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Global proteogenomic analysis of human MHC I peptides derived from non­canonical reading frames


Using high­throughput mass spectrometry, we probed the six­reading­frame translation of human B cells’ transcriptome. We report that about 10% of MHC I­associated peptides (MAPs) derive from non­canonical reading frames. These so­called cryptic MAPs originate from allegedly non- coding genomic sequences and from out­of­frame translation. Their biogenesis and properties differ in many ways from those of conventional MAPs. Thus, cryptic MAPs come from very short proteins with atypical C­termini, and they are coded by transcripts bearing long UTRs selectively enriched in destabilizing elements. Cryptic MAPs increase the complexity of the immunopeptidome and represent an heretofore unexploited source of potential tumor­specific epitopes. In a more general context, the features of cryptic MAPs suggest that mRNA instability is instrumental in the biogenesis of MAPs. Associated RNA-seq accession: GSE67174 .

Sample Processing Protocol

MAPs were eluted from B-LCL and sequenced by mass spectrometry as previously described : Granados,D.P. et al. Impact of genomic polymorphism on the repertoire of human MHC class I-associated peptides. Nat Commun 5, 3600 (2014)

Data Processing Protocol

Mascot search engine (Matrix Science) was used in combination with custom databases including reverse sequences. Mass tolerance on the precursor and fragment ions were set to 5 p.p.m and 0.02 Da, respectively. Searches were performed without enzyme specificity and cysteinylation, phosphorylation (on Ser, Thr and Tyr), oxidation (Met) and deamidation (Asn, Gln) were used as variable modifications. Following each database search, we converted raw files to peptide maps containing m/z values, charge state, retention time and intensity above detection threshold (≥ 8,000) using ProteoProfile ( Peptide maps were further aligned to derive a list of peptides identified by each database as well as their abundance across the four replicates.


Olivier Caron-Lizotte, University of Montreal - IRIC
Olivier Caron-Lizotte, IRIC - University of Montreal ( lab head )

Submission Date


Publication Date



    Laumont CM, Daouda T, Laverdure JP, Bonneil É, Caron-Lizotte O, Hardy MP, Granados DP, Durette C, Lemieux S, Thibault P, Perreault C. Global proteogenomic analysis of human MHC class I-associated peptides derived from non-canonical reading frames. Nat Commun. 2016 Jan 5;7:10238 PubMed: 26728094


Showing 1 - 2 of 2 results
# Accession Title Proteins Peptides Unique Peptides Spectra Identified Spectra View in Reactome
1 46779 Cryptic Immunopeptide in Subject 3 1699 10041 1828 79049 8956
2 46780 Cryptic Immunopeptides of Subject 4 442 3076 491 96860 2558