Table 1.
Characteristics of RCC-presented peptides identified by MS
| Peptide | HLA | Protein | Gene ID | Gene symbol | UniProtKB ID | Position | RT exp. (min) | RT calc. (min) | (M+H)+ calc. | (M+2H)2+ calc. | (M+2H)2+ obs. |
|---|---|---|---|---|---|---|---|---|---|---|---|
| LTYEALGLCP | n.d. | Sterol carrier protein 2 | 6342 | SCP2 | P22307 | 56–65 | 54.7 | 43.9 | 1079.537 | 540.2683 | 540.29 |
| STDHIPILY | A*01 | Glutamine-fructose-6-phosphate transaminase 1 | 2673 | GFPT1 | Q06210 | 218–226 | 80.2 | 52.1 | 1058.544 | 529.772 | 529.77 |
| NTDSPLRY | A*01 | Ribosomal protein SA | 3921 | RPSA | P08865 | 149–156 | 31.6 | 21.6 | 965.4611 | 483.2306 | 483.24 |
| ALADGVQKV | A*02 | Apolipoprotein L, 1 | 8542 | APOL1 | O14791 | 160–168 | 27.8 | 13.9 | 900.5073 | 450.7537 | 450.74 |
| SIFEVVWAI | A*02 | Calcium channel, voltage-dependent, α 1E subunit | 777 | CACNA1E | Q15878 | 462–470 | 69.6 | 57.4 | 1063.575 | 532.2874 | 532.29 |
| LLMVLSPRL | A*02 | Clathrin, heavy chain | 1213 | CLTC | Q00610 | 1422–1430 | 122.2 | 56.7 | 1041.641 | 521.3207 | 521.34 |
| RLLDVLAPL | A*02 | Collagen, type XVIII, α 1 | 80781 | COL18A1 | P39060 | 14–22 | 138.1 | 50.4 | 1009.633 | 505.3164 | 505.34 |
| AGLPRPDLSL | A*02 | Hypothetical LOC400614 | 400614 | LOC400614 | XP_378693 | 2–11 | 51.3 | 40.9 | 1038.587 | 519.7933 | 519.78 |
| RIGSGLKALL | A*02 | Chromosome 2 open-reading frame 54 | 79919 | C2orf54 | Q53QU5 | 219–228 | 75.3 | 35.8 | 1027.655 | 514.3273 | 514.28 |
| RLLEVPVML | A*02 | LSM8 homolog, U6 small nuclear RNA associated | 79763 | LSM8 | O95777 | 49–57 | 135.8 | 46.2 | 1069.636 | 535.3182 | 535.35 |
| VLIPKLPQL | A*02 | ORM1-like 3 (S. cerevisiae) | 94103 | ORMDL3 | Q8N138 | 118–126 | 124.3 | 61.9 | 1020.674 | 510.8369 | 510.84 |
| LVLMVLYLI | A*02 | Phosphatidylinositol glycan anchor biosynthesis, class M | 93183 | PIGM | Q9H3S5 | 153–161 | 70.6 | 80.2 | 1076.671 | 538.8356 | 538.79 |
| VMLDVPIRL | A*02 | RAS protein activator like 2 | 9462 | RASAL2 | Q9UJF2 | 855–863 | 129.5 | 52.7 | 1055.621 | 528.3103 | 528.3 |
| IMLEALERV | A*02 | Small nuclear ribonucleoprotein polypeptide G | 6637 | SNRPG | P62308 | 68–76 | 103 | 29.1 | 1073.595 | 537.2975 | 537.31 |
| TLSDLRVYL | A*02 | Sulfiredoxin 1 | 140809 | SRXN1 | Q9BYN0 | 114–122 | 114.7 | 38.5 | 1079.602 | 540.301 | 540.32 |
| RVMAPRALL | A*02/ B*07 | Major histocompatibility complex, class I, C | 3107 | HLA-C | P10321 | 2–10 | 45.7 | 35.7 | 1026.617 | 513.8083 | 513.77 |
| TAHLMVVVL | A*02/ B*07 | Olfactory receptor, family 13, subfamily F, member 1 | 138805 | OR13F1 | Q8NGS4 | 242–250 | 53.7 | 45.7 | 982.5679 | 491.784 | 491.75 |
| APRAVFPSI | B*07 | Actin, α 1, skeletal muscle | 58 | ACTA1 | P68133 | 28–36 | 71.9 | 43.1 | 957.5441 | 479.2721 | 479.26 |
| RPELVRPAL | B*07 | Aldo-keto reductase family 1, member C3 | 8644 | AKR1C3 | P42330 | 91–99 | 39.3 | 29.2 | 1050.634 | 525.8172 | 525.79 |
| FPNIPGKSL | B*07 | Degenerative spermatocyte homolog 1, lipid desaturase | 8560 | DEGS1 | O15121 | 265–273 | 59.4 | 49.2 | 972.5436 | 486.7718 | 468.75 |
| VPATDRNAL | B*07 | Eukaryotic translation initiation factor 3, subunit 6 48 kDa | 3646 | EIF3S6 | P60228 | 109–117 | 23.1 | 20.2 | 956.5084 | 478.7542 | 478.77 |
| PSRDSLPLPV | B*07 | G-protein signaling modulator 1 (AGS3-like, C. elegans) | 26086 | GPSM1 | Q86YR5 | 418–427 | 123.1 | 39.1 | 1080.597 | 540.7986 | 540.84 |
| RPQKVCSFL | B*07 | Guanine nucleotide binding protein (G protein), γ 5 subunit | 79218 | Gng5 | P63218 | 60–68 | 46.5 | 25.6 | 1077.58 | 539.2899 | 539.31 |
| MPRGVVVTL | B*07 | HECT domain containing 1 | 25831 | HECTD1 | Q9ULT8 | 851–859 | 69.7 | 38 | 971.5631 | 486.2816 | 486.28 |
| RPTLWAAAL | B*07 | Insulin-like growth factor binding protein 3 | 3486 | IGFBP3 | P17936 | 5–13 | 95.6 | 49.3 | 998.5706 | 499.7853 | 499.79 |
| APRTLVLLL | B*07 | Major histocompatibility complex, class I, A | 3105 | HLA-A | P16189 | 5–13 | 130.8 | 44.7 | 995.6535 | 498.3268 | 498.34 |
| IPRSITVLV | B*07 | Minichromosome maintenance complex component 7 | 4176 | MCM7 | P33993 | 73–81 | 82.6 | 48 | 997.6328 | 499.3164 | 499.31 |
| IPRAALLPL | B*07 | HtrA serine peptidase 1 | 5654 | HTRA1 | Q92743 | 3–11 | 94.6 | 59.6 | 963.6273 | 482.3137 | 482.31 |
| LPKQPPLAL | B*07 | RAN binding protein 9 | 10048 | RANBP9 | Q96S59 | 691–699 | 64.1 | 54.7 | 976.6112 | 488.8056 | 488.8 |
| GPRAVFVLL | B*07 | Transcription factor binding to IGHM enhancer 3 | 7030 | TFE3 | P19532 | 18–26 | 125.5 | 49.9 | 971.5961 | 486.2981 | 486.28 |
| APRPGLLSL | B*07 | Widely interspaced zinc finger motifs | 58525 | WIZ | Q96IG5 | 80–88 | 76.3 | 43.7 | 923.5596 | 462.2798 | 462.3 |
| ISVGISLLLL | B*07? | GRB2-binding adaptor protein, transmembrane | 202309 | GAPT | Q8N292 | 12–21 | 101.3 | 65.5 | 1027.668 | 514.3342 | 514.31 |
| LSLENLEKI | B*07? | Inositol polyphosphate-5-phosphatase F | 22876 | INPP5F | Q5W135 | 667–675 | 127.6 | 24.8 | 1058.602 | 529.8008 | 529.82 |
| REAPSPLMI | B*49 | Bromodomain-containing 4 | 23476 | BRD4 | O60885 | 1060–1068 | 66.5 | 35.6 | 1013.537 | 507.2687 | 507.25 |
| LEVIPRTLI | B*49 | Chaperonin-containing TCP1, subunit 3 γ | 7203 | CCT3 | P49368 | 406–414 | 104.4 | 50.9 | 1053.659 | 527.3295 | 527.33 |
| GEYPKLLRL | B*49 | Component of oligomeric golgi complex 5 | 10466 | COG5 | Q9UP83 | 411–419 | 68.6 | 38.3 | 1088.639 | 544.8193 | 544.83 |
| TEITHAVVI | B*49 | Eukaryotic translation initiation factor 3, subunit 8, 110 kDa | 8663 | EIF3S8 | Q99613 | 322–330 | 49 | 32.9 | 982.5492 | 491.7746 | 491.75 |
| AEFIKFTVI | B*49 | GTF2IRD2 β | 389524 | GTF2IRD2B | Q6EKJ0 | 397–405 | 129.6 | 51.9 | 1067.606 | 534.303 | 534.31 |
| KEFDGKSLV | B*49 | Heat shock protein 90 kDa α, class B member 1 | 3326 | HSP90AB1 | P08238 | 526–534 | 31.6 | 12.8 | 1022.544 | 511.7721 | 511.77 |
| RESFSLVQV | B*49 | HLA-B-associated transcript 3 | 7917 | BAT3 | P46379 | 820–828 | 76.3 | 15.1 | 1064.566 | 532.783 | 532.81 |
| GEFIIGRVI | B*49 | LIM and senescent cell antigen-like domain 2 | 55679 | LIMS2 | Q7Z4I7 | 80–88 | 107.2 | 46.1 | 1003.586 | 502.293 | 502.29 |
| RESFPMILV | B*49 | Muscle RAS oncogene homolog | 22808 | MRAS | O14807 | 116–124 | 134.6 | 44.9 | 1091.584 | 546.2922 | 546.31 |
| IEIERILSV | B*49 | Myosin IE | 4643 | MYO1E | Q12965 | 816–824 | 114.7 | 32 | 1071.633 | 536.3167 | 536.33 |
| REFLFNAI | B*49 | Ribonucleotide reductase M2 B (TP53 inducible) | 50484 | RRM2B | Q7LG56 | 152–159 | 113.8 | 42.4 | 1009.539 | 505.2696 | 505.28 |
| VEVGRVAYV | B*49 | Ribosomal protein L14 | 9045 | RPL14 | P50914 | 7–15 | 29.5 | 15.3 | 991.5497 | 496.2749 | 496.26 |
| REMIPFAVV | B*49 | Septin 9 | 10801 | Sep 09 | Q9UHD8 | 485–493 | 114.7 | 41.8 | 1061.574 | 531.2869 | 531.29 |
| GEHTLLVTV | B*49 | Similar to CG14977-PA | 392758 | LOC392758 | XP_374498 | 77–85 | 63 | 28.9 | 968.5335 | 484.7668 | 484.77 |
| REANLQALI | B*49 | Ubiquitin 1 | 29979 | UBQLN1 | Q9UMX0 | 562–570 | 73.2 | 22 | 1027.582 | 514.291 | 514.25 |
| IYAHGALPII | HLA-C? | Progestin and adipo Q receptor family member IV | 124222 | PAQR4 | Q8N4S7 | 52–61 | 70.7 | 68.2 | 1067.617 | 534.3086 | 534.31 |
The table lists the identified peptide sequence along with the respective HLA class I restriction element, the protein name, the gene ID, gene symbol, the UniProtKB ID, the relative position of the identified peptide within the open-reading frame, the experimental (RT exp.) and calculated (RT calc.) retention time of the peptide within the total ion current as well as its calculated/observed ion masses (M+H); n.a., not assigned.