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 |