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

Nebiyu Abshiru, Olivier Caron-Lizotte, Roshan Elizabeth Rajan, Adil Jamai, Christelle Pomies, Alain Verreault () and Pierre Thibault ()
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Nebiyu Abshiru: Université de Montréal
Olivier Caron-Lizotte: Institute for Research in Immunology and Cancer, Université de Montréal
Roshan Elizabeth Rajan: Institute for Research in Immunology and Cancer, Université de Montréal
Adil Jamai: Institute for Research in Immunology and Cancer, Université de Montréal
Christelle Pomies: Institute for Research in Immunology and Cancer, Université de Montréal
Alain Verreault: Université de Montréal
Pierre Thibault: Université de Montréal

Nature Communications, 2015, vol. 6, issue 1, 1-9

Abstract: Abstract 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.

Date: 2015
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DOI: 10.1038/ncomms9648

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