qpMerge: Merging different peptide isoforms using a motif centric strategy

Matthew M Hindle, Thierry Le Bihan, Johanna Krahmer, Sarah F Martin, Zeenat B Noordally, T. Ian Simpson, Andrew J. Millar

Research output: Working paper

Abstract / Description of output

Accurate quantification and enumeration of peptide motifs is hampered by redundancy in peptide identification. A single phosphorylation motif may be split across charge states, alternative modifications (e.g. acetylation and oxidation), and multiple miss-cleavage sites which render the biological interpretation of MS data a challenge. In addition motif redundancy can affect quantitative and statistical analysis and prevent a realistic comparison of peptide numbers between datasets. In this study, we present a merging tool set developed for the Galaxy workflow environment to achieve a non-redundant set of quantifications for phospho-motifs. We present a Galaxy workflow to merge three exemplar dataset, and observe reduced phospho-motif redundancy and decreased replicate variation. The qpMerge tools provide a straightforward and reusable approach to facilitating phospho-motif analysis. The source-code and wiki documentation is publically available at http://sourceforge.net/projects/ppmerge. The galaxy pipeline used in the exemplar analysis can be found at http://www.myexperiment.org/workflows/4186.
Original languageEnglish
PublisherbioRxiv, at Cold Spring Harbor Laboratory
Number of pages9
Publication statusPublished - 5 Apr 2016


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