SUPPLEMENTAL DATA Supplemental Table: MHC Class II (I-Ab) and Class I (H-2kb and H-2Db)-bound self peptides derived from mouse proteome. Only one representative peptide is shown when multiple peptides for the same epitope were identified. MHC Class I: Representative Peptide Source protein Entrez Gene ID ERASFITPVPGGVGP C1-tetrahydrofolate synthase 217676 KKAGYITPVPGGVGP Methylenetetrahydrofolate dehydrogenase 17768 QGGVYASPSIAGSRPG Sphingosine phosphate lyase 1 20397 DDGHGGYKPFQNPVPNQSPSS Interleukin 4 receptor 16190 IIQGLRSGGTSRHPGPL Histocompatibility 2, class II antigen A, alpha 14960 GGDTHFDSAEPWTVQNE Matrix metallopeptidase 14 (membrane-inserted) 17387 VGAGHFRSPHTTEVVG Integrin alpha 4 16401 GDSNFGAPSASVAAAPAP Adaptor protein complex AP-1, beta 1 subunit 11764 EEYEVAEMGAPHGSASVR Interferon induced transmembrane protein 3 66141 YLNEYGAPDAGGLE Glucosamine (N-acetyl)-6-sulfatase 75612 INDYKGAVIVVSHDAR ATP-binding cassette, sub-family F, member 1 224742 APDTRFVAPGALGNAPW Ring finger protein 149 67702 NPGDGAFYGPKIDIQIK Threonyl-tRNA synthetase 110960 DGEEAGAYDGPRTADGIVS Disulfide isomerase associated protein 3 14827 1 SVGAWTGPMGNWAM Myeloid-associated differentiation marker 50918 APVEGASPTSISAVDG Histocompatibility 2, class II, locus DMa 14998 IFYGASIASLSASH Integrin alpha M 16409 VEPYEVHNPVPLIVG Integrin alpha M 16409 GPPPYHESLAGASQPP Scotin 66940 KSLQWFGATVRAHGSS Integrin alpha 5 subunit (fibronectin receptor) 16402 GPVPEFSGATVERVSED Crystallin, lamda 1 68631 APMYYRGAQAAIVVY RAB5C, member RAS oncogene family 19345 APFDWEGAQASQA Peptide-histidine transporter 4 100561 DIYVWRGAQATLSNTT Flightless I homolog 14248 ITQVQWNDPGAQYSLVNK Cadherin 17 12557 ITYSYAGARAPMGQG LDL receptor-related protein 10 65107 APETRSQVTPSVPSEALDD LDL receptor-related protein 10 65107 ITDKFWGPSGAESVIG Glypican-1 14733 GPGLDFEGPDAKLSGPN AHNAK 66395 GPGSAVSPYPSFNVS Annexin A1 16952 DFAGPAIHGSAV Voltage-dependent anion channel protein 2 674496 GPPGFEDYVELPPSVSQAAKSPPG Colony stimulating factor 2 receptor, beta 1 12983 LPNVQVEGPTPNRP Colony stimulating factor 2 receptor, beta 1 12983 LPNSFDGPVTITIVNR CD44 antigen 12505 DEGKLLEAKGPVTDVAYSHDG WD repeat domain 1 22388 EQIYYAGPVNNPGLDVPQ Ly86 protein 17084 FGPYYTEPVIAGLDPK Proteasome subunit, beta type 3 26446 2 LSYIGPSVNKA Niemann Pick type C1 18145 DTIEFRGPNGLLVYQG Cytochrome b-5 reductase, diaphorase 1 109754 NSEFDPPGPNVATTT Eukaryotic translation initiation factor 3 53356 DPAGPNFEYAEAPSRLSPDD Lipoprotein lipase 16956 APTSALGPKASPAPS CCR4-NOT transcription complex, subunit 3 232791 RMAPYQGPDAAPGALD Actinin alpha 4 60595 RGPEITVQPAAQPTEQ Flk-1 16542 DYRSPFIASVSD Flk-1 16542 RDLDWLWPNAQRDSEE Flk-1 16542 HNYEGPETHTSL MHC class II antigen A beta 14961 GRPDAEYWNSQPEILER Histocompatibility 2, class II antigen A, beta 1 14961 LSRFTSGVPSFVLDTE Serine protease inhibitor, Kunitz type 1 20732 VTKADSGVYTLLT CEA-related cell adhesion molecule 9 26368 SSVAFIKPGVNKAEVT CD84 leukocyte antigen 12523 GVDFIGSTVGLAK Disintegrin and metalloprotease domain 8 11501 HVEGYEGSAASIS Disintegrin and metalloprotease domain 8 11501 YTPIPNGLYPS Lectin, galactose binding, soluble 9 16859 FRPAHQAPMAQTTIH Lectin, galactose binding, soluble 9 16859 WSDAAAPFAGLSTDQ Interleukin-four induced protein-1 14204 GIPVYRFVLPANAFA CD36 antigen 12491 AFSNPSAGISVDVK Phospholipase D family, member 4 104759 LPYKSPGINVDS Icos ligand 50723 GIDPYDQPNAIYIER Sortilin-related receptor, LDLR class A repeats 20660 3 GMAFRVPTPNVSVVD Similar to glyceraldehyde-3-phosphate dehydrogenase 545741 DISNYGFPRSVQAID Matrix metalloproteinase 8 17394 VPIYEGYALPHAILR Actin, gamma, cytoplasmic 1 11465 ETFNTPAMYVAIQ Actin, gamma, cytoplasmic 1 11465 LPYDTPVPGYMNNT Liver glycogen phosphorylase 110095 AQRAGYKAAIVHNVDSD Rnf13 protein 24017 TSSYSNPTIGYENR Cyclophilin C-associated protein 19039 LPQDPTFHTPLDLYAYAR Cyclophilin C-associated protein 19039 TNTAYVGSAILSEET Pleckstrin homology domain containing, family B (evectins) member 2 226971 LEDFYGSPIPSVS CD97 antigen 26364 EVQWQSAEPGSTPR Colony stimulating factor 2 receptor alpha chain 12982 RDNMFSGSKINYTE Glucose phosphate isomerase 1 14751 FGTGHSAPSASPAFG Nucleoporin 153 218210 ADDFFQGTKAALAGGT Collapsin response mediator protein 1 12933 DSVTTDHISPAGNIAR Cytoplasmic aconitase 11428 NEKDDLYKDSSGNTSAESS Trans-golgi network protein 2 22135 DGNHTLFHNPHVNPLPT Cytochrome c oxidase polypeptide VIa-liver, mitochondrial precursor 12862 VPWNFHEPQPGQYEF Galactosidase, beta 1 12091 ADNQIYIAGHPAFVN Hnrpl protein 15388 GRFTYQNAAAQPETGPG Tumor necrosis factor receptor superfamily, 21933 4 member 10b GDLSQHATPLPTPAVLPG Target of Myb protein 1 21968 DGDSYRSPWSN Capping protein (actin filament) muscle Z-line, beta isoform 12345 VEYEASAAGLIR Dipeptidylpeptidase III 75221 APAAAATTAAPAAAAAPAK Arbp protein 11837 AEPQAEAPAAAASSEQ Brain abundant, membrane attached signal protein 1 70350 NVLRIINEPTAAAIA Heat shock protein 2 15512 VPPTPQPVAPTPSAAPAGP Dihydrolipoamide S-acetyltransferase (E2 component of pyruvate dehydrogenase complex) 235339 EKPVPAAPVPSPVAPAP Hematological and neurological expressed sequence 1 15374 DARSYTAAVANRAK Myotubularin related protein 4 170749 TSWTYNPAAVSKVAPA Ubiquitin ligase mind bomb 225164 EIQDWSASSPHSA Ubiquitin ligase mind bomb 225164 SQELVRAPTAALSPEPQ Scaffold attachment factor B2 224902 IPPTHYAASRAASVAE Latexin 17035 VELPPSVSQAATSPP Colony stimulating factor 2 receptor, beta 1, low- affinity (granulocyte-macrophage) 12984 REYLWSPSAARLVSSR Neuropilin 2 18187 TNDRYVASLAARNK Interleukin 6 signal transducer 16195 FVAPAVTPVK Acid sphingomyelinase-like phosphodiesterase 3a 57319 5 APISSHTAPRPNPTPA Protein tyrosine phosphatase, non-receptor type 104831 IKVYWDAPSPAPDHIR Stromal cell derived factor receptor 2 635993 EVSSVEAPSVSPAR Low density lipoprotein-related protein 12 239393 EDNVFEAPTLVKV Activated leukocyte cell adhesion molecule CD166 11658 DEATRYLAPTILTDVDPN Aldehyde dehydrogenase family 3, subfamily A2 11671 LDSQYRASAPNSHVP Eosinophil peroxidase 13861 LVFDVTAPNTFKTLD RAB7, member RAS oncogene family 19349 LHLRFSAPQIENEPET Interleukin 10 receptor, beta 16155 SPHPYQLPQALAPHVD Tripeptidyl peptidase I 12751 RPVQFPYVTPAPHEPVK Mahogunin, ring finger 1 17237 RYMAPEVLDDSIN TGF-beta type I receptor 21812 LPPYDDATAVPSTAKEPPPP Lysosomal-associated protein transmembrane 4B 114128 WKALYTDPKSSETAA Serine carboxypeptidase 1 74617 RSYSSPDITQALQEE Ubiquitin specific peptidase 8 84092 IARQNFTEPTAIQAQG DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 13207 ITPSYVAFTPEGER Heat shock 70kD protein 5 (glucose-regulated protein) 14828 DPTPDPNTAYASYPSASVEN Synaptogyrin 2 20973 TVIHFNNPKVQASLAA Basic transcription factor 3 218490 IASFKDPKISTSLPV Lymphocyte cytosolic protein 1 18826 ESPDQWSSSSPHSASDWS Notch2 protein 18129 ESPDQWSSSSPHSNIS Notch 1 protein 18128 6 KPVSQMRMATPLLMRP Ia antigen-associated invariant chain, CD74 antigen 16149 KNLDYVATSIHEAVT Glutamate oxaloacetate transaminase 1, soluble 14718 FPKPPSYNVATTLPSYDE Nedd4 WW domain-binding protein 5 22381 RDYVPPTANLDQKD Staphylococcal nuclease domain containing 1 56463 VQIYHNPTANSFR Vasodilator-stimulated phosphoprotein 22323 IPEAQWQSSLARTSSAE Fatty acid synthase 14104 SARTVITPDPNLSIDQ Polymerase (RNA) II (DNA directed) polypeptide A 20020 INYQPPTVVPGGDL Tubulin, alpha 1 22142 RYNPPIIHQGFQ Small inducible cytokine A6 20305 NPPSYYTQPVPVPN Nedd4 WW domain-binding protein 3 22379 SSEVYTFPVPERHLE Cadherin 1 12550 KPTVTVVSPLPNDSIN Ecotropic viral integration site 2b 216984 FTYQQPQPLSVEPR Similar to Plexin-B2 precursor isoform 21 NONE NVTELNEPLSNEERNL 3-monooxgenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide 22628 IEVSSPITLQAL Apob protein 238055 RSNEFDYPSVGQLA CD18 antigen preprotein 16414 ELDYYDSPSVNAR Actinin, alpha 1 109711 SDLYNWKNNNPSFSEDPG Melanoma antigen 17276 SIVYWMTSQPSDAVR ATP-binding cassette, subfamily G, member 1 11307 YPDSWSTPHSYFS Interleukin 12b 16160 7 NPEKHIYSSITTWETTER Amica1 protein 270152 LETSIRRIADLQ Myosin XVIIIb 74376 GPFPGGVVSPQPHSSY C330002I19Rik protein 77480 RRAVATPAAAAAEEE Solute carrier family 7 (cationic amino acid transporter, y+ system), member 5 20539 RYMAPEVLDETIN Activin A receptor, type 1B 11479 DAGKKASWDAPKVWGLR Similar to melanoma antigen 1403805 VNIEFKDL ATP-binding cassette, subfamily G, member 1 11307 ASYEFVQRL Dynein, cytoplasmic, heavy chain 1 13424 VAVTFSERL Solute carrier family 7 (cationic amino acid transporter, y+ system), member 11 26570 KALINADEL Spectrin alpha 2 isoform 1 NONE YGLKNLTAL Phosphoinositide-3-kinase adaptor protein 1 83490 DGELTYENVQVSPVPGGPPG PREDICTED: similar to B-cell differentiation 669118 antigen CD72 NQLEALVGPEANVGPYG Mannosidase 2, alpha B1 17159 EVLDYSTPTTNGTPE Signal recognition particle receptor 67398 SMGKNPTDEYL Myosin light chain, regulatory B-like 67268 ISGDITLTSANHAMI Galectin 3 16854 TEWEAATPAVAETPDIK Ribosomal protein S5 20103 EPPPAYEPPAPAPAPLPPP Secretory carrier membrane protein 3 24045 LQVYAPEVSPESIM Interferon gamma inducible protein 30 65972 8 MHC Class I: VNMEGLGGKL AHNAK nucleoprotein 66395 RSYSFLNSSL Deoxyribonucleadeoxyribonuclease 1-like 1 69537 SNFNYEQRGAF Clone:6230411L24 product, unknown protein NONE VFYEREVQM Serum/glucocorticoid regulated kinase 242341 VALDFEQEM Serum/glucocorticoid regulated kinase 11461 QSIEFSRL Exportin 1, CRM1 homolog (yeast) 13669 IGVDFTVRSL CD74 antigen (invariant polypeptide of MHC, class II antigen-associated) 19331 KTYQFLNDI Similar to activating signal cointegrator 1 complex subunit 3 isoform a 224823 KSLTYYTNL Solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 4 208795 SQLEFRQNL Tripartite motif protein 12 228071 KSFEWLSQM