PRIDE Assigned Tags:Biological Dataset
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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 (http://proteomics.iric.ca/tools/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.
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