 3.1509 2 1 2 Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein
151 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table .KDLNGIDLTPVQD.T Q96BJ3 1 2.4953 2 .ICVTCKECEDLGV.E Q96E18 1 2.5068 2 .KISSTKNISIK.Q Q96CB8 1 2.4415 2 Q.QGRELEAECPVCW.NK.LGDSWDVKLGA.LL.CGLLEASGGGRALPQ.LT I.ELTEMESMKTTLKEEVNELQY.RG.FYHLRIAYYASK.GA.EPTAAPHPVLKQV.I Q96D59 Q96DA0 Q96DZ1 1 Q96EA4 1 1 2.5543 2 2 2.6438 2.5704 Q96ES2 2.6952 Q96F28 2 2 2 1 1 2.4674 2.2739 2 2 K.LTVLGQPK.AA.RLVQSVLRVWQ.VM.TGTPKTQEGAKDLEVDMNK.TA.DVEDVTEEDC.AL.GWGRERELCVKCL.LV H.MPQPVNPELTAGPITGLV.YH.SPPSAVLLR.AL.EAAGRFLL.P Q8WW03K.FDAKILHLPTYSVDK.L Q8WUK4 Q8WUY4 1P 21 1 Q8WYY9 2.6201 Q96AR0 2.2198 Q96BQ3 2.444 2 3 2 1 2 1 2.9394 2.3784 Q96BT6 Q96C45 3.8355 2 Q96C12 2 3 1 1 1 2.5522 2.6998 2.3887 2 2 2 Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein ProteinHypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Peptide Hypothetical protein Hypothetical protein
152 (continued) MMMDDAVLCMCFSR.D Q9BU59 1 2.5506 2 .SVSLSLGEAPGGGLFLPPP.S Q96IQ8 1 2.4053 2 .KIDGSLEVPLERAK.D Q96HM2 1 2.5623 2 H.NSWSSSSRHPNQATPKK.SA.LVLAVGGGGLLAGVVAGLLEV.GI.YAKLEEIEADKA.PS.SEDAKIHEKTSR.TL.ALAPDLSTEQRRRR.RI.VKESLTEEDVLNCQKT.IY Q96GA7 Q96F86 1 2 2.4513 Q96GS8 3.058 Q96GV0 2 Q96HB5 2 Q96HM2 1 1 1 2.524 1 2.5182 2.5643 2 2.2343 2 2 1 K.AGVETTKPSK.QQ.VTVLGQPK.AH.SEEPLTIFSGA.LV E.LEQEVQRLKKE.QS.TVQVCNSILCPKTGR.ER.IHLMAGR.VK.GDTFSCMVGHEALPLAFTQE.TM.VGHEALPLAFTQE.TG.HEALPLAFTQE.T Q96I69E.SWVTDMCKVGASSDP.C Q96I69M.QHCNLLCLPENYQMKYYLYHGLSWP.Q Q96IH6 19S.FSDLYSSYVIF.Y 1 Q96J23F. Q96QE5 1 2.9767 Q9BRV0 2.5323 2 Q9BSU3 2.3929 1 1 4 Q9BRV0 2 Q96S83 1 Q9BS82 3.1605 3.0091 Q9BRV0 1 4.9399 2 1 2 2 2 3.9429 1 5 3.442 2.0391 3 Q9BTX1 3.4029 3.4416 2 1 2 2 3 2.7715 2 Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein
153 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table .LLKGLQTVGCMPPPVSSA.V Q9H0M9 1 2.4845 2 KNHNEIIQTKLKEIT.E Q9UFE4 1 3.4016 2 .GGHTSLAGVFPASPSVSLKQ.V Q9H0H3.LFSPCLVYGSVADMP.F 1 3.0259 2 Q9HAF5 1 2.5125 2 .SGSAEGSLQKAEK.V Q9H0K5 1 2.6018 2 I.YAGLANGSILVYDVR.NL.GLISPAYLFLW.PN.EGGAKPELASQATE.GV I.LKADIAILRQEICTMKN.DT A.LCSTLIEGQKKRSQV.SW Q9BUI8L.EVDILDSSLQALTSR.KE.VNDIITTFDSIV.G Q9BWC3 1 Q9BUN8V Q9H0H6 2.5755K.MTLPNLPR.L 2 1I.ISLSFLSLGWNIFVCL.F 2 1 3.2948 2.5815E.GYIAVVLPKFEESK.S Q9H0L3L.QNGHLRFPGIKTYIDP.D 2 2 2.7003T. 1 Q9HA85L.NYLFLQILLVE.S 2 Q.AFCIEFSRIR.E 2.2753 Q9HAD3 1 2 2.7372 1 Q9NW96 Q9NUJ7 2 Q9NX38 2.4469 Q9UF33 1 1 2 1 2.5119 2 2.4134 Q9UFQ7 2 2.8054 2.8565 2 Q9UKZ1 2 1 2 1 2.4772 2 2.4258 2 ProteinHypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Peptide Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein Hypothetical protein
154 (continued) .RRESEYPFIDGLQ.N Q9Y3H6 1 3.1806 2 .SEADCIAVQHVCTIVSF.R Q96EH2 1 3.0043 2 .EKVFESAVDPGA.V Q9NWF6 1 2.8126 2 L.QDNIMKDIAEL.RT Q.LLRIFELLADAG.VF R.AAAPRAGAAASMAPSPR.TN.QNGVLDFFFQK.PL.LAGSSAGGTGVLLNV.DL.SFHSVSGILVCQAGCVLE.EL.GSRASLADALPLHIAPR.W Q9UNU8E.CLAPLGALEFLRLNG.N Q9Y3N6N.LQDLENTTPAQPK.N O95902 1K.QNVNILIDTEK.F 7C.ARLAAGPGAAEPLPV.E 2.2277 1 Q8N3C2 Q8N410P 2 Q8N465 3.4086S.SSPGGLPPVL.S 3.2144 Q8ND25 2 3 1A.KVKLVMWPLSSLRRY.G 2 1 Q8ND46A.LQVDTQREGTLISLAKQ.A 1 2.7652 2.5011S.DLANLGA.E 2.557 Q8NDG1 2 1 2 A.ADSTEELAEVEEGVG.V 2.7087 2 Q96BV2K.EVERFLAQ.L Q96BR4 1 2 2.5802 2.5179 1 1 1 Q96HI2 2 Q96IF6 Q96HG1 2.4451 2.0954 2 1 1 1 1 Q9BTP1 3.1477 Q9BSB5 2.412 3.1485 2 1 2 2 Q9BW53 1 2.4903 2.2143 1 2 1 2.5507 2 Hypothetical protein Hypothetical protein (BA6J24.2) Hypothetical protein (Fragment) Hypothetical protein (Fragment) Hypothetical protein (Fragment) Hypothetical protein (Fragment) Hypothetical protein (Fragment) Hypothetical protein (Fragment) Hypothetical protein (Fragment) Hypothetical protein (Fragment) Hypothetical protein (Fragment) Hypothetical protein (Fragment) Hypothetical protein (Fragment) Hypothetical protein (Fragment) Hypothetical protein (Fragment) Hypothetical protein (Fragment) Hypothetical protein (Fragment) Hypothetical protein (Fragment) Hypothetical protein
155 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table .NGQATKTPEPSS.P Q8N3L4 1 2.5309 2 L.LSRSPSVASMKAVPAA.SS.GRIHRLALTGEKRADIQL.NK.ILRELVHDRFHK.QE.PLVEEAAQVLIV.TQ.TPKDDPAITLL.ND.CPITAHMY.ED.FPTENPNDNSVLGNL.R Q9C074L.FRSPDSEHATSCPR.L Q9NPR9K.VRSEEAPAGCGAE.G 1M.FSGQPPGPPQAPPGL.P 1 Q9NSJ3K.IVNLGSSKTDLFYE.R 2.3189 Q9NT34 2.8377M.EELPRVLYLPLFMEAF.S 1 2 L.SQCPSISQLKTLDLSGIRLTNYSL.V Q9NT45 2 L.YMNSVSFLE.G Q9UG33 6F 2.2765 Q9UFV0 1 Q9Y3Y1L.LMQNLNKLQTPEEKFD.F 3.1535 2 1 Q9BUL9K.VLVFNFLNCFA.S 1 2.519 2 Q9H204L.QELDLKSNNIRT.I 1 2.2081 O60810 2 2.4132 1 Q9UH06 O95521 1 1 3.2626 2 2.5178 1 1 2 2.4134 1 2 O60810 2 2.3913 2.5241 Q8N3L3 2.5047 2 2 2 1 1 Q9NW15 Q9NVW3 2.7255 3.1095 1 10 2 2 2.8562 2.9369 2 2 Protein (Fragment) Hypothetical protein (Fragment) Hypothetical protein (Fragment) Hypothetical protein (Fragment) Hypothetical protein (Fragment) Hypothetical protein (Fragment) Hypothetical protein (Fragment) Hypothetical protein (Fragment) Hypothetical protein Peptide (RNase PHypothetical protein subunit p25) protein ANGIOGENESIS marker) (Tumor Hypothetical protein BK223H9.2/MGC1346 Hypothetical protein (Fragment) DJ1198H6.1 Hypothetical protein DJ845O24.2 (Fragment) Hypothetical protein DKFZp451E012 (Fragment) Hypothetical protein DKFZp451F022 (Fragment) Hypothetical protein FLJ10375 Hypothetical protein FLJ10470 Hypothetical protein
156 (continued) STSPASPKGLHTGGTK.R Q9H8T7 2 2.468 2 .AGRKWGPGEQRALLPGQ.G.ELKEMVSDVDLSFNKLSFISLEL.C.DANEGIQAQTVA.N Q9H9T4 Q9H9A6 1.FRLEEGVASDEEAEEAQP.G 1 2.5869 3.6294 2 Q8N442 3 1 Q9H882 2.5887 2 1 2.7824 2 .LRERFLQPLMALLYPDCGGGRLDSHRA.F Q9H8K6 1 2.9367 2 .EYQQVAFQPSILTE.P Q9H9N0 1 2.6536 2 Q.EYGELDAK.DK.QQEEQTRVALLEQQMQACTLDFENEK.LE.PVTQLYVSVDASTK.DD.FHRLLTVELQF.KA.AATIILY.F Q9NVS7L.VTVLGAGLL.CV 4F V 3.6972 Q9NVU7N.EAIVPVGAWVEP.A Q9NV66 3 V 1T. Q9NV09 1E.RLQSESLVNR.R 2.2064 2.598P 4 Q9NUS2 Q9NUM3 1 A.PAFLLLLLLWPQ.G 2 2.6564V 1 3L.CACEEYLSNLA.H 2 Q9H8U7 2.2122 2.3368N.MLATANKTEKTEFL.GL.VTVSSASPTSPK.V 1 2 G.QGTLVTVSSASPTSPK.V 1 3.3425 Q9GZX5 2 Q9H8E9 1 2 Q9H876 2.5954 Q9H7U8 2 Q96K68 3.2813 Q96K68 1 3 2 2 2.415 2.6133 4 2 3.3974 2 3.207 2 2 Hypothetical protein FLJ10498 Hypothetical protein FLJ10540 Hypothetical protein FLJ10900 Hypothetical protein FLJ11006 Hypothetical protein FLJ11175 Hypothetical protein FLJ11274 Hypothetical protein FLJ12562 Hypothetical protein FLJ12647 Hypothetical protein FLJ12889 Hypothetical protein FLJ13215 Hypothetical protein FLJ13220 Hypothetical protein FLJ13236 Hypothetical protein ZBRK1) FLJ13405 (Zinc-finger protein Hypothetical protein FLJ13491 Hypothetical protein FLJ13693 Hypothetical protein FLJ13881 Hypothetical protein FLJ13898 (Fragment) Hypothetical protein FLJ14235 Hypothetical protein FLJ14473 Hypothetical protein
157 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table VTVSSASPTSPK.V Q96K68 1 2.6845 2 L .FVAGKESRGARGV.R Q9NWY0 1 2.7128 2 .ADADEILQEEIKE.Y Q96T18 1 2.4409 2 .SSLFNLQKSSL.S Q9NXD0 1 2.5566 2 .AADSQKLSMGGLHSSRP.L.FDAARGADF.D Q96K30 1 3.0482 2 Q9NXL6 2 2.3403 1 .ESPLELSAQ.G Q96SY1 1 2.9682 2 G.TLVTVSSASPTSPK.VQ.GTLVTVSSASPTSPK.VT. Y F K.RQVAPGAPSAPRRGRGGHRGGRGRFGI.RP S.LLSICPEAK.QA.SWDEPQFSDNSGAE.L Q96K68S.QPCKNGATCKDGANSF.R Q96K68 Q96SN5P I.SRSDLEEILDT.E 8 14 1T 2.2883 3.1154D.RRAYPAQITPKMCLL.E 2.7384V 1 2 2 L.WETVALALGVQ.R Q96JU7 Q96JU7G.VSRASPLLLLLLVPSPRLAAAAPRRQLG.D Q96JY1N.KKENSETVVTGSL.D 1 1G.SCLSSQHFGR.P 1 2.3588 Q9NXG0 2.4041 Q9H7F8 Q9NX74 2.7845 1 2 2 2 1 5 Q9NWK6 2.9279 4.144 2.472 2 Q9GZS3 1 3 2 2.4382 Q9H721 5 2 3.0895 1 2 2.6853 2 Protein FLJ14500 Hypothetical protein FLJ14568 Hypothetical protein FLJ14737 Hypothetical protein FLJ14827 Hypothetical protein FLJ14900 (Fragment) Hypothetical protein FLJ14964 Hypothetical protein Peptide FLJ20174 Hypothetical protein FLJ20276 Hypothetical protein FLJ20315 Hypothetical protein FLJ20399 Hypothetical protein FLJ20539 Hypothetical protein FLJ20772 Hypothetical protein FLJ20958 Hypothetical protein FLJ21101 Hypothetical protein FLJ21497 Hypothetical protein
158 (continued) .LPPPPQVLPLLSPAR.G.QGGGQFCPSGSAFLG.V Q8TCH9 1 Q8N7I6 2.5064 1 2 2.5004 2 .DWHTRSPALTF.T Q8TEC6 1 2.431 2 Q.MSNKVILTLSAIATLDR.IS.RSVALFRGY.HD.PDVFNQIVKIL.HL.DPDVFNQIVKIL.HE.LLEPVVDDVPKTTA.TR.KPCKLMLQVVK.IL.DLPSLTSLLSEKAKEFLMENR.VA.CNCDLLQLKTW.L Q9H720A.FNGLGLLKQLHINHNSLE.ID.LIYGPVLPLSAIAGLVGKEAETFR.P 1N.YENYIDI.V Q9H6U8S.QVEKLNVFLSPPDVINYLALTEA.T Q9H6T3 Q9H6T3 3.0042 Q9H6N4T Q9H668 1 2 V 2 1 Q9GZU1 1R.EGPENMVRIALQLDD.G Q9H5W3 2.5199 1 Q9H5Y7 2.4173L.KSGTTPPPPGA.A 2.2656 Q9H5Y7 1 2.4451 2 1 2.4916V 2 Q8NE42 1 2 2 Q.AGGGIHFTVERTRQAT.E 2.2174 2 1 2.5535 2.57G.SQLEVLVHVQ.D 1 1 2 L.VEKCTVSVK.D 2.9191 Q9H5L4 2 3.9174 2 Q96LS5 3 3 2.3005 1 Q96DK4 Q96NU7 1 2.6723 1 1 2 Q969Y0 2.3111 3.2805 Q96NT3 2 1 2 2 2.3859 2.7278 1 2 Hypothetical protein FLJ21511 Hypothetical protein FLJ21845 Hypothetical protein FLJ21908 Hypothetical protein FLJ22052 Hypothetical protein FLJ22449 (Mucolipin) (Mucolipidosis type Hypothetical protein FLJ22559 Hypothetical protein FLJ22774 Hypothetical protein FLJ22944 Hypothetical protein FLJ23323 Hypothetical protein FLJ23537 Hypothetical protein FLJ23651 Hypothetical protein FLJ23865 Hypothetical protein FLJ25122 Hypothetical protein FLJ25270 Hypothetical protein FLJ25506 Hypothetical protein FLJ30055 Hypothetical protein FLJ30102 Hypothetical protein FLJ30119 Hypothetical protein
159 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table .AMHEVFLQRLA.A Q96NG4 1 3.1109 2 .RPDSSPFRPAARPR.M Q96NR7 1.LPEEAPSNDER.T 2.6359 2 Q96DN4 1 2.8396 2 S.EAQEGLQKFKVVRA.GR.PSQETTPPDRSHHSGFGLFCGD.PT A.SSRGSIQMSAPDLSTALR.GD.PPTLSGAECYACIGV.HV M.KVFSKNVSK.C Q96NS8S.QEKKEEAITLLKDSI.K Q96NT0A.KVELSPGPPKP.A 1L.QTLPLSTLESE.N 1 Q96NP8K.SALIVHQHTHSK.G 2.4474N.KFQGPVTLKDVIV.E 2.2353 Q96DR2 2 1T 1 I.SLHPSGHFIVVGFADK.L 1 2.3143G.GLELEEETAFQGALTSRQLPSGCP.E Q96N52 Q96N64 1 A.MACEIFNELR.L 3.1211A.DAIKTLHMAMSLPGMK.R Q96IA7 2 1E.VINADDLDVAYQKLSQLI.R 1 Q96MY0 Q96MU2 Q96MU2 2.7493 2.5034 1 Q96MC3 1 2 Q96MR6 2 1 2.736 1 1 2.4131 2.2723 2 1 2.7191 Q96MA4 3.8413 1 2 Q96M69 Q96MC0 2 2.4155 3 1 2 1 1 2.4563 2.6101 2.716 1 2 2 Protein FLJ30131 Hypothetical protein FLJ30136 Hypothetical protein FLJ30277 Hypothetical protein FLJ30384 Hypothetical protein FLJ30469 Hypothetical protein FLJ30934 Hypothetical protein FLJ31359 Hypothetical protein FLJ31400 Hypothetical protein Peptide FLJ31409 (Fragment) Hypothetical protein FLJ31726 (Fragment) Hypothetical protein 25) FLJ31890 (Zinc finger protein Hypothetical protein FLJ31897 Hypothetical protein FLJ32000 Hypothetical protein FLJ32658 Hypothetical protein FLJ32662 Hypothetical protein FLJ32706 (Fragment) Hypothetical protein FLJ32786 Hypothetical protein
160 (continued) .FVHREIYPGSKI.T Q8NAD9 1 2.7928 2 .YEFEGGVK.L Q8N267 1 2.2153 1 M.ETKRTQEGE.AK.AYKCSSTLSK.HI.IQVIYVEE.KL.LFFYINGAGGR.EL.FVEANMNSEKKGIRVN.FK.VVHGDVTPYDLV.RF E.REEILKR.YL.KSRVKNIKTGSDFSMFEALRDTIY.S Q96M31A.ISDGEEGGGEPG.A Q96M04A.SNHTNQTLS.D 1 Q8N2C0N.PDLSWYHHANPI.L Q96LY9 Q8NBD7 1D.EIKNNSEVQNQE.C 3.1226 Q8NBC6 1L.LAFTSVAELELLGLE.K Q8NB85 2.334 1 2 2 Y 3.0213 2 1 2.553 2.275K.ENGQMAVSDGSVKGLLSVVRGWSR.G 1 2 S.LGIFLLFREDQPPGK.V 2.7881 2 Q8NBA2 1 Q8NB73 4.0571L.KIKGKEDIDL.D 2 E.DQIESDESELK.K 3 1 Q8NAR9 Q8NAR6 1 Q8NAC9 Q8N157 2.5699 Q8NAG7 1 2.4386 1 2 1 4 2 2.2192 1 2.767 3.8517 Q8NA94 1 3.0675 2 2.2182 3 2 1 2 Q8NA19 Q96HJ4 2.4338 1 2 1 2.4464 2.6729 2 2 Hypothetical protein FLJ32867 Hypothetical protein FLJ32933 Hypothetical protein FLJ32978 Hypothetical protein FLJ33401 Hypothetical protein FLJ33516 Hypothetical protein FLJ33697 Hypothetical protein FLJ33868 Hypothetical protein FLJ34011 Hypothetical protein FLJ34087 Hypothetical protein FLJ34146 (Fragment) Hypothetical protein FLJ34889 (Fragment) Hypothetical protein FLJ34907 Hypothetical protein FLJ34943 Hypothetical protein FLJ35382 Hypothetical protein FLJ35502 Hypothetical protein FLJ35552 Hypothetical protein FLJ35727 Hypothetical protein FLJ35936 Hypothetical protein FLJ36029 Hypothetical protein
161 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table .FIMAILVGV.K Q8N994 2 2.6735 2 .SCPQLPPRDSPR.C Q8N1N9 1 2.5228 2 G.GGRRVLSGGGRTAFGGGGRTAFGDGGRTAF.GR.IQLQILE.AA.SFLEWASAVLPTGPPEPL.S Q8N9U9L.SRVVPYCSNNMPPICVQ.NR.FRKVLGCELPPSPAPDL.L 1D.FEENAYSYASV.DK.ALPDVELVQ.H 2.4533A.LSLPSPEGLSLKATPGAAH.KP 2 Q8N9T9I.QGIFMGE.H Q8N9S7V Q8N9U0 1L.NSSVPPGEPLEIK.G Q8N9G9L.QVFDEIR.S 1 2.201 1L.LLAHPACDSSLTDK.A 2 Q8N1W2 Q8N1N9 2.4527K.KLVMLKEMDKDLNSVVIA.V 2 2.2941 2.4634 Q8N1P7A.ISAGTGASGIVEVLTEV.P 2 1 1 1 K.HDLFTPEPHYV.P 2 3R.IDCGEKPYKCNECGKTFGQ.N 2.6097 2.4346 Q8N9A1 2 2 2.6266 Q8N922 2 Q8N8K6 1 Q8N8S2 1 Q8N8W3 Q8N897 2.4581 1 1 2.4341 Q8N823 1 1 2.4401 3 2 2.4902 Q8N830 2.4137 1 2 2 2.9438 2 1 2.609 2 2.4522 2 2 Protein FLJ36186 Hypothetical protein FLJ36557 Hypothetical protein FLJ36558 Hypothetical protein FLJ36601 Hypothetical protein FLJ37161 Hypothetical protein FLJ37393 Hypothetical protein FLJ38020 Hypothetical protein FLJ38072 Hypothetical protein Peptide FLJ38144 Hypothetical protein FLJ38183 Hypothetical protein FLJ38508 (Fragment) Hypothetical protein FLJ38763 Hypothetical protein FLJ38940 Hypothetical protein FLJ39325 (Fragment) Hypothetical protein FLJ39787 Hypothetical protein FLJ40100 Hypothetical protein FLJ40115 Hypothetical protein
162 (continued) TCLHAILNILEK.G Q92621 4 2.7687 2 .LDHATVIHSGDYF.L Q92508 4 2.7606 2 R R.EPQIVEFVFLL.SH.HNKKHGVFSKLPRNPKTPTERIYW.AD.WEQSAESLQPVQEDMA.LK.LHPNQAGLDSKV.LE.LFTIEDLQNSVTQLQL.QQ.FDASTPKNDISPPGR.FS.INPFNTSLFQFSSV.K Q8N7Y9H.IYGYFDEEMAVK.YL.ALFNSAIVMQESGEVKL.R 1R.AGRHPQLLPRLPAL.H Q8N815 Q8N7R5E.SSVKALDFDISETRTEV.E 2.5698R.IYCEDKQTFLQ.D 1L.AAFTKLYESLL.P 1 2 Q8N1K5 Q8NCI1Q.WEGQLVNLFARLATDNIGYIDW.D Q8NCI1 2.5132 2.6961R.ILLYSSTLR.W 1 Q8NCI1 1 1 A.AESLTAIPEPASPQ.L 2 Q8NC50 Q8NCD6 1 3.4389A.VFEAYQEHIEEQNLERQV.L 2.2697 1 Q8N2J0 2.4815N.PLSMLLNGIVDPAVMGGFAKY.E 1 1 2 Q9P2X3 1 2.4921 Q14997P. 2 2.73 2.79 1W Q9P2X3 2 1L.DFTEDLPGVPES.V 1 P42695 2 2 2.9247 2.5932 7 2 2.5523 Q14687 Q92608 2 1 Q14676 Q14667 2.8824 2 2.3359 2 1 1 1 1 2 3.2366 2.4592 2.4246 2.2669 2 2 2 Q92549 2 1 2.5514 2 Hypothetical protein FLJ40137 Hypothetical protein FLJ40201 Hypothetical protein FLJ40441 Hypothetical protein FLJ40584 (Fragment) Hypothetical protein FLJ90238 Hypothetical protein FLJ90323 Hypothetical protein FLJ90492 (Fragment) Hypothetical protein FLJ90562 Hypothetical protein (Imprinted and ancient) IMPACT Hypothetical protein KIAA0056 (Fragment) Hypothetical protein KIAA0077 (Fragment) Hypothetical protein KIAA0100 (Fragment) Hypothetical protein KIAA0170 Hypothetical protein KIAA0182 (Fragment) Hypothetical protein KIAA0209 (Fragment) Hypothetical protein KIAA0225 (Fragment) Hypothetical protein KIAA0233 Hypothetical protein KIAA0261 (Fragment) Hypothetical protein
163 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table .RAMDTDTLTQVKEKI.L Q9Y4D7 1 2.5666 2 .LKDTKGAQKVINWHMK.I O15078 1 2.5515 2 .WGSGVGGGGTVRLLL.I.KDKSSTGDGTQNK.R O14524 1 2.663 2 O43148 1 2.4942 2 A.YPYVESETVEQ.DR.HLLAEVSK.QP L.NPLLLSNILYP.GS.PKANGQNQ.AR.PASPARSGSPAPETTNE.SK.FSVNGDFIISNVDGK.GT L.FMEGLADSALED.V Q92551P Q.EAGELRRSLGEGAKEREAL.R Q9Y469 1A.MLDYELHSDFVSSL.I O15047 O15025I.NCSSGSSSRDSLREPP.A 1 2.3222L.HAFIAEVFAMVRAHV.A O15047 O15070 1 2 1A.EGLAGPVQEVACLFNTVMLQLVA.A 1.9753G.EGPGETEARDK.G 1 1 1 2.6665 2.8732 O15085 O75033L.IGRPNKVTTVDRFQGQQNDYIL.L 2.5256 2 2 2.3676V 1 1 1 2 O75051 O60287 O60275 2.7367 O60280 3.902 1 1 2 O60306 1 2 2 2.4797 2.2008 O60303 2.5865 1 2 2.3769 2 2 2 1 2.5749 2 2.3033 1 Protein KIAA0263 (Fragment) Hypothetical protein KIAA0278 (HARG) (Activity-regulated Hypothetical protein KIAA0286 (HA6800) (Fragment) Hypothetical protein KIAA0308 (Fragment) Hypothetical protein KIAA0339 (Fragment) Hypothetical protein KIAA0364 Hypothetical protein KIAA0373 Hypothetical protein KIAA0380 Hypothetical protein Peptide KIAA0398 (RNAHypothetical protein (Guanine-7-) KIAA0445 (DJ37C10.5) Hypothetical protein KIAA0463 (Fragment) Hypothetical protein KIAA0522 (Fragment) Hypothetical protein KIAA0528 (Fragment) Hypothetical protein KIAA0539 (Fragment) Hypothetical protein KIAA0556 (Fragment) Hypothetical protein KIAA0560 (Fragment) Hypothetical protein KIAA0620 (Fragment) Hypothetical protein
164 (continued) .KSKACEKVISVGQTVITK.H.SLSATGPQFLSVEPAH.S.DRCLFYYKDEKEESILGS.I O94877 2 3.3772 2 Q9Y2H2 Q9Y2H5 5 1 2.6663 2.8695 1 2 .KLDEVVTSEGK.T O94877 1 2.8465 2 G.ACGGVLAPPAGTAASSKA.VI.MEVVGLEEQGQNF.VA.GGPKVGGASKEGGAGAVDEDDFIKAFT.DD.FEKKGGISFGRAKGT.SE.DFDFKHYNKTLF.AD.PEGVALEALPVQESVHIME.GK.LPVPQGPNPVVVVLQ.Q O75122 O75119K.DGSLLEVEKVSLQQRLNQ.FT 1V 1 O75121L.NMQQHQPLTMQQP.L 2.5381 3.048L.SSAEDSGVDEGQ.G O75129 O75189 9 2 L.FDHLEPIELAEHLTFL.E 2 O75189I.RNNLTVIDMIGVEGFGA.R 2.5827 2 O94829 9 O94873V 2 1V 3.1103 3.0571 1 2G.AAGAGTGGAGPAGRLLPPPA.P 2 2.9994 2 R.SSIIKDGTKQK.R O94900 2.5097 2.5197 2 A.KFPDYKSTWSPDPIGH.N 2 O94928 2 I.SHLSKQGQEVEPPRRGPAVPPAR.P O94931 2 Q9H065 1 3.4005 3 Q9Y2K2 1 2 3.3494 2.8713 2.2343 1 2 Q9ULT2 2 2 Q9UPQ9 2.4821 Q9UPR0 1 2 1 1 4.0233 2.9137 2.8611 3 2 2 Hypothetical protein KIAA0623 Hypothetical protein KIAA0626 Hypothetical protein KIAA0627 (Fragment) Hypothetical protein KIAA0634 (Fragment) Hypothetical protein KIAA0710 Hypothetical protein 13) KIAA0724 (RAN binding protein Hypothetical protein KIAA0775 Hypothetical protein KIAA0780 (Fragment) Hypothetical protein KIAA0808 Hypothetical protein KIAA0842 (Fragment) Hypothetical protein KIAA0846 Hypothetical protein KIAA0922 Hypothetical protein KIAA0966 Hypothetical protein KIAA0969 Hypothetical protein KIAA0999 (Fragment) Hypothetical protein KIAA1092 (Fragment) Hypothetical protein KIAA1093 (Fragment) Hypothetical protein (Fragment) KIAA1138 Hypothetical protein
165 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table YELWYK.L Q9ULE8 4 2.4782 2 L HELRAVKGPLLYCAR.P Q8N1G4 2 2.9629 2 .AREIPRYKQMVERY.Y Q9ULL4 1 2.3485 2 .VGDLDKVVNLLLSLSGRLARVENAL.N Q9ULL8 1.GGMNRIGGGIGFGGLEAMNSMGG.F 2.4292 2 Q9P2K5 1 2.691 2 D.YNPCEEDLFVLF.FL.FDGHAGSGAAVVASR.LT. S.EGRKNNHLLGHGGK.SF Y N.KDFLLGVNFPLSFPNL.CN.LKLEDARR.E Q9ULR3 Q9ULS3Y. K.LKSEMEEKVYNLT.R 1 1S.FSFNPHPGYLTPSMK.K Q9ULM5S.YLNALKKL.Q 2.4185 2.9733 1F Q9ULG1 2 2 K.KSAWSSAQVK.V 2.4517G.EPYQHNTPLHYAAR.H 1 2 K.DVPPFGPPIPKGVTF.P Q9ULF2L.LPFLLEMIVLL.L 2.5547 Q9ULE5 Q9ULE4 2 1 1 1 2.5046 Q9P2Q2 2.3025 2 2.7122 Q9P2G1 Q9P2I4 1 3 2 Q9P2F8 1 1 2.7195 Q9P2E7 1 3.8319 2 2.314 2.3461 3 1 2 1 2.254 2 Protein (Fragment) KIAA1147 Hypothetical protein (Fragment) KIAA1157 Hypothetical protein KIAA1185 Hypothetical protein (Fragment) KIAA1195 Hypothetical protein KIAA1202 (Fragment) Hypothetical protein KIAA1206 (Fragment) Hypothetical protein KIAA1259 (Fragment) Hypothetical protein KIAA1268 (Fragment) Hypothetical protein Peptide KIAA1272 (Fragment) Hypothetical protein KIAA1275 (Fragment) Hypothetical protein KIAA1276 (Fragment) Hypothetical protein KIAA1294 (Fragment) Hypothetical protein KIAA1341 (Fragment) Hypothetical protein KIAA1363 (Fragment) Hypothetical protein KIAA1386 (Fragment) Hypothetical protein KIAA1389 (Fragment) Hypothetical protein KIAA1400 (Fragment) Hypothetical protein
166 (continued) .LFDIQLPNIYPAVPPHFCYLSQC.S Q9C0C9 1 3.7657 3 .SDVKRGAPKRQSDPSIR.T Q9C0D7 1 2.4465 2 .FKLMIGSSNAMGRL.Y.IGCYLALSMTAVGHSIEK.F Q9P267 1 2.8413 2 Q9HCE0 1 2.7601 2 L.CPWGTHLAGPTT.MG.LQPLVEPCLRQTLKLL.SI.RMAFMAATDHSNQ.LM.PPNKEASGLSSSPAGL.IQ.PPTTVLSLLRQSQMDSSA.VP A.FNAAGDGPRSTPTQGQTQQ.AA.QRGSPGGPEFLKTPL.GA.FLRDLAEQNSGKYG.V Q9P2E5 Q9P2E4S.YVGGFAVVEYSTA.E Q9P2D3I.VPTITQGSRDGHRSPA.R 1 Q9P2A5 1 Q9P267A.VHPEIISVLLDRVQE.TP Q9P214 2 2.4456 2.7764I.KKITQELSDLQQ.E 1 1S.LLSESNKKLHNQEQVIKHL.T 2 2 2.4486 1N.DDDEDVQVEVAEKVQ.K Q9HCM0 2.4004 2.651 2 I.KLTDSNFLRILENSIR.L Q9HCJ9 2 2.5971 1T 2 Q9HCJ3 2 Q9HCF8I.ISGLGSNKWIQQNLQ.C 1 2.5401S.REELIKR.G Q9HCE0 3 3.1602 1 1Y Q9HCD9 2 1 2.4614 Q9HCD9 2.2369 Q9C0H0 1 2 2.7363 2 Q9C0G6 2 1 2.9723 2 2 2.6026 Q9C0D3 2 3.5023 1 2 3.0952 1 Q9C0D0 2 2.5608 2 4 2.6635 2 Hypothetical protein KIAA1402 (Fragment) Hypothetical protein KIAA1403 (Fragment) Hypothetical protein KIAA1414 (Fragment) Hypothetical protein KIAA1443 (Fragment) Hypothetical protein KIAA1461 (Fragment) Hypothetical protein KIAA1514 (Fragment) Hypothetical protein KIAA1552 (Fragment) Hypothetical protein KIAA1573 (Fragment) Hypothetical protein KIAA1579 (Fragment) Hypothetical protein KIAA1614 (Fragment) Hypothetical protein KIAA1632 (Fragment) Hypothetical protein KIAA1633 (Fragment) Hypothetical protein KIAA1693 (Fragment) Hypothetical protein KIAA1697 (Fragment) Hypothetical protein KIAA1726 (Fragment) Hypothetical protein KIAA1730 (Fragment) Hypothetical protein KIAA1733 (Fragment) Hypothetical protein KIAA1734 (EC 6.3.2.19) (Ubiquitin- Hypothetical protein
167 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table VPKPIPLPGV.R Q8NCM4 2 2.3681 2 ALLQPDAAGPGGGGVSAGVAVL.G Q96JP2 1 2.704 1 R T .SSLVMGSQTESA.L Q96JN0 2 2.4595 2 .RSHLNQHQ.R Q96JJ8 1 2.4038 2 .GSEGVVLSPNYPHNYTAGQ.I Q96PZ7 1 2.9081 1 .ACHVLLDSFGTYALTGE.P Q8WYP7 1 3.0272 2 K.GKSPPMAEATPVIVTTEEIAEIKRKNE.LF P. Y Q9C093 1 3.3549 2 I.ARSAAATALSLLVPVFII.SK.AWCWASYLEEEK.AE.NVILQEKEIYSKSK.EM.KSCCFAGDRDQYILS.GY Q96JM8 Q96JM7 1 Q96JM4 Q96JK2 2.3742 3 1 2 1 2.4841 2.8299 2 2.3743 2 1 T K.VFSGTASPSPGEETF.EM.EATGSRATGMEATGVSATGV.EE.EEEEEMK.QV. I.EALHKDEGNEAV.ER.PSSLSASNSTQTFSVTM.SI.QQHMVSPEPASLKE.KA.FPNGTLEIGATGAG.D Q8TF21 Q96PV4 1 1 2.7809 Q8NCM4 2.4241 Q8IVG6 Q8IVF3 2 2 Q8IVP0 1 4 1 Q8N644 2.4536 2 2.7358 2.5465 1 2 2 2 3.0187 2.9531 2 2 Protein KIAA1770 (Fragment) Hypothetical protein KIAA1777 (Unc5h4) Hypothetical protein KIAA1783 (Fragment) Hypothetical protein KIAA1795 (Fragment) Hypothetical protein Peptide Hypothetical protein KIAA1797 (Fragment) Hypothetical protein KIAA1798 (Fragment) Hypothetical protein KIAA1801 (Fragment) Hypothetical protein KIAA1824 (Fragment) Hypothetical protein KIAA1829 (Fragment) Hypothetical protein Hypothetical protein KIAA1890 (Fragment) Hypothetical protein KIAA1934 (Fragment) Hypothetical protein KIAA1981 (Fragment) Hypothetical protein KIAA2001 (Fragment) Hypothetical protein KIAA2004 (Fragment) Hypothetical protein KIAA2018 (Fragment) Hypothetical protein MGC27277 Hypothetical protein MGC3103 Hypothetical protein MGC45474 (Fragment) Hypothetical protein
168 (continued) WPLPLLLLLLLLLGP.A Q8NBP7 1 2.7108 2 TLHVAANFSVPVVSAPH.S O75144 1 2.7797 2 .GLVFIMGYSVVAGA.A Q8N4M1 2 2.6515 2 .FSCMVGHEALPLAFTQK.T P01876 1 2.533 2 T W. S.GSSNSSGDALVTRISILLRDLPTLK.AE.ELALQGQPGNSKYSCKV.CE.DVAAFSSSDDV.GR.PYECNECGKSFQ.DR.RHSSEGGVK.S Q8NBH7V. R.DGRKLVPWVDTIKE.S 1K.GDTFSCMVGHEALPLAFTQK.T O15060K.SGNTFRPEVH.LK.TPLTATLSK.SE.PSQGTTTFAVTSILR.V 3.8008G.TTTFAVTSILR.VK.KGDTFSCMVGHEALPLAFTQK.T 1 3 K.SAVQGPPER.D O75132K.TFTCTAAYPESK.T Q8TF45K.YLTWASR.Q 2.306G.HEALPLAFTQK.TL.SVTWSESGQGVTAR.N 1R.NFPPSQDASGDLYTTSSQLTLPATQCLAGK.S Q9BYB6 P01876 1 1R.WLQGSQELPR.E Q9Y6Y4T 2.2714R.DLCGCYSVSSVLPGCAEPWNHGK.TR.DASGVTFTWTPSSGK.S 2.425 2 P01876 4R.VAAEDWK.K 1 1R.QEPSQGTTTFAVTSILR.V P01876 P01876 P01876R.LSLHRPALE.D 2 2.162R.LSLHRPALED.L 4.2155 P01876 2.6865 1 P01876 1 14 2 2 3 2 P01876 P01876 61 3.6474 P01876 P01876 P01876 1 2.601 2.5593 3.6236 P01876 2 12 2.3437 9 2 2 2 2 P01876 2.4676 2 P01876 5 2 15 2.8006 P01876 2.7096 2 3.8025 2.9064 63 3.2742 2 80 2.2961 2 P01876 2 16 2 P01876 2 P01876 3.6482 2 3.8378 3 3.5276 2 2 2 1 2 2.205 2.4597 2.5596 2 2 2 γ -1 chain C region α Hypothetical protein NT2RP2000279 Hypothetical protein NT2RP3002337 Hypothetical protein KIAA0352 Hypothetical zinc finger protein KIAA0637 Hypothetical zinc finger protein KIAA1956 Hypothetical zinc finger protein ICB-1 ICOS ligand (B7 homolog 2) (B7-H2) (B7-like IDN3 protein Ig
169 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table .NWYVDGVEVHNAK.T P01857 6 3.4653 2 R.DLCGCYSVSSVLPGCAQPWNHGE.TR.DASGATFTWTPSSGK.SK.VPTGGVEEGLLER.HR.SLEVSYVTDHGPM.-K.GFYPSDIAVEWESNGQPENNYK.TK.THTCPPCPAPELLGGPSVFLFPPKPK.DK.STSGGTAALGCLVK.DK.THTCPPCPAPELLGGPSVFLFPPK.P P01877K.THTCPPCPAPELLGGPSVF.LK.GPSVFPLAPSSK.SK.TTPPVLDSDGSFFLYSK.LG.GPSVFLFPPKPK.DL.TVLHQDWLNGK.E 1K.GFYPSDIAVE.W P01877 P01857K.NQVSLTCLVK.G P01857D.PEVKFNWYVDGVEVHNAK.T 3.0137 P01880E.LLGGPSVFLFPPKPK.D P01857K.TTPPVLDSDGSFFL.Y P01880 27G.PSVFLFPPKPK.D 29 2 18K.TTPPVLDSDGSFFLYS.KL.DSDGSFFLYSK.L 12 P01857 P01857 3.3717K.DYFPEPVTVSWN.S 4.293 7 1 3.1534K.FNWYVDGVEVHNA.KK.DYFPEPVTVSWNSG.A 2 2.5157 P01857K.DYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVT 3 2 45 2 4.2223K.FNWYVDGVEVHNAK.T P01857 2.9273D.SDGSFFLYSK.L 2 P01857 P01857 P01857L.GGPSVFLFPPKPK.D 220 P01857 3 2 2.7781K.DTLMISR.T 3.379 174F P01857L.LGGPSVFLFPPKPK.D P01857 P01857 2 2.5482 73 1 2 4 P01857 8 2.2058 P01857 2 1 3.0976 P01857 3.8436 4.2197 1 5 8 3.2111 P01857 P01857 1 P01857 2 3 3 P01857 2.7814 1 2 2.4965 2.4121 22 P01857 2.4787 2 4 2 2.4591 2 5 1 2.9777 1 P01857 1 69 P01857 1 3.3127 2.6834 2.6017 2 P01857 2.649 P01857 2.4171 71 2 2 1 3 1 2 7 3.2669 23 2.76 2 2.4243 2.5384 2 2 2 chain C region -2 chain C region -1 chain C region α δ γ ProteinIg Ig Ig Peptide
170 (continued) -2 chain C region γ .YVDGVEVHNAK.T P01857 12 3.1898 2 TLPPSRDELTK.N P01857 7 2.6529 2 CPPCPAPELLGGPSVFLFPPKPK.D P01857 1 4.2484 3 APELLGGPSVFLFPPKPK.D P01857 1 2.407 2 .FPLAPSSK.S.SVLTVLHQDWLNGK.E.PSSSLGTQTYICNVNHKPSNTK.V.DGVEVHNAK.T.VTVPSSSLGTQTYICNVNHKPSNTK.V P01857 P01857.VSVLTVLHQDWLNGK.E P01857 1 10 P01857 3.5693 1 4.1905 P01857 2 1 2 2.367 3.155 5 1 P01857 2 2.354 1 1 3.7549 2 .VDGVEVHNAK.T P01857 2 3.2388 2 .PPVLDSDGSFFLYSK.L.KGPSVFPLAPSSK.S P01857 12 2.4497 P01857 2 4 2.5896 2 .PVLDSDGSFFLYSK.L P01857 2 2.4667 1 K.FNWYVDGVEVH.ND.GSFFLYSK.LA.PELLGGPSVFLFPPKPK.DK.VSNKALPAPIEK.TG.PSVFLFPPK.PK.ALPAPIEK.TC.PAPELLGGPSVFLFPPKPK.DK.TTPPVLDSDGSFFLY.SC.VVVDVSHEDPEVK.FG.PSVFPLAPSSK.ST R.EPQVYTLPPSRDELTK.NR.EPQVYTLPPSR.DV V N.WYVDGVEVHNAK.T P01857 P01857V T Y. P01857 P01857 P01857Y 14 23V P. P01857 P01857R.TPEVTCVVVDVSHEDPEVK.F P01857 2.978 P01857 4.4611 1T. 2 7V P01857W 3 P01857 2 P 1 1 4.3712 3.2332 2.4997R.TPEVTCVVVDVSHED.P 5 4S.DGSFFLYSK.L P01857 24 3 V 2 2.4892 2 2.4916 P01857R.VVSVLTVLHQDWLNGK.E 5 1.9172 2.8205N.KALPAPIEK.TIg 2 1 2.5186 51K.GPSVFPLAPCSR.S 1 2 2.8708 37K.CCVECPPCPAPPVAGPSVFLFPPKPK.D P01857 2 D.PEVQFNWYVDGVEVHNAK.T 2.3134L.TVVHQDWLNGK.E 2 K.TTPPMLDSDGSFFLY.S 3.3426 2 8 2 P01857 3.8225 P01859 P01857 3 14 P01857 P01859 54 1 P01857 2.9117 P01859 2 4.6671 2.9336 2 1 P01859 P01859 1 24 2 2 2.9834 4.6311 1 3 2 2.4135 2.7903 3 2 2 2.4944 2.4332 1 2
171 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table AGPSVFLFPPKPK.D P01859 8 3.0164 2 V PVAGPSVFLFPPKPK.D P01859 1 3.0878 2 .SVLTVVHQDWLNGK.E P01859 3 2.9983 2 .PPMLDSDGSFFLYSK.L P01859.PPVLDSDGSFFLYSR.L 9 5.4691 2 P01861 1 3.5294 2 .APPVAGPSVFLFPPKPK.D P01859 1 3.2122 2 K.TTPPMLDSDGSFFLYSK.LP. P. P N.KGLPAPIEK.TT R.TPEVTCVVVDVSHEDPEVQ.FR.KCCVECPPCPAPPVAGPSVFLFPPKPK.DR.STSESTAALGCLVK.DQ.TYTCNVDHKPSNTK.VV R.VVSVLTVVHQDWLNGK.EK.TPLGDTTHTCPR.C P01859K.SCDTPPPCPR.CR.TPEVTCVVVDVSHEDPEVQFK.W P01859K.YGPPCPSCPAPEFLGGPSVFLFPPKPK.D 25 P01859G.PPCPSCPAPEFLGGPSVFLFPPKPK.DK.YGPPCPSCPAPEFLGGPSVFLFPPK.P 1K.TTPPVLDSDGSFFLYSR.L 2.8899R.WQEGNVFSCSVMHEALHNHYTQK.S P01859T 6 P01859R.EPQVYTLPPSQEEMTK.N 3.7995 P01859 1 P01859-.QVQLVQSGAEVK.K P01861 P01860 3 1 4.2699Q.VQLVQSGAEVK.K 79 P01861 8S.QTQLVQSGAEVR.K 21 3 P01860 P01861 2.4636 19K.ALEWLAR.I P01861 3 2.4073 P01860 3.2012 4.1463 2 -.EVQLVESGGGLVQPGGSLR.L 2 2 E.VQLVESGGGLVQPGGSLR.L 3.974 5 1 3.731 P01861 2 2 2 2 4.0916 3 3.4342 P01861 2.449 2 56 3.5959 3 2.5104 2 2 P01742 2 2 2.6959 2 P01742 P01744 2 P01766 2.4219 8 P01766 1 2 1 P01814 2.5261 26 2.405 1 2 2.7477 4.1628 1 2 2.6194 2 2 2.2803 2 2 -3 chain C region (Heavy chain disease protein) (Heavy chain disease protein) -3 chain C region -4 chain C region γ γ ProteinIg Peptide Ig EU region Ig heavy chain V-I ND (Fragments) region Ig heavy chain V-I OU region Ig heavy chain V-II BRO region Ig heavy chain V-III
172 (continued) .PPSDEQLK.S P01834 2 2.3414 1 -.EVQLVESGGGLVQ.PQ.LVESGGGLVQPGGSLR.LE.LVESGGGVVZPGR.SQ.VELVESGGGVVZPGR.S-.QVKLVQAGGGVVQPGR.S-.DVQLVESGGGLVKPGGSLR.LQ.LVESGGGLVKPGGSLR.LL.YYADSVK.G-.QVQLVQSGGGLVKPGGSLR.LQ.SGGGLVKPGGSLR.L P01766E.SGGGLVQPGGSLR.L P01766G.GGLVQPGGSLR.LC.EVQLLESGGGLVQPGGSLR.L P01768Q.LLESGGGLVQPGGSLR.L P01768 3 P01771 1-.QVQLVDSGGGLVEPGGSLR.L P01780G.LVEPGGSLR.L 3.5268 1 P01780 3-.TVAAPSVFIFPPSDEQLK.S 4.2614 2D.NALQSGNSQESVTEQDSK.D P01762 2C.LLNNFYPR.E 2 2 2.9024C.EVTHQGLSSPVTK.S 2.6592G.NSQESVTEQDSK.D 5 2.2302 P01762A.SVVCLLNNFYPR.E 2.9562 2 1 2 P01762D.STYSLSSTLTLSK.A P01764 1 A.PSVFIFPPSDEQLK.S P01764 3.5131 2 F P01764 P01764 2.6661A.APSVFIFPPSDEQLK.S P01763 1K.VYACEVTHQGLSSPVT.K 2 1 8K.SGTASVVCLLNNFYPR.E 1 1K.VDNALQSGNSQESVTEQD.S 2.5929K.VYACEVTHQGLSSPVTK.S 5 P01834 P01834 1 2 2.433 3.4551K.DSTYSLSSTLTLSK.A 2.5381 P01763 2 2.5825 2 2.5369 1 2.9525 69 2 1 P01834 2 P01834 2 P01834 2 1 P01834 3.2727 4.436 P01834 P01834 7 2.4395 P01834 1 P01834 1 2 1 P01834 P01834 1 2 P01834 3.0244 1 13 2.73 2.5045 3 1 2.5007 16 2 3 P01834 2.5117 2.4003 2 39 2 1 3.5838 3.077 2.7916 4.2554 2 1 436 2.3083 2 2 1 2 2 2.37 2 chain C region κ Ig heavy chain V-III region CAM region Ig heavy chain V-III HIL region Ig heavy chain V-III JON region Ig heavy chain V-III TRO region Ig heavy chain V-III VH26 region Ig heavy chain V-III WEA region Ig heavy chain V-III Ig
173 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table .KVDNALQSGNSQESVTEQDSK.D P01834 1 3.8391 2 EFTLTISS.L P01598 1 2.2579 1 .ACEVTHQGLSSPVTK.S P01834 6 3.0483 2 K.VDNALQSGNSQESVTEQDSK.DQ.SGNSQESVTEQDSK.DN.SQESVTEQDSK.DW Y S.GNSQESVTEQDSK.DN.ALQSGNSQESVTEQDSK.D-.DIQMTQSPSSLSASVGDR.VM.TQSPSSLSASVGDR.VQ.SPSSLSASVGDR.V P01834-.DIQLTQSPSSLSASVGDR.V-.DIQMTQSPSTLSASVGDR.VQ.SPSTLSASVGDR.V 20 P01834-.BIZMTQSPSSLSASVGDR.V P01834 2.2791 P01834K.ASSLESGVPSR.FT. 9 P01834 P01593 2 K.LLIYKASTLETGVPSR.F 1 4 2.2825 P01593K.LLIYGASTR.E 1 P04430 2 P01593 3.077K.LLIYDASNLETGVPSR.F 1 5.2592 P01596-.DIQMTQSPSSLSATVGDR.V 2.3199 1 2.2449 2 S.YLBWYZZKPGK.A 2 4 P01597 7 1 P01596-.DIQMTQSPSSVSASVGDR.V 4 1 2.9558R.FSGSGSGTDFTLK.I 5.6874 3.3596R.FSGSGSGTDFTLKISR.V 2 4 5.0292 3 P01598 2 P01604 2 2 5.4398 3.2201 P01613 P01613 2 1 2 2 P01605 2.6842 P01611 3.3818 2 2 P01606 6 2 2 4.0476 2.6146 P01614 4 P01614 3.1042 1 2 2 4.9907 2 1 3.0164 42 2 2 3.2331 3.3221 2 2 chain V-I region AG region chain V-I BAN region chain V-I CAR region chain V-I DEE region chain V-I EU region chain V-I Kue region chain V-I Lay region chain V-I Ni region chain V-I OU region chain V-I Wes region chain V-I Cum region chain V-II κ κ κ κ κ κ κ κ κ κ κ ProteinIg Ig Ig Peptide Ig Ig Ig Ig Ig Ig Ig Ig
174 (continued) .KAGVETTTPSK.Q P01842 2 2.4483 2 .SCQVTHEGSTVEK.T P01842 1 3.305 2 R.FSGSGSGTBFTLK.IL.TZSPGTLSLSPGZR.AG.NYLAWYQQK.PG.EIVMTQSPATLSVSPGER.AM.TQSPATLSVSPGER.AQ.SPATLSVSPGER.AG.EIVLTQSPGTLSLSPGESA.T-.EIVLTQSPGTLSLSPGER.AR.FSGSGSGTDFTLTISR.LQ.SPGTLSLSPGER.AR.LLIYGASSR.A P01616L.TQSPATLSLSPGER.AG.EIVLTQSPATLSLSPGER.A P01619 P04207Q.SPATLSLSPGER.AR.LLIYDASNR.A P01619 3 P04207M.TQSPDSLAVSLGER.A 1 P06311G.DIVMTQSPDSLAVSLGER.A 8 P04207K.SSQSVLYSSNNK.N 2.613D.SLAVSLGER.A 1 P01620 2.6157L.WISGAYGDIVMTQSPDSLA.V 2 4.6199 8 P01620 2 A.ASSYLSLTPEQWK.S 2 2.5088 2 K.ADSSPVKAGVETTTPSK.Q 2 2.6809 15 P01620K.YAASSYLSLTPEQWK.S 3.4162K.AGVETTTPSK.Q 2 P04433 19 3.4452 P04433K.AAPSVTLFPPSSEELQANK.A 2 P01620R.SYSCQVTHEGSTVEK.T 4.4352 2 S.SYLSLTPEQWK.S 2 7 P04433 4.4635V P06312 2 2Y P06312 2 5 P04433 2 3.2608 P06312 4.1295 2 P06312 2.8327 7 2.6433 2 1 2 9 P01842 P06312 2 1 2.6078 2 P01842 4.5946 1 P01842 P01842 3.0771 2.2025 2 2.8694 2 1 1 2 P01842 2.3894 P01842 2 2 63 2 5 2.7622 2.4892 2 P01842 3.3712 25 2.0906 32 3.2199 2 2 2 1 1 4.4168 1 2.6242 2 2 2.402 2 R.FSGSLLGGK.A P04211 1 2.238 2 chain V-II region MIL region chain V-II B6 region chain V-III CLL region chain V-III (Rheumatoid factor) IARC/BL41 region chain V-III SIE region chain V-III VG (Fragment) region chain V-III (Fragment) region chain V-IV chain C regions chain V region 4A chain V region κ κ κ κ κ κ κ λ λ Ig Ig Ig Ig Ig Ig Ig Ig Ig
175 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table .YCSSYVDNNNFVFGGG.T P01710 1 2.9867 2 K.RPSGVPDR.FK.SGTSASLAISGLR.S P01700 P01700 2 3 3.4573 2.7482 2 2 K.RPSGIPDR.IQ.SVLTQPPSVSAAPGQK.V P01701 P01701 3 2.6266 3 2 2.7973 2 Q.SVLTQPPSVSGAPGQR.V P01703 4 2.6021 2 K.LLIYDNNK.RQ.SVLTQPPSVSAAPGQE.V P01702 P01702 2 1 3.8645 2 2.3171 2 Y H.FVSWYQQHPGK.A P01706 1 2.4998 2 K.YVSWYQQHPGK.A P01708 2 3.211 2 K.RPSGVSNR.F P01705 1 3.1271 2 K.LMIFDVTKRPSGVPDR.L P01707 1 2.2649 2 N.RPSGVSDR.F P01711 1 2.6662 2 -.YVLTQPPSVSVAPGETAR.LD.RPSGIPER.F-.YVLTQPPSVSVAPGE.TQ.PPSVSVAPGETAR.LR.FSGSNSGNTATLTISR.V P80748 P80748 9 P80748 P80748 P80748 4.4932 4 7 1 2 2 3.3739 4.2559 2.2112 2.5831 2 2 1 2 -.SELTQDPAVSVALGQTVR.I P01714 3 3.5615 2 K.RPSGIPZR.F P06889 5 2.8532 2 chain V-I region HA region chain V-I chain V-I region NEW region chain V-I chain V-I region NEWM region chain V-I chain V-I region NIG-64 region chain V-I chain V-II region BO region chain V-II chain V-II region BOH region chain V-II chain V-II region BUR region chain V-II chain V-II region NEI region chain V-II chain V-II region TRO region chain V-II chain V-II region VIL region chain V-II chain V-III region LOI region chain V-III chain V-III region SH region chain V-III chain V-IV region MOL region chain V-IV λ λ λ λ λ λ λ λ λ λ λ λ λ ProteinIg Peptide Ig Ig Ig Ig Ig Ig Ig Ig Ig Ig Ig Ig
176 (continued) PLPVIAELPPK.V P01871 6 2.253 1 .LKQSLSFSTC.G O95163 1 2.5016 2 .PPSSEELQANK.A P15814 21 2.2249 1 D.FMLTQPHSVSESPGK.T-.DFMLTQPHSVSESPGK.TA.NFMLTQPHSVSESPGK.TR.FSGSIDSSSNSASLTISGLK.TK.QVGSGVTTDQVQAEAK.EK.NVPLPVIAELPPK.VK.DVMQGTDEHVVCK.VG.SGVTTDQVQAEAK.EK.YAATSQVLLPSK.DQ.VGSGVTTDQVQAEAK.EV. P01721 P01721I.PPSFASIFLTK.SK.VSVFVPPR.D P06319K.QVGSGVTTDEVEAEAK.E P06318G.VTTDEVEAEAK.E 1K.GVALHRPDVYLLPPAR.E 1G.SGVTTDEVEAEAK.E P01871K.GVALHRPDVY.L 1K.YVTSAPMPEPQAPGR.Y 3.3123 1 3.1402R.EGKQVGSGVTTDEVEAEAK.E P01871 P01871S.GVTTDEVEAEAK.E 18 4.8848 2 P01871R.DGFFGNPR.K 2 P01871 3.179Q.VGSGVTTDEVEAEAK.E P01871R.VFAIPPSFASIFLTK.S 2 17 4.2165 4 2 Y 3 1 2 P04220 31 2.6365R.SSEDPNEDIVER.N 4.0172 P04220 P04220 2.4402F 2 2.8292 P04220 2 P04220L.FPPSSEELQANK.A 3.5133 P04220 4 P04220K.YAASSYLSLTPEQWR.S 2 P04220Q.LTVLSQPK.A 2 56 9 2 R.SYSCQVMHEGSTVEK.T P04220 13 3.163 1 1 8 P04220 P04220 4.8415 15 2.2694 2.1894 2 1 2.6993 P04220 P04220 3 3.0036 1 4.2639 3.3754 1 15 1 2 2.9459 2 2 2 4 P01591 4 4.4638 2.5829 2 P15814 P15814 2 2.8897 2 2.3233 P15814 11 2 2 P15814 1 1 2.8919 1 2 2.6749 2.4549 1 2.9023 2 1 2.4388 2 2 -like polypeptide 1 λ chain C region (BOT) heavy chain disease protein chain V-VI region AR region chain V-VI EB4 region chain V-VI WLT region chain V-VI λ λ λ µ µ B kinase complex-associated protein B kinase complex-associated protein κ Ig Ig Ig Ig Ig I Immunoglobulin J chain Immunoglobulin
177 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table LAVGSMKTLMLNVSLFN.A P13612 2 2.9236 2 .KESLHEVSKSDLGRKIKEGVEEAA.K O43615 1 2.3745 2 .WRAEGGQCPSLLFDLR.D P08514 1 2.715 2 -2 subunit) subunit) D.VGPVVQHIYEL.R P06756 1 2.4892 2 L.ALGAVKNISLNISISNLGDDAYDAN.VA.EGGQCPSLLFDL.RP Q13797 1 3.3476 P08514 2 1 2.5607 2 A.KLIPGATVGLLQKDSGNIL.Q P18564 1 2.3196 2 V R.EVMPLLLAYLK.S Q8TEX9 1Y. 2.6054 2 L.NNIGDSSPLIRA.TK.YYVDSVK.GING1LP member 1-like) family, (P33) (Inhibitor of growth L.KEIDDVYEK.YQ.VNTLFMKSHSNMVQRA.AS.LVANPVK.EE.DLEEAGV.QS.VMKAFKCHHVVRLLGV.VR.AFWLDVSHNR.LR.DFALQNPSAVPR.FR.LEALPNSLLAPLGR.L Q92973E.KDLLIVRSQNDK.F Q14571 Q9ULB6 1 O95698 1 2.3136 3 P14616 1 Q96PC2 2 2.8487 1.9731 O15357 2.9282 2 1 1 P35858 1 P35858 P35858 2 1 2.524 2.3799 P56199 1 2 1 2.2202 2 1 2.9077 4 1 2.337 2.3599 2 2 2 2.5754 2 β α -RLC) -IV) (VLA-4) (CD49d) α α -2 subunit (Karyopherin -V (Vitronectin receptor receptor -V (Vitronectin -IIb -9 (Integrin -1 (Laminin and collagen receptor) (VLA-1) -1 (Laminin and collagen receptor) -4 (Integrin -6 β α β α α α α Integrin Integrin Integrin ProteinImport inner membrane translocase subunit TIM44 Importin 4 Importin Peptide Integrin Imunoglobulin heavy chain (Fragment) type 2 Inositol 1,4,5-trisphosphate receptor Inositol hexakisphosphate kinase 3 Inositol polyphosphate 5-phosphatase (EC 2.7.1.112) protein Insulin receptor-related complex acid labile factor binding protein Insulin-like growth Integrin Integrin
178 (continued) .FGGSEIVVAGK.F P19823 1 2.4048 2 .FGKAAPAPQEATA.T P13598 1 2.5933 2 K.GSEMVVAGK.LK.ETLFSVMPGLK.MK.SPEQQETVLDGNLIIR.YK.YIFHNFMERLWA.YK.NVVFVIDK.SK.ILDDLSPR.DK.LALDNGGLAR.RG.RYSLFCLGFGFDVSYA.FR.GPDVLTATVSGK.LR.FKPTLSQQQK.SR.LGVYELLLK.VR.QGPVNLLSDPEQGVEVTGQYER.ER.PSLVPASAENVNK.AR.VQGNDHSATR.ER.AISGGSIQIENGYFVHYFAPEGLTTMPK.N Q14624T Q14624 Q14624N.CSTDCPSSEKIALETSL.S Q14624 1 Q14624 2 Q14624 1 Q14624 Q14624 Q14624 1 Q14624 Q14624 4.3896 2.0274 2.2593 1 Q14624 1 1 2.6452 1 2 8 Q14624 1 Q14624 9 1 20 2.621 2 2.3516 Q14624 2.5834 3.7068 2.2457 1 2.4285 3.4357 1 2 2 2 P32942 1 2 2 2 2.4047 2 1 2.4273 2.4013 2 1 2.4617 2 2 2 2.4588 2 K.PLLVDVDLQYPQDAVLALTQNHHK.QK.ELAAQTIK.KK.AAISGENAGLVR.AK.LDAQASFLPK.ER.GMADQDGLKPTIDKPSED.SK.HADPDFTR.KK.FYNQVSTPLLR.NK.VQFELHYQEVK.W P19827K.IQPSGGTNINEALLR.AK.AHVSFKPTVAQQR.IR.SILQMSLDHHIVTPLTSLVIENEAGDER.MR.SSALDMENFR.TR.TEVNVLPGAK.V 1R.FLHVPDTFEGHFDGVPVISK.GR.IYLQPGR.LR.IYGNQDTSSQLK.K P19827 4.5499Y P19827 P19827 P19823 2 P19827 1 15 P19823 1 P19823 P19823 1 P19823 2 2.8903 3.8034 P19823 P19823 1.9788 3.0428 2 19 2.651 2 8 1 2 P19823 1 P19823 2 3 2 2 2.6328 2.629 2.3268 3.6727 P19823 3.1648 3 P19823 2 3.6127 2 4 2 2 2 1 3 2.4109 2.472 1 2 2.2484 2 2.2451 2 2 -trypsin inhibitor heavy chain H4 -trypsin inhibitor heavy chain H1 -trypsin inhibitor heavy chain H2 α α α Inter- adhesion molecule-2 (ICAM-2) Intercellular adhesion molecule-3 (ICAM-3) Intercellular Inter- Inter-
179 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table ) YRGFKNECPSGI.V Q96T43 9 2.6627 2 L α EPPPFEDQPEPE.V Q9BR39 1 3.0921 2 SYRIISCGGVF.N O60494 1 2.6294 2 .VSGGAEPCSRPR.R Q9UKQ9 1 2.4031 2 .KGKTVEEALTIKNTDI.A Q9H1K1 1 2.5701 2 V R.LGFTDLFSK.WR.VGSALFLSHNLK.F P29622 P29622 2 2 2.8753 2.3991 2 2 S.WASAELHAPPGSPG.TF. V E.RKKEELASTAEK.TA.CVSLNQPGTVVASASQ.KS.ELLGEDLPLEPSVTKAERSHLI.VP. Q01344 1S.PILGPQPPDAPASGTEATR.GV. Q8IZX7 Q9Y484 Q9UKB3 3.1002 2 1 2 2 2.8982 2.576 2.9507 Q9BZS0 2 2 2 2 2.8609 2 L.VAVGPWVLSAAAGGK.NE.QEQLLKEGFQK.ES.LNSSSLLMNGLRNNQ.RL.SLPLMEGLSTDQTETSS.L P17181 2 P19525 P32455 Q8NFM7 2.4844 1 1 3 2 3.9521 2.434 3.3877 3 1 2 N.LKKYFNAG.H P01579 1 2.2278 1 chain (IFN- chain (IL-5R- α α ) (Immune interferon) γ eceptor r β (IFN- / α γ B and V(D)J recombination signal sequences binding B and V(D)J recombination Kallikrein 9 (EC 3.4.21.-) (Kallikrein-like protein 3) protein 9 (EC 3.4.21.-) (Kallikrein-like Kallikrein inhibitor 4) inhibitor) (Protease Kallistatin (Kallikrein κ Intrinsic factor-B12 receptor (Intrinsic factor-vitamin receptor Intrinsic factor-B12 ISCU2 1 J domain containing protein JM5 protein JNK-associated leucine-zipper protein Junctophilin 2 (Junctophilin type 2) (JP-2) KCHIP2.5 Interferon-induced guanylate-binding protein 1 guanylate-binding protein Interferon-induced double-stranded RNA-activated protein Interferon-induced, long form protein Interleukin 17 receptor-like Interleukin-5 receptor Protein Interferon Interferon- Peptide
180 (continued) .RLQSRSRPSAPE.T Q9Y4F4 6 2.6956 2 .SGGGGGGGLGSGGSIR.S P35527 4 3.6493 2 K.GSLGGGFSSGGFSGGSFSR.GR.ALEESNYELEGK.IR.LASYLDKVR.AL.QLETEIEALKE.ER.GGSGGSHGGGSGFGGE.SR.FSSSSGYGGGSSR.VR.GGSGGSYGGGGSGGGYGGGSGSR.GT K.SKAEAESLYQSK.YR.GGGGGGYGSGGSSYGSGGGSYGSGGGGGGGR.G P13645R.SLVNLGGSK.SR.TNAENEFVTIKK.DK.FASFIDKVR.F P13645 1 P04264 P35527G.LGVGFGSGGGSSSSVK.F P13645 P35527Q.DLVEDFKNKYEDEINKRTAAE.N 3.5353 P05783 1 1L.DRNQLSALPP.E 3 P35527 2 1 1G.IKEEVQLTSKQK.E 3.1253 1 3.0315 4.8523Q.MKKTDYFFLEV.Q P04264 3.1079 1 2.4812 2 2 Y 2 2.7114 2 P04264 2 P04264 2.4463 P02538 2 1 P13647 2 P35908 5 2.9608 1 1 2 2 3.2352 1 2.5239 3.1645 Q14160 2.4956 Q92616 2 2 2 2.8317 O43149 2 9 2 4 1 2.6107 3.1104 2 2.5174 2 2 L.QDLLSDRNKQVL.EL.KENLNKQPNKQ.WA.TEGAECLNVDDQ.DS.QGENLEGK.YL.KAFFAEVVSDGVPLVLAL.V O75042 O75048 O75049 O60288 3 1 O75049 2.4408 2 1 2.4056 2 2.4896 1 2.2059 2 2 1 2.8289 2 Keratin, type I cytoskeletal 10 (Cytokeratin 10) (K10) (CK Keratin, type I cytoskeletal 18 (Cytokeratin 18) (K18) (CK Keratin, type I cytoskeletal 9 (Cytokeratin 9) (K9) (CK Keratin, type II cytoskeletal 1 (Cytokeratin 1) (K1) (CK (67 Keratin, type II cytoskeletal 2 epidermal (Cytokeratin 2e) (K2e) Keratin, type II cytoskeletal 5 (Cytokeratin 5) (K5) (CK Keratin, type II cytoskeletal 6A (Cytokeratin 6A) (CK (Fragment) KIAA0147 protein (Fragment) KIAA0219 protein (Fragment) KIAA0399 protein (Fragment) KIAA0423 protein KIAA0454 protein (Fragment) KIAA0454 protein (Fragment) KIAA0460 protein (Fragment) KIAA0461 perotein (Fragment) KIAA0540 protein
181 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table ALVGVIDGGSTSCN.E Q9P2D5 1 2.9777 2 WCATRPSDPASA.T Q9P228 1 2.6831 2 .LEPIFSSEDINQ.Q Q9P2D7 1 2.4844 2 .PQVSSLPPLSQPY.V O60293 1 2.7533 2 P Q.NELKTTENCE.NI.KDPDKEIDELI.PI.CIGILLRSAELA.LK.VGKQIVENFSPNQTK.FQ.HELNEVKERA.EL.QIIHDTEKSPH.TS.VYSVHALTLLSEVLAHL.LH.AGSSDQPHPSIQQ.GL.EPLIGDMPLVGALSI.F O60335A.NNLEDIASTLVR.H O75179Y O94856 O75183 1K.SYLPVQFQSPDKAETQ.RW. 2 2.4296 Q9Y2K3 1 1D.IIQSPSSTGLLKSGK.T Q9UPN5 Q9UPS4 2.2181 1 D.KDQMLQEKDKQ.I 2.5469 2.2502 1 Q9ULJ6L.KAVDADTEAESVTFTIVQ.P 6 2 G.ASIGSALAAIMLLLL.V 2 Q9ULJ2 1 2 V. 2.6383 2.6006 1 Q9ULG5 2.4905 2 1 2 Q9P2D5 3.0545 2 1 2.8363 2 1 Q9P2D0 2.8331 2 Q9P228 Q9P2B0 2.7666 2 1 Q9P228 2 1 1 2.4135 1 3.1696 2 3.1799 2 2.487 2 2 Protein (Fragment) KIAA0546 protein (Fragment) KIAA0594 protein (Fragment) KIAA0697 protein (Fragment) KIAA0701 protein (Fragment) KIAA0756 protein (Fragment) KIAA1000 protein (Fragment) KIAA1078 protein (Fragment) protein KIAA1117 Peptide (Fragment) KIAA1224 protein (Fragment) KIAA1228 protein (Fragment) KIAA1255 protein (Fragment) KIAA1410 protein (Fragment) KIAA1412 protein (Fragment) KIAA1417 protein (Fragment) KIAA1438 protein (Fragment) KIAA1500 protein
182 (continued) .TQEQVYNACAKQIVKDVLEGYN.G O60282 1 3.0149 2 .LRRVHSTSSLDSQKFVTVPSSNEVVTNLEV.L Q96JI7 1 2.4395 2 .NSSSVQCQNTSYS.Y Q9HCM2 1 2.6203 2 A.VGGFKVGLDLLVE.FR.NIPPFEGCIWNLVI.N P24043 P24043 1 1 3.1133 2.4962 2 2 K.AVDAALKK.YK.TVGSDTFYSFK.YK.AATGECTATVGK.RK.YNSQNQSNNQFVLYR.IR.DIPTNSPELEETLTHTITK.LR.VQVVAGK.K GLIS2 zinc finger protein Kruppel-like L.LPGTVLDLSTGV.NM.ASLIIVLKLCGYVIFRGA.N P01042 P01042 P01042 P01042 P01042 6 5 3 2 2 Q14739 Q9BZE0 P01042 2.4246 2.6002 2.5254 3.2797 2.6129 1 1 3 2 2 2 2 2 2.4691 2.5489 2.0947 2 2 1 F E.SSTIASYVTLRK.TI.NPQDLTVNLVANVPQ.DS.TGQPLVTHSGSSKQKEY.LK.SLLENAEAK.KP R.WCCNKKNAVVMDQE.PL.HREGKFNDTLRLTGE.LT Q9C0H4N.AIQIVQQAVKYVGQLAVLKGSKLH.F Q9C0H7S.FLPGICKELIGSSLDFF.G Q9C0F0R.VNEDPKDTLLREFQEEIARLKAQLEK.R 1 1N.EIEEVKVAFEIK.K 1 Q96JM2 2.4158 P43628 2.821 2.9771 Q15058 2 Q9Y5Q4 2 1 2 O14782 1 1 2 2.5222 Q15058 2.7714 2 3.1006 1 2.6951 2 3.9542 1 2 2 Q9H3R5 3 2.4068 5 2 3.5338 2 -2-thiol proteinase inhibitor) -2-thiol proteinase α -2 chain (Laminin M chain) α Lamin B receptor Lamin B receptor Laminin KIAA1550 protein (Fragment) KIAA1550 protein (Fragment) KIAA1686 protein (Fragment) KIAA1689 protein (Fragment) KIAA1713 protein (Fragment) KIAA1803 protein (Fragment) KIAA1840 protein 2DL3 Killer cell immunoglobulin-like receptor 2-2-2 (Fragment) Killer inhibitory receptor Kinesin heavy chain isoform 5C KIF14 Kinesin-like protein KIF3C Kinesin-like protein CENP-H protein Kinetochore Kininogen (
183 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table VPITSPAVSKVTSTNNMAYNKAPR.P O60705 2 3.2345 2 .HDTSPYRWGGK.S Q9HAR2 1 2.5366 2 binding protein 4 binding protein A.FPKNRIIGSGCN.LL.TQPRGVNWCERTTLSNGGCQYL.CD.ATQGKTWSAFQNGTDRR.VA.TIYTADLSSKSSITALIPSIL.SH.RDCITIFDADSE.EM.DRVAFVK.LK.ISNIPDEYFK.R P01130K.SLEDLQLTHNK.I Q9BYZ2 P98164 1 Q8N705 1 2.4776 1 2 1 2.4368 Q9BX84 2.6886 2 2.4388 2 Q96QT4 1 2 P51884 P51884 3.0198 1 1 9 2 2.2076 2.3599 3.3003 1 2 2 K.ALGHLDLSGNR.LI.YLYENDL.DM.AAVPLLGGSKYGASPLCLPL.PI.RCSLESVGSSATL.YG.GFGGGGGACTAGGGGGGY.RE.INGIHDESNAFESK.AC.FKCVACECDLGGSSSGA.EP. O75473 P02750 P29376 1 Q9NZU1 4 Q93033 2.4232 2.3843 Q8WWI1 1 2 Q8WWI1 2 1 2 2.3803 2.6929 1 1 2.9578 2 2 2.4465 2.6768 2 2 2 G.CHRCDCNILGSR.R Q13751 1 2.5088 2 C.ENHLACPGQECVNSPGSFQCRACP.SY O75441 12 3.4879 2 β 3) β -2-glycoprotein (LRG) -2-glycoprotein α -3 chain (Laminin 5 β TRPC6 channel kinase 2 TRPC7 L-lactate dehydrogenase A-like (EC 1.1.1.27) L-lactate dehydrogenase (LDL receptor Low-density lipoprotein receptor) 2 protein receptor-related Low-density lipoprotein LSDR L L lumican) Lumican (Keratan sulfate proteoglycan Leucine-rich repeat transmembrane protein FLRT1 FLRT1 transmembrane protein Leucine-rich repeat 5 receptor G protein-coupled Leucine-rich repeat-containing Leukocyte surface protein (EC 2.7.1.112) kinase receptor Leukocyte tyrosine LIM domain only 7 LIM protein ProteinLaminin factor- Latent transforming growth Peptide Lectomedin-3 Leucine-rich
184 (continued) ALGLVFLTSLAGLGLWL.L O95867 1 2.4238 2 P .EAQPLSPLDER.A Q9UJ55 1 2.2726 1 .PEATGMTPAEVSIVVL.S P40967 1 2.7689 2 .MAVSSRGNADSIVASLVLM.V Q9H3S5 1 3.0963 2 .STLAPEAWPA.M Q92675 2 2.5225 2 L.KKALWFQGRCV.KG.PGLGGDTHFDADEPW.TQ.LLSFTLLAGLLVQVSK.VR.PRPLSVYSHKLFN.GT F N.AGNIFVVSLAVADLVVA.I P51511 P43243 Q96QQ8 1 1 Q8IZV8 1 2.5166 2.3797 P48039 2.4284 2 2 2 2 2.7443 2 2 2.4727 2 R.FNALQYLR.LR.LKEDAVSAAFK.GR.NNQIDHIDEK.AR.LPSGLPVSLLTLYLDNNK.ID.SSQDPDPTTQPIVLLLPG.IT. Q.ARCTARGGSLAQPADR.QI.TVLAVLALVPQDQ.GI.VLGVFIVCWLPAFSILLLDYAC.PL.KTPQVTNEGEPEKEL.S P51884 P51884G.GGVGAGAAAVASAGVIY.P P51884 Q96SE0 P51884V 2L.FWDDGQSIDTYGK.G 8 Q9Y240 1 1 1P 3.6577 O95136 3.0523 2.2921 2.2638 Q06643 1 2.5147 2 2 2 1 1 2 Q13342 Q08397 2.4084 1 2.4452 2 1 2.5791 1 2 O43451 2 3.0131 2.2414 2 1 3 2.4646 2 ) (Tumor necrosis factor C) (TNF-C) necrosis ) (Tumor β (LT- β hydrolase protein 1 protein hydrolase β / α ymphocyte antigen 6 complex locus G6C protein ymphocyte antigen 6 complex locus G6C protein C-type lectin ymphocyte secreted ymphotoxin- Edg5 ysosphingolipid receptor ysyl oxidase homolog 1 (EC 1.4.3.-) (Lysyl YSp100 protein (Lymphoid-restricted homolog of Sp100) (Lymphoid-restricted YSp100 protein Matrin 3 (EC 3.4.24.-) (MMP-15) Matrix metalloproteinase-15 MDC-SIGN1A type II isoform MEGAP transcript variant a Pmel 17 Melanocyte protein sulfate proteoglycan Melanoma-associated chondroitin type 1AMelatonin receptor (Mel-1A-R) Lung L L L L L L nM15) 1) (Protein 2 (Necdin-like protein MAGE-like protein Maltase-glucoamylase, intestinal [Includes: Maltase FLJ90174) Mannosyltransferase (Hypothetical protein
185 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table .LFDFAADFID.G.LSAQLLDGGIFHEQTG.Q Q9UMX9 1 2.3025 1 Q96PK2 1 2.7991 2 .FPWDGAEVPPQR.Q.QSKLQARKALSKDGRIFGESIMI.G Q13505 1 2.5034 Q8TDJ1 2 1 4.2342 3 .EVRCGSGGPPIITK.P.VEPTSTSWNPRGW.P Q14833 1 Q9UNZ8 2.5465 2 1 2.4027 2 .LRVFLFFRPF.R.RESILNDIR.K Q9Y2Q9 Q99683 5 2.5593 1 2 2.4098 2 V A.NASFTWVASDGWGAQESIIKGSEH.VT L.GGLFPVHAKGER.GI.HLCNYIEPWE.DY Q14832T V 1F I.FHIVENDL.Y 2.9402F S.TEDENQGTIKR.C O00222 2 A.AFAVEPQGPALGSE.PY Q99727 1L.HLEEDKTTVSQE.SK.SSNILLLEEIEH.D 2.6596 2A.SLGSPAPPKGAAAPSA.S 2 N.KTQPILDILLK.N 2.6213 Q9Y2Q9 2 Q8IVH8 Q8TDJ1 1 1 2 Q9BWE8 2.3048 Q9H2W2 Q8WWN1 2.6721 1 2.4275 2 2 1 3 2 Q9Y376 2.4147 2.2246 2.8236 2 2 2 2 2.6734 1 β Protein (AIM-1 protein) Membrane-associated transporter protein 3 (mGluR3) glutamate receptor Metabotropic 4 (mGluR4) glutamate receptor Metabotropic 8 (mGluR8) glutamate receptor Metabotropic inhibitor 4 (TIMP-4) Metalloproteinase Metaxin 1 splice variant 2 Methyl-CpG binding protein factor 1, isoform 4 crosslinking Microtubule-actin Peptide S28 (S28mt) (MRP-S28) Mitochondrial 28S ribosomal protein kinase 5 (EC 2.7.1.-) Mitogen-activated protein kinase 3 Mitogen-activated protein 44 Mitotic phosphoprotein protein Mitotic spindle coiled-coil related Mixed lineage kinase 4 MIX) 1 (Homeodomain protein Mix-like homeobox protein (CGI-66) MO25 protein
186 (continued) isoform .YKPEVVAAY.R P13535 1 2.6702 2 α H.KTQPIVEILLK.NI.QNPISLEDSPEAGGE.RI.GDGAGVGKGRTIAGIIYENYLLS.RS.NLNRQFLFRPHHIQK.PL.RMHLSNTLLDGEMI.IK.AKVVDLMSITEQKRE.EA.AAVAAVVAA.AC.FFFILAIRAASF.H Q9H3T8A.SMAAVLL.G Q9H9S4 Q03989L.QIFLRLFGVFASS.I 1A.VIGGVLGVVLLL.L Q9H3T7 1 1 2.7968C.REMPQNLSTKPQDLC.A O60942 12 3.0324A.LASVLLAL.L P78312 2.5282 2 D.RGKKDNANANK.G 1 1 1 2.4761E.EAIVELVE.N O75446 1 2 R.ALEEALEAK.E Q9H3F3 2.44 2.7777V 1 O95255 2 O75485G.PSISKPAAKPAAAGAPPAK.T 1 2 P25189 Q9UL68K.AEVARLSKQVKTISEFE.K 2.4033 2.4837 1 1 1 1 3 2 P13533 2.1341 P24158 2.4437 3.0473 2.3345 1 2 1 P35579 2 P14649 2 1 P35580 2.4115 Q9NQX4 2.2013 1 1 1 2 2 6 2.2888 2.5164 2.9337 1 2 2.562 2 2 MO25-like protein factor I (Fragment) Modulator recognition MOP-3 MOP-4 mRNA capping enzyme (HCE) (HCAP1) mRNA, complete cds, clone:RES4-22B MSin3A associated polypeptide p30 MSTP031 6 protein resistance-associated Multidrug TRC8 Multiple membrane spanning receptor zero) (Myelin protein Myelin P0 protein Myelin transcription factor 1-like Myeloblastin (EC 3.4.21.76) muscle Myosin heavy chain, cardiac A Myosin heavy chain, nonmuscle type Myosin heavy chain, nonmuscle type B Myosin heavy chain, skeletal muscle, perinatal AMyosin light chain 1, slow-twitch muscle isoform (MLC1sa) Myosin Vc (Myosin 5C)
187 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table β AKILIVGGGV.A Q13423 1 2.9169 2 .TTLSQGSAATLHMAVRDLVR.S Q9GZX3 1 2.9387 2 P .SAFSKKPRSVEVAAGS.P Q14896 1 2.4212 2 .ASVAVAGILAA.L Q16798 1 2.5236 2 T R.SNDTVLEATAALYN.QN.ERKYRQHPDTVKFTSVPDSM.GQ.PPDKLKFTSVTDSLEQV.LK.DVKYLKKEDANRKTF.TS.RLPSLFSQNIIPE.Y P20929 Q9NRD9 P20929 1 1 Q8IZP8 1 4.0472 2.4706 Q9ULX6 1 3 2 2.4422 2.6379 2 1 2 3.0061 2 W C.QSTTSVYSSFVFNL.FP. Q96MN2 1 2.7715 2 V K.IIWMKNKMEIQGN.PK.GLEWVGR.I-.EVQLVESGGGLVKPGGSLR.LK.TDGGTTDYAAPVK.G-.EVQLVESGGGLVK.P-.EVQLVESGAEVK.KE.VQLVESGAEVK.KK.DTERPSGIPER.FI.VVEKPGRIVPGVIGLMR.AK.KSDQKTTESTVTR.KG.GSMITGYIVEKR.DE.KEQALIRKKMAK.D Q13203 Q9UL88 Q9UL88 11 1 Q9UL88 Q9UL88 Q9UL92 3.5112 2.6362 5 Q9UL92 1 Q8WZB3 2 2 2 31 Q9UL82 3.0079 7 Q8WZB3 2.3207 4.2997 1 Q8WZB3 2 2.8077 Q8WZB3 4 2 2 2.6125 1 2 2.6007 1 2 2.2157 1 2 2.4025 2 2.859 2.4414 2 2 2 -acetylglucosamine 6-O-sulfotransferase GST-4 NADP-dependent malic enzyme, mitochondrial oxidase 1 NADPH thyroid Nebulin 3 Nectin-like protein 95 A-kinase anchoring protein Neighbor of NACHT-, LRR- and PYD-containing protein 4 LRR- and PYD-containing protein NACHT-, mitochondrial NAD(P) transhydrogenase, Protein MyBP-C) (Cardiac C, cardiac-type Myosin-binding protein H (MyBP-H) (H-protein) Myosin-binding protein immunoglobulin heavy chain variable region Myosin-reactive immunoglobulin light chain variable region Myosin-reactive N2B-titin isoform Peptide N
188 (continued) SSPSVLPPLVEENGGLQKP.P O15194 1 3.0037 2 .SITVSIFSLVLIAVERHQLII.N P25929 1 3.502 3 .PLVEENGGLQKP.P O15194 1 3.2103 2 .PEELLRSSADFLQRLSAILRTSLRF.R Q9UM47 9 2.7004 2 .KVSMPDVDLNLKGPKL.K Q09666 1 2.4233 1 L.VRKVKRTLPSP.PA.NEIVLLEAGHE.PV K.KELLQEQ.LH.ECQWVVEDA.PD.SHLENKINIILSETDR.DR.LELEDKVR.HS.CKTHVLLLVLHGGNILDTGAGDPSCKA.AG.ETKTEESPASDEAGEKEA.K Q9UPA5M.PSSDLADEK.V O95502C.LVGANLLVK.I 1 Q9BZ71I.TDAEKNEYEKDSPRLTKT.N 1 2.4179P. Q9Y6K9 Q9GZT8 Q9BZQ8P 1 2.4725 2 1 2 1 2 P05114 2.5153 Q9UH61 2.4268 2.651 2 2.523 1 1 2 2 P48552 2 Q99590 3.2398 2.537 Q16288 2 1 1 2 1 2.7777 2.812 2.6534 2 2 2 L.FLAAREGSYEAAK.IP Q04721 1 2.5615 2 L.DQEIARPLENENQEFLK.SL.RPLARVLVTGLLQ.LG.PDPKLKVPKVKMPEINIK.AP P48681 Q09666 O95156 2 4 2.4831 1 2 2.9037 2.4959 2 2 B essential modulator (NEMO) κ Neuronal double zinc finger protein Neuronal pentraxin receptor Neuronal Y Neuropeptide type 1 (NPY1-R) receptor NF- Niban protein 1 NIF3-like protein Ninein NIR1 HMG-14 protein Nonhistone chromosomal SR129 domain protein, Novel member of serine-arginine (EC 2.7.1.112) factor receptor growth NT-3 1) interacting protein Nuclear factor RIP140 (Nuclear receptor factor 1 Nuclear LIM interactor-interacting Neurogenic locus notch homolog protein 2 locus notch homolog protein Neurogenic 3 locus notch homolog protein Neurogenic Nestin 2 (Fragment) Neurexophilin AHNAK associated protein differentiation Neuroblast
189 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table .ASFSCELSHEDEEVE.W Q96AA2 1 2.8326 2 VRTAAKTTWFIMGILNPAQGFLLSLAF.Y P51810 1 2.8424 2 LHELEEK.M O75694 3 2.2444 1 .EGQSQGSVLAFTRTFIA.T Q9GZY0 1 2.3934 2 .YVAPSAVHSQLLSKVF.S Q9GZK7 2 2.2275 2 N.IINHFTCEILAVQKLACAD.IF L.NPLVYSLRNKEVKSAF.K Q96R43 1 Q96R08 3.7938 1 3 2.7789 2 F. A.TGLEEIDRA.LV R.FNPKTFFILHDINS.DK.KKVLLGVGDPKIGAAIQ.EL.LGEGFADESL.DD.RETGSSKGFGFVDF.NL.RERIIPRSVLY.FA.EADFKMVSEPVAHGVAEEEMASSTSD.SR.PPYERPELPTCLYVIGLTGISGSGKSSI.A Q9Y6Q9D.CSGNDLEQ.L O00567 Q02818A.HEISQITNDL.A 3W Q99457 1 1P. P19338 Q8TEZ1 2.5105 Q13057 1 2.9175 2.7697 2 1 P55209 1 1 2 2 2.5528 2.3393 2.5402 2.5609 2 1 2 2 2 Q8WYB0 Q8WZ77 2.5208 1 2 1 2.204 2.2852 1 2 α Olfactory receptor (Fragment) Olfactory receptor (Hs6M1-18) 11A1 Olfactory receptor 5B16 Olfactory receptor Protein Nup155 (Nucleoporin Nup155) complex protein Nuclear pore coactivator 3 (EC 2.3.1.48) (NCoA-3) Nuclear receptor Nuclear RNA 2) (TAPL-2) protein export factor 2 (TAP-like Nucleobindin 1 (CALNUC) 5A) Nop56 (Nucleolar protein Nucleolar protein Nucleolar RNA-associated protein C23) Nucleolin (Protein protein) 1-like 1 (NAP-1 related Nucleosome assembly protein Peptide 1-like 3 Nucleosome assembly protein (NBP) (POV-2) Nucleotide binding protein NUP196 nucleoporin O-acetyltransferase Obscurin Ocular albinism type 1 protein
190 (continued) ) β .QKTYSEDTYRLARIL.V P49116 2 2.1216 1 .EAASLAADI.S O00146 1 2.2877 2 .QRPELQLPLFLL.F Q9GZM6 1 2.7681 2 .DEASSACSTDWVI.P P55055 1 2.4166 2 .VTGSTEMAITNQ.T Q8WXI7 1 2.9486 2 .LSFMLRAVSIF.V Q03431 1 2.9378 2 T H.SAPLPAATAHPAAAAHA.AQ.DGMVTNTSLTSSTK.SE.SLMKKMKENPLEHK.TA.HQELGTAAAAAAAASRSA.MK.PDKAMRAPSSAG.GM.SNLLAGAACLVMIFISPDL.HK.GREDRAPLLK.T Q13516V F P23515 2A.IVSMSTTTWPESTRART.E O95948S.QSLGRVSSVLSESTTEGVTDS.S Q9UNA1I.MEEKRMNGIIYEI.I 2.9077 1 1 O15245S.MVESIKHCIVLLQIAK.D 1 2 Q8IZA3 2.4244 2.7902 2.6498 4 1 1 2 2 O95190 2.5134 Q8WXI7 Q8WXI7 2.2817 2 1 1 1 1 P56715 Q96SU4 2.3462 3.0726 2.5337 2 2 1 1 2 2.4683 2.7163 2 2 T V L.MKGTHSGAALAV.AS.LLLLSTCVALLL.QA.ALVRERGADLVVIE.GF O14680 P01298 Q9NVE7 1 1 2 2.3308 2 2.88 2.602 2 2 (Liver X receptor (Liver X receptor β Olfactory receptor 8D2 (Olfactory receptor-like protein JCG2) protein 8D2 (Olfactory receptor-like Olfactory receptor transcription factor 2 (Basic helix-loop-helix Oligodendrocyte glycoprotein Oligodendrocyte-myelin like protein Oligophrenin-1 One cut domain family member 2 Oocyte-specific histone H1 cation transporter Organic Ornithine decarboxylase antizyme 2 (ODC-Az 2) (AZ2) TAK1) TR4 (Orphan nuclear receptor Orphan nuclear receptor tumor marker CA125 Ovarian cancer related 1 (Retinitis pigmentosa RP1 protein Oxygen-regulated 9 protein binding protein-related Oxysterol LXR- receptor Oxysterols P120E4F transcription factor (Fragment) P53 induced protein polypeptide) (PP) hormone (Pancreatic Pancreatic Pantothenate kinase 4 (EC 2.7.1.33) peptide hormone-related hormone/parathyroid Parathyroid
191 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table subunit β WDSELQREGVSHYR.L Q969N2 1 2.4526 2 R .SLVPTLALLLGLPI.P Q8TEQ8 1 2.2148 2 .FLAILGGAKVADK.I P00558 3 2.9481 1 .RPLPARPR.D O00459 1 2.401 2 .SLYEVALVTQ.G.FRDIWVFQF.C Q9Y6C5 1 Q96RV3 2.4288 1 2 2.7288 2 G.GEVKLSISYKNNKLFI.MV R.IADVTSGLIGGEDGR.VR.VYAEADSQ.EK.ALESPERPFLAILGGAK.VP O00750 1 P80108 P00558 2.5008 1 O95394 2 5 2.9622 1 2 3.7099 2.3207 3 1 G.YLLSPIQ.RP Q8TCU6 1 2.2952 1 F R.TKEEIIELLVLEQYLTI.IF R.RAAGAAVLLVEML.EK.EYGVVLAPDGSTVAVEPLLAGLEAGLQGR.RR.PSLSHLLSQYYGAGVAR.DR.DGSPDVTTADIGANTPDATK.GR.AGLLRPDYALLGHR.QA.QERKTQLKV.A Q96PD5K.ELAEQRAELEKIFQDKNQAERALRNL.E Q9GZU2S.EAMYNKMNISELSAMI.P 2T. 3 Q9P2X9 Q96PD5 Q96PD5 6.0437 O95613 2.6722 3 1 Q96PD5 1 1 2 1 2.5192 2.9672 2 4.3083 Q13356 P78562 2 4.1235 2 3 3.5976 3 1 1 3 2.7412 2.5371 2 2 Phosphatidylinositol-4-phosphate 3-kinase C2 Phosphatidylinositol-glycan biosynthesis, class O protein Phosphatidylinositol-glycan-specific phospholipase D 1 Phosphoacetylglucosamine mutase (EC 5.4.2.3) (PAGM) Phosphoglycerate kinase 1 (EC 2.7.2.3) Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac Phosphatidylinositol 3-kinase regulatory Protein homolog 2 (PTC2) Patched protein gene 3 isoform 1 Paternally expressed 1 Pecanex-like protein Peptide transporter 3 L protein Peptidoglycan recognition cis-trans isomerase like 2 (EC 5.2.1.8) Peptidyl-prolyl Pericentrin 2 (Kendrin) Peptide neutral endopeptidase (EC 3.4.24.-) Phosphate regulating Phosphatidyl inositol glycan class T (DJ453C12.7)
192 (continued) SRVANVKNFVSLSKLCIA.C Q8NFD8 1 2.508 2 .TTPEPTPIPTIATSPTILV.S P07359 1 2.7724 2 .LDPVSRRPPTSCW.P Q16221 5 2.332 2 A.QDKAPDSSQISAPTP.AK.APRVSTAQDVIQQT.LF K.PLGLTVMRDVTISK.SL.KHQIKQEFR.RK.TSLEDFYLDEER.TK.LQSLFDSPDFSK.IR.ALYYDLISSPDIHGTYK.EK.YIFNSLDDVAHVNTV.M Q8WWN8K.DSVTGTLPK.V Q9HBX6K.VSEGNHDIALIK.L 1K.EIIIHQNYK.VA.LTPKILDLLVHAISINSA.Y 2 O14832 2.7141L.DEEEEENPDKAS.KD.SSLQSLETSV.- 2 2.8144K.LSSPAVITDK.V Q9Y6V0 2 P36955 P36955R.YEFLNGR.V 2 R.NPDGDVGGPWCYTTNPR.K P36955 O14632R.HSIFTPETNPR.A 2.3167Platelet factor 4 variant (PF4var1) (PF4alt) 1R.HITSLEVIK.A 2 1 2 4P 1 2.8833 P03952 for type III collagen (Fragment) Platelet receptor P03952 Q16720 3.3162 2.728F. L.TILRKMSHVGL.T 2.3572 2 2.2935 P03952 2 2 7 P23634 1 2 2 1 P00747 1 P23634 2.3523 2.3597 2.348 P00747 1 2 2.5645 2 3 2 P00747 P00747 1 2.5576 2 2 5.1004 P10720 2 2.4529 1 17 2.467 2 2 Q8NFD8 2.3082 2.6175 1 2 2 2 1 2.8528 2 2.2125 2 chain α Phosphoinositide-binding proteins Phosphoinositide-specific phospholipase C PLC-epsilon Phosphorylase kinase catalytic subunit PHKG2 homolog Phytanoyl-CoA dioxygenase, peroxisomal (Aczonin) (Fragments) Piccolo protein Pigment epithelium-derived factor (PEDF) (EPC-1) PKY kinase protein (EC 3.4.21.34) (Plasma Plasma kallikrein 3 ATPase Plasma membrane calcium-transporting 4 ATPase Plasma membrane calcium-transporting Angiostatin] Plasminogen (EC 3.4.21.7) [Contains: Ib Platelet glycoprotein
193 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table YNISFTSL.P P98196 2 2.528 2 L ) β LT AY .LPSQAGATPTPRTKAKLIPTGRDVGPVPLKPVPGKSTPKL.N Q92796 1 3.8574 3 .DSCQSGGVPTA.V Q13310 1 2.5145 2 R.LDNMLLAEGVAGPEKGGGSA.AL.NDMYAPPDYASTFTALA.DT S.SFERAPAMVVNSL.CL.QQQPLCTSVNTIYDNA.VE.ISAPVQVITF.K P40424 Q92796 1 2.4949 1 Q9P1I8 Q9P189 2 2.2022 1 1 2 Q9H3A0 2.8836 2.4082 3 2 2 2.5596 2 K.EWIREISESKSLPQSV.IT H.GSLPEVIVT.CS.VEFSNVSAG.SQ.AIDESTNGFTY.KQ.YLCQAGDDSNSNK.KG.LPASLALVATLR.HS.YSELKEQ.Q Q9NRJ5R.SALNLVDLV.AL.AILFGATFF.I 1L.LIIVGNPLLLGH.DT. Q8TCZ9 2.4495 Q8TCZ9 Q9NTG1 P01833 2 1 4 Q9Y2U2 1 8 2.3634 2.6867 2.9572 2 Q9UJ96 1 2.8531 Q8TDN2 1 2 2.5818 2 P20648 Q9HCE1 4 1 2 1 2.689 2.7792 1 2 1 2.9244 2.2942 2 1 chain 1 (EC 3.6.3.10) α (EC 2.7.7.19) (PAP β Pre-B-cell leukemia transcription factor-1 leukemia transcription factor-1 Pre-B-cell SAP102 protein Presynaptic PRO1635 (Hypothetical protein) PRO1855 PRO2523 ProteinPoly(A) polymerase Peptide Polyadenylate-binding protein 4 (Poly(A)-binding protein 4) 4 (Poly(A)-binding protein Polyadenylate-binding protein Polycystic kidney and hepatic disease 1 for egg jelly related Polycystic kidney disease and receptor Polymeric-immunoglobulin receptor Potassium channel subfamily K member 7 Potassium voltage-gated channel subfamily G member 2 Potassium voltage-gated channel subfamily V member 2 Potassium-transporting ATPase Potentail helicase MOV-10 IH (EC 3.6.3.1) ATPase Potential phospholipid-transporting
194 (continued) NNDNTAPAEDVIIMIQVPQ.S Q96PH3 1 3.4172 2 .DTLGAEKFLWILLILL.F.EMACSFRGSGSPSYSL.E Q9H583 Q96N03 1 1 2.3212 2.4767 2 2 .VEINNTDAEGRLVLA.D Q8NDH3 1 2.919 2 T C.SAPSTVVATAVGV.LA.GGLGPFRPLWALLAFALPALLLLGA.YN.LSPLTAFLKLTSLGFIIGVSVVGNLL.IL.EVPQEGLSTDPFRPA.LY. Q9BZJ7 Q9NPD1 O00270 1 1 2.4797 1 P57059 2.5816 2 2.5785 2 1 2 2.4149 2 L.KEGDLVKIDL.GI.GNGQRKDRKKTSLGPG.GA.EFFTSIGHMTDLIY.AG.EDCGSVSVAFPITML.LV V E.DGVLGGVIVL.RL.EKKLSELSNSQQ.S Q9NQ31D.TESEASILGDSGEYK.M Q9UQ80K.KPTWTCPVCDK.K O15460 1A.NKVKAALKSLIPTLEK.T P43115 1A.SGVDIEEETEKNLE.K 2.6369 1 2.3656S.TKEQVLAAVRRLR.Y 1 2 2 3.0333 2.6994 Q9H6P5 2 Q9NQG5 Q9Y3E5 2 6 1 Q15397 Q9Y6X2 1 2.3734 Q9P2E3 3.5134 2.5078 1 1 1 Q9P218 2 2 1 2.7316 2.8794 1 2 2 3.1212 2.7169 2 2 -2 subunit (EC 1.14.11.2) α Probable aminopeptidase NPEPL1 (EC 3.4.11.-) aminopeptidase NPEPL1 (EC 3.4.11.-) Probable GPR31 receptor G protein-coupled Probable GPR62 (hGPCR8) receptor G protein-coupled Probable GPR85 (Super receptor G protein-coupled Probable kinase SNF1LK (EC 2.7.1.-) protein serine/threonine Probable protein potential-related Proliferation Proliferation-associated protein 2G4 - protein Proliferation-associated BCA3 protein Proline-rich 4-hydroxylase Prolyl EP3 subtype E2 receptor, Prostaglandin BAP28 Protein C20orf102 Protein C20orf13 Protein C20orf77 Protein CGI-147 Protein 3 protein inhibitor of activated STAT Protein KIAA0020 Protein KIAA1404 Protein KIAA1510 Protein
195 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table ) (Protein ) (Protein µ VFFVLLSLSGA.G Q9NRJ7 3 2.4812 2 L .QTEKHVFE.Q P41743 2 2.4365 2 .EVCLTGDSGAGE.F Q9Y5E4 2 2.4851 2 .KSENLDNPIQ.T Q15155 4 2.6561 2 .IALAALVYCVK.K P17152 1 2.4911 2 E.VNLQNGILFVNSR.IV. Y Q9Y5I3 1 3.0855 2 L.RFFRQSVAGLAARLQR.QV Q9BXM7 1 3.1386 2 R.SATFEDFQIR.PG.PKCGENSECKNWNTKA.TA.ATCGHINLVKIL.VT Y G.VRFKRSKKIMPAGLVAGLSL.MA.YRGVLNSPVKAVRDTLI.TI.RVGFVTYNKVLHF.Y Q92832K.LTNPVQLDDF.DG.DPELSCCDSSTISF.I Q15139K.LAACLEGNCAEGLGTNYR.G 1 Q96T49R.TATSEYQTFFNPR.TR.ELLESYIDGR.I 26 Q9Y6G1R.ETAASLLQAGYK.G 2.6256 1 2.4224 P53992 2 1 2 2.2873 P53992 2.4138 1 2 P00734 Q9UBF0 2 Q16827 1 2.5364 P00734 2 2 2 2.5524 1 P00734 P00734 2 2.5121 3.1127 10 2.5215 2 2 3 2 2.9578 1 2.5217 2 2.4292 2 2 16) 1) 5) β α β type (EC 2.7.1.-) (nPKC- µ 1 (PCDH- 16 (PCDH- 5 (PCDH- β β α Protocadherin Protocadherin Protein kinase BRPK (PTEN induced putative 1) Protein kinase C, iota type (EC 2.7.1.37) (nPKC-iota) (Atypical Protein kinase C, Protein Peptide Protocadherin Protein kinase C-binding protein NELL1 (NEL-like kinase C-binding protein Protein inhibitor subunit 16B (TGF- phosphatase 1 regulatory Protein PM1 Protein pM5 Protein TS58) (Protein PTD011 Protein C) protein Sec24C (SEC24-related transport protein Protein O truncated phosphatase receptor-type tyrosine Protein O phosphatase, receptor-type, Protein-tyrosine (EC 3.4.21.5) (Coagulation factor II) Prothrombin Protocadherin
196 (continued) .QIQWSNNKGENI.P Q99420 1 2.601 2 .AHGNEVIPTIIRARA.M Q8IVM8 2 2.475 2 A.KVPEVELKDLSPSEA.EL.DKNEVKKVLDKFYKR.KQ.STGGPAAGAALGL.GR.SGLSGFSLQHPGVTG.PR.SASLCVWGSVSETLCLSLG.LF I.IVPFVTCGDLS.SL.FISLVFLLVNL.T Q96HN2 O43630M.QAKEDFKKMMEEA.KL.RSENKRLQDQR.Q 1 Q9H4B9L.MEVTVYLQSDKD.M 1 P98177 Q8TDV3 2.4557R.LLLVKEHSNPMQ.V 2 2.823A.GVTISSIEKKLS.A 2 1 1 2.8871 2 2.5648 2.6171 2 Q9UET6 O14776 2 O60478 2 1 Q13145 1 2 P59045 2.519 P59046 2.4429 1 2.616 2 1 P32322 1 2 2.6512 1 2.5442 2 1 3.2529 2 2 2.4898 2 E.KKGFLSAPQSLL.ES.NMSLSLFVLDQNDNAPE.ID.PDTGFNGVQHYELLNGQ.SK.LCAGASYAEENE.CR.EGLDDQGL.TN.GLTLDVDGR.TP Q9Y5G5 Q9Y5D6 Q9HC56 1 1 Q9HC56 1 3.1752 2.5771 3.062 1 Q969N9 2 O75870 2 2 2.4405 1 1 2 2.5178 2.5754 2 2 A1 short form protein A8 γ γ Putative adenosylhomocysteinase 3 (EC 3.3.1.1) mitochondrial RNAATP-dependent Putative helicase Putative DMO orthologue (Fragment) AFX1 Putative fork head domain transcription factor coupled receptor Putative G-protein Putative integral membrane transport protein Putative ribosomal RNA methyltransferase 1 (EC 2.1.1.-) (Similar to Putative seven pass transmembrane protein Putative transcription factor CA150 NMA Putative transmembrane protein protein 6 PYRIN-containing APAF1-like 7 (Monarch-1) protein APAF1-like PYRIN-containing (EC 1.5.1.2) (P5CR) reductase Pyrroline-5-carboxylate Protocadherin Protocadherin Protocadherin Protocadherin-9 LPTB-like protein 2) (Polypyrimidine tract binding protein PTPsigma (Fragment) Put. B7,3 molecule of CD80-CD86 family
197 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table TKLVK.E Q9NQC3 2 2.2658 1 L TA LKSEMPPVQF.K P52306 1 2.4927 2 .EKIVEAILQE.K Q8TDV9 1 2.5251 2 .TIGGRVLYSGLSLL.I Q15303 1 2.5501 2 V E.KSSMLFYIDEER.K Q8NHQ3 1 3.0942 2 Q.PDDEVVGILPL.DI.AQETFDAAVR.EC.GWASVKYKGQKLDK.YG.SSVSGGGGGGGAG.AL.QSPLPLPTTLPLL.SI.GPLSYTGGVSELAR.IA.EKMEEMEQE.RS.NGFGFKDAVFDGS.SR.LQNECRGYNLQP.DQ.KVKLQDFK.G O95825 Q9Y2P2F. O94999 Q9Y2P2L.RAHLGALLSALSRSVRAC.P 1V 1 Q8TDJ6 1 Q8TDJ6 1 2.6793D.NTTSLTDKHLDPIR.E 3.0607Q.VLIEVGLVPVK.D 2.5581 2 Q9Y2J0 1 P04049 2.2495 1P. 2 2 O15211 1 2.2485 2.4273 1 1 O43374 2 P47736 2 1 2.6021 3.0119 2.5585 1 2 2 1 Q13546 2 2.7946 2.5617 Q13127 2 1 2 2 3.1589 2 2.5042 2 Retinal short chain dehydrogenase reductase Retinal short chain dehydrogenase 8 Retinoblastoma binding protein Protein 1 (QOH-1) Quinone oxidoreductase-like R30923_1 (Fragment) (Fragment) partial protein R31167_1, Rabconnectin Rabphilin-3A kinase serine/threonine-protein RAF proto-oncogene 2 Ral guanine nucleotide dissociation stimulator-like Peptide 1 (Rap1GAP) Rap1 GTPase-activating protein Rap1 GTPase-GDP dissociation stimulator 1 2 RasGAP-activating-like protein kinase erbB-4 Receptor protein-tyrosine kinase 2 protein serine/threonine Receptor-interacting REST protein inhibitor) (Nogo protein) Reticulon 4 (Neurite outgrowth
198 (continued) TLLMDPMNVF.Y Q9NZJ4 1 2.1683 1 .KEILKEQ.E O14805 1 3.0995 2 .LEVNLAILGRRGAGK.S.EPEPEPELEPEK.A Q9NYN1 1 2.471 2 P21817 1 2.9356 2 .FPVVSFSAGVKVRF.L P21817 1 2.4891 2 R.GREEWESAALQNANTK.CD.FYKVIESFIKAE.GQ.QTINKLTK.DS.IKAAAQWVR.DK.DLNENLAATQGLA.HL.QFLYTGQ.LD.LRAAANVISR.A Q8TDN5R.LGWGSGWDVLLPK.GL.TFSNELISRDEGLHCD.F 1D.PEFTAKTPKDSPGLPASANAHQL.F P06400P 2.243 O14777V Q96QB1 1 Q8NEX9 2 Q.EIVFPLDMGIV.G 1D.LAITSLLLLNQCLEELQ.G 3.2513 2 1 Q9UK32L.LVIGTAYLEAQ.G O94844 Q9H477 Q99575 2 2.437 2.7136 P31350F 2.6492P 1 2 1 2 3 2 1E.DLVGIISIPLK.L 1E.KVDEEGLKK.L 2.6972 2.3455 2.5389 2.3405Y. 2.4983 2 1 2 2 Q14690 P16499 2 1 Q92545 1 3.6169 2.7598 1 2 Q15413 2 2.4146 P29034 1 2 1 2.4907 2.6263 2 2 6 (EC 2.7.1.37) α W1 protein (Fragment) W1 protein 1 (Skeletal muscle-type ryanodine yanodine receptor (RyR3) 3 (Brain-type ryanodine receptor) yanodine receptor Retinoblastoma-associated factor 600 (P105-RB) (RB) (PP110) Retinoblastoma-associated protein HEC Retinoblastoma-associated protein similar protein Retinol dehydrogenase 7 Rho-GTPase-activating protein 1 BTB domain-containing protein Rho-related Ribokinase (EC 2.7.1.15) Ribonucleases P/MRP subunit POP1 (EC 3.1.26.5) protein M2 chain (EC Ribonucleoside-diphosphate reductase S6 kinase Ribosomal protein Ris subunit regulatory RNA-binding protein Rod cGMP-specific 3’,5’-cyclic phosphodiesterase homolog (Fragment) RRP5 protein R R R A2 (S-100L S100 calcium-binding protein (CAN19) protein) Sacsin
199 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table .SVGAVPVLSKECASGERGRRMSQ.M Q96T21 1 2.4606 2 .GLLLPVLFILF.L Q9NR16 1 2.2491 1 R.SPRKPQGPPPQGGNQPQGPPPPPGKPQ.GQ.APPAGKPQGPPPPPQ.GR.SPPGKPQGPPQQEG.NR.SPPGKPQGPPQ.QR.SPPGKPQGPPQQ.ER.SPPGKPQGPPQQE.G Q15214R.SPPGKPQGPPQQEGNKPQ.GR.SPPGKPQGPPPQ.GR.APPGKPQGPPQQEGNNPQ.GR.APPGKPQGPPQQE.G 1F 5.1993 P10162V K.LPTDSELAPR.S 3 P10163R.CQAYGAACADCCLARDPY.C P10163 1 P10163 P10163 P10163K.HTQLVEQLDES.S 1 P04280 4.0888S.RDLPDDVL.T 1 1 P04280D.EKADIALIKIDHQGK.L 1 3.4706 2 1 P04280 1K.SRAEGRAPNPARK.A 3.8327 2 3.1865 3.3821 2.8876I.QQEITVLSQCDSPYIT.R 3 2 4.2882 1 2 Q13275N.GFALPLKEEHKIF.L 2 2 2 3.1891 2.7704 P49908 2 1 2 Q9NTN9 1 2.4417 Q92743 Q9H3T2 1 2 Q15831 2.4386 O00506 1 2.4081 2 1 1 Q13362 2 2.2121 1 2.4384 2.3568 1 2 1 2.4364 2 2 2.7473 2 Protein 1 (Fragment) protein Salivary proline-rich PO (Allele K) protein Salivary proline-rich PO (Allele S) protein Salivary proline-rich (Clones CP3, CP4 and protein Salivary proline-rich M160 cysteine-rich type 1 protein Scavenger receptor Peptide 2 SECIS-binding protein PSelenoprotein (SeP) Semaphorin 3F (Semaphorin IV) (Sema Semaphorin 4G Y) Y) (Sema Semaphorin 6C (Semaphorin HTRA1 (EC 3.4.21.-) (L56) Serine protease (EC 2.7.1.37) kinase 11 protein Serine/threonine kinase 25 (EC 2.7.1.37) protein Serine/threonine phosphatase 2A, 56 kDa regulatory protein Serine/threonine
200 (continued) LNENPLRALYLI.A Q13153 1 2.5894 2 .FPDHVVFKD.L Q13315 1 3.4185 2 D.FTNSSSQEEIDKLLMD.LG.LSPEIHTLDDI.RY. K.EGYYGYTGAFR.CK.SVIPSDGPSVACVK.KK.HSTIFENLANK.AG.LVYDAYLAPNNLKPVVAEFYGSK.EK.EFQLFSSPHG.KD.GGFVYIAGK.C Q06190K.EFQLFSSPH.GK.EDPQTFYYAVAVVK.KK.KSASDLTWDNLK.GK.HQTVPQNTGGK.NK.EDLIWELLNQAQEHFGK.D 1 P16299K.EFQLFSSPHGK.DK.AVANFFSGSCAPCADGTDFPQLCQLCPGCGCSTLNQYF P02787I.PSDGPSVACVK.K 3.9559D.PQTFYYAVAVVK.K P02787I.PMGLLYNK.I 1 P02787 P02787I.PIGLLYCDLPEPR.K 1 I.WELLNQAQEHFGK.D 1M.YLGYEYVTAIR.N P02787 2.5767K.ADRDQYELLCLDNTR.K 1 17K.DSGFQMNQLR.G 55 4.2449 P02787K.ASYLDCIR.A 2 P02787 199 P02787K.DYELLCLDGTR.K P02787 3.6486H.LAQVPSHTVVAR.S P02787 3 P02787 2.4635 3.2135K.CSTSSLLEACTFR.R P02787K.DCHLAQVPSHTVVAR.S 2.559 3 1 18 2 D.TPEAGYFAVAVVK.K 2 4K.DGAGDVAFVK.H 5 P02787 6 1G.YYGYTGAFR.C 2 21 2.7861 3.3916 P02787 P02787 2.3451 3.4271 3.3119 2.6511 2 76 2 P02787 P02787 2.825 1 P02787 P02787 2 50 2 1 2 P02787 2.6227 2 P02787 1 4 2.6492 2.3234 4 1 1 P02787 P02787 2 P02787 P02787 2 P02787 3.8974 2.9344 1 38 3.8917 P02787 2.2426 3.0606 2 1 2 7 P02787 3 1 3 1 3.3749 1 2 P02787 2 2.8348 2 2.5453 3.5316 2.4503 104 3.5589 2 2.9156 2 2 2 2 2 3.8588 2 2 2.6529 2 P Serine/threonine protein phosphatase 2A, 72/130 kDa protein Serine/threonine phosphatase 2B catalytic subunit protein Serine/threonine 1 kinase PAK Serine/threonine-protein (Siderophilin) (Transferrin) Serotransferrin Serine-protein kinase ATM (EC 2.7.1.37) ATM kinase Serine-protein
201 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table YGYTGAFR.C P02787 1 2.5168 2 LAPNNLKPVVAEF.YLAPNNLKPVVAEFY.G P02787 P02787 1 1 2.3204 2.3829 2 2 G.YFAVAVVK.KK.DSAHGFLK.VD.SGFQMNQLR.GK.SKEFQLFSSPHG.KL.DGGFVYIAGK.CK.NPDPWAK.NK.NLNEKDYELLCLDGTR.KK.SASDLTWDNLK.GK.SCHTAVGR.TK.MYLGYEYVTAIR.NK.SKEFQLFSSPH.GK.IECVSAETTEDCIAK.IK.SKEFQLFSSPHGK.DE.KYLGEEYVK.AL.GYEYVTAIR.NL.KPVVAEFYGSK.EK.LCMGSGLNLCEPNNK.EG.GFVYIAGK.C P02787E.GYYGYTGAFR.C P02787 P02787 P02787G.AGDVAFVK.H P02787K.YLGEEYVK.A P02787K.IMNGEADAMSLDGGFVYIAGK.C 1K.KDSGFQMNQLR.G P02787 48 P02787R.KPVDEYK.D 1 1 1Y. P02787R.AIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSK.E 1 2.4601 P02787 P02787 2.3397Y. P02787 2.5966 P02787 2.4908 56R.FDEFFSEGCAPGSK.K 1 4.2783 P02787 2 R.DDTVCLAK.L 218 2.4901 2 N.NLKPVVAEFYGSK.E 2 2 P02787 2 1R.LKCDEWSVNSVGK.I P02787 3.0296 4 2.3352 5Y. 2 P02787 P02787 4 P02787 4.4578 6R.WCAVSEHEATK.C 2 R.KPVEEYANCHLA.R 2 2.0609 4.373R.APNHAVVTR.K 4 2 2.6662 P02787 P02787 3 4.6121 3.6338 2 1 1 2 P02787 2 2 3 P02787 P02787 4.0563 3 2.4243 2 2.783 1 3.2149 4.8013 2 2 5 P02787 18 2 P02787 3 3 2 2.5645 2.4729 P02787 3.0831 P02787 2 1.9693 1 P02787 3.6875 1 13 2 1 P02787 3 P02787 7 2.0546 4.2736 6 12 P02787 1 3.9039 12 2 1 3.2895 2.0125 3 22 3.1044 2 1 3.2487 2 2.2269 2 2 Protein Peptide
202 (continued) LAPNNLKPVVAEFYGSK.E P02787 5 2.7084 2 Y. R.SMGGKEDLIWELLNQAQEHFGK.DR.TAGWNIPMGLLYNK.IR.KPVEEYANCHLAR.AR.DQYELLCLDNTR.KC.VADESAENCDK.SC.PFEDHVK.LD.LPSLAADFVESK.DM.DDFAAFVEK.CM.PADLPSLAADFVESK.D P02787D.LGEENFK.AC.FSALEVDETYVPK.EL.VNEVTEFAK.TC.TAFHDNEETFLK.KC.IAEVENDEMPADLPSLAADFVESK.D 2K.YICENQDSISSK.L P02787K.VPQVSTPTLVEVSR.N P02787L.AADFVESK.D 5.0312L.DELRDEGK.A P02787C.ELFEQLGEYK.F 34D.FAAFVEK.C 2 P02768L.KAVMDDFAAFVEK.C 3L.HTLFGDK.L P02768 P02768 3.7701 5A.FHDNEETFLKK.Y P02768A.FHDNEETFLK.K P02768 4.223 P02768D.DFAAFVEK.C 1 2 A.LEVDETYVPK.E P02768 2.342 79A.DESAENCDK.S 39 2 2 P02768L.PSLAADFVESK.D P02768 6 2.2135L.VAASQAALGL.- P02768 4 1 A.KTYETTLEK.C 2.7488 3.6317 15 P02768L.GEYKFQNALLVR.Y P02768 4.6841 1 2.4761L.FEQLGEYK.F 1 2.9142 27 2 D.KLCTVATLR.E 2 11 3.1639 2 K.YLYEIAR.R 293 P02768 2 211A.PELLFFAK.R 2 P02768 P02768 P02768 2.5048A.DLPSLAADFVESK.D 2.9649 2 2.2693 2.1218 P02768 3.5211 2 2 P02768 5 1 15 P02768 3 1 P02768 1 2 P02768 2.2232 1 P02768 2.4699 2.6057 1 2.5176 P02768 P02768 1 4 1 P02768 2 2.5063 2 2 P02768 12 3.1543 8 P02768 2.7119 89 2.7915 1 2 2 P02768 P02768 4 3.2249 2.4105 2 1 2 P02768 1 2.4573 2.2606 P02768 P02768 2 1 2.8057 2 2.7272 1 1 4 2.7902 16 2 237 25 2 3.0426 2 2.7819 3.4824 2.4334 2.9489 2 2 2 2 2 Serum albumin Serum
203 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table APELLFFAK.R P02768 1 2.2134 1 Y DEFKPLVEEPQNLIK.Q P02768 19 3.74 2 .KPLVEEPQNLIK.Q.GDKLCTVATLR.E P02768.SALEVDETYVPK.E 18 P02768 4.1808 2 1 2.5301 P02768 2 17 2.7027 2 D.KAACLLPK.LK.SHCIAEVENDEMPADLPSLAADFVES.KK.QNCELFEQLGEYK.FK.QNCELFEQLGEYKFQNALLVR.YK.KVPQVSTPTLVEVS.RK.KVPQVSTPTLVEV.SK.QTALVELVK.HK.AEFAEVSKLVTDLTK.VK.KVPQVSTPTLVE.VK.AEFAEVSK.L P02768G.DLLECADDR.AE.MPADLPSLAADFVESK.DE.VDETYVPK.EK.KVPQVSTPTL.V P02768 1F H.TLFGDKLCTVATLR.EK.LVAASQAALG.LK.LVAASQAALGL.- P02768 3.5931 P02768K.SLHTLFGD.K 3 P02768E.FKPLVEEPQNLIK.Q 2 K.AVMDDFAAFVEKCCK.A P02768F P02768 16 2.2681 1K.RMPCAEDYLSVVLNQLCVLHEK.T P02768 27F. P02768K.LKECCEKPLLEK.S 2 P02768 4.7689 1K.LDELRDEGKASSAK.Q 28 2.5052K.LDELRDEGK.A 2.6297 P02768 P02768I.CENQDSISSK.L 2 7 2 K.LDELRDEG.K 2.9706 6 3.1275 2 1K.AVMDDFAAFVEK.C P02768 P02768 P02768F. 2.2255 2 78F 2 1 3.1839K.NYAEAK.D P02768 P02768 4.7383K.LVAASQAAL.G P02768 P02768 2 K.NYAEAKDVFLGMFLYEYAR.R 1 1 2.949 3 2 P02768 2.8032 2 P02768 1 6 105 2 2 3.7417 3.0762 2.7253 1 5 P02768 P02768 4.7732 2 2 2 2 2.4727 2.4283 4.4214 3.2151 2 2 2 P02768 2.6868 2 7 15 P02768 P02768 2 P02768 P02768 2 211 2.8938 3.0054 164 3 P02768 2 2 1 2.6603 4 P02768 2.2103 2.3516 2 2.5294 3.509 2 2 1 8 2 3 2.7578 1.9491 2 1 Protein Peptide
204 (continued) HDNEETFLK.K P02768 20 3.0986 2 .HADICTLSEK.E P02768 1 3.2448 2 K.KVPQVSTPTLVEVSR.NF F. K.LCTVATLR.EK.VHTECCHGDLLECADDR.AK.SHCIAEVENDEMPADLPSLAADFVESK.DK.PLVEEPQNLIK.QK.KYLYEIAR.RE.VENDEMPADLPSLAADFVESK.DK.SLHTLFGDK.LK.LDELRDE.GK.DLGEENFKALVLIAFAQYLQQCPFEDHVK.LK.AAFTECCQAADK.A P02768K.AAFTECCQA.AK.DLGEENFK.A P02768K.VFDEFKPL.VK.LVNEVTEFA.K P02768 28K.VFDEFKPLV.E P02768 140K.VFDEFKPLVE.E P02768K.VFDEFKPLVEE.PG.DKLCTVATLR.E 3.9947 24 P02768K.VFDEFKPLVEEPQN.L 3.8393K.TYETTLEK.C P02768 1 2 K.VFDEFKPLVEEPQNL.I 1 3 3.8658K.EFNAETFTFHADICTLSEK.E P02768K.VFDEFKPLVEEPQNLI.K 2 4.089K.VFDEFKPLVEEPQNLIK.Q P02768 62 2 2.6557K.ECCEKPLLEK.S P02768K.LVTDLTK.V P02768 2.2198 3 14K.VFDEFKPLVEEPQNLIKQ.N 2 3.3402 P02768 321K.LVNEVTEFAK.T 122K.DVFLGMFLYEYAR.R 2 P02768K.VFDEFKPLVEEPQ.N 11 2.9725 2 P02768 P02768K.ADDKETCFAEEGK.K 2.0783K.KQTALVELVK.H P02768 2.7853 1 P02768 2 K.SLHTLFGDKL.C P02768 95 2.4045 P02768 1 K.SLHTLFGDKLCTVAT.L P02768 P02768 2 H.KDDNPNLPR.L 3 P02768 1 2.2315 2 1 P02768 10 2.7377 P02768 29 P02768 2 1 2.5767 10 2.8405 1 2 P02768 1 3.2405 2.479 2.8304 14 307 2 2 2.4758 P02768 2.4651 2 2.4117 2 3.4544 2 2 P02768 P02768 3 2 3.6136 4.0127 P02768 2 2 P02768 2.3174 P02768 2 8 1 3 4.2323 1689 17 P02768 P02768 2 3 39 P02768 2.8553 3 7 2.5788 2.3683 P02768 1.9185 214 2 1 2.985 3.5972 52 2 1 1 2.444 2 2.9609 2 2 2.4257 2 2 2.7154 2 2
205 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table .ADESAENCDK.S P02768 2 2.4039 1 .KAEFAEVSK.L.ADLPSLAADFVESK.D.SLAADFVESK.D.KLDELRDEGK.A.YFYAPELLFFAK.R P02768 P02768 P02768 P02768 P02768 2 1 3 2.5425 3 25 3.1145 2 3.029 3.2511 2.5656 2 2 2 2 .KDLGEENFK.A P02768 1 2.7087 2 K.ADDKETCFAEEGKK.LK.KLVAASQAALGL.-K.KLVAASQAALG.LK.CCAAADPHECYAK.VK.SLHTLFGDKLCTVATLR.EK.TYETTLEKCCAAADPHECYAK.VK.DVCKNYAEAK.DK.TYETTLEKCCAAAD.PK.CCTESLVNR.RK.DDNPNLPR.LK.FQNALLVR.YH.DNEETFLKK.YK.TCVADESAENCDK.SK.AAFTECCQAADKAACLLPK.LK.TPVSDRVTK.C P02768F P02768K.KVPQVSTPT.L P02768K.ALVLIAFAQYLQQCPFEDHVK.L P02768 P02768 P02768N.DEMPADLPSLAADFVESK.D 10P P 5 11P 33 P02768 3.4938 8P P02768 1P 3.0864R.LSQRFPKAEFAEVSK.L 2.6686 2 P02768 3.508R.HPYFYAPELLFF.A P02768 2.9973 2.5443 3V 2 P02768 3 2 P02768R.NECFLQHKDDNPNLPR.L P02768 3 P02768 P02768 2 R.NECFLQHK.D 2 R.MPCAEDYLSVVLNQLCVLHEK.T 1 12 2.5775 2.5606R.RHPDYSVVLLLR.L P02768 70 32R.LVRPEVDVM.C P02768 149 2 R.RHPYFYAPELLFF.A 2 3.1123 2 2 2.3707R.LSQRFPK.A P02768 2.3939S.ALEVDETYVPK.E 3.6576 2.8479 2 2 2 4 4.6559 2.727 2 2 2 2 2.9968 P02768 2 2 2.4127 P02768 P02768 2 P02768 2.4089 2 1 2 9 4 P02768 1 P02768 3.0029 P02768 2.4544 P02768 4.5359 2.7031 2 29 8 2 P02768 2 P02768 2 1 3 3.5491 2.7011 7 2.5794 2.7478 1 3 2 2 2.9068 2 2.5011 2 2 Protein Peptide
206 (continued) KLVNEVTEFAK.T P02768 26 3.5777 2 NEVTEFAK.T P02768 2 2.3415 1 APELLFFAK.R P02768 7 2.2681 1 .FDEFKPLVEEPQNLIK.Q.PQVSTPTLVEVSR.N P02768 11.MDDFAAFVEK.C 2.5653 2 P02768 43 3.1281 P02768 2 3 2.241 1 .FYAPELLFFAK.R.GEMADCCAK.Q.KAAFTECCQAADK.A P02768 P02768 80 P02768 1 2.9079 2.2502 6 2 1 2.8013 2 .YGEMADCCAK.Q.AFHDNEETFLK.K.PTLVEVSR.N P02768 P02768 1 P02768 12 2.3849 1 2.5615 25 1 2.5143 2 R.LAKTYETTLEK.CV. R.HPYFYAPELLFFAK.RR.HPYFYAPELLFFA.KR.LVRPEVDVMCTAFHDNEETFLK.KS.TPTLVEVSR.NR.YTKKVPQVSTPTLVEVSR.NR.VTKCCTESLVNR.RY Y R.RPCFSALEVDETY.VT S.LAADFVESK.DV T P02768Y T P02768 P02768R.RPCFSALEVDETYVPK.ER.RHPYFYAPELLFFAK.R P02768 27 P02768R.RHPYFYAPELLFFA.KS.KLVTDLTK.V 4 62R.FPKAEFAEVSK.L 3.9553R.HPYFYAPELL.F P02768 P02768 2R.AFKAWAVAR.L 3Q.TALVELVK.H 3.3129 2.8061 2 V P02768R.FKDLGEEN.F 2.5292 13 3.6723 2 2 R.FKDLGEENF.K 1R.FKDLGEENFK.A 2 R.DAHKSEVAHR.F P02768 3 1 2.7069R.FKDLGEENFKAL.V 3.2955 P02768R.ETYGEMADCCAK.QR.HPDYSVVLLLR.L P02768 2 V. 2 2.6754 4 P02768V 30Y. 2 15 2.7609 P02768 P02768 1 2.7881 P02768 P02768 2 4.0128 2 P02768 2.9058 10 3 3 4 P02768 P02768 1 2 P02768 2.85 3.3056 P02768 P02768 37 P02768 2.3487 2.5953 2 2 P02768 16 204 2 2.9732 1 1 1 2 36 2.7486 2 2.4418 2.8391 43 2.7348 3.547 2.1802 2 2 2 2.2205 2 1 2 2 R.FRPDGLPK.KR.GPGGVWAAK.L P35542 P35542 3 1 2.948 2.4699 2 2 Serum amyloid A-4 protein A-4 protein amyloid Serum
207 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table .MFILLGFTDHPELQ.A Q8NGJ0.PISNTGILELR.R 1 2.2971 1 O15389 1 2.3276 1 .SFPITNYLAPVSASVSPSA.V P11831 1 2.4813 2 .CDVPPILALSCSNVDIN.I Q8NH90 1 2.5365 1 K.YVYIAELLAHK.IR.IQNILTEEPK.VP E.DHGYSLVNR.LS.TCGAHVTVVTVYYVPC.AG.VALLITSVAPL.LT N.KVVSVIGLGVFVRA.LL.STTTVPKALAIFWLQAH.N P27169G.PNVIDHFSCDASPLL.A P27169L.LLVSYIVILVSVP.K Q8NGC4 1F Q9Y6P5 5E.VTSKPLNIQVQGV.P 2 2.4299E.GGENVDTCTVYADGQAFMVDKPPV.P Q8NGE2 3.4774 1 2 A.QLDAASVSSIQVVGVVEAL.I 3.6623 Q8NGJ4 Q8NGM7 2 T 1 2.4525 2 L.LRVEIHNPLLEE.E Q8NGQ2 1 1 2 2.6255-.MVLLESEQFLTELTR.L Q9UPX8 Q8NH43 1 2.45 2.4457 2 2 1 Q96P30 2.6759 2 2 Q9Y3L3 2 2.6305 2.4447 1 1 2 2 2.6009 2.3908 Q9BZZ2 P37108 2 2 1 1 3.127 2.8671 2 2 Protein paraoxonase/arylesterase 1 (EC 3.1.1.2) Serum factor (SRF) response Serum PA26) protein Sestrin 1 (p53-regulated Seven transmembrane helix receptor Seven transmembrane helix receptor Seven transmembrane helix receptor Seven transmembrane helix receptor Seven transmembrane helix receptor Peptide Seven transmembrane helix receptor Seven transmembrane helix receptor Seven transmembrane helix receptor 2b SH2 domain-containing phosphatase anchor protein 2 (Shank2) domains protein SH3 and multiple ankyrin repeat 1 (3BP-1) SH3-domain binding protein Sialic acid binding Ig-like lectin 5 (Siglec-5) Sialoadhesin (Sialic acid binding Ig-like lectin-1) (SRP14) particle 14 kDa protein Signal recognition
208 (continued) subunit β .EDTVQPLLQE.Q.FFSGRPLTDKMKFEELK.I Q9BUT3 1 Q8WUN7 2.4046 2 1 2.8603 2 .AIDESWKGGGPV.T Q8WU96 1 2.3186 2 .FVVGDVPEESKELLLQRA.L Q8TC38 2 2.8499 2 .DIRNTTVTPNVTKDVALAAVLVPVLVMVLTTLI.L Q8N6M4 1 2.4262 2 .IVDETLDFGGL.S.YVASFPVALPLQP.P Q9BV77 Q8N195 1 1 2.4964 2.5895 2 2 Q.DLWEVYQ.RL.VLLVLGQQPVI.S Q8IZ32 Q8TBY7 1 1 2.4001 2.2758 1 2 A.TSPASKAARE.SD.LDLLHKIVLKV.GF F P Q.YGHYSTAEVLLRAGVSRDARTKVDRT.PK.QLCRPLTCEKSKPVPLK.L Q9BQ28Y Q8IVW4 1 1 Q8TAK5 2.4803 4.1075 1 2 2 Q8TBR6 3.7882 3 1 2.2541 2 W K.DFLRRYVLSFVGCGLAVVGTYLL.VI.LFGGEYFNGQKT.FI.NEDLDSGTQIPFIK.RR.PFVEEYIPTQEIQV.TW Q9BVE6S.PSRSIDGMQYPIVIKNTK.GV M.NRITTKEATSSCPP.K 1 3.0387 Q96F29 Q8WUF8 2 Q8IWK1 1 1 Q9BRR1 2 2.4756 2.4551 1 2 2.9171 Q96AS3 2 3.8619 2 1 3 2.2543 1 Similar to Fgd1 family, member 2 Similar to Fgd1 family, Similar to fring Similar to GA transcription factor, binding protein Similar to chromosome 6 open reading frame 32 6 open reading Similar to chromosome Similar to cyclin-dependent kinase-like 3 display and activated by p53 Similar to differential 2 Similar to early development regulator Similar to endothelial and smooth muscle cell-derived Similar to gene near HD on 4p16.3 Similar to hypothetical protein Similar to hypothetical protein 384D8_6 Similar to hypothetical protein dJ462O23.2 Similar to hypothetical protein DKFZp434G0522 Similar to hypothetical protein DKFZp564D172 Similar to hypothetical protein FLJ10101 (Fragment) Similar to hypothetical protein FLJ11807 Similar to hypothetical protein FLJ12618 Similar to hypothetical protein FLJ14840 Similar to hypothetical protein FLJ14886 (Fragment) Similar to hypothetical protein
209 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table QPIIKEILKNFPK.E Q8N4J0 1 2.4011 2 .FSRLWEDF.K Q9BSY6 2 2.4966 2 .YVELLLR.N Q9BS16 4 2.4892 2 K.NTKLDMQFIKDSR.QK.EAAAAGAAAGAATGTVAG.AP N.LPGVHCGPSSGAGPGFGPGSW.SN.DNQDNENPGNTNCHDVV.LR.PVPLSARVQPVCLPVP.GL.VEHLELLQK.K Q8IYT1G.HTVTLTLTYLFIKEY.S Q96BG7Q.CMYGTSNQYPAQETL.D Q96II8 1L.GKENSWKPRL.P 1 Q8NEQ4Y 2.525 1K.GLAEEVKSRWEK.E 3.4999 Q8N171 1G.SCLLLLGGFSLALSFAPW.C 2 2.7274 2 Y. 2.6838 2 1 Q8NHU3 Q8N179 Q8HWS3 2 2.8921 1 1 1 2 Q9BSE9 2.5384 2.4289 Q96B33 3.2101 Q8WVF5 2 1 2 2 1 3 2.1571 2.4652 2.9673 1 2 2 A.AWDALIVR.PI.TWIVTQVAISY.TI.ELLANQYSIQVQVEDL.T Q9BRR6 Q96CB9 Q96KY4 1 2 1 2.5324 2.5181 2.4325 2 2 2 Protein FLJ22582 Similar to hypothetical protein MGC26988 Similar to hypothetical protein FKSG14 (P33) Similar to leucine zipper protein protein Similar to leucine-rich neuronal factor receptor Similar to opioid growth (Fragment) serine, 8 (Prostasin) Similar to protease, (Inhibitor) subunit phosphatase 1, regulatory Similar to protein Similar to putative Peptide factor X, 4 Similar to regulatory Similar to RIKEN cDNA 0610037N03 gene Similar to RIKEN cDNA gene (Fragment) 1110014F24 Similar to RIKEN cDNA 2210017A09 gene Similar to RIKEN cDNA 2310014B08 gene (Fragment) Similar to RIKEN cDNA 2410127L17 gene Similar to RIKEN cDNA 2610017G09 gene Similar to RIKEN cDNA 2810049G06 gene Similar to RIKEN cDNA 2810405F18 gene
210 (continued) PLQKGLEKAAAVADKRK.S Q8NEN5 1 2.7077 2 PILVDLLEK.S Q8NEM7 5 2.9085 2 .EQPVFAANFI.K.EDVMQFVREADP.Q Q8TBF3 1 Q96GD3 2.3337 2 2 2.4147 2 .NDLYVSDAFHK.A Q8TCE1 3 2.9396 2 I.ANGPNLTLLVR.QA.DVERFFNYCGLDPEELE.NA.NDRVPYGISAIER.N Q8TC76 Q8TC15 Q8TC76 1 1 1 3.0521 2.5907 2 2.4778 2 2 K.GSDLDPEEPIKVEE.PK.ASPAVALPK.RQ.SRLAALGRQVGAR.VV I.ILQEQKTVLASVFSVLSAIYAS.QI.FQLLALLF.FF V Q96BD8L.VQVPQGLTLSLLAR.QV. Q8IUR0 Q8WVL0 3 Q96ER3P. 2.9097 1 1 1 2 2.4339 2.4761 2.5631C.HKFIALSDKEGK.L Q8N6K9 2 2 L.YINSELQDFQKV.P 2 Q8TC65R.CEGTIVDCSNQK.L 4Q.GHTSEPRDLNSVNCDELGPLPPGWE.V 3L.LDKNSSGDIGKK.E 2.6741Q.NSADISITLR.N 2.5592 2 2 Q9HCE7 Q9Y6F0 O94813 1 O75094 1 3.8803 5 2.6037 Q9H3U0 1 3 2.4956 2 Q96SB8 2.2704 1 2 2 2.4879 1 2 2.474 2 protein) (BA57G10.4) protein) α Similar to ubiquitin-protein isopeptide ligase (E3) Similar to ubiquitin-protein Similar to unknown Sirtuin type 1 (SIR2 Similar to RIKEN cDNA 2810433K01 gene Similar to RIKEN cDNA 3300001M08 gene Similar to RIKEN cDNA 4021401A16 gene Similar to RIKEN cDNA 4930521I23 gene Similar to RIKEN cDNA 5031425D22 gene Similar to RIKEN cDNA 9030623N16 gene clade C inhibitor, Similar to serine (or cysteine) proteinase Similar to sex comb on midleg-like 1 (Drosophila) Similar to solute carrier family 26, member 8 Similar to sperm specific antigen 2 Similar to transcription factor (p38 interacting protein) (h-Slit-2) Slit protein (MEGF5) protein SLIT-3 factor 1 (EC 6.3.2.-) Smad ubiquitination regulatory SMAP-2b SMC6 protein
211 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table -4 chain -1 chain α α .GNIPAGLVPPVA.P Q9BXS9 1 3.0686 2 .LSITHVNSLK.L O95233 1 2.6351 2 .SAVPSPGAGDDTR.H P31645 1 2.4466 2 .IGLVETGAIIG.P P46721 1 2.4178 2 .LADMTLSEVHVVMTGGY.A O00337 1 2.5407 2 .FVSIVVVQW.A P05023 1 2.7097 2 K.GAPERILEFCSTFLLNGQEY.SY Q13733 1 2.533 2 Q.SAPSCPSSSPSPGEEPEGEGETDPEK.VR.TLSRRSFDACVK.AY Q9H2X9 1 2.4138 Q9Y666 2 2 2.9436 2 R.RAVCRYYNNDL.LS.PTFVGYTWKGLRKSDN.SV A.CVLGKIMYIFGGYEQ.QR.RYSEFELLR.SS.GGLSQPAGWQSL.L Q9UGH3 O94956 3 Q96GH7 1 3.0681 2.5026 1 2 Q8TCJ2 O95219 2 2.4475 1 2 1 2.7635 2.3472 2 2 F E.EVGALTQSGAVQE.ID.GIEDMIGYR.PM.QGVLESFLGTAVS.GV Y Q12766 O15153 P31641 2 3.0359 1 6 2 3.1812 2.4274 2 2 L.YGVFLCFSI.M Q9HC58 1 2.3913 2 Sodium-dependent serotonin transporter (5HT transporter) Sodium-dependent serotonin Solute carrier family 12 member 5 Solute carrier family 12 member 7 Solute carrier family 21 member 3 Solute carrier family 21 member 9 Solute carrier family 23, member 2 1) Solute carrier family 26 member 6 (Pendrin-like protein Sortilin 1 Sorting nexin 4 of immunodominant MHC-associated peptides Source Sodium/potassium-transporting ATPase Sodium/potassium-transporting ATPase Protein (Fragment) SMF protein Sodium- and chloride-dependent taurine transporter Sodium bicarbonate cotransporter Sodium/nucleoside cotransporter 1 (Na(+)/nucleoside Peptide Sodium/potassium/calcium exchanger 3 Sodium/potassium-transporting ATPase
212 (continued) VEPDRRNQSPVDQ.G P18827 1 2.77 2 VETTRRK.E Q09428 1 2.5774 2 QTKFMELLEPLNE.R Q01082 1 3.14 2 A R .VLSQAPEDEGGSPEK.G Q12770 1 2.6603 2 S.QLALPIQPIPCKP.VS.SSSGPQEREGA.GA.EEDSEEMPSLLTSTV.QL.EAQSHFRKVEDLFLTFAKKASAF.NV. S.FYGQLEYIGRSVHYWK.KR.SRSRSRSKSRSVSRSPV.PA.DSSEEKFL.R Q9UN79 Q13813N.ALVSHLLVVEPEK.LP O60248 Q9HB58 1S.LRRLAHSFRPAYR.K 1K.VQQTVQDLFGR.A 1 1 2.4151 Q99666 2.9413D.EENDMIEGIPEGKDKHRMNKHKIG.N 1 2.8075 Q13243N.GSIGEETDSS.P 2.4355 2 1A.KAWPTVLQ.T 2 2 T. 1 P11474 2.4871 P02808 Q13033 2.7201 2 Q12772 1 2 1 1 P38646 2.8693 1 2.2224 3.7522 2 1 2 2.4275 Q13586 3 P31040 2.2248 2 1 2 1 2.6759 2.4621 1 2 D.KVNQLEEK.TQ.YLRQEVLRRAEATAA.SV. O95721 Q15431 1 1 2.5487 2.7568 2 2 chain, brain chain, brain 1 α β SOX-13 protein (Type 1 diabetes autoantigen ICA12) (Type SOX-13 protein (SOX-20 protein) SOX-15 protein kDa) (Speckled 110 nuclear body protein Sp110 Spectrin Spectrin BS-63 Sperm membrane protein 5 arginine/serine-rich Splicing factor, Statherin ERR1 hormone receptor Steroid cleavage-activating element binding protein regulatory Sterol (SREBP-2) element binding protein-2 regulatory Sterol mitochondrial protein, Stress-70 Striatin 3 (Cell-cycle autoantigen SG2NA) (S/G2 antigen) interaction molecule 1 Stromal subunit, [ubiquinone] flavoprotein Succinate dehydrogenase 1 receptor Sulfonylurea Synaptonemal complex protein 1 (SCP-1 protein) Synaptonemal complex protein 29 (SNAP-29) Synaptosomal-associated protein Syndecan-1 (SYND1) (CD138 antigen)
213 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table ) δ ) (CCT- δ .QHNDKNIGGDE.D P07766 2 2.6309 2 .KVETTTLNI.Q P34741 1 2.7336 2 K.MIQDGKGDVTITNDGA.T P50991 1 2.4246 2 R.VNNSNCLLSEPP.S Q99973 1 2.9339 2 E.RLAPGTRRGLSAQ.E Q8IZW7 1 2.2837 1 Q.MLCIDNSRTRELKALHLV.P Q9Y4I5 2 4.2081 2 G.YSFLSLY.R Q9NS86 1 2.3742 1 R.LDTLAQEVALLK.E P05452 1 2.6208 2 P E.KIQQRNQYERKGEKAP.KK.IKEFEDVDPKVKLKDGLVRKEK.E Q9BQS9 Q9UNK0 1 1 2.7377 2.389 2 1 A.ASLGAEDPETQVVL.I Q9Y490 1 2.2588 2 K.ILNDYKTK.N Q9NYW0 1 2.5404 1 G.SWCVSVFFPALF.A Q9NYV8 1 2.9541 2 H.KRAIRIILSFFFLF.LK.ALLEEAFDNLKDE.MK.MKSLIRTLEQ.ER.RISPADTPVSESSSPL.KW Q9NYW6 P82094 2 Q16650 O60343 1 2.224 2.6797 1 1 1 2 2.7184 2.5496 1 2 subunit (TCP-1- δ element modulatory factor (TMF) TA brain-1 protein (T-box brain protein 1) (TBR-1) (TES-56) brain protein (T-box brain-1 protein -cell surface glycoprotein CD3 epsilon chain -cell surface glycoprotein 1, -complex protein AFII140 protein (Fragment) AFII140 protein elomerase-associated protein TP-1 elomerase-associated protein ensin 3 esmin (Metallothionein-like 5, testis-specific) estis-specific adriamycin sensitivity protein estis-specific adriamycin sensitivity protein etranectin (TN) alin 1 aste receptor type 2 member 10 (T2R10) aste receptor aste receptor type 2 member 14 (T2R14) aste receptor aste receptor type 2 member 3 (T2R3) aste receptor T T T T T Protein Syndecan-2 (Fibroglycan) Syntaxin 8 T T Peptide T T T TA TBC1 domain family member 4 T- T T
214 (continued) ) (c-erbA-1) α .LEEKVSVAFRQEV.V Q8WZ42 1 2.3421 2 .SSREATQILSVPKVDDE.I.WLAQWLGPLLLVSLW.G.DPSIRHFDVAHVSTAA.T.EEEEEEEGGAVGPHKRQ.H P42166 Q9NQE7 P01266 1 1 2.8232 2 2.8826 2 P20396 2 2.6669 2 1 2.5278 2 .TFLFFK.N O76003 1 2.5753 2 .ILAPVKDKQTELG.E Q9UHV7 1 2.6392 2 .KDLSLDDFK.G P30048 1 2.528 2 G.GVLSSIETGVSIII.PR.DNAGDRADFW.RE.EKVLVAVTKKEAPPKA.RE.EIVPEEEVLPEE.EV Q.QAIPDSTVEFKA.I Q07157 Q8WZ42 Q9UDY2 1 Q8WZ42 1 1 Q8WZ42 2.6547 2.5971 2.4206 1 2 2 2 2 3.8064 2.5622 2 2 V V V K.PSKVECGSDPEENSARS.PD.CTNFLLQECGK.QF V K.NALALFVLPK.E P10827 O75448 1 3.0209 1 2 P05543 2.4542 2 1 2.5162 2 A.AAAAAALLPGA.TL.EKLKEVVHFQKEKDDVSERGY.VG.PEDPEEELPPEE.VF E.FKDLSLDDFK.GP Q9NVV9 P36897 1 Q9P2T0 2.5077 1 2 2.4867 P30048 1 2 3.0214 36 2 2.6402 2 K.QIAAKQGTKKAR.E Q9Y5Y9 1 2.2206 2 ) α (C-erbA- α (TP α eceptor type I (EC 2.7.1.37) (TGFR-1) r β ght junction protein ZO-2 (Zonula occludens 2 protein) ght junction protein ght junction protein ZO-1 (Zonula occludens 1 protein) ght junction protein itin etrodotoxin-resistant voltage-gated sodium channel etrodotoxin-resistant Ti T Thymus-specific serine protease (EC 3.4.-.-) Thymus-specific serine protease Thyroglobulin hormone receptor Thyroid complex 100 protein hormone receptor-associated Thyroid complex 240 protein hormone receptor-associated Thyroid hormone) (TRH) releasing (Thyrotropin Thyroliberin globulin (T4-binding globulin) Thyroxine-binding Ti T THAP 1 domain protein gene) haploid expressed (Testicular THEG protein mitochondrial reductase, peroxide Thioredoxin-dependent protein Thioredoxin-like Thymopoietin, isoform TGF-
215 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table LIENKMQLYVPQPEEDIYELLYKEI.E Q13009 1 3.8712 3 .VPEKKVPVPPPKKPEVPPTKVPEVPKVAV.P.HKLTIADVR.A Q8WZ42 2 3.9008 3 Q8WZ42 1 2.6629 2 .EVFDQVTQEGAG.H.RQMDLQTPDSHLR.Q Q9HBG7 Q9NRV3 1 2.5509 1 2 2.6315 2 .TRGIFPEVEPPEAIPE.I Q8WZ50 1 3.1555 2 .NNGPNGGGGNV.A Q15542 1 2.2735 1 V V A.SKEVIREEKVPLAPPKEP.EK.VPEALQEIVPEKKTL.VT K.EAEKTAVTKVVVAADK.AY F. Y M.KEKLLAELEGK.L Q8WZ50 Q8WZ50G.DGGSVSGGGSSNR.H 2 Q92762Q.DKDVNEGETSDGVRK.S 1D.GKVRQVIPIFTDVA.L 2.5663 1D.FFSGTVSLP.G 2.7658 2 R.GQQSAEEENFKKPT.R 2.6574 2 -.MAAPLLHTRLPGDAAA.S 2 Q13077T Q.KQIDNMKGKLQE.T Q8NG57 Q9Y5Q9 1 1 Q9UKN8 2.6457 1 2.4436 2 Q15014 1 3.2655 Q9H4F0 Q01201 2 2 2.9354 1 1 1 2 Q15545 2.7287 2.5418 2.2607 2 2 1 1 2.9982 1 R.IANIQDAIWNSRK.I O60602 1 2.6799 2 itin fetal isoform (Fragment) itin Z-disc (Fragment) (Lymphocyte -lymphocyte surface antigen Ly-9 1 -lymphoma invasion and metastasis inducing protein ranscription factor IIIC102 ranscription factor IIIC90 ranscription factor RelB (I-Rel) MRGX protein ranscription factor-like ranscription initiation factor IA protein ranscription initiation factor TFIID 100 kDa subunit ranscription initiation factor TFIID 55 kDa subunit (TAFII-55) ranscription elongation factor Elongin A3 ranscription elongation factor Elongin oll-like receptor 5 oll-like receptor ProteinT T T T TNF intracellular domain-interacting protein associated factor 1 TNF receptor Peptide T T T T T T T T T
216 (continued) ) α (TIF1- PPPPPEVIPEPEVSTQPPPEEPGCGSETVPVPDGPR.S O95359 1 2.4276 2 .ARDDGLFSGDPNWFPKK.S P37802.ETAFERLQQELEQQ.R 1 3.0173 2 Q9C019 1 2.4086 2 .FRKVGIPIII.A.VTSVPKQPGVAPI.N Q9NRS4 1 2.4867 2 Q9H4I2 1 2.5015 2 E.EKEVDLSDIINTPLPR.V P49848 1 2.974 2 A.SAAASGGPSAAP.SL.ELMPEKGLKEEE.KK.ICDELIAKLGKTD.-K.AGNSCPELVPSRRSK.LP. V L.LVGCAVAVLAV.HK.KIQVLREVE.KT O15164K.AADDTWEPFASGK.T Q8NI51K.TSESGELHGLTTEEEFVEGIYKVEIDTK.SR.KAADDTWEPFASGK.T O75410 O75410 3R.RYTIAALLSPYSYSTTAVVTNPK.E 1K.GTSEVTESGKKK.T 2.9144 1 1V 2.4118 2 K.PLGSRDVLPNNRQL.Y P02766 Q9Y5Z9 1.9926 2.6635 1 K.ENNLENEKMVKNK.P 1 2 T Q8TDI7 P02766 2 1 P02766S.AGFGGALNTNASFGCAVST.S P02766A.LFFKVIK.D 3.0804 4.2219 1 1 6 2 2 Q13061 4 2.5057 5.0544 4.1857 P29144 2 4.5456 2 1 2 Q8IZK1 2 Q12816 2 2.3366 1 2 2.9988 1 2.2188 2 3.0144 P49815 2 2 1 2.4878 2 α homolog) α ophinin ranscription initiation factor TFIID 70 kDa subunit (TAFII-70) ranscription initiation factor TFIID 70 kDa subunit (TAFII-70) ranscription intermediary factor 1- ransgelin 2 (SM22- ranscriptional repressor CTCFLranscriptional repressor (CCCTC-binding factor) 1 ransforming acidic coiled-coil-containing protein 2 ransforming acidic coiled-coil-containing protein ransitional EPITHELIA protein response 2 protein ransmembrane cochlear-expressed serine 4 (EC 3.4.21.-) ransmembrane protease, (TTR) (ATTR) (TBPA) (Prealbumin) ransthyretin riadin B7) 15 (Zinc finger protein ripartite motif protein ripeptidyl-peptidase II (EC 3.4.14.10) (TPP-II) ripin riple homeobox 1 protein 2 protein) sclerosis uberin (Tuberous T T T T T T T T T T T T T T T Tr T
217 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table PISIAPSSPLLPL.H Q9UPU5 2 2.5867 2 .LGAICYCDLFCNRTVSD.C Q9GZM7 1 2.5505 2 .VIDEVRTGTY.R.DPWTLPQLKDTSQPW.K P05209 2 2.4574 2 Q8N130 1 2.9532 2 .QDRPSFTELREDL.E P30530 1 2.5225 2 .TMASCTSESHSH.W Q9HAV5 1 2.5449 2 A.RLVKLAQEDTPPETDY.RL.LKTPGVVENHG.YK.ISFKSLVASL.A Q9UHP3 1 Q14139 2.4768 P22314 24 2 2.4569 1 2 2.5135 2 T L.LERAESVERLEE.AY A.LSLTFVLGLLSGFLVWR.RF E.ELAELEDALR.NI.FIPSPSLEEQSNDG.KI.QVQTLNLSQEE.ET Q15814L.KMNAAIKML.K Q9NP84P 13G.ELADKKDRDA.S 1I.SSTLNPQAPEF.I 2.6337P. Q15628 3.5492 Q12888 2 2 Q9UJ47 1 1 2.5394 P35590 4 2.4352 2 2 2.4625 O43188 1 1 Q14694 2.1605 3 1 1 2.5245 2.4219 2 2 -tubulin 1) α -1 chain ( α osine-protein kinase receptor Tie-1 Tie-1 kinase receptor osine-protein UFO (EC kinase receptor osine-protein r r ubulin cofactor C) C (Tubulin-folding ubulin-specific chaperone superfamily member Fn14 factor receptor umor necrosis superfamily member XEDAR factor receptor umor necrosis type 1 associated DEATH factor receptor umor necrosis 1 p53-binding protein umor suppressor ype I transmembrane receptor FLJ38680) ype IIc Na+/Pi cotransporter (Hypothetical protein Ubiquitin carboxyl-terminal hydrolase 25 (EC 3.1.2.15) Ubiquitin carboxyl-terminal hydrolase A Ubiquitin conjugation factor E4 Ubiquitin-activating enzyme E1 (A1S9 protein) ProteinT T TUBULOINTERSTITIAL protein NEPHRITIS antigen-related T T T T T Peptide T Ty Ty U5 snRNP 100 kDa protein 10 (EC 3.1.2.15) Ubiquitin carboxyl-terminal hydrolase 24 (EC 3.1.2.15) Ubiquitin carboxyl-terminal hydrolase
218 (continued) .YLNNIYPEVYVPDLN.P Q14435 3 2.9917 2 .SKEFFQLVVEE.I Q05086 1 2.4546 2 .DFPPLSEELISE.M Q13432 1 2.4414 2 .VGTQVCLRNNPLYHAGAVAFSISAGIPK.V O95071 1 2.7194 2 .ALLMTNCYATPSSNA.T P07911 1 2.4672 2 V T R.SRGISSECLDYNSPDNNPTG.AW S.MNYLTKKGMSSK.EK.VWELQDLSFQAASQIMSTPVYD.AL.LLGFSDAMTFKERV.WS.QDIDHILETLSA.L O00208E.VQGLVDERPFLHYDCV.NY 1 Q9NYU1 Q9NYU2 2.5949 1 2 Q9HAW7 1 2.418 Q9BZM6 1 Q9Y223 2 2.9609 1 2 2.4397 1 2 2.5731 2.4435 2 2 M.LLVLGLCGAAYRPTEEIDL.RR.KDDGVAHR.DF K.SVYVVGNATASLVSKIGLD.TL.LDTFLEEGKEYIF.VQ.TLQKEIEKVYLDNKLLK.ES.CDICNTARRGLKRKSLQPNLQLSKKLK.T Q9H1C4 1 P10746 Q96PH5 4.7339 P15918 3 1 1 Q9BZF9 Q07131 1 2.4584 1.9622 14 3.8467 1 2 1 2.6899 3 2.4088 2 1 I.LTKLLEVSDDPQVLA.VA.LKQSFLELTELK.Y Q9UI12 Q9HBG4 1 1 2.6539 2 2.4288 2 -acetylgalactosaminyltransferase -acetylgalactosaminyltransferase N N ) (Retinoic acid early transcript 1) β -acetylglucosamine-2-epimerase N acuolar ATPacuolar H synthase subunit H (EC 3.6.3.14) (V-ATPase acuolar proton pump 116 kDa accessory subunit pump 116 acuolar proton Ubiquitin-protein ligase E3AUbiquitin-protein (EC 6.3.2.-) ligase EDD (EC 6.3.2.-) Ubiquitin—protein UDP-GalNAc:polypeptide UDP-GalNAc:polypeptide glucosyltransferase 1 UDP-glucose:glycoprotein glucosyltransferase 2 UDP-glucose:glycoprotein 1-7 , microsomal UDP-glucuronosyltransferase UDP- (ALCAN- ULBP1 protein 4) (HRG4) homolog (Retinal protein protein Unc-119 Unc-93 related protein Unc-93 related transporter UT-A1 Urea urinary glycoprotein) (Tamm-Horsfall Uromodulin synthase (EC 4.2.1.75) (UROS) Uroporphyrinogen-III UTP—glucose-1-phosphate uridylyltransferase 1 (EC 2.7.7.9) Uveal autoantigen 1 (RAG-1) activating protein V(D)J recombination V V
219 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table .GQGTLVTVSSASTK.G Q9Y509 6 2.7864 2 .EKAENSSLNLIGK.A P46459 1 2.7272 2 G.RIGAIGRTNLFYKLLSTFDL.IF K.KSNDSNPYDTDK.MG.TLVTVSSASTK.GQ.GTLVTVSSASTK.GW R.VTISVDTSK.ND.TEAMKRALASIDSK.L Q9Y2P4K.ELSSFIDK.GK.VPTADLEDVLPLAEDITNILSK.CK.FPSGTFEQVSQLVK.EK.HLSLLTTLSNR.V 3K.KELSSFIDK.GK.LCDNLSTK.N P46459L.PLAEDITNILSK.C 4.5431K.YTFELSR.RR.VCSQYAAYGEK.K Q9Y509 Q9Y509R.THLPEVFLSK.V 3 1K.IETISHEDLQR.Q P02774K.VYFAGFPR.K 9 P18206 15R.NNLELSTPLK.I 1.9378 O95973G.PIDAAFTR.I 1 2.883 2.6799E.GPIDAAFTR.I 5 P02774E.DGVLDPDYPR.N 1 1K.AVRPGYPK.L P02774 2 2 R.VDTVDPPYPR.S P02774 2.2519R.DVWGIEGPIDAAFTR.I 2.4261 1.9445 3 P02774 P02774 P02774 2 4 2 12 1 P02774 2.483 P02774 P02774 2.165 2 1 2.938 1 P07225 2 1 1 2.7126 P07225 2 1 P07225 30 2.6748 1.9832 2.8862 1 2 1 1 P04004 1.9585 2.5169 P04004 P04004 1 P04004 2 1 3.2217 P04004 P04004 1 2 2.2473 1 2.2884 1 2 2 1 3 2 2 2 2.5102 2.7643 2.5678 3.7382 2.2912 2 2.8167 2 2 2 2 2 inculin (Metavinculin) (DBP) itamin D-binding protein S itamin K-dependent protein factor) (S-protein) spreading (Serum itronectin ery long-chain acyl-CoA synthetase homolog 1 (EC 3.6.4.6) ATPase esicle-fusing ProteinV V (Fragment) VH3 protein (Fragment) VH4 heavy chain variable region V V Peptide V V
220 (continued) -1F subunit α AMDICATGPTAC.P Q9H1B6 3 2.5892 2 T -8 subunit .RASSIFPILSAI.L.VKVEPSDNGP.L Q8WXS5 1 2.5263 2 Q99986 1 2.4935 2 -4 subunit γ R.SIAQYWLGCPAPGHL.-R.FEDGVLDPDYPR.NR.DWHGVPGQVDAAMAGR.IV K.HKTVAVASAQR.SD.GAVEDYEPVFEK.YK.VIVIPVGIGPHANLK.QE.RARGTGASMAVAAR.SA.VFPGLPTSAELFILPPK.N P04004 P04004V P04004R.KNKIYSINPK.K 1 1I.DRPGMLCSFRIPGA.W 11 O60840M.KSRYTTEFHELEKIGSGEF.G 3.2347 3.2158 Q8IZS9 2.9316I.FAITSAGVTHSVARSCSEGSI.E P04275 2 2 C.HCALPGENQTVQPMATPA.A Q8WY21 1 2 Q9UPU3 1E.RLKQIKIPDIQILNEKV.C 1 2.2868I.YPKPKPPYYPQPENPDSG.G 1 2.4891 1L.IEEAAKMKKI.K 2.4553 2 2.4231 2 A.IASSHDVQELDVSGILATQVYT.W P30291 Q8WV16 2 Q8WWQ0 2.4664W. P04628 2 2 O75851K.QNSKMIFGVRMYE.D 1 1 1 1 2.2513 Q9Y6U6 2.2799 1 3.3044 P55808 2.3768 2 Q9Y485 2 2 2.5051 1 2 1 2 Q8NFD2 2 2.6856 2.4266 2 2.4652 1 Q9Y2K1 2 2 2.2001 2 2 3.1442 2 δ (2) α ltage-dependent L-type calcium channel ee1-like protein kinase (EC 2.7.1.112) (WEE1hu) kinase (EC 2.7.1.112) ee1-like protein oltage-dependent calcium channel oltage-gated calcium channel factor (vWF) on Willebrand V Vo V V SorCS1 VPS10 domain-containing receptor SorCS3 VPS10 domain-containing receptor VRK1 (Fragment) protein domain 11 WD repeat 21 protein WD-repeat W protein Wnt-1 proto-oncogene (Fragment) WUGSC:H_DJ0751H13.1 protein (Fragment) WUGSC:H_RG015P03.1 protein PBDX) (Protein XG glycoprotein X-kinase X-like 1 protein Xylosyltransferase I (EC 2.4.2.26) (Fragment) 1 Zinc finger and BTB domain containing protein
221 e State d Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table .YDAPSSYSLQQ.A Q9ULC8 1.QDCVSGVDSPTMVSEEVL.V 2.5384 2 Q9Y462 1 3.4986 2 .QDVMLENFRNLLSVGHHPFKHDV.F Q14588 1 3.9568 3 .NRSAILIKHK.R O43345 1 2.4712 2 D.PPSVVVTSHQAPGEK.KK.AREDIFMETLK.DE.RPEGETGDLGKR.E P25311 P25311 7 Q9Y4I0 1 3.8944 1 3 3.8465 2.4184 2 1 V S.ILTAGMQEQESSGPQELET.VK.LYKCEECGKAFNSSSNL.TF E.DIMKVSL.LY S.DGENKTKIGKPASEE.GR.RSPLTRHQR.I O95625N.DQLIPFIDAVLK.D Q03924A.LVDGLRREPGG.P 1M.VYMAVKDSSQEEDDI.SV 1 3.9003K.VPHGPGDFDAP.G 3 2.506A.GQVAVLPEVQVT.Q Q14591 Q9UJU3 2 1 1 Q14592 O94822 2.2496 Q9Y462 P28698 2.2314 1 1 1 1 1 1 P10071 2.2283 2.4703 Q03164 2.5665 2 2.5421 2 1 2 2 1 2.486 2.7056 2 2 -2-glycoprotein) -2-glycoprotein) α -2-glycoprotein (Zn- -2-glycoprotein α Zinc-finger helicase Protein 8 Zinc finger DHHC domain containing protein Zinc finger protein HPF9) (Fragment) (Zinc finger protein 117 Zinc finger protein 208 Zinc finger protein 228 Zinc finger protein HZF4) (Fragment) 234 (Zinc finger protein Zinc finger protein HZF7) 271 (Zinc finger protein Zinc finger protein HZF8) (Fragment) 272 (Zinc finger protein Zinc finger protein Peptide 294 Zinc finger protein 42 (Myeloid zinc finger 1) (MZF-1) Zinc finger protein 6 Zinc finger protein GLI3 Zinc finger protein protein) HRX (ALL-1) (Trithorax-like Zinc finger protein Zinc-
222 (continued) .AMGMVGSGTNNAR.L Q13200 1 2.4579 2 I.EHCSNFKEENMDT.SD.REQLLQR.AG.EQVELKEEAEAPVEDGSQPPPPEPKGDA.TM.DQIFTEVEMTTLEKVI.NK.QPVENQE.KE.EPFVFEKILMPEL.AN.FQTLDVAMQLNAGVF.E Q9Y4L1D.IQENDEEAVQVKE.QF O00156 1C.DLLMEIEQVDMLEKDID.EL.SSEGLARCRKAGFDGA.V Q9Y4L1 2.4267 1 Q04917K.YAEVLRYVDSSKAVIE.T 2 K.GLQLYQSNQTEKALQV.W 1 2.5284G.LNMEYCR.G 1 Q01970 Q00722 Q13018 1 K.KDNLIPCKEAGLK.F 2.7068 2.4934 O00231R.TSTIGKKSVQTISNEQ.R 1 2 2 Q13200 4L.GGCWVIPTFISF.L 2 Q9BQ50K.VRGVDVVVGGHSNTFLY.T 1 2.4052 3.3143 2.4235D.PLKMDEVYKVILPNFL.A 3 Q08752 2 2 Q13702E.FNAEVHRKHIMGQN.V 1 1 4.1121 3.9041 2 1 2.6104 1 3 Q00013 2 2.5893 O43422 P41595 2.7615 2 P21589 2 1 Q13639 1 P21589 1 2.7915 P46777 1 2.6228 2.6535 1 1 2 2 2.4808 2 1 2.5467 2.4639 2 2 3.3221 2 2 ZYG homologue AS1) eta (Protein 14-3-3 protein (Orp150) protein 150 kDa oxygen-regulated 180 kDa transmembrane PLA2 receptor 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase subunit 11 regulatory non-ATPase 26S proteasome subunit 2 regulatory non-ATPase 26S proteasome 3’-5’ exonuclease TREX2-like protein cis-trans isomerase (EC 5.2.1.8) 40 kDa peptidyl-prolyl of the synapse (RAPSYN) protein 43 kDa receptor-associated kinase of the inhibitor protein 52 kDa repressor (p55) membrane protein 55 kDa erythrocyte (5-HT-2B) 2B receptor 5-hydroxytryptamine receptor) (Serotonin (5-HT-4) 4 receptor 5-hydroxytryptamine 5’-nucleotidase (EC 3.1.3.5) (Ecto-5’-nucleotidase) L5 60S ribosomal protein
223 e State d C terminal to
Xcorr c Count b Swiss-ProtAccession Peptide Charge (continued) a Supplementary Table 1 Supplementary Table .VVDIVTGHARL.S Q9UBM7 4 2.9046 2 R.QTATQLLK.LP P11518 1 2.2646 2 SEQUEST cross correlation score. correlation SEQUEST cross Sequences of the peptides identified by tandem MS are bracketed by periods, outside of which are the residues immediately N and the residues bracketed by periods, outside of which are Sequences of the peptides identified by tandem MS are Swiss-Prot protein accession references. protein Swiss-Prot Number of times a peptide was identified in the 140 {__LC-MS/MS analyses. Charge state of the peptide molecular ion chosen for tandem MS. Charge a b c d e Protein 3) L7a (Surfeit locus protein 60S ribosomal protein (EC 1.3.1.21) reductase 7-dehydrocholesterol Peptide the identified peptide.
224 Analysis of the Human Serum Proteome ______225
Acknowledgments of prostate cancer. J Natl Cancer Inst 2002;94: 1576–1578. This project has been funded in whole or in 8. Adkins JN, Varnum SM, Auberry KJ, et al. part with Federal funds from the National Toward a human blood serum proteome: anal- Cancer Institute, National Institutes of Health, ysis by multidimensional separation coupled under Contract No. NO1-CO-12400. By accep- with mass spectrometry. Mol Cell Proteomics tance of this article, the publisher or recipient 2002;1:947–955. 9. Pieper R, Gatlin CL, Makusky AJ, et al. The acknowledges the right of the US Government human serum proteome: Display of nearly to retain a nonexclusive, royalty-free license 3700 chromatographically separated protein and to any copyright covering the article. The spots on two-dimensional electrophoresis gels content of this publication does not necessarily and identification of 325 distinct proteins. Pro- reflect the views or policies of the Department teomics 2003;3:1345–1364. of Health and Human Services, nor does men- 10. Tirumalai RS, Chan KC, Prieto DA, Issaq HJ, Conrads TP, Veenstra TD. Characterization of tion of trade names, commercial products, or the low molecular weight human serum pro- organizations imply endorsement by the US teome. Mol Cell Proteomics 2003;2:1096–1103. Government. 11.Washburn MP, Wolters D, Yates JR. Large- scale analysis of the yeast proteome by multi- References dimensional protein identification technology. 1. Aebersold R, Mann M. Mass spectrometry- Nature Biotechnology 2001;19:242–247. based proteomics. Nature 2003;422:198–207. 12. Grossklaus DJ, Smith JA, Shappell SB, Coffey 2. Anderson NL, Anderson NG. The human CS, Chang SS, Cookson MS. The free/total plasma proteome: history, character, and diag- prostate-specific antigen ratio (%fPSA) is the nostic prospects. Mol Cell Proteomics 2002;1: best predictor of tumor involvement in the rad- 845–867. ical prostatectomy specimen among men with 3. Petricoin EF, Ardekani AM, Hitt BA, et al. Use an elevated PSA. Urol Oncol 2002;7:195–198. of proteomic patterns in serum to identify 13. Janini GM, Conrads TP, Veenstra TD, Issaq HJ. ovarian cancer. Lancet 2002;359:572–577. Development of a two-dimensional protein- 4. Conrads TP, Zhou M, Petricoin EF, 3rd, Liotta peptide separation protocol for comprehen- L, Veenstra TD. Cancer diagnosis using pro- sive proteome measurements. J Chromatogr B teomic patterns. Expert Rev Mol Diagn 2003;3: Analyt Technol Biomed Life Sci 2003;787: 411–420. 43–51. 5. Li J, Zhang Z, Rosenzweig J, Wang YY, 14. Yousef GM, Diamandis EP. The new human Chan DW. Proteomics and bioinformatics tissue kallikrein gene family: structure, func- approaches for identification of serum tion, and association to disease. Endocr Rev biomarkers to detect breast cancer. Clin Chem 2001;22:184–204. 2002;48:1296–1304. 15. Luo LY, Katsaros D, Scorilas A, et al. The serum 6. Adam BL, Qu Y, Davis JW, et al. Serum pro- concentration of human kallikrein 10 represents tein fingerprinting coupled with a pattern- a novel biomarker for ovarian cancer diagnosis matching algorithm distinguishes prostate and prognosis. Cancer Res 2003;63:807–811. cancer from benign prostate hyperplasia and 16. Rumble B, Retallack R, Hilbich C, et al. Amy- healthy men. Cancer Res 2002;62:3609–3614. loid A4 protein and its precursor in Down’s 7. Petricoin EF, 3rd, Ornstein DK, Paweletz CP, syndrome and Alzheimer’s disease. N Engl J et al. Serum proteomic patterns for detection Med 1989;320:1446–1452.
Volume 1, 2004 ______Clinical Proteomics