qpMerge: Merging different peptide isoforms using a motif centric strategy
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Date
2016Author
Hindle, Matthew M.
Le Bihan, Thierry
Krahmer, Johanna
Martin, Sarah F.
Noordally, Zeenat B.
Simpson, T. Ian
Millar, Andrew J.
Metadata
Abstract
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.