Reduction of Ambiguity in Phosphorylation-site Localization in Large-scale Phosphopeptide Profiling by Data Filter using Unique Mass Class Information

Abstract

Department of Applied Chemistry, College of Applied Science, Kyung Hee University, Yongin, Gyeonggi 446-701, KoreaReceived September 21, 2013, Accepted October 1, 2013The rapid development of shotgun proteomics is paving the way for extensive proteome profiling, whileproviding extensive information on various post translational modifications (PTMs) that occur to a proteomeof interest. For example, the current phosphoproteomic methods can yield more than 10,000 phosphopeptidesidentified from a proteome sample. Despite these developments, it remains a challenging issue to pinpoint thetrue phosphorylation sites, especially when multiple sites are possible for phosphorylation in the peptides. Wedeveloped the Phospho-UMC filter, which is a simple method of localizing the site of phosphorylation usingunique mass classes (UMCs) information to differentiate phosphopeptides with different phosphorylation sitesand increase the confidence in phosphorylation site localization. The method was applied to large scalephosphopeptide profiling data and was demonstrated to be effective in the reducing ambiguity associated withthe tandem mass spectrometric data analysis of phosphopeptides. Key Words : Phosphoproteomics, Phosphorylation site, Unique mass class IntroductionProtein phosphorylation plays an important role in under-standing cell signaling cascade for many signal transduc-tions in eukaryotes.