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Discovery of protein acetylation patterns by deconvolution of peptide isomer mass spectra.

Abshiru N, Caron-Lizotte O, Rajan RE, Jamai A, Pomies C, Verreault A, Thibault P

Department of Chemistry, Université de Montréal, PO Box 6128, Station centre-ville, Montréal, Québec, Canada H3C 3J7.

Protein post-translational modifications (PTMs) play important roles in the control of various biological processes including protein-protein interactions, epigenetics and cell cycle regulation. Mass spectrometry-based proteomics approaches enable comprehensive identification and quantitation of numerous types of PTMs. However, the analysis of PTMs is complicated by the presence of indistinguishable co-eluting isomeric peptides that result in composite spectra with overlapping features that prevent the identification of individual components. In this study, we present Iso-PeptidAce, a novel software tool that enables deconvolution of composite MS/MS spectra of isomeric peptides based on features associated with their characteristic fragment ion patterns. We benchmark Iso-PeptidAce using dilution series prepared from mixtures of known amounts of synthetic acetylated isomers. We also demonstrate its applicability to different biological problems such as the identification of site-specific acetylation patterns in histones bound to chromatin assembly factor-1 and profiling of histone acetylation in cells treated with different classes of HDAC inhibitors.

Nat Commun 2015;6:8648.

Pubmed ID: 26468920

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