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