Supplemental Table S3. Annotation of identified proteins. Number of Sequence Accession Number of Theoretical Subcellular Number Locus ID Gene Name Protein Name Identified Coverage Theoretical pI Protein Family NSAF Number Amino Acid MW (Da) Location of TMD Peptides (%) (O08539) Myc box-dependent-interacting protein 1 O08539 BIN1_MOUSE BIN1 (Bridging integrator 1) (Amphiphysin-like protein) 3 10.5 588 64470 5 Nucleus other NONE 5.73E-05 (Amphiphysin II) (SH3-domain-containing protein 9) (O08547) Vesicle-trafficking protein SEC22b (SEC22 O08547 SC22B_MOUSE SEC22B 5 30.4 214 24609 8.5 Cytoplasm other 2 0.000262 vesicle-trafficking protein-like 1) (O08553) Dihydropyrimidinase-related protein 2 (DRP-2) O08553 DPYL2_MOUSE DPYSL2 5 19.4 572 62278 6.4 Cytoplasm enzyme NONE 7.85E-05 (ULIP 2 protein) O08579 EMD_MOUSE EMD (O08579) Emerin 1 5.8 259 29436 5 Nucleus other 1 8.67E-05 (O08583) THO complex subunit 4 (Tho4) (RNA and transcription O08583 THOC4_MOUSE THOC4 export factor-binding protein 1) (REF1-I) (Ally of AML-1 1 9.8 254 26809 11.2 Nucleus NONE 2.21E-05 regulator and LEF-1) (Aly/REF) O08585 CLCA_MOUSE CLTA (O08585) Clathrin light chain A (Lca) 2 4.7 235 25557 4.5 Plasma Membrane other NONE 0.000287 (O08600) Endonuclease G, mitochondrial precursor (EC O08600 NUCG_MOUSE ENDOG 4 23.1 294 32191 9.5 Cytoplasm enzyme NONE 0.000134 3.1.30.-) (Endo G) (O08638) Myosin-11 (Myosin heavy chain, smooth O08638 MYH11_MOUSE MYH11 8 6.6 1972 227026 5.5 Cytoplasm other NONE 3.13E-05 muscle isoform) (SMMHC) (O08648) Mitogen-activated protein kinase kinase O08648 M3K4_MOUSE MAP3K4 kinase 4 (EC 2.7.11.25) (MAPK/ERK kinase kinase 4) 2 1.7 1597 179948 6.5 Cytoplasm kinase NONE 7.03E-06 (MEK kinase 4) (MEKK 4) (O08663) Methionine aminopeptidase 2 (EC 3.4.11.18) O08663 AMPM2_MOUSE METAP2 (MetAP 2) (Peptidase M 2) (Initiation factor 2-associated 2 7.7 478 52922 5.8 Cytoplasm peptidase NONE 3.52E-05 67 kDa glycoprotein) (p67) (p67eIF2) (O08709) Peroxiredoxin-6 (EC 1.11.1.15) (Antioxidant protein 2) (1-Cys peroxiredoxin) (1-Cys PRX) (Acidic O08709 PRDX6_MOUSE PRDX6 calcium-independent phospholipase A2) (EC 3.1.1.-) 14 53.4 223 24739 6 Cytoplasm enzyme NONE 0.00146 (aiPLA2) (Non-selenium glutathione peroxidase) (EC 1.11.1.7) (NSGPx) (O08749) Dihydrolipoyl dehydrogenase, mitochondrial O08749 DLDH_MOUSE DLD precursor (EC 1.8.1.4) (Dihydrolipoamide 22 38.3 509 54212 7.9 Cytoplasm enzyme 1 0.002183 dehydrogenase) (O08756) 3-hydroxyacyl-CoA dehydrogenase type-2 (EC 1.1.1.35) (3-hydroxyacyl-CoA dehydrogenase type II) O08756 HCD2_MOUSE HSD17B10 (Type II HADH) (3-hydroxy-2-methylbutyryl-CoA 5 23.1 260 27287 8.4 Cytoplasm enzyme NONE 0.00082 dehydrogenase) (EC 1.1.1.178) (Endoplasmic reticulum- associated amyloid beta-peptide-binding (O08759) Ubiquitin-protein ligase E3A (EC 6.3.2.-) O08759 UBE3A_MOUSE UBE3A 2 2.7 885 101176 5.1 Nucleus enzyme NONE 1.27E-05 (Oncogenic protein-associated protein E6-AP) TCOF1 (O08784) Treacle protein (Treacher Collins syndrome O08784 TCOF_MOUSE (includes 1 1.3 1320 135001 9.3 Nucleus transporter NONE 8.5E-06 protein homolog) EG:6949) (O08788) Dynactin-1 (150 kDa dynein-associated O08788 DYNA_MOUSE DCTN1 2 3 1281 141727 6 Cytoplasm other NONE 1.31E-05 polypeptide) (DP-150) (DAP-150) (p150-glued) (O08795) Glucosidase 2 subunit beta precursor (Glucosidase II subunit beta) (Protein kinase C O08795 GLU2B_MOUSE PRKCSH 14 23 521 58793 4.5 Cytoplasm enzyme NONE 0.000334 substrate, 60.1 kDa protein, heavy chain) (PKCSH) (80K- H protein) (O08912) Polypeptide N- acetylgalactosaminyltransferase 1 (EC 2.4.1.41) (Protein- UDP acetylgalactosaminyltransferase 1) (UDP- O08912 GALT1_MOUSE GALNT1 1 2.3 559 64255 7.7 Cytoplasm enzyme 1 1E-05 GalNAc:polypeptide N-acetylgalactosaminyltransferase 1) (Polypeptide GalNAc transferase 1) (GalNAc-T1) (pp- GaNTase 1) (O08914) Fatty-acid amide hydrolase (EC 3.1.-.-) O08914 FAAH_MOUSE FAAH 1 3.8 579 63221 7.9 Plasma Membrane enzyme 1 9.69E-06 (Oleamide hydrolase) (Anandamide amidohydrolase) (O08915) AH receptor-interacting protein (AIP) (Aryl- transcription O08915 AIP_MOUSE AIP 2 10 330 37605 6.4 Nucleus NONE 3.4E-05 hydrocarbon receptor-interacting protein) regulator (O08997) Copper transport protein ATOX1 (Metal O08997 ATOX1_MOUSE ATOX1 2 20.6 68 7338 6.5 Cytoplasm transporter NONE 0.000413 transport protein ATX1) 1 (O09043) Napsin-A precursor (EC 3.4.23.-) (Kidney- O09043 NAPSA_MOUSE NAPSA 3 11.2 419 45544 7.5 Extracellular Space peptidase NONE 0.000134 derived aspartic protease-like protein) (KDAP-1) (KAP) (O09044) Synaptosomal-associated protein 23 (SNAP- O09044 SNP23_MOUSE SNAP23 23) (Vesicle-membrane fusion protein SNAP-23) 11 51.4 210 23261 5 Plasma Membrane transporter NONE 0.000802 (Syndet) (O09051) Guanylate cyclase activator 2B precursor O09051 GUC2B_MOUSE GUCA2B 1 15.1 106 11628 6.5 Extracellular Space other 1 5.3E-05 [Contains: Uroguanylin (UGN)] (O09061) Proteasome subunit beta type 1 (EC 3.4.25.1) (Proteasome component C5) (Macropain subunit C5) O09061 PSB1_MOUSE PSMB1 8 35.4 240 26372 7.8 Cytoplasm peptidase NONE 0.000491 (Multicatalytic endopeptidase complex subunit C5) (Proteasome gamma chain) (O09111) NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial precursor (EC O09111 NDUBB_MOUSE NDUFB11 1.6.5.3) (EC 1.6.99.3) (NADH-ubiquinone 9 27.2 151 17444 5.2 Cytoplasm enzyme 2 0.000966 oxidoreductase ESSS subunit) (Complex I-ESSS) (CI- ESSS) (Neuronal protein 15.6) (p15.6) (Np15.6) (O09131) Glutathione transferase omega-1 (EC O09131 GSTO1_MOUSE GSTO1 3 20.4 240 27498 7.4 Cytoplasm enzyme NONE 0.000304 2.5.1.18) (GSTO 1-1) (p28) (O09159) Lysosomal alpha-mannosidase precursor (EC 3.2.1.24) (Mannosidase, alpha B) (Lysosomal acid alpha- O09159 MA2B1_MOUSE MAN2B1 2 2.4 1013 114604 8.1 Cytoplasm enzyme 1 4.43E-05 mannosidase) (Laman) (Mannosidase alpha class 2B member 1) (O09164) Extracellular superoxide dismutase [Cu-Zn] O09164 SODE_MOUSE SOD3 2 14.7 251 27392 6.8 Extracellular Space enzyme 1 8.95E-05 precursor (EC 1.15.1.1) (EC-SOD) O09167 RL21_MOUSE RPL21 (O09167) 60S ribosomal protein L21 4 16.4 159 18431 10.5 Cytoplasm other NONE 0.000494 (O09174) Alpha-methylacyl-CoA racemase (EC O09174 AMACR_MOUSE AMACR 13 38.4 380 41587 7.4 Cytoplasm enzyme NONE 0.001359 5.1.99.4) (2-methylacyl-CoA racemase) (O35099) Mitogen-activated protein kinase kinase MAP3K5 kinase 5 (EC 2.7.11.25) (MAPK/ERK kinase kinase 5) O35099 M3K5_MOUSE (includes 2 2.1 1380 154459 5.7 Cytoplasm kinase NONE 8.13E-06 (MEK kinase 5) (MEKK 5) (Apoptosis signal-regulating EG:4217) kinase 1) (ASK-1) (O35129) Prohibitin-2 (B-cell receptor-associated protein transcription O35129 PHB2_MOUSE PHB2 14 45.8 299 33296 9.8 Cytoplasm NONE 0.002027 BAP37) (Repressor of estrogen receptor activity) regulator (O35134) DNA-directed RNA polymerase I largest O35134 RPA1_MOUSE POLR1A subunit (EC 2.7.7.6) (RNA polymerase I 194 kDa 2 1.3 1717 194109 6.9 Nucleus enzyme NONE 6.54E-06 subunit) (RPA194) (O35166) Golgi SNAP receptor complex member 2 (27 O35166 GOSR2_MOUSE GOSR2 2 5.2 212 24725 8.2 Cytoplasm transporter 1 5.3E-05 kDa Golgi SNARE protein) (Membrin) (O35206) Collagen alpha-1(XV) chain precursor O35206 COFA1_MOUSE COL15A1 2 2.6 1367 140525 4.9 Extracellular Space other 2 8.21E-06 [Contains: Endostatin (Endostatin-XV)] (O35215) D-dopachrome decarboxylase (EC 4.1.1.84) O35215 DOPD_MOUSE DDT 10 64.1 117 12946 6.5 Cytoplasm enzyme NONE 0.002879 (D-dopachrome tautomerase) (O35226) 26S proteasome non-ATPase regulatory O35226 PSD4_MOUSE PSMD4 subunit 4 (26S proteasome regulatory subunit S5A) 3 11.4 376 40704 4.8 Cytoplasm other NONE 8.96E-05 (Rpn10) (Multiubiquitin chain-binding protein) (O35250) Exocyst complex component 7 (Exocyst O35250 EXOC7_MOUSE EXOC7 2 4.7 697 79960 7 Plasma Membrane transporter NONE 1.61E-05 complex component Exo70) (O35295) Transcriptional activator protein Pur-beta transcription O35295 PURB_MOUSE PURB (Purine-rich element-binding protein B) (Vascular actin 6 39.3 323 33770 5.4 Nucleus NONE 0.000278 regulator single-stranded DNA-binding factor 2 p44 component) (O35309) N-myc-interactor (Nmi) (N-myc and STAT transcription O35309 NMI_MOUSE NMI 2 8.3 314 35236 5 Cytoplasm NONE 5.36E-05 interactor) regulator (O35381) Acidic leucine-rich nuclear phosphoprotein 32 family member A (Potent heat-stable protein O35381 AN32A_MOUSE ANP32A phosphatase 2A inhibitor I1PP2A) (Acidic nuclear 2 7.7 247 28538 4.1 Nucleus other NONE 4.55E-05 phosphoprotein pp32) (Leucine-rich acidic nuclear protein) (O35386) Phytanoyl-CoA dioxygenase, peroxisomal precursor (EC 1.14.11.18) (Phytanoyl-CoA alpha- O35386 PAHX_MOUSE PHYH 5 11.8 338 38607 7.5 Cytoplasm enzyme NONE 0.000116 hydroxylase) (PhyH) (Phytanic acid oxidase) (Lupus nephritis-associated peptide 1) (O35387) HS1-associating protein X-1 (HAX-1) (HS1- O35387 HAX1_MOUSE HAX1 5 33.9 280 31654 4.9 Nucleus other NONE 0.000241 binding protein) 2 (O35409) Glutamate carboxypeptidase 2 (EC 3.4.17.21) (Glutamate carboxypeptidase II) (Membrane glutamate O35409 FOLH1_MOUSE FOLH1 carboxypeptidase) (mGCP) (N-acetylated-alpha-linked 13 18.5 752 84635 7.5 Plasma Membrane peptidase 1 0.000299 acidic dipeptidase I) (NAALADase I) (Pteroylpoly- gamma-glutamate carboxypeptidase) (F (O35459) Delta3,5-delta2,4-dienoyl-CoA isomerase, O35459 ECH1_MOUSE ECH1 11 34.9 327 36118 7.7 Cytoplasm enzyme NONE 0.001562 mitochondrial precursor (EC 5.3.3.-) (O35465) 38 kDa FK506-binding protein homolog O35465 FKBP8_MOUSE FKBP8 3 12.7 355 38615 7 Cytoplasm other 1 7.91E-05 (FKBPR38) (FK506-binding protein 8) (muFKBP38) (O35479) Heterogeneous nuclear ribonucleoprotein G O35479 HNRPG_MOUSE RBMXL1 2 7.5 388 42234 10