Table 1.

The majority of minor H antigens (30/50) identified by an unbiased forward strategy are (predicted to be) differentially processed.

Levels of differential peptide processing	Minor H antigen	HLA restrictiona	Peptide sequenceb,c	C-terminal cleavage scorec,d	TAP scorec,d	HLA affinity score (nM)c,d	References
Transcription	UGT2B17/A29	HLA-A*29:02	AELLNIPFLY				(79)
			–
	UGT2B17/B44	HLA-B*44:03	AELLNIPFLY				(79)
			–
	UGT2B17/A2	HLA-A*02:06	CVATMIFMI				(50)
			–
	ACC-6	HLA-B*44:02/03	MEIFIEVFSHF				(31)
			–
	ZAPHIR	HLA-B*07:02	IPRDSWWVEL				(80)
			–
Translation	LRH-1	HLA-B*07:02	TPNQRQNVC				(28)
			–
	PANE1	HLA-A*03:01	RVWDLPGVLK				(81)
			–
C-terminal or internal proteasome cleavage	ACC-4	HLA-A*31:01	ATLPLLCAR	0.26	0.68	17	(82)
			ATLPLLCAG	0.03	−0.57	11313
	ACC-5	HLA-A*33:03	WATLPLLCAR	0.26	0.65	210	(82)
			WATLPLLCAG	0.03	−0.59	29173
	HA-3e	HLA-A*01:01	VTEPGTAQY	0.97	1.25	13	(16)
			VMEPGTAQY	0.97	1.31	134
	SP110e	HLA-A*03:01	SLPRGTSTPK			54	(83)
			SLPGGTSTPK			155
	LB-FUCA2-1V	HLA-B*0702	RLRQVGSWL	0.90	0.48	38	(84)
			RLRQMGSWL	0.53	0.48	24
	LB-GEMIN4-1V	HLA-B*07:02	FPALRFVEV	0.97	0.04	65	(53)
			FPALRFVEE	0.24	−0.78	3208
	LB-GEMIN4-2V	HLA-B*08:01	FPALRFVEV	0.97	0.04	23	(71)
			FPALRFVEE	0.24	−0.78	405
TAP transport	HA-8	HLA-A*02:01	RTLDKVLEV	0.96	0.23	35	(30)
			PTLDKVLEV	0.96	−0.08	3665
HLA-binding	HA-1	HLA-A*02:01	VLHDDLLEA	0.95	−0.19	29	(25)
			VLRDDLLEA	0.93	−0.18	321
	HA-2	HLA-A*02:01	YIGEVLVSV	0.96	0.12	7	(10)
			YIGEVLVSM	0.96	0.11	58
	TRIM22	HLA-A*02:01	MAVPPCCIGV	0.95	0.17	620	(85)
			MAVPPCRIGV	0.89	0.17	3046
	LB-APOBEC3B-1K	HLA-B*07:02	KPQYHAEMCF	0.26	0.95	278	(53)
			EPQYHAEMCF	0.26	0.82	9507
	LB-BCAT2-1R	HLA-B*07:02	QPRRALLFVIL	0.94	0.33	253	(53)
			QPTRALLFVIL	0.92	0.30	2753
	DPH1	HLA-B*57:01	SVLPEVDVW	0.45	0.50	217	(34)
			SLLPEVDVW	0.59	0.44	1582
	LB-TRIP10-1EPC	HLA-B*40:01	GEPQDLCTL	0.96	0.26	176	(52)
			GGSQDLGTL	0.87	0.21	15676
	LB-C16ORF-1R	HLA-B*07:02	RPCPSVGLSFL	0.9	0.38	643	(71)
			WPCPSVGLSFL	0.9	0.26	3010
	LB-NCAPD3-1Q	HLA-A*02:01	WLQGVVPVV	0.91	0.18	13	(71)
			WLRGVVPVV	0.91	0.22	108
	UTA2-1	HLA-A*02:01	QLLNSVLTL	0.97	0.46	39	(27)
			QLPNSVLTL	0.97	0.45	222
	LB-TMEM8A-1I	HLA-B*07:02	RPRSVTIQPLL	0.97	0.41	11	(71)
			RPRSVTVQPLL	0.97	0.41	28826
	LB-ERAP1-1R	HLA-B*07:02	HPRQEQIALLA	0.96	−0.45	692	(53)
			HPPQEQIALLA	0.97	−0.48	12460
	LB-ADIR-1F	HLA-A*02:01	SVAPALALSPA	0.89	−0.08	490	(86)
			SVAPALALFPA	0.91	−0.08	1555
TCR affinity	HB-1	HLA-B*44:03	EEKRGSLHVW	0.9	0.29	184	(48)
			EEKRGSLYVW	0.89	0.29	188
	ACC1	HLA-A*24:02	DYLQYVLQI	0.9	0.20	115	(31)
			DYLQCVLQI	0.77	0.20	197
Yet unknown	LB-ECGF-1	HLA-B*07:02	RPHAIRRPLAL	0.91	0.42	9	(73)
			RPRAIRRPLAL	0.91	0.43	5
	SLC5A1	HLA-B*40:02	AEATANGGLAL	0.96	0.49	48	(50)
			AEPTANGGLAL	0.96	0.48	50
	LB-WNK1-1I	HLA-A*02:01	RTLSPEIITV	0.97	0.30	58	(53)
			RTLSPEMITV	0.95	0.30	78
	LB-NDC80-1P	HLA-A*02:01	HLEEQIPKV	0.97	0.09	82	(71)
			HLEEQIAKV	0.97	0.09	184
	LB-ZDHHC6-1Y	HLA-B*07:02	RPRYWILLVKI	0.97	0.23	338	(71)
			RPRHWILLVKI	0.95	0.18	334
	LB-SON-1R	HLA-B*40:01	SETKQRTVL	0.92	0.37	58	(52)
			SETKQCTVL	0.95	0.37	28
	LB-SWAP70-1Q	HLA-B*40:01	MEQLEQLEL	0.94	0.43	178	(52)
			MEQLEELEL	0.92	0.43	141
	LB-NUP133-1R	HLA-B*40:01	SEDLILCRL	0.90	0.28	194	(52)
			SEDLILCQL	0.90	0.28	80
	P2RX7	HLA-A*29:02	WFHHCHPKY	0.95	1.40	6	(34)
			WFHHCRPKY	0.85	1.40	15
	LB-TTK-1D	HLA-A*02:01	RLHDGRVFV	0.89	0.26	30	(51)
			RLHEGRVFV	0.84	0.26	33
	LB-EBI3-1I	HLA-B*07:02	RPRARYYIQV	0.96	0.15	26	(53)
			RPRARYYVQV	0.96	0.15	19
	LB-ARHGDIB-1R	HLA-B*07:02	LPRACWREA	0.42	−0.07	10	(53)
			LPRACWPEA	0.42	−0.07	35
	LB-SSR1-1S	HLA-A*02:01	VLFRGGPRGSLAVA	0.89	−0.14	1403	(87)
			VLFRGGPRGLLAVA	0.86	−0.14	649
	LB-PRCP-1D	HLA-A*02:01	FMWDVAEDL	0.92	0.49	8	(53)
			FMWDVAEEL	0.95	0.49	3
	LB-MOB3A-1C	HLA-B*07:02	CPRPGTWTC	NAf	−0.13	442	(71)
			SPRPGTWTC		−0.09	69
	LB-PNP-1S	HLA-B*13:01	TQAQIFDYSEI	0.57	0.28	NAg	(71)
			TQAQIFDYGEI	0.4	0.28
	LB-GSTP1-1V	HLA-B*08:01	DLRCKYVSL	0.77	0.24	8	(71)
			DLRCKYISL	0.71	0.24	13
	C19ORF48	HLA-A*02:01	TAWPGAPEV	0.97	0.38	163	(72)
			TAWPGAPGV	0.96	0.38	268
Predicted not to bind HLAh	LB-C19ORF48-2E	HLA-B*51:01	TAWPGAPEV	0.97	0.38	24822	(71)
			TAWPGAPGV	0.96	0.38	25920
	LB-PDCD11-1F	HLA-B*07:02	GPDSSKTFLCL	0.97	0.15	7364	(53)
			GPDSSKTLLCL	0.96	0.15	7408
	LB-ZNFX1-1Q	HLA-B*40:01	NEIEDVWQLDL	0.94	0.47	5834	(71)
			NEIEDVWHLDL	0.96	0.47	4026
	LB-APOBEC3B-1K	HLA-B*08:01	KPQYHAEMCF	0.26	0.95	9287	(71)
			EPQYHAEMCF	0.26	0.82	4709
	LB-CCL4-1T	HLA-A*02:01	CADPSETWV	0.15	0.08	8014	(71)
			CADPSESWV	0.29	0.08	9995

^aFor B

^*44:02/03 binding mHags, only scores for B*44:03 are depicted.

^bThe upper peptide sequence corresponds to minor H antigen and the bottom to allelic counterpart.

^cBold values indicate the level of (predicted) differential peptide processing.

^dPredictions made by NetChop3.1, IEDB and NetMHC4.0.

^eHA-3 and SP110 are generated through differential internal proteasome cleavage and proteosome-catalyzed peptide splicing.

^fThe C-terminus of the MOB3A antigen is the C-terminus of the MOB3A protein.

^gThe HLA-B*13:01 binding prediction is not available at NetMHC4.0, but both peptides harbor the HLA-B*13 binding motif.

^hBecause the NetMHC4.0 affinity scores indicated no binding to HLA (>> 1,000 nM), it is currently complicated to assess potential differential HLA-binding, so we excluded these five minor H antigens from the analyses.