Table II.

List of Qa-1b-binding peptides isolated from TAP-positive and TAP-negative tumor cells

Peptide number Peptide sequence Peptide location Protein length UniProtKB or SwissProt number Protein description 
TAP-positive 
1 AMAPRTLLL 3-11 362 P01899 H-2 class I histocompatibility antigen, D-B alpha chain 
2 AQAERTPEL 691-699 1274 A2RT67 DENN domain-containing protein 3 
3 IINTHTLLL 1302-1310 1657 Q80UW7 IQ motif containing GTPase activating protein 1 
4 PKFEVIDKPQS 98-108 108 P97450 ATP synthase-coupling factor 6, mitochondrial 
5 PTEEESPV 486-493 493 P53986 Monocarboxylate transporter 1 
6 QAIPQGAIQ 246-254 461 Q8BG99 Homeobox protein PKNOX2 
7 QLQPQQPLPQPQ 125-136 672 Q9WVH4 Forkhead protein FKHR2 
TAP-negative 
1 AAIENIEHL 1193-1201 1392 Q6PB66 Leucine-rich PPR motif-containing protein, mitochondrial 
2 AALKLGQEL 799-807 1271 Q9JJ28 Protein flightless-1 homologue 
3 AAPTNANSLNSTF 454-466 575 Q8BT14 CCR4-NOT transcription complex subunit 4 
4 AAPTSPDHSPA 699-709 709 Q66L44 Protein Dos 
5 AAVIAHDFL 153-161 292 P30282 G1/S-specific cyclin-D3 
6 AGIENDEAF 44-52 248 B1AWD9 Clathrin light polypeptide 
7 AGPENSSKI 383-346 2075 Q80XK6 Autophagy-related protein 2 homologue B 
8 AGQFNQDYL 45-53 503 Q921F1 Annexin A11 
9 AGVRNPQQHL 515-524 636 Q8BN32 Pabpc1 protein 
10 ASLQNFNISNL 2103-2113 2128 B2RRJ7 Wnk1 protein 
11 KSISNPPGSNL 2115-2125 2128 B2RRJ7 Wnk1 protein 
12 ASQQNSEEM 202-210 210 Q9CXE2 B-cell CLL/lymphoma 7 protein family member A 
13 ASVLNVNHI 2195-2203 2603 Q99NH0 Ankyrin repeat domain-containing protein 17 
14 ASYRAQPSVSL 270-280 573 Q62019 16 kD protein 
15 ATPGRLIDFL 256-265 648 Q5U222 Ddx5 protein 
16 AVSEGTKAVTKYTSAK 111-126 126 Q8CGP1 Histone H2B type 1-K 
17 FAPLPRLPTL 17-26 156 Q9CR21 Acyl carrier protein, mitochondrial 
18 FAPVNVTTEVKSVE 280-293 462 P10126 Elongation factor 1-alpha 1 
19 FAYEGRDYI 137-145 184 Q62143 Qa-2 cell surface antigen 
20 FGPVNHEEL 33-41 147 P46414 Cyclin-dependent kinase inhibitor 1B 
21 FQIVNPHLL 634-642 792 Q6NZB3 Ribonucleoside-diphosphate reductase 
22 FQVTHTVAL 113-121 361 Q9QYA2 Mitochondrial import receptor subunit TOM40 homologue 
23 GGPINPATA 1036-1044 1107 Q80X50 Ubiquitin-associated protein 2-like 
24 GLGVLLAF 5-12 113 Q8QZT4 Crumbs protein homologue 3 
25 HSIQNSQDM 61-69 210 Q91YN9 BAG family molecular chaperone regulator 2 
26 IQKTPQIQVY 21-30 119 P01887 Beta-2-microglobulin 
27 KAPPPLPPLVVF 27-38 499 P16277 Tyrosine-protein kinase BLK 
28 KAPTNEFYA 190-198 198 O35988 Syndecan-4 
29 KCSVSIQVVDVNDNYPEL 328-345 794 Q91XZ8 Protocadherin beta 22 
30 KSAVGHEYV 96-107 486 Q922I8 Hematopoietic cell specific Lyn substrate 1 
31 LAIRNDEEL 93-101 137 Q64426 Histone H2A 
32 LVRPGTALEL 2294-2303 2883 NP_076331 desmoplakin 
33 METLTATPQ 976-984 1241 B2RXW8 Ppfia1 protein 
34 NSIRNLDTI 100-108 475 P28658 Ataxin-10 
35 PADIVKNLK 12-20 341 Q8VDZ8 Calcium binding protein 39 
36 PDTGISSKA 52-60 126 Q8CGP2 Histone H2B type 1-P 
37 PEAFPALA 385-392 392 Q9CY58 Plasminogen activator inhibitor 1 RNA-binding protein 
38 PNKLVELNK 138-146 943 Q6DFV7 Nuclear receptor coactivator 7 
39 PPSAKAAID 97-105 323 Q5SSG6 TATA box binding protein (TBP)-associated factor 
40 PPTAKAAVE 425-433 661 Q5SUS9 Ewing sarcoma breakpoint region 1 
41 PVKAVEIEI 155-163 930 Q7TSZ1 Xeroderma pigmentosum, complementation group C 
42 RSPENPPSKEL 171-181 181 Q9CQA0 Centromere protein M 
43 RSPGNSPTPM 186-195 469 Q8CI61 BAG family molecular chaperone regulator 4 
44 SALINLSSF 7-15 161 Q8VE65 Transcription initiation factor TFIID subunit 12 
45 SAPENAVRM 28-36 126 O35127 Protein C10 
46 SAPSNFEHR 12-20 593 Q8BTW9 Serine/threonine-protein kinase PAK 4 
47 SAPTGSGKTL 227-236 639 Q6P9R1 ATP-dependent RNA helicase DDX51 
48 SAVISLEGKPL 156-166 166 P18760 Cofilin-1 
49 SAVSNNYIQTL 168-178 911 P30999 Catenin delta-1 
50 SHRKFSAPR 2-10 403 Q3U9L3 ribosomal protein L3P family member 
51 SLGINPHVL 966-974 1170 B2RQL0 Nup98 protein 
52 SLGKNPTDAYL 60-70 172 Q3THE2 Myosin regulatory light chain MRLC2 
53 SQPESKVFYL 110-119 245 P63101 Protein kinase C inhibitor protein 1 
54 SSTTNPKLSTL 726-736 959 Q5NBZ5 Eukaryotic translation initiation factor 4E nuclear import factor 1 
55 STIRLLTSL 458-466 545 P80318 T-complex protein 1 subunit gamma 
56 TNPESKVFYL 155-160 284 P68254 14-3-3 protein theta 
57 TQGQNIQHL 431-439 2326 Q80YT7 Myomegalin 
58 VAVTNGPRS 371-379 393 Q9D6J1 LAG1 longevity assurance homologue 4 
59 VPPVQVSPLIKFGRY 2-16 71 Q5EBI8 ATP synthase, H+ transporting, mitochondrial F1F0 complex 
60 VQVSNFKSGKGDSTL 254-268 579 Q80WJ7 Metastasis adhesion protein 
61 VSLLDIDHL 473-481 679 Q8BQM4 HEAT repeat-containing protein 3 
62 VSLLNPPETL 411-420 422 Q8BRG1 Cyclin A2, isoform CRA 
63 VTLVNHGSTF 15-24 640 P59110 SUMO-1 protease 2 
64 YGYSNRVVDLM 316-326 333 P16858 Glyceraldehyde-3-phosphate dehydrogenase 
65 AAPRSGPSV 611-619 641 Q923D5 WW domain-binding protein 11 
66 AAPRSGPSVA 611-620 641 Q923D5 WW domain-binding protein 11 
67 AGIENKFGL 648-656 676 Q9QXX4 Calcium-binding mitochondrial carrier protein Aralar2 
68 AGIENKFGLYL 648-658 676 Q9QXX4 Calcium-binding mitochondrial carrier protein Aralar2 
69 AGIENKFGLYLP 648-659 676 Q9QXX4 Calcium-binding mitochondrial carrier protein Aralar2 
70 TKAVTKYTSSK 117-127 127 A0JNS9 Histone H2B 
71 GTKAVTKYTSSK 116-127 127 A0JNS9 Histone H2B 
72 SEGTKAVTKYTSSK 114-127 127 A0JNS9 Histone H2B 
73 VSEGTKAVTKYTSSK 113-127 127 A0JNS9 Histone H2B 
74 AVSEGTKAVTKYTSSK 112-127 127 A0JNS9 Histone H2B 
75 PEPAKSAPAPK 2-12 126 Q64478 Histone H2B type 1-H 
76 PEPAKSAPAPKKG 2-14 126 Q64478 Histone H2B type 1-H 
77 LGVKNSEPA 59-67 576 Q80UG5 Septin-9 
78 LGVKNSEPAA 59-68 576 Q80UG5 Septin-9 
79 SSPANISSLEFEDA 583-596 773 P51125 Calpastatin 
80 SSPANISSLEFEDAK 583-597 773 P51125 Calpastatin 
81 SSPANISSLEFEDAKLS 583-599 773 P51125 Calpastatin 
82 SSPANISSLEFEDAKLSA 583-600 773 P51125 Calpastatin 
83 KPLFEILNG 1138-1146 1735 Q9IZU3 Endogenous mouse mammary tumor virus Mtv1 
84 KPLFEILNGD 1138-1147 1735 Q9IZU3 Endogenous mouse mammary tumor virus Mtv1 
Peptide number Peptide sequence Peptide location Protein length UniProtKB or SwissProt number Protein description 
TAP-positive 
1 AMAPRTLLL 3-11 362 P01899 H-2 class I histocompatibility antigen, D-B alpha chain 
2 AQAERTPEL 691-699 1274 A2RT67 DENN domain-containing protein 3 
3 IINTHTLLL 1302-1310 1657 Q80UW7 IQ motif containing GTPase activating protein 1 
4 PKFEVIDKPQS 98-108 108 P97450 ATP synthase-coupling factor 6, mitochondrial 
5 PTEEESPV 486-493 493 P53986 Monocarboxylate transporter 1 
6 QAIPQGAIQ 246-254 461 Q8BG99 Homeobox protein PKNOX2 
7 QLQPQQPLPQPQ 125-136 672 Q9WVH4 Forkhead protein FKHR2 
TAP-negative 
1 AAIENIEHL 1193-1201 1392 Q6PB66 Leucine-rich PPR motif-containing protein, mitochondrial 
2 AALKLGQEL 799-807 1271 Q9JJ28 Protein flightless-1 homologue 
3 AAPTNANSLNSTF 454-466 575 Q8BT14 CCR4-NOT transcription complex subunit 4 
4 AAPTSPDHSPA 699-709 709 Q66L44 Protein Dos 
5 AAVIAHDFL 153-161 292 P30282 G1/S-specific cyclin-D3 
6 AGIENDEAF 44-52 248 B1AWD9 Clathrin light polypeptide 
7 AGPENSSKI 383-346 2075 Q80XK6 Autophagy-related protein 2 homologue B 
8 AGQFNQDYL 45-53 503 Q921F1 Annexin A11 
9 AGVRNPQQHL 515-524 636 Q8BN32 Pabpc1 protein 
10 ASLQNFNISNL 2103-2113 2128 B2RRJ7 Wnk1 protein 
11 KSISNPPGSNL 2115-2125 2128 B2RRJ7 Wnk1 protein 
12 ASQQNSEEM 202-210 210 Q9CXE2 B-cell CLL/lymphoma 7 protein family member A 
13 ASVLNVNHI 2195-2203 2603 Q99NH0 Ankyrin repeat domain-containing protein 17 
14 ASYRAQPSVSL 270-280 573 Q62019 16 kD protein 
15 ATPGRLIDFL 256-265 648 Q5U222 Ddx5 protein 
16 AVSEGTKAVTKYTSAK 111-126 126 Q8CGP1 Histone H2B type 1-K 
17 FAPLPRLPTL 17-26 156 Q9CR21 Acyl carrier protein, mitochondrial 
18 FAPVNVTTEVKSVE 280-293 462 P10126 Elongation factor 1-alpha 1 
19 FAYEGRDYI 137-145 184 Q62143 Qa-2 cell surface antigen 
20 FGPVNHEEL 33-41 147 P46414 Cyclin-dependent kinase inhibitor 1B 
21 FQIVNPHLL 634-642 792 Q6NZB3 Ribonucleoside-diphosphate reductase 
22 FQVTHTVAL 113-121 361 Q9QYA2 Mitochondrial import receptor subunit TOM40 homologue 
23 GGPINPATA 1036-1044 1107 Q80X50 Ubiquitin-associated protein 2-like 
24 GLGVLLAF 5-12 113 Q8QZT4 Crumbs protein homologue 3 
25 HSIQNSQDM 61-69 210 Q91YN9 BAG family molecular chaperone regulator 2 
26 IQKTPQIQVY 21-30 119 P01887 Beta-2-microglobulin 
27 KAPPPLPPLVVF 27-38 499 P16277 Tyrosine-protein kinase BLK 
28 KAPTNEFYA 190-198 198 O35988 Syndecan-4 
29 KCSVSIQVVDVNDNYPEL 328-345 794 Q91XZ8 Protocadherin beta 22 
30 KSAVGHEYV 96-107 486 Q922I8 Hematopoietic cell specific Lyn substrate 1 
31 LAIRNDEEL 93-101 137 Q64426 Histone H2A 
32 LVRPGTALEL 2294-2303 2883 NP_076331 desmoplakin 
33 METLTATPQ 976-984 1241 B2RXW8 Ppfia1 protein 
34 NSIRNLDTI 100-108 475 P28658 Ataxin-10 
35 PADIVKNLK 12-20 341 Q8VDZ8 Calcium binding protein 39 
36 PDTGISSKA 52-60 126 Q8CGP2 Histone H2B type 1-P 
37 PEAFPALA 385-392 392 Q9CY58 Plasminogen activator inhibitor 1 RNA-binding protein 
38 PNKLVELNK 138-146 943 Q6DFV7 Nuclear receptor coactivator 7 
39 PPSAKAAID 97-105 323 Q5SSG6 TATA box binding protein (TBP)-associated factor 
40 PPTAKAAVE 425-433 661 Q5SUS9 Ewing sarcoma breakpoint region 1 
41 PVKAVEIEI 155-163 930 Q7TSZ1 Xeroderma pigmentosum, complementation group C 
42 RSPENPPSKEL 171-181 181 Q9CQA0 Centromere protein M 
43 RSPGNSPTPM 186-195 469 Q8CI61 BAG family molecular chaperone regulator 4 
44 SALINLSSF 7-15 161 Q8VE65 Transcription initiation factor TFIID subunit 12 
45 SAPENAVRM 28-36 126 O35127 Protein C10 
46 SAPSNFEHR 12-20 593 Q8BTW9 Serine/threonine-protein kinase PAK 4 
47 SAPTGSGKTL 227-236 639 Q6P9R1 ATP-dependent RNA helicase DDX51 
48 SAVISLEGKPL 156-166 166 P18760 Cofilin-1 
49 SAVSNNYIQTL 168-178 911 P30999 Catenin delta-1 
50 SHRKFSAPR 2-10 403 Q3U9L3 ribosomal protein L3P family member 
51 SLGINPHVL 966-974 1170 B2RQL0 Nup98 protein 
52 SLGKNPTDAYL 60-70 172 Q3THE2 Myosin regulatory light chain MRLC2 
53 SQPESKVFYL 110-119 245 P63101 Protein kinase C inhibitor protein 1 
54 SSTTNPKLSTL 726-736 959 Q5NBZ5 Eukaryotic translation initiation factor 4E nuclear import factor 1 
55 STIRLLTSL 458-466 545 P80318 T-complex protein 1 subunit gamma 
56 TNPESKVFYL 155-160 284 P68254 14-3-3 protein theta 
57 TQGQNIQHL 431-439 2326 Q80YT7 Myomegalin 
58 VAVTNGPRS 371-379 393 Q9D6J1 LAG1 longevity assurance homologue 4 
59 VPPVQVSPLIKFGRY 2-16 71 Q5EBI8 ATP synthase, H+ transporting, mitochondrial F1F0 complex 
60 VQVSNFKSGKGDSTL 254-268 579 Q80WJ7 Metastasis adhesion protein 
61 VSLLDIDHL 473-481 679 Q8BQM4 HEAT repeat-containing protein 3 
62 VSLLNPPETL 411-420 422 Q8BRG1 Cyclin A2, isoform CRA 
63 VTLVNHGSTF 15-24 640 P59110 SUMO-1 protease 2 
64 YGYSNRVVDLM 316-326 333 P16858 Glyceraldehyde-3-phosphate dehydrogenase 
65 AAPRSGPSV 611-619 641 Q923D5 WW domain-binding protein 11 
66 AAPRSGPSVA 611-620 641 Q923D5 WW domain-binding protein 11 
67 AGIENKFGL 648-656 676 Q9QXX4 Calcium-binding mitochondrial carrier protein Aralar2 
68 AGIENKFGLYL 648-658 676 Q9QXX4 Calcium-binding mitochondrial carrier protein Aralar2 
69 AGIENKFGLYLP 648-659 676 Q9QXX4 Calcium-binding mitochondrial carrier protein Aralar2 
70 TKAVTKYTSSK 117-127 127 A0JNS9 Histone H2B 
71 GTKAVTKYTSSK 116-127 127 A0JNS9 Histone H2B 
72 SEGTKAVTKYTSSK 114-127 127 A0JNS9 Histone H2B 
73 VSEGTKAVTKYTSSK 113-127 127 A0JNS9 Histone H2B 
74 AVSEGTKAVTKYTSSK 112-127 127 A0JNS9 Histone H2B 
75 PEPAKSAPAPK 2-12 126 Q64478 Histone H2B type 1-H 
76 PEPAKSAPAPKKG 2-14 126 Q64478 Histone H2B type 1-H 
77 LGVKNSEPA 59-67 576 Q80UG5 Septin-9 
78 LGVKNSEPAA 59-68 576 Q80UG5 Septin-9 
79 SSPANISSLEFEDA 583-596 773 P51125 Calpastatin 
80 SSPANISSLEFEDAK 583-597 773 P51125 Calpastatin 
81 SSPANISSLEFEDAKLS 583-599 773 P51125 Calpastatin 
82 SSPANISSLEFEDAKLSA 583-600 773 P51125 Calpastatin 
83 KPLFEILNG 1138-1146 1735 Q9IZU3 Endogenous mouse mammary tumor virus Mtv1 
84 KPLFEILNGD 1138-1147 1735 Q9IZU3 Endogenous mouse mammary tumor virus Mtv1 
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