Supplementary Table S5

Supplementary table S5

HLA class II LiTAAs and LiTAPs

Protein/Peptides / Number of positive AMLs
[rep. frequency] / PSM
A1BG alpha-1-B glycoprotein / 6 [50%] / 11
APVELILSDETLPAPE / 3 / 3
ETPDFQLFKNGVAQEPV / 1 / 2
LAPLEGARFALVRED / 2 / 2
SPDRIFFHLNAVALGD / 1 / 1
SPDRIFFHLNAVALGDG / 2 / 3
CORO1A coronin, actin binding protein, 1A / 5 [41.7%] / 11
EEMRKLQATVQELQKR / 1 / 1
EEPLSLQELDTSSG / 4 / 5
EMRKLQATVQELQKR / 1 / 1
HLEEPLSLQELDTSSG / 1 / 1
LEEPLSLQELDTSSG / 2 / 3
RPS5 ribosomal protein S5 / 5[41.7%] / 14
AGTVRRQAVDVSPLR / 5 / 6
IGRAGTVRRQAVDVSPLR / 1 / 1
RAGTVRRQAVDVSPLR / 4 / 5
TVRRQAVDVSPLR / 1 / 2
C19orf10 chromosome 19 open reading frame 10 / 5[41.7%] / 18
GVVHSFSHNVGPGDK / 2 / 3
GVVHSFSHNVGPGDKY / 1 / 2
GVVHSFSHNVGPGDKYT / 1 / 2
KTEEFEVTKTAVAHRP / 1 / 2
KTEEFEVTKTAVAHRPG / 3 / 5
VRPGGVVHSFSHNVGPGDK / 1 / 2
VRPGGVVHSFSHNVGPGDKYT / 1 / 2
PLIN3 perilipin 3 / 4 [33.3%] / 8
AEKGVRTLTAAAVSGAQ / 1 / 1
AQPILSKLEPQIASASE / 1 / 1
EKGVRTLTAAAVSGAQ / 3 / 3
EKGVRTLTAAAVSGAQP / 1 / 1
GVRTLTAAAVSGAQ / 1 / 1
KGVRTLTAAAVSGAQ / 1 / 1
CLSTN1 calsyntenin 1 / 4 [33.3%] / 8
DVNEYAPVFKEKSYK / 1 / 2
HRSFVDLSGHNLA / 1 / 1
HRSFVDLSGHNLANPH / 1 / 1
HRSFVDLSGHNLANPHP / 3 / 4
HSP90B1 heat shock protein 90kDa beta (Grp94), member 1 / 4 [33.3%] / 19
ALPEFDGKRFQNVAKEG / 1 / 1
DSNEFSVIADPRG / 1 / 2
DSNEFSVIADPRGN / 1 / 2
DSNEFSVIADPRGNT / 1 / 2
DSNEFSVIADPRGNTL / 1 / 2
DSNEFSVIADPRGNTLG / 1 / 2
PEFDGKRFQNVAK / 1 / 1
SDSNEFSVIADPRGNTLG / 1 / 2
SQKKTFEINPRHPLIR / 1 / 1
ALPEFDGKRFQNVAKEG / 1 / 1
PEFDGKRFQNVAK / 2 / 2
PEFDGKRFQNVAKE / 1 / 1
B4GALT1 UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1 / 4 [33.3%] / 11
LNSLTYQVLDVQRYP / 1 / 1
LPQLVGVSTPLQG / 2 / 3
LPQLVGVSTPLQGG / 1 / 1
LPQLVGVSTPLQGGS / 3 / 4
RLPQLVGVSTPLQGGS / 1 / 1
SDVDLIPMNDHNAYR / 1 / 1
SPN sialophorin / 4 [33.3%] / 10
GRRKSRQGSLAMEELK / 1 / 2
RKSRQGSLAMEELK / 3 / 6
SGPSLKGEEEPLVASEDGAVD / 1 / 1
SGSGPSLKGEEEPLVASEDGAVD / 1 / 1
METAP1 methionyl aminopeptidase 1 / 4 [33.3%] / 9
IKPGVTTEEIDHAVH / 4 / 5
KPGVTTEEIDHAVH / 3 / 4
HSPG2 heparan sulfate proteoglycan 2 / 4[33.3%] / 11
DGVLRIQNLDQS / 4 / 5
GAYFHDDGFLAFPG / 1 / 2
TPYSFLPLPTIKDAYR / 1 / 2
YPTPDISWSKLDGSLPP / 1 / 1
YPTPDISWSKLDGSLPPD / 1 / 1
QSOX1 quiescin Q6 sulfhydryl oxidase 1 / 3 [25.0%] / 6
ASHFEQMAAASMHR / 3 / 6
MANBA mannosidase, beta A, lysosomal / 3 [25.0%] / 8
GGQVIVAIPKLQTQQ / 1 / 2
GQVIVAIPKLQTQ / 1 / 2
GQVIVAIPKLQTQQ / 1 / 2
IESTFDVVSSKPVG / 2 / 2
CREG1 cellular repressor of E1A-stimulated genes 1 / 3 [25.0%] / 7
DWGALATISTLEAVRG / 1 / 1
GRPFADVLSLSDGPPG / 1 / 1
WGALATISTLEAVR / 2 / 2
WGALATISTLEAVRG / 2 / 2
LDHA lactate dehydrogenase A / 3 [25.0%] / 6
ADELALVDVIEDK / 1 / 2
GVSLKTLHPDLGTDK / 2 / 3
IVSGKDYNVTANSKL / 1 / 1
CP ceruloplasmin (ferroxidase) / 3 [25.0%] / 6
DDNIKTYSDHPEK / 1 / 1
DKVYVHLKNLASRPY / 1 / 1
GDKVYVHLKNLASRPY / 1 / 1
LDDNIKTYSDHPEK / 1 / 1
TGDKVYVHLKNLASRPY / 1 / 1
VYVHLKNLASRPY / 1 / 1
COL1A1 collagen, type I, alpha 1 / 3 [25.0%] / 13
KTSRLPIIDVAPLDVGAPD / 1 / 1
KTSRLPIIDVAPLDVGAPDQE / 1 / 1
LPIIDVAPLDVGAPD / 1 / 1
RLPIIDVAPLDVGAPD / 3 / 4
RLPIIDVAPLDVGAPDQE / 2 / 2
SRLPIIDVAPLDVGAPD / 1 / 1
SRLPIIDVAPLDVGAPDQE / 1 / 1
TSRLPIIDVAPLDVGAPD / 1 / 1
TSRLPIIDVAPLDVGAPDQE / 1 / 1
CRP C-reactive protein, pentraxin-related / 3 [25.0%] / 15
DTSYVSLKAPLT / 2 / 2
DTSYVSLKAPLTKP / 1 / 1
DTSYVSLKAPLTKPL / 1 / 1
ESDTSYVSLKAPLT / 2 / 2
ESDTSYVSLKAPLTKPL / 1 / 1
SDTSYVSLKAPLT / 3 / 4
SDTSYVSLKAPLTKP / 2 / 2
SDTSYVSLKAPLTKPL / 2 / 2
APRT adenine phosphoribosyltransferase / 3 [25.0%] / 4
DPASFRAAIGLLARH / 3 / 4
MBL2mannose-binding lectin 2 / 3 [25.0%] / 3
TEGQFVDLTGNRLTYT / 3 / 3
IFI30 interferon, gamma-inducible protein 30 / 3 [25.0%] / 9
ALDFFGNGPPVNYK / 1 / 1
ALDFFGNGPPVNYKTG / 1 / 1
DFFGNGPPVNYKTG / 2 / 3
LDFFGNGPPVNYK / 1 / 2
LDFFGNGPPVNYKTG / 1 / 1
QALDFFGNGPPVNYKTG / 1 / 1
LBP lipopolysaccharide binding protein / 3 [25.0%] / 10
AISDYVFNTASLVYH / 1 / 1
AISDYVFNTASLVYHEE / 2 / 3
ISDYVFNTASLVYH / 1 / 1
ISDYVFNTASLVYHEE / 3 / 4
YVFNTASLVYHEE / 1 / 1
RAB5A RAB5A, member RAS oncogene family / 3 [25.0%] / 6
IVIALSGNKADLA / 1 / 1
SPNIVIALSGNKADL / 1 / 1
SPNIVIALSGNKADLA / 3 / 4
ICAM3 intercellular adhesion molecule 3 / 3 [25.0%] / 8
TPPRLVAPRFLEVE / 1 / 1
TPPRLVAPRFLEVET / 1 / 2
TPPRLVAPRFLEVETS / 3 / 5
MAN1A1 mannosidase, alpha, class 1A, member 1 / 3 [25.0%] / 17
EIQRDILLEKKKVAQDQ / 1 / 2
FGAIFFLPDSSK / 1 / 2
IQRDILLEKKKVAQ / 1 / 2
IQRDILLEKKKVAQD / 1 / 2
IQRDILLEKKKVAQDQ / 1 / 2
LSGVLFHSSPALQPA / 1 / 2
RDILLEKKKVAQDQ / 1 / 2
SSKLLSGVLFHSSPA / 1 / 2
SSPALQPAADHKPGPG / 1 / 1
RBMX RNA binding motif protein, X-linked / 3 [25.0%] / 5
APPTRGPPPSYGGS / 1 / 1
GNSRSAPPTRGPPPSYGGSSRY / 1 / 2
RDYGHSSSRDDYPS / 1 / 1
SPRDDGYSTKDSY / 1 / 1
PBX2 pre-B-cell leukemia homeobox 2 / 3 [25.0%] / 4
GGSAAAAAAAAASGG / 1 / 1
DNMLLAEGVSGPEK / 2 / 3
YARS tyrosyl-tRNA synthetase / 3 [25.0%] / 5
ADSLYVEKIDVGEAEPR / 3 / 5
TPM4 tropomyosin 4 / 3 [25.0%] / 2
RIQLVEEELDRAQER / 2 / 1
RRIQLVEEELDRAQER / 1 / 1
RPL36A ribosomal protein L36a / 3 [25.0%] / 2
HQPHKVTQYKKGKDSLY / 2 / 1
RKKAKTTKKIVL / 1 / 1
GANAB glucosidase, alpha; neutral AB / 3 [25.0%] / 4
DVFRQYASLTGTQALPP / 1 / 1
GTAQGELFLDDGHT / 1 / 2
VFRQYASLTGTQALPP / 1 / 1
HSP90B2P heat shock protein 90kDa beta (Grp94), member 2, pseudogene / 3 [25.0%] / 3
PEFDGKRFQNVAK / 1 / 1
PEFDGKRFQNVAKE / 2 / 1
ALPEFDGKRFQNVAKEG / 1 / 1
LAIR1 leukocyte-associated immunoglobulin-like receptor 1 / 3 [25.0%] / 15
ASPSESEARFRIDSVSEGNAGPY / 1 / 1
EARFRIDSVSEGNAGP / 1 / 1
ESEARFRIDSVSEGNAGP / 1 / 1
ESEARFRIDSVSEGNAGPY / 1 / 1
FRIDSVSEGNAGP / 1 / 2
FRIDSVSEGNAGPY / 1 / 2
SEARFRIDSVSEGNAGPY / 3 / 5
SPSESEARFRIDSVSEGNAGPY / 1 / 2
GALNT7 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7) / 3 [25.0%] / 9
GNQLFRINEANQL / 1 / 2
GNQLFRINEANQLMQ / 2 / 3
SPAMAGGLFAIERE / 1 / 4
ARRDC1 arrestin domain containing 1 / 3 [25.0%] / 9
FIGNIAVNHAPVSPR / 1 / 2
FIGNIAVNHAPVSPRPG / 1 / 2
IGNIAVNHAPVSPRP / 3 / 4
IGNIAVNHAPVSPRPG / 1 / 1
ERGIC1 endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1 / 3 [25.0%] / 10
FEGQFSINKVPGNFH / 3 / 4
FEGQFSINKVPGNFHVS / 2 / 3
RFEGQFSINKVPGNFH / 2 / 3

Top 36 highest ranking HLA class II ligandome derived tumor-associated antigens (LiTAAs) with representation frequencies >20% in AML patients(n=12) and representing HLA ligands (LiTAPs). Abbreviations: rep., representation; PSM, peptide spectrum matches.