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qpMerge: Merging different peptide isoforms using a motif centric strategy

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qPMerge_bioarXive.pdf (540.3Kb)
Date
2016
Author
Hindle, Matthew M.
Le Bihan, Thierry
Krahmer, Johanna
Martin, Sarah F.
Noordally, Zeenat B.
Simpson, T. Ian
Millar, Andrew J.
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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.
URI
http://hdl.handle.net/1842/15770
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