Supplemental Figures 1 (PDF)

Supplemental Figure 1 A Peptide length Run 1 Run 2A Run 2B Total number Unique number Supplemental Figure 1. Information on eluted peptides from Mamu-A2*05:01. (A) Number of peptides found in each 8-mer 40 32 61 133 87 run with a mascot ion score equal or higher than 35. (B) List 9-mer 22 11 26 59 41 of 8-, 9-, and 10-mer eluted natural peptides with a mascot 10-mer 8 12 14 34 22 ion score of 35 or higher for Mamu-A2*05:01 for the 3 runs. B Protein name Protein accession number Peptide sequence Mascot ion score Length Run 1 KIAA0415 gene product IPI00465123,IPI00807569,IPI00872712 TRIPVEQF 55,3 8 Transforming protein RhoA IPI00478231 NRIGAFGY 54,2 8 Isoform A of Proline/serine-rich coiled-coil protein 1 IPI00027963,IPI00448173,IPI00828052 QRLNLPVm 48 8 Isoform 2 of Protein FAM60A IPI00607866,IPI00639887,IPI01014821 NRTPVFSF 47,7 8 Isoform 2 of U5 small nuclear ribonucleoprotein 200 kDa helicase IPI00168235,IPI00420014,IPI01018841 ARSLQYEY 47,5 8 triosephosphate isomerase isoform 2 IPI00465028,IPI00797270,IPI01013543 VDIINAKQ 46,6 8 TH1-like (Drosophila), isoform CRA_b IPI00164949,IPI00759539 IRFPVVAm 45,9 8 Uncharacterized protein IPI00005416,IPI00029019,IPI00181306,IPI00514856,IPI00646016,IPI00946257,IPI00977741 TRFPLDYY 45,9 8 Baculoviral IAP repeat-containing protein 6 IPI00939720 QSPSANVL 44,7 8 Dual specifcity protein kinase TTK IPI00151170,IPI00640529 GRVPVNLL 43,8 8 Isoform 1 of Cell division cycle and apoptosis regulator protein 1 IPI00217357,IPI00939119,IPI01009531,IPI01011002 LNKVVLRE 43,3 8 Isoform 3 of Tyrosine-protein phosphatase non-receptor type 13 IPI00006714,IPI00030246,IPI00337648,IPI01015899 SVASLNRS 43 8 Isoform 1 of Telomere-associated protein RIF1 IPI00293845,IPI00375454,IPI00964181 QRFPVATm 42,4 8 Isoform Long of E3 ubiquitin-protein ligase SMURF1 IPI00217054,IPI00219332,IPI00979334 TRVPLQGF 41,7 8 Isoform 1 of Krueppel-like factor 3 IPI00027726,IPI00607675 SHLQQPLm 40,6 8 Angiotensinogen IPI00032220,IPI00908365 DRVYIHPF 40,3 8 Thrombomodulin IPI00010737,IPI00902498 AEATVPSE 40,1 8 Isoform 2 of DNA replication licensing factor MCM7 IPI00219740,IPI00299904,IPI00925989,IPI01009615 VRSPQNQY 40,1 8 Isoform 1 of Heterogeneous nuclear ribonucleoprotein K IPI00216049,IPI00216746,IPI00514561,IPI00640296,IPI00807545,IPI00910458,IPI01015770 RYDGmVGF 39,6 8 G2 and S phase-expressed protein 1 IPI00160901,IPI00871779 SRPLIDLm 39,1 8 Olfactory receptor 6A2 IPI00029412 DHGQLISF 39 8 Uroporphyrinogen decarboxylase IPI00301489,IPI00514662,IPI00514944,IPI00885017,IPI00909873 GRVPLIGF 38,8 8 Protein S100-A9 IPI00027462 NQGEFKEL 38,4 8 Actin-related protein 2/3 complex subunit 3 IPI00005162,IPI00911088 mRAYLQQL 38,2 8 Isoform 1 of Rho GTPase-activating protein 35 IPI00334715,IPI00718985,IPI01015086 VRLPVNSF 38,2 8 Isoform LAMP-2A of Lysosome-associated membrane glycoprotein 2 IPI00009030,IPI00216172,IPI00739827,IPI00922445,IPI00980890 IRIPLNDL 38 8 Keratin, type II cytoskeletal 8 IPI00554648,IPI01021414,IPI01021596,IPI01021753,IPI01022187,IPI01022329,IPI01022891,IPI01023071 SRISSSSF 37,4 8 L-xylulose reductase IPI00448095,IPI00797249 NRIPLGKF 37,1 8 Uncharacterized protein IPI00053288,IPI00171127,IPI00238081,IPI00552603,IPI01013830 SRLPVDYY 37 8 Isoform 1 of Disintegrin and metalloproteinase domain-containing protein 9 IPI00440932 NRFAVPTY 36,8 8 Hydroxymethylglutaryl-CoA synthase, cytoplasmic IPI00008475,IPI00963899 ARmLLNDF 36,3 8 Probable phospholipid-transporting ATPase IF IPI00240793,IPI00789084,IPI00908989 NRFPQNGL 36,1 8 Melanoma antigen preferentially expressed in tumors IPI00019282,IPI00893980,IPI00894164,IPI00894404,IPI01010791 NRASLYSF 36 8 Inactive hydroxysteroid dehydrogenase-like protein 1 IPI00171459,IPI00909286 SRALQYEY 36 8 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit IPI00152377 TRNILDDF 35,8 8 STT3B Keratin, type I cytoskeletal 10 IPI00009865 FNEKSKEL 35,7 8 Fatty acid synthase IPI00026781 SRLSIPTY 35,6 8 MIT domain-containing protein 1 IPI00103065,IPI00916058,IPI00916171,IPI00917485,IPI00917655 SRYPQALV 35,3 8 Acyl-CoA desaturase IPI00299468,IPI00646334 ARLPLRLF 35,2 8 Isoform 1 of RNA-binding protein 4 IPI00003704,IPI00719549,IPI00974578 ARNSLYDm 35 8 cDNA FLJ54957, highly similar to Transketolase IPI00643920,IPI00940673,IPI00942979,IPI00946864 IRmPSLPSY 49,4 9 Keratin, type I cytoskeletal 9 IPI00019359 GLGSGGSIR 47,4 9 Isoform 1 of Heterogeneous nuclear ribonucleoprotein K IPI00216049,IPI00216746,IPI00514561,IPI00640296,IPI00807545,IPI00910458,IPI01015770 DRYDGMVGF 46,2 9 Tetraspanin-13 IPI00000735 RFVGGIGLF 45,1 9 Isoform 1 of Ataxin-2-like protein IPI00456359,IPI00456361,IPI00456363,IPI00456365,IPI00456367,IPI00456369,IPI00883782 AHYPSQPVF 44,7 9 Isoform 1 of Filamin-C IPI00178352,IPI00302592,IPI00333541,IPI00413958,IPI00552416,IPI00552858,IPI00644576,IPI00657767,IPI00910863 HVPGSPFQF 43,3 9 Golgi SNAP receptor complex member 1 IPI00029447,IPI00477701,IPI00479817 NRFPAVNSL 42,4 9 Similar to Condensin-2 complex subunit H2 IPI00644022,IPI00745556,IPI00853120,IPI00889043 SRFPQLNEW 42,1 9 Isoform 1 of Fanconi anemia group I protein IPI00019447,IPI00306518,IPI00784704,IPI00884225,IPI01011483 ELLPIILTA 42 9 Heterogeneous nuclear ribonucleoprotein U-like protein 2 IPI00456887,IPI00929107 DRYGGQPLF 41,5 9 Putative heat shock protein HSP 90-alpha A2 IPI00031523,IPI00382470,IPI00414676,IPI00455599,IPI00604607,IPI00784295 YIDQEELNK 41,5 9 Isoform Long of ATP-binding cassette sub-family B member 8, mitochondrial IPI00019022,IPI00383931,IPI00443945,IPI00719730,IPI00945897,IPI00946428,IPI00946804,IPI00946831,IPI01011632 ELGRGIALF 41,4 9 Zinc fnger protein 148 IPI00010833,IPI00448928 SRAGIATQF 41,4 9 Uncharacterized protein IPI00005416,IPI00029019,IPI00181306,IPI00514856,IPI00646016,IPI00946257,IPI00977741 TRFPLDYYS 40,7 9 Isoform 1 of MAP kinase-activating death domain protein IPI00103536,IPI00107843,IPI00107844,IPI00237706,IPI00292094,IPI00292095,IPI00788877,IPI00914569,IPI00914603,I- SHYPFFSTF 39,7 9 PI01011225,IPI01012296 Isoform 1 of Zinc fnger protein Gf-1b IPI00003110,IPI00479652 RYSPGmDAY 38,3 9 Isoform 2 of Zinc fnger CCCH-type antiviral protein 1 IPI00332936,IPI00410067,IPI00410069 GGRmALDAL 38,2 9 Isoform 1 of NudC domain-containing protein 1 IPI00797537,IPI00974288 LDAAVAEVK 38,1 9 Isoform 1 of Ataxin-2-like protein IPI00456359,IPI00456361,IPI00456363,IPI00456365,IPI00456367,IPI00456369,IPI00883782 QQFPGQPAm 37,7 9 HLA class I histocompatibility antigen, A-1 alpha chain IPI00026569,IPI00384279,IPI00471951,IPI00472013,IPI00472035,IPI00472112,IPI00472222,IPI00472448,IPI00472825,I- VmAPRTLLL 35,9 9 PI00472855,IPI00472903,IPI00472921,IPI00644748,IPI00646225,IPI00647457,IPI00647634,IPI00651697,IPI00743716,I- PI00744964,IPI00745649,IPI00749025,IPI00790450,IPI00794678,IPI00795906,IPI00796489,IPI00797121,IPI00847335,I- PI00885217,IPI00889629,IPI00892768,IPI00892834,IPI00892868,IPI00893004,IPI00893023,IPI00893133,IPI00893894,I- PI00894106,IPI00922944,IPI00942050,IPI00970871,IPI00976792,IPI00980405,IPI00981135,IPI00981298,IPI00982121,I- PI01010897,IPI01011050,IPI01014600,IPI01020664,IPI01022401,IPI01024754 cDNA FLJ52551, highly similar to Beta-soluble NSF attachment protein IPI00908301,IPI00942239 VKASHSFLR 35,8 9 Isoform R-type of Pyruvate kinase isozymes R/L IPI00027165,IPI00743713,IPI00909829,IPI00941093 QVENGGVLG 35,2 9 Isoform 1 of Filamin-C IPI00178352,IPI00302592,IPI00333541,IPI00413958,IPI00552416,IPI00552858,IPI00644576,IPI00657767,IPI00910863 QHVPGSPFQF 46,8 10 Nuclear pore complex protein Nup107 IPI00028005,IPI00448974,IPI01011062 SRATPGLQKF 46,4 10 Putative uncharacterized protein DKFZp686N02209 IPI00384938,IPI00399007,IPI00418153,IPI00423463,IPI00423464,IPI00423466,IPI00426051,IPI00645363,IPI00784817,I- TQKSLSLSPG 39,6 10 PI00784842,IPI00816314,IPI00876888,IPI00892671,IPI00930072,IPI00930124,IPI00973474,IPI00973588 Salivary acidic proline-rich phosphoprotein 1/2 IPI00299078,IPI00377025,IPI00847261 GPPPQGGRPQ 38 10 Isoform 1 of ADP-ribosylation factor GTPase-activating protein 1 IPI00175169,IPI00217354,IPI00922590,IPI00973726,IPI01014630,IPI01023007 TRKSPSSDSW 37,7 10 Isoform 2 of Ficolin-2 IPI00025052,IPI00871650 PGPPGKAGPP 36,8 10 Moesin IPI00219365,IPI00922115 AQmVQEDLEK 35 10 Keratin, type II cytoskeletal 1 IPI00220327 SmDNNRSLDL 35 10 Run 2A Isoform 1 of Delta(14)-sterol reductase IPI00019018,IPI00334970,IPI00980101,IPI00982040,IPI00984558 LRYPINGF 47,1 8 Isoform 1 of Actin-related protein 3B IPI00007068,IPI00028091,IPI00554433,IPI00916399,IPI00916540 TGYTKLGY 45,8 8 KIAA0415 gene product IPI00465123,IPI00807569,IPI00872712 TRIPVEQF 45,7 8 Isoform 1 of Dynamin-2 IPI00033022,IPI00181352,IPI00218889,IPI00221332,IPI00413140,IPI00444873,IPI00480085,IPI00514550,IPI00641436,I- IRNLVDSY 45,2 8 PI00657691,IPI00816287,IPI00887273,IPI00888758,IPI00895844,IPI00977141,IPI00980135,IPI00980612,IPI01011821,IPI01015103 Isoform 2 of Protein FAM60A IPI00607866,IPI00639887,IPI01014821 NRTPVFSF 45,2 8 Desmin IPI00465084 YRHQIQSY 44 8 Isoform 2 of U5 small nuclear ribonucleoprotein 200 kDa helicase IPI00168235,IPI00420014,IPI01018841 ARSLQYEY 43,3 8 MIT domain-containing protein 1 IPI00103065,IPI00916058,IPI00916171,IPI00917485,IPI00917655 SRYPQALV 42,4 8 Isoform 1 of Telomere-associated protein RIF1 IPI00293845,IPI00375454,IPI00964181 QRFPVATm 42,1 8 Uncharacterized protein IPI00022434,IPI00745872,IPI00966829 FQNALLVR 41,2 8 Dual specifcity protein kinase TTK IPI00151170,IPI00640529 GRVPVNLL 40,9 8 Isoform 2 of Probable ubiquitin carboxyl-terminal hydrolase FAF-X IPI00003964,IPI00221012 GRHLQQYF 40,6 8 Isoform 4 of E3 ubiquitin-protein ligase NEDD4-like IPI00023287,IPI00163321,IPI00166830,IPI00304945,IPI00384495,IPI00640924,IPI00643856,IPI00644256,IPI00645053,I- SRVPmNGF 40,4 8 PI00940829,IPI00941170,IPI00945379,IPI00964065,IPI00969091 Transforming protein RhoA IPI00478231 NRIGAFGY 39,1 8 Uncharacterized protein IPI00022434,IPI00745872,IPI00966829 DDNPNLPR 39 8 Probable phospholipid-transporting ATPase IF IPI00240793,IPI00789084,IPI00908989 NRFPQNGL 38,8 8 Uncharacterized protein IPI00178959 ARLPQELL 38,2 8 Isoform 1 of Krueppel-like factor 3 IPI00027726,IPI00607675 SHLQQPLm 38,2 8 Hemoglobin subunit zeta IPI00217473 SVLTEKYR 37,6 8 Protein name Protein accession number Peptide sequence Mascot ion score Length Run 2A L-xylulose reductase IPI00448095,IPI00797249 NRIPLGKF 37,4 8 cont. TH1-like (Drosophila), isoform CRA_b IPI00164949,IPI00759539 IRFPVVAm 37,3 8 Isoform 1 of Probable histone-lysine N-methyltransferase ASH1L IPI00020546,IPI00642422 SRTPLLSm 37,3 8 UPF0556 protein C19orf10 IPI00056357 VALRPAEA 36,9 8 Melanoma antigen preferentially expressed in tumors IPI00019282,IPI00893980,IPI00894164,IPI00894404,IPI01010791 NRASLYSF 36,5 8 Hydroxymethylglutaryl-CoA synthase, cytoplasmic IPI00008475,IPI00963899 ARMLLNDF 36,3 8 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-2 IPI00003348,IPI00012451,IPI00026268,IPI00642117,IPI00924758,IPI00925530 GRLLLAGY 35,7 8 Isoform 2 of F-box only protein 21 IPI00025647,IPI00069507,IPI00216812,IPI00794860,IPI01021707 SRHPSLAF 35,6 8 Keratin, type II cytoskeletal 8 IPI00554648,IPI01021414,IPI01021596,IPI01021753,IPI01022187,IPI01022329,IPI01022891,IPI01023071 SRISSSSF 35,5 8 Tetratricopeptide repeat protein 37 IPI00005634,IPI00965004,IPI00965347 YRHFIQSL 35,5 8 Isoform 1 of Casein kinase I isoform alpha IPI00183400,IPI00448798,IPI00965679,IPI00966927,IPI00976381 ARHPQLLY 35,2 8 Isoform 1 of Heterogeneous nuclear ribonucleoprotein K IPI00216049,IPI00216746,IPI00514561,IPI00640296,IPI00807545,IPI00910458,IPI01015770 RYDGMVGF 35,2 8 ADP-ribosylation factor GTPase-activating protein 2 IPI00297322,IPI00937554,IPI00941529,IPI00976984 SRSQLDLF 35 8 Isoform 1 of Heterogeneous nuclear ribonucleoprotein K IPI00216049,IPI00216746,IPI00514561,IPI00640296,IPI00807545,IPI00910458,IPI01015770 DRYDGMVGF 41,6 9 Hemoglobin subunit epsilon IPI00217471,IPI00220706,IPI00554676,IPI00657911,IPI00744503,IPI00749035,IPI00939160,IPI00939544 HVDPENFKL 43,8 9 cDNA FLJ54957, highly similar to Transketolase IPI00643920,IPI00940673,IPI00942979,IPI00946864 IRmPSLPSY 43 9 PRELI domain-containing protein 1, mitochondrial IPI00001638,IPI00157883,IPI00965823,IPI00967050,IPI00967292 IVDPQNQTm 38,5 9 Golgi SNAP receptor complex member 1 IPI00029447,IPI00477701,IPI00479817 NRFPAVNSL 35,9 9 Tetraspanin-13 IPI00000735 RFVGGIGLF 40,5 9 Isoform 1 of Ephrin type-A receptor 3 IPI00298105,IPI00418427 RNPGSLKII 38,4 9 40S ribosomal protein S4, X isoform IPI00217030,IPI00646114,IPI01024803 SIDKTGENF 35,2 9 Similar to Condensin-2 complex subunit H2 IPI00644022,IPI00745556,IPI00853120,IPI00889043 SRFPQLNEW 48,4 9 Isoform 1 of DNA polymerase theta IPI00794779,IPI00873495,IPI01012356 SRYTGINQF 44,8 9 Isoform 3 of Bromodomain-containing protein 8 IPI00016570,IPI00019226,IPI00148057,IPI00828194,IPI00878385,IPI00878545,IPI00879787,IPI01013224 VGDPHTVTV 42,3 9 26S proteasome non-ATPase regulatory subunit 14 IPI00024821 AAMLDTVVFK 51,2 10 Actin, cytoplasmic 1 IPI00021439,IPI00021440,IPI01015522 AGFAGDDAPR 56,2 10 T-complex protein 1 subunit zeta IPI00027626,IPI00552590,IPI01013273,IPI01013629 GRAQLGVQAF 43,3 10 Ubiquitin-60S ribosomal protein L40 IPI00456429 IIEPSLRQLA 41,9 10 Histone H3.2 IPI00171611,IPI00216402,IPI00219038,IPI00419884,IPI00465070,IPI00784001,IPI00909530 ImPKDIQLAR 42,5 10 Isoform 1 of Zinc fnger protein Gf-1b IPI00003110,IPI00479652 LRYSPGmDAY 35,8 10 Uncharacterized protein IPI00022434,IPI00745872,IPI00966829 LVNEVTEFAK 43,7 10 Isoform 1 of Filamin-C IPI00178352,IPI00413958 NHIPGSPLQF 40,3 10 Eukaryotic translation initiation factor 3 subunit G IPI00290460 NVEWAKPSTN 47,7 10 Heat shock protein HSP 90-beta IPI00414676,IPI00555614 SNASDALDKI 66,9 10 Nuclear pore complex protein Nup107 IPI00028005,IPI00448974,IPI01011062 SRATPGLQKF 38,9 10 Isoform 1 of Transcription factor Sp3 IPI00025807,IPI00555936,IPI00852622,IPI00852778,IPI00853503,IPI01014738 VTVSGNETmE 38 10 Run 2B Transcription elongation factor B polypeptide 1 IPI00300341,IPI00791185 MAANFLDc 68,5 8 CAD protein IPI00301263,IPI00893035,IPI00893143 LATVLGRF 52,9 8 Desmin IPI00465084 YRHQIQSY 51,2 8 Uncharacterized protein IPI00178959 ARLPQELL 46,7 8 Hemoglobin subunit beta IPI00654755 VHLTPEEK 46,5 8 Isoform 1 of Probable histone-lysine N-methyltransferase ASH1L IPI00020546,IPI00642422 SRTPLLSm 46 8 KIAA0415 gene product IPI00465123,IPI00807569,IPI00872712 TRIPVEQF 46 8 RNA-binding protein 4B IPI00027838,IPI00978512 TRNSLYDm 45,3 8 Isoform 2 of Protein FAM60A IPI00607866,IPI00639887,IPI01014821 NRTPVFSF 45,1 8 Uncharacterized protein IPI00022434,IPI00745872,IPI00966829 FQNALLVR 44,9 8 Alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase-like IPI00100033 ILNHPANL 43,8 8 protein LOC641515 26S proteasome non-ATPase regulatory subunit 10 IPI00003565,IPI00027699,IPI00183104,IPI00552190,IPI00647839 NRHEIAVm 43,5 8 UPF0556 protein C19orf10 IPI00056357 VALRPAEA 42,8 8 Isoform 2 of Uncharacterized protein C1orf131 IPI00470641,IPI00513772,IPI00641845,IPI00646945,IPI00845227 HRFGITGY 42,7 8 MIT domain-containing protein 1 IPI00103065,IPI00916058,IPI00916171,IPI00917485,IPI00917655 SRYPQALV 42,2 8 Isoform 1 of Actin-related protein 3B IPI00007068,IPI00028091,IPI00554433,IPI00916399,IPI00916540 TGYTKLGY 42,1 8 TH1-like (Drosophila), isoform CRA_b IPI00164949,IPI00759539 IRFPVVAm 41,8 8 Eukaryotic translation initiation factor 3 subunit A IPI00029012,IPI01014951 IRNQLTAm 41,4 8 Dual specifcity protein kinase TTK IPI00151170,IPI00640529 GRVPVNLL 41,3 8 Keratin, type II cytoskeletal 8 IPI00554648,IPI01021414,IPI01021596,IPI01021753,IPI01022187,IPI01022329,IPI01022891,IPI01023071 SRISSSSF 41 8 Isoform Long of E3 ubiquitin-protein ligase SMURF1 IPI00217054,IPI00219332,IPI00979334 TRVPLQGF 41 8 Isoform 5 of Kin of IRRE-like protein 2 IPI00063735,IPI00395833,IPI00439945 GMVPPCRL 40,7 8 Uncharacterized protein IPI00053288,IPI00171127,IPI00238081,IPI00552603,IPI01013830 SRLPVDYY 40,5 8 Isoform 3 of Lactadherin IPI00334005,IPI00966900 ALLcAPSL 40 8 Transforming protein RhoA IPI00478231 NRIGAFGY 39,8 8 Uncharacterized protein IPI00022434,IPI00745872,IPI00966829 DDNPNLPR 38,9 8 Probable phospholipid-transporting ATPase IF IPI00240793,IPI00789084,IPI00908989 NRFPQNGL 38,7 8 Isoform 1 of Disintegrin and metalloproteinase domain-containing protein 9 IPI00440932 NRFAVPTY 38,6 8 Isoform 1 of Heat shock cognate 71 kDa protein IPI00003865,IPI00037070,IPI00910870,IPI00980651,IPI00981268,IPI00981429,IPI00981943,IPI00983926,IPI01008803 RPKVQVEY 38,5 8 Isoform 1 of RNA-binding protein 4 IPI00003704,IPI00719549,IPI00974578 ARNSLYDm 38,3 8 Isoform 1 of Dynamin-2 IPI00033022,IPI00181352,IPI00218889,IPI00221332,IPI00413140,IPI00444873,IPI00480085,IPI00514550,IPI00641436,I- IRNLVDSY 38,3 8 PI00657691,IPI00816287,IPI00887273,IPI00888758,IPI00895844,IPI00977141,IPI00980135,IPI00980612,IPI01011821,IPI01015103 Isoform 1 of Ankyrin repeat and FYVE domain-containing protein 1 IPI00159899,IPI00375301,IPI00909909,IPI00914539,IPI01019010 NRFQLQLL 38,2 8 Myotubularin-related protein 13 IPI00654703,IPI00719299,IPI00893307 RSFPIASI 38,2 8 Isoform 1 of Krueppel-like factor 3 IPI00027726,IPI00607675 SHLQQPLm 38,1 8 Hemoglobin subunit zeta IPI00217473 SVLTEKYR 38,1 8 Transmembrane protein 59, isoform CRA_e IPI00550038,IPI00643279 NRYPASSL 37,8 8 Isoform 1 of Serine/threonine-protein phosphatase 2A regulatory subunit B’’ IPI00550228,IPI00790787,IPI00827645,IPI01024789,IPI01025029,IPI01026452 GRISImQF 37,5 8 subunit gamma Melanoma antigen preferentially expressed in tumors IPI00019282,IPI00893980,IPI00894164,IPI00894404,IPI01010791 NRASLYSF 37,5 8 Calmodulin IPI00075248,IPI00794543,IPI00916600,IPI00945782 FVQmmTAK 37,4 8 Tripartite motif-containing protein 59 IPI00432462,IPI00945336,IPI00945495,IPI00946083,IPI00946493,IPI00947059,IPI00947483 YRQPLNVY 37,4 8 Isoform 1 of Heterogeneous nuclear ribonucleoprotein K IPI00216049,IPI00216746,IPI00514561,IPI00640296,IPI00807545,IPI00910458,IPI01015770 RYDGMVGF 37,3 8 Isoform 2 of Ubiquitin-associated protein 2-like IPI00029019,IPI00181306,IPI00514856,IPI00646016,IPI00946257 TRFPLDYY 37,2 8 Isoform 4 of E3 ubiquitin-protein ligase NEDD4-like IPI00023287,IPI00163321,IPI00166830,IPI00304945,IPI00384495,IPI00640924,IPI00643856,IPI00644256,IPI00645053,I- SRVPmNGF 37,1 8 PI00940829,IPI00941170,IPI00945379,IPI00964065,IPI00969091 Isoform 2 of F-box only protein 21 IPI00025647,IPI00069507,IPI00216812,IPI00794860,IPI01021707 SRHPSLAF 36,9 8 ADP-ribosylation factor GTPase-activating protein 2 IPI00297322,IPI00937554,IPI00941529,IPI00976984 SRSQLDLF 36,8 8 Isoform 2 of Cytosolic non-specifc dipeptidase IPI00165579,IPI00177728 YEVSQLKD 36,7 8 cDNA FLJ55237, highly similar to Homo sapiens activating signal cointegrator IPI00434390,IPI01013403 QRFTVDSF 36,5 8 1 complex subunit 1 (ASCC1), mRNA Isoform 1 of Dolichol-phosphate mannosyltransferase subunit 3 IPI00004454,IPI00297475,IPI01018998 VGYRVATF 36,5 8 Proteasome maturation protein IPI00006377 LRNIQGLF 36,4 8 Isoform 1 of COP9 signalosome complex subunit 1 IPI00156282,IPI00300386,IPI00414289,IPI00921488 NRALIQYF 36,4 8 Isoform 2 of DNA replication licensing factor MCM7 IPI00219740,IPI00299904,IPI00925989,IPI01009615 VRSPQNQY 36,4 8 E3 ubiquitin-protein ligase SMURF2 IPI00329664 SRVPLQGF 36,1 8 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-2 IPI00003348,IPI00012451,IPI00026268,IPI00642117,IPI00924758,IPI00925530 GRLLLAGY 35,7 8 Nucleolar protein 56 IPI00411937,IPI00642697,IPI00984526 YRQSLHTY 35,7 8 Isoform 1 of Cullin-3 IPI00014312,IPI00382458,IPI00382459 DRFLLESF 35,6 8 Angiotensinogen IPI00032220,IPI00908365 DRVYIHPF 35,6 8 Isoform 2 of Dynactin subunit 2 IPI00220503,IPI00789792,IPI00973457,IPI00973500,IPI01015908,IPI01018647,IPI01021112,IPI01021277,IPI01022555,IPI01026290 SRPEQDKF 35,6 8 Isoform 2 of DDB1- and CUL4-associated factor 5 IPI00382979,IPI00411906,IPI00783277,IPI01024870,IPI01025647 SRLPVFQF 35,5 8 Isoform 1 of Regulator of nonsense transcripts 3B IPI00023409,IPI00074183 YRKFLESY 35,4 8 Isoform 1 of Rho GTPase-activating protein 35 IPI00334715,IPI00718985,IPI01015086 VRLPVNSF 35,2 8 N-alpha-acetyltransferase 10, NatA catalytic subunit IPI00013184,IPI00641919,IPI00791664,IPI00793465,IPI00853145 NRAALHLY 35,1 8 Isoform 1 of Reactive oxygen species modulator 1 IPI00016046 mAIGmGIRc 56,4 9 Transcription elongation factor B polypeptide 1 IPI00300341,IPI00791185 LmAANFLDc 55,9 9 Hemoglobin subunit epsilon IPI00217471,IPI00220706,IPI00554676,IPI00657911,IPI00744503,IPI00749035,IPI00939160,IPI00939544 HVDPENFKL 48 9 Similar to Condensin-2 complex subunit H2 IPI00644022,IPI00745556,IPI00853120,IPI00889043 SRFPQLNEW 47,3 9 26S proteasome non-ATPase regulatory subunit 14 IPI00024821 AmLDTVVFK 47 9 cDNA FLJ54957, highly similar to Transketolase IPI00643920,IPI00940673,IPI00942979,IPI00946864 IRmPSLPSY 46,3 9 Ubiquitin-60S ribosomal protein L40 IPI00456429 IIEPSLRQL 45,2 9 40S ribosomal protein S4, X isoform IPI00217030,IPI00646114,IPI01024803 SIDKTGENF 44,6 9 Protein name Protein accession number Peptide sequence Mascot ion score Length Histone H2B type 2-E IPI00003935,IPI00018534,IPI00020101,IPI00152785,IPI00152906,IPI00220403,IPI00303133,IPI00329665,IPI00419833,IP- TSREIQTAV 44,5 9 I00477495,IPI00515061,IPI00554798,IPI00646240,IPI00794461,IPI00815755,IPI00930174 Actin, cytoplasmic 1 IPI00021439,IPI00021440,IPI01015522 ASLSTFQQm 44,3 9 Tetraspanin-13 IPI00000735 RFVGGIGLF 43,5 9 Isoform 1 of Ephrin type-A receptor 3 IPI00298105,IPI00418427 RNPGSLKII 43,4 9 40S ribosomal protein S23 IPI00218606,IPI00966986,IPI00983798 VGDIPGVRF 40,8 9 TRAF-type zinc fnger domain-containing protein 1 IPI00009146 VIRPPQNLY 40,7 9 Isoform 1 of Filamin-C IPI00178352,IPI00413958 HVPGSPFQF 40,4 9 Heterogeneous nuclear ribonucleoprotein U-like protein 2 IPI00456887,IPI00929107 DRYGGQPLF 40 9 Isoform 2 of Zinc fnger CCCH-type antiviral protein 1 IPI00332936,IPI00410067,IPI00410069 GGRmALDAL 38,3 9 Isoform 1 of Protein phosphatase 1 regulatory subunit 7 IPI00033600,IPI00395771,IPI00759705,IPI00759816,IPI00893379,IPI00893539,IPI00893764,IPI00893774,IPI00893943,IPI00894184 RNIEGVDKL 38,3 9 Isoform 1 of DNA polymerase theta IPI00794779,IPI00873495,IPI01012356 SRYTGINQF 37,4 9 60S ribosomal protein L31 IPI00026302 TTFKNLQTV 37,3 9 Isoform 2 of Chromodomain-helicase-DNA-binding protein 7 IPI00472901,IPI00794880,IPI00954579 THFDHYNQY 36,8 9 Uroporphyrinogen decarboxylase IPI00301489,IPI00514662,IPI00514944,IPI00885017,IPI00909873 AGRVPLIGF 36,4 9 Golgi SNAP receptor complex member 1 IPI00029447,IPI00477701,IPI00479817 NRFPAVNSL 36 9 Isoform 1 of Heterogeneous nuclear ribonucleoprotein K IPI00216049,IPI00216746,IPI00514561,IPI00640296,IPI00807545,IPI00910458,IPI01015770 DRYDGmVGF 35,4 9 Isoform R-type of Pyruvate kinase isozymes R/L IPI00027165,IPI00743713,IPI00909829,IPI00941093 QVENGGVLG 35,1 9 Isoform 2 of Ubiquitin-associated protein 2-like IPI00029019,IPI00181306,IPI00514856,IPI00646016,IPI00946257 TRFPLDYYS 35,1 9 Heat shock protein HSP 90-beta IPI00414676,IPI00455599,IPI00555614 SNASDALDKI 73,9 10 Actin, cytoplasmic 1 IPI00021439,IPI00021440,IPI01015522 AGFAGDDAPR 70,7 10 26S proteasome non-ATPase regulatory subunit 14 IPI00024821 AAMLDTVVFK 66,4 10 HIG1 domain family member 2A IPI00020883 LAVTAmKSRP 50,1 10 T-complex protein 1 subunit zeta IPI00027626,IPI00552590 GRAQLGVQAF 48 10 Eukaryotic translation initiation factor 3 subunit G IPI00290460 NVEWAKPSTN 47,4 10 Isoform 1 of Filamin-C IPI00178352,IPI00413958 QHVPGSPFQF 43,8 10 Uncharacterized protein IPI00022434,IPI00745872,IPI00966829 LVNEVTEFAK 40,9 10 Isoform 1 of Filamin-C IPI00178352,IPI00413958 NHIPGSPLQF 40,5 10 Histone H3.2 IPI00171611,IPI00216402,IPI00219038,IPI00419884,IPI00465070,IPI00784001,IPI00909530 ImPKDIQLAR 40,4 10 Nuclear pore complex protein Nup107 IPI00028005,IPI00448974,IPI01011062 SRATPGLQKF 40,1 10 Ubiquitin-60S ribosomal protein L40 IPI00456429 IIEPSLRQLA 38,8 10 Dynein light chain 1, cytoplasmic IPI00019329,IPI00062037,IPI00902978 QVAILLFKSG 36,2 10 Trypsin-1 IPI00011694,IPI00169276,IPI00945846,IPI00946754,IPI01009918 TLNNDImLIK 35,6 10 Supplemental Figure 2

A P2 PΩ M P Y S V S D I Q Q A C N K L E G R E F D

V M

8-mer H

R L

T Y S W Q I K G F R A D R A F S C

9-mer N I V

M M

G L L K H V Y T W P Y R N Q F

L N

I L

10-mer V I K Q E

M A

R G

H G P B Mamu-B Mamu-A haplotype fr (N=2377) Mamu-A haplotype B*008:01 A1*006:02 A2*05:01 A4*14 4,84 A1*008:01 A2*05:03 A3*13:03/11 20,4 A1*011:01/04 A2*05 2,69 A1*012:01 A2*05:11/19 5,55 A1*016:02 A3*13:06 1,85 A1*019:01 A2*05:29 A4*14 1,18

Supplemental Figure 2. Summary on peptide data and information on the MHC haplotypes of BPRC macaques. (A) Pie charts showing the amino acid preferences at the second residue (p2) and the C-terminus (pΩ) of the eluted 8-, 9-, and 10-mer peptides of Mamu-A2*05:01. The amino acids are depicted by the conventional one-letter code. (B) Overview of the Mamu-A haplotypes found in combination with Mamu-B*008:01 in the Indian rhesus macaques of the BPRC. The frequency (fr) in which the Mamu-A haplotypes are present in the 2377 typed rhesus macaques (N) is provided in the last column. Supplemental Figure 3

Δ A DRYGGCPLF RRDNRRGL (Vif RL8) RRAIRGEQL (Vif RL9) RRHRILDIYL(Nef RL10) 100 100 100 100 IC50 = 0.37 IC50 = 1.06 IC50 = 0.94 IC50 = 1.09 80 Slope = 0.367 80 Slope = 0.26 80 Slope = 0.391 80 Slope = 0.348

60 60 60 60

40 40 40 40

p6-labeling 20 20 20 20

100 100 100 100 Inhibition (%) IC50 = 3.35 IC50 = 0.05 IC50 = 145.49* IC50 = 13.8 80 Slope = 0.474 80 Slope = 0.268 80 Slope = 0.381 80 Slope = 0.528

60 60 60 60

40 40 40 40

p7-labeling 20 20 20 20

0 0 0 0 25 25 25 25 100 100 100 100 6.25 6.25 6.25 6.25 0.0015 0.0061 0.0244 0.0977 0.3906 1.5625 0.0015 0.0061 0.0244 0.0977 0.3906 1.5625 0.0015 0.0061 0.0244 0.0977 0.3906 1.5625 0.0015 0.0061 0.0244 0.0977 0.3906 1.5625 Peptide concentration (µm) B SRYDPSISF Δ 100 100 100 IC50 = 0.06 IC50 = 0.21 100 IC50 = 0.07 IC50 = 0.32* 80 Slope = 1.101 Slope = 0.964 Slope = 1.062 80 Slope = 0.943 80 80 60 60 60 60 40 40 40 40

p6-labeling 20 20 20 20 0 0 0 0 25 25 25 25 100 100 6.25 100 100 6.25 6.25 6.25 0.0015 0.0061 0.0244 0.0977 0.3906 1.5625 0.0015 0.0061 0.0244 0.0977 0.3906 1.5625 0.0015 0.0061 0.0244 0.0977 0.3906 1.5625 0.0015 0.0061 0.0244 0.0977 0.3906 1.5625

100 100 100 100 Inhibition (%) IC50 = 4.12 IC50 = 0.5* IC50 = 0.62* IC50 = 2.98 80 Slope = 0.754 80 Slope = 1.059 80 Slope = 1.154 80 Slope = 1.719

60 60 60 60

40 40 40 40

p7-labeling 20 20 20 20

0 0 0 0 25 25 25 25 100 100 100 100 6.25 6.25 6.25 6.25 0.0015 0.0061 0.0244 0.0977 0.3906 1.5625 0.0015 0.0061 0.0244 0.0977 0.3906 1.5625 0.0015 0.0061 0.0244 0.0977 0.3906 1.5625 0.0015 0.0061 0.0244 0.0977 0.3906 1.5625 Peptide concentration (µm) C ARSLQYEY Δ 100 100 100 100 IC50 = 0.18 IC50 = 98196418.45* IC50 = 5.51* IC50 = 288086.66* 80 Slope = 0.563 80 Slope = 0.073 80 Slope = 0.597 80 Slope = 0.138

60 60 60 60

40 40 40 40

p6-labeling 20 20 20 20

100 100 100 100 Inhibition (%) IC50 = 0.45 IC50 = 1020009.9* IC50 = 10.68* IC50 = 441.1* 80 Slope = 0.503 80 Slope = 0.114 80 Slope = 0.48 80 Slope = 0.239

60 60 60 60

40 40 40 40

p7-labeling 20 20 20 20

Supplemental Figure 3. Individual dose-inhibition curves for the stadardized competitor (SC) peptide and the peptides Vif RL8, Vif RL9, and Nef RL10 tested against the 9-mer indicator peptides labeled at the p6 or p7 position. (A) Mamu-A2*05:01, (B) Mamu-B*008:01, (C) Mamu-A1*002:01. The indicated IC50 values (μM) are derived from the regression curves of four individual experiments. A triangle marks the standardized competitor (SC; peptide similar to the biotin-labeled indicator peptide). An asterisk, near the IC50 values, indicates a binding affinity statistically significantly higher or lower than the SC.