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We utilized the largest published version of the human immunopeptidome that we know of, downloaded from the Schubert lab on February 13th, 2011. The immunopeptidome contained 1510 unique protein identifications across 107 unique lysates across 44 distinct tissues (figures 2D and 3D). We excluded from our analysis proteins that mapped to multiple human proteins (Figures 2E and 3E). This included those proteins containing known modifications like posttranslational amino acid residues. From the remaining 226,187 nonredundant protein identifications, the major and minor histocompatibility antigen immunopeptidome is comprised of just 164 proteins (Figures 2F and 3F).

The advent of innovative technologies have revealed a more complex organization of the cellular proteome than was originally thought. For example, transcript variants of the same gene (e.g., myosin heavy chain-4 (MYH4)) may yield distinct proteins (MYH4-1, MYH4-2, MYH4-3). This leads to the use of alternative polyadenylation sites and alternative splicing to generate multiple mRNA and protein isoforms, respectively. In a recent study, the authors found that there were a large number of splice isoforms of angiotensinogen generated by alternative splicing, with splice variants of 15-20% of the transcriptome defined in human tissue proteomes.33 76 In the same study, a comparable number of tissue-specific splice variants were found to be expressed in human tissue proteomes, and these were found to be largely independent of tissue of origin, which demonstrates that splice isoforms of human proteins are independent of their tissue of origin. In addition to alternative splicing, we observed multiple polyadenylation sites of transcripts that encode the same protein.

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