Table I. Phosphorylated ligands displayed by HLA-B*40:02.
| N | Sequence | AN | Protein name | IMAC | TiO2 | Reference |
|---|---|---|---|---|---|---|
| 1 | AEL[pS]PVEQKL | Q9Y5P8 | Protein phosphatase 2A 48 kDa regulatory subunit | + | + | This study |
| 2 | REL[pS]PQRNL | Q96F44 | E3 ubiquitin-protein ligase TRIM11 | + | − | This study |
| 3 | TER[pS]PGPRL | O14978 | Zinc finger protein 263 | + | + | This study |
| 4 | IES[pS]PQYRL | Q8WWM7 | Ataxin-2-like protein | + | + | (53) |
| 5 | KEKDF[pS]PEAL | O15372 | Eukaryotic translation initiation factor 3 subunit H | + | − | (54) |
| 6 | GEW[pS]ASLPHRF | O43164 | E3 ubiquitin-protein ligase Praja-2 | + | − | This study |
| 7 | SEA[pS]PSREAI | Q13111 | Chromatin assembly factor 1 subunit A | + | + | (55) |
| 8 | YEG[pS]PIKVTL | P06748 | Nucleophosmin | + | + | (56) |
| 9 | HERSI[pS]PLL | Q9UBT6 | DNA polymerase κ | + | + | This study |
| 10 | VEKKKIR[pS]L | O75394 | 39S ribosomal protein L33, mitochondrial | + | − | This study |
| 11 | AEN[pS]PTRQQF | Q86XP3 | ATP-dependent RNA helicase DDX42 | + | − | (56) |
| 12 | QEV[pT]PSRSTL | P49454 | Centromere protein F | + | + | (57) |
| 13 | RE[pS]PPPSAL | Q86VE0 | Myb-related transcription factor, partner of profilin | + | − | This study |
| 14 | REK[pT]PSEDKL | Q8NFC6 | Biorientation of chromosomes in cell division protein 1-like 1 | + | − | This study |
| 15 | GEDR[pS]PPTAL | Q9BUB5 | MAP kinase-interacting serine/threonine-protein kinase 1 | + | − | (51) |
| 16 | REV[pS]PAPAVA | O60292 | Signal-induced proliferation-associated 1-like protein 3 | + | − | (50) |
| 17 | KEV[pT]PKPVL | P17544 | Cyclic AMP-dependent transcription factor ATF-7 | + | − | This study |
| 18 | HEL[pS]PPQKRM | Q9BXP5 | Serrate RNA effector molecule homolog | + | − | (55) |
| 19 | RE[pT]PSPRPM | Q9UQ35 | Serine/arginine repetitive matrix protein 2 | + | − | (58) |
| 20 | REYG[pS]PLKA | Q9UQ88 | Cyclin-dependent kinase 11A | + | − | (51) |
| 21 | KEM[pS]PTRQL | Q4G0N7 | Protein FAM229B | + | + | This study |
| 22 | GENK[pS]PLLL | Q8IZD2 | Histone-lysine N-methyltransferase MLL5 | + | + | This study |
| 23 | VEFPH[pS]PEI | Q9BR61 | Acyl-CoA-binding domain-containing protein 6 | + | + | This study |
| 24 | YEKAN[pT]PEL | Q9H8V3 | Protein ECT2 | + | + | (55) |
| 25 | VEK[pS]PRPPL | Q7L590 | Protein MCM10 homolog | + | − | This study |
| 26 | QEK[pS]PKQAL | O43683 | Mitotic checkpoint serine/threonine-protein kinase BUB1 | + | − | (51) |
| 27 | GEI[pS]PQREV | Q8WWI1 | LIM domain only protein 7 | + | − | (56) |
| 28 | HEFH[pS]QENL | Q9Y3M8 | StAR-related lipid transfer protein 13 | + | − | (59) |
| 29 | REG[pS]GRFSL | P57764 | Gasdermin-D | + | − | This study |
| 30 | GEN[pS]GIGKL | Q6P0N0 | Mis18-binding protein 1 | + | − | (51) |
| 31 | SEI[pS]PIKGSV | Q7Z5K2 | Wings apart-like protein homolog | + | − | (56) |
| 32 | SEK[pS]LENETL | P23588 | Eukaryotic translation initiation factor 4B | + | − | (56) |
| 33 | RED[pS]QRPGAHL | Q32P51 | Heterogeneous nuclear ribonucleoprotein A1-like 2 | + | − | (60) |
| 34 | RED[pS]GTFSL | O75569 | Protein activator of the interferon-induced protein kinase | + | − | (51) |
| 35 | REA[pS]PSRLSV | O75122 | CLIP-associating protein 2 | + | + | This study |
| 36 | SEQ[pS]LGQKL | P33991 | DNA replication licensing factor MCM4 | + | − | (55) |
| 37 | REV[pS]PAPAV | O60292 | Signal-induced proliferation-associated 1-like protein 3 | + | − | (50) |
| 38 | SERM[pS]LPLL | Q15398 | Disks large-associated protein 5 | + | − | (61) |
| 39 | SES[pS]PPKAM | Q9UHB6 | LIM domain and actin-binding protein 1 | + | − | (51) |
| 40 | SEV[pS]PSGVGF | Q6ULP2 | Aftiphilin | + | − | This study |
| 41 | REK[pS]PGRML | O14578 | Citron Rho-interacting kinase | + | − | (50) |
| 42 | SEF[pS]DVDKL | O75665 | Oral-facial-digital syndrome 1 protein | + | − | This study |
| 43 | REA[pS]PLSSNKL | Q9Y462 | Zinc finger protein 711 | + | − | This study |
| 44 | REIES[pS]PQYRL | Q8WWM7 | Ataxin-2-like protein | + | − | (53) |
| 45 | REY[pS]PPYAP | Q9UPT8 | Zinc finger CCCH domain-containing protein 4 | + | − | (51) |
| 46 | KEKEV[pS]QEL | A8MX76 | Calpain-14 | + | + | This study |
| 47 | KEL[pS]PPPGL | Q7Z4S6 | Kinesin-like protein KIF21A | + | + | (51) |
| 48 | RER[pS]PSPSF | P49585 | Choline-phosphate cytidylyltransferase A | + | − | (56) |
| 49 | GET[pS]LMRTL | O96017 | Serine/threonine-protein kinase Chk2 | + | − | (62) |
| 50 | AEK[pS]PGPIV | Q86WB0 | Nuclear-interacting partner of ALK | + | − | (51) |
| 51 | REN[pS]PVQSI | Q7Z2Z1 | Treslin | + | − | This study |
| 52 | RET[pS]PNRIGL | Q7Z460 | CLIP-associating protein 1 | + | + | This study |
| 53 | REG[pS]FRVTTA | P49757 | Protein numb homolog | + | − | This study |
| 54 | PEV[pS]PRPAL | Q96L73 | Lysine N-methyltransferase 3B | + | − | This study |
| 55 | KEL[pS]PAGSI | O95453 | Poly(A)-specific ribonuclease PARN | + | − | (55) |
| 56 | REG[pS]YDRYL | Q9HCD5 | Nuclear receptor coactivator 5 | + | − | (63) |
| 57 | S[pS]YGNIRAV | Q8N122 | Regulatory-associated protein of mTOR | + | − | (64) |
| 58 | GEPHS[pS]PEL | Q9NUA8 | Zinc finger and BTB domain-containing protein 40 | + | − | This study |
| 59 | REK[pS]PGRMLST | O14578 | Citron Rho-interacting kinase | + | − | This study |
| 60 | SEL[pS]PGRSV | Q8NFF5 | FAD synthase | + | − | (50) |
| 61 | HEFS[pS]PSHL | Q9H3D4 | Tumor protein 63 | + | − | This study |
| 62 | QEK[pS]PEERL | Q7RTP6 | Protein-methionine sulfoxide oxidase MICAL3 | + | − | (51) |
| 63 | KEQ[pS]PEPHL | Q5VV52 | Zinc finger protein 691 | + | − | (65) |
| 64 | NEA[pS]PVKRPRL | Q9H8U3 | AN1-type zinc finger protein 3 | + | − | (66) |
| 65 | G[pS]FSRFYSL | P22695 | Cytochrome b-c1 complex subunit 2, mitochondrial | + | − | This study |
| 66 | REF[pS]KEPEL | Q9NQS7 | Inner centromere protein | + | − | (57) |
| 67 | SEKPV[pS]PKSGTL | Q14155 | Rho guanine nucleotide exchange factor 7 | + | − | (63) |
| 68 | REL[pS]PLISL | P51825 | AF4/FMR2 family member 1 | + | − | (50) |
| 69 | RE[pT]PVPPAM | Q9Y2F5 | Uncharacterized protein KIAA0947 | + | − | (56) |
| 70 | REP[pS]PSSSSL | O60336 | Mitogen-activated protein kinase-binding protein 1 | + | − | This study |
| 71 | LEKRT[pS]PQVL | Q7Z417 | Nuclear fragile X mental retardation-interacting protein 2 | + | − | (51) |
| 72 | REL[pS]GTIKEI | P30050 | 60S ribosomal protein L12 | + | − | This study |
| 73 | GEA[pS]PSHII | Q9ULL5-3 | Proline-rich protein 12 | + | − | This study |
| 74 | GEQ[pS]PNVSL | Q58WW2 | DDB1- and CUL4-associated factor 6 | + | − | (51) |
| 75 | KE[pT]PDKVEL | Q13610 | Periodic tryptophan protein 1 homolog | + | − | (57) |
| 76 | NEFH[pS]PIGL | Q06413 | Myocyte-specific enhancer factor 2C | + | + | This study |
| 77 | REV[pS]PEPIV | Q8N103 | T-cell activation Rho GTPase-activating protein | + | − | This study |
| 78 | NEK[pS]PYASL | Q6IQ21 | Zinc finger protein 770 | + | − | This study |
| 79 | REL[pS]GTIKEIL | P30050 | 60S ribosomal protein L12 | + | − | This study |
| 80 | SERIMQL[pS]L | Q81IY63 | Angiomotin-like protein 1 | + | − | This study |
| 81 | R[pS]FPTLPTL | Q13761 | Runt-related transcription factor 3 | + | − | This study |
| 82 | KES[pS]PIPSP | Q01082 | Spectrin β chain, non-erythrocytic 1 | + | − | (51) |
| 83 | SE[pS]GSNLHAL | Q6P4F7 | Rho GTPase-activating protein 11A | + | − | This study |
| 84 | KELARQI[pS]F | Q9Y385 | Ubiquitin-conjugating enzyme E2 J1 | + | − | This study |
| 85 | KEN[pT]PPAL | P31350 | Ribonucleoside-diphosphate reductase subunit M2 | + | − | (50) |
The sequence, accession number (AN), and putative parental protein are indicated. + and − symbols specify whether the peptide was sequenced from the IMAC or the TiO2 fraction. If the described phosphorylation was annotated in the HPRDB and/or the UniProt database, a reference is given. Peptides phosphorylated at P2 (n + 57, 65, and 81) are shown in bold letters. Phosphoserine and phosphothreonine are represented as [pS] and [pT], respectively.