RT Journal Article
SR Electronic
T1 qpMerge: Merging different peptide isoforms using a motif centric strategy
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 047100
DO 10.1101/047100
A1 Matthew M. Hindle
A1 Thierry Le Bihan
A1 Johanna Krahmer
A1 Sarah F. Martin
A1 Zeenat B. Noordally
A1 T. Ian Simpson
A1 Andrew J. Millar
YR 2016
UL http://biorxiv.org/content/early/2016/04/05/047100.abstract
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.