PT  - JOURNAL ARTICLE
AU  - Matthew M. Hindle
AU  - Thierry Le Bihan
AU  - Johanna Krahmer
AU  - Sarah F. Martin
AU  - Zeenat B. Noordally
AU  - T. Ian Simpson
AU  - Andrew J. Millar
TI  - qpMerge: Merging different peptide isoforms using a motif centric strategy
AID  - 10.1101/047100
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 047100
4099  - http://biorxiv.org/content/early/2016/04/05/047100.short
4100  - http://biorxiv.org/content/early/2016/04/05/047100.full
AB  - 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.