Table II. Peptide intensities derived from the same protein and intensities of different HLA-presented peptides from some selected proteins. As shown in Fig. 7, proteins can be represented by several peptides in the HLA ligandome. Here, three proteins were chosen that are represented by seven, five, and fvie peptides in HLA in B-LCL-HHC. As can be seen, these peptides can be presented by different alleles and have greatly differing hydrophobicity. Importantly, peptides derived from the same protein differ greatly in abundance. So, the abundance of an HLA ligand derived from a certain protein does not correlate with simply its protein intensity.

Protein name	Peptide sequence	Intensity	HLA allele	BMI	NetMHC (nM)	Gravy
Isoform 1 of clathrin heavy chain 1	NENSLFKSL	7.60E+07	B44	59	359	−0.622
	NPASKVIAL	2.64E+07	B7	51	13	0.7
	AEELFARKF	2.27E+07	B44	39	351	−0.267
	EEAFAIFRKF	6.45E+06	B44	47	17	0.11
	AETGQVQKI	5.32E+06	B44	41	671	−0.556
	FVHDLVLYL	3.30E+06	A2	41	13	1.622
	LLMVLSPRL	1.09E+06	A2	43	16	1.6
Mediator of RNA polymerase II transcription subunit 24	SLVEQLTMV	1.98E+07	A2	70	12	1.044
	SPTDRSMSSSL	1.87E+07	B7	56	10	−0.782
	KERWSDYQW	6.45E+06	B44	36	123	−2.533
	AEQMHKTGF	3.59E+06	B44	53	594	−0.967
	SLMDPPGTAL	1.31E+06	A2	35	31	0.27
Isoform 1 of Dedicator of cytokinesis protein 2	KMWEEAISL	3.42E+08	A2	58	9	−0.067
	SPRLSQTFLQL	5.26E+07	B7	52	21	−0.109
	IPGMVGPIL	5.20E+07	B7	36	89	1.656
	LEAYIQQHF	4.28E+06	B44	39	145	−0.233
	ILLQVAALKYI	1.71E+06	A2	49	63	1.773