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qpMerge: Merging different peptide isoforms using a motif centric strategy

Matthew M. Hindle, Thierry Le Bihan, Johanna Krahmer, Sarah F. Martin, Zeenat B. Noordally, T. Ian Simpson, Andrew J. Millar
doi: https://doi.org/10.1101/047100
Matthew M. Hindle
1SynthSys and School of Biological Sciences, University of Edinburgh, UK, EH9 3BF
2Institute of Structural and Molecular Biology, University of Edinburgh, UK, EH9 3BF
4Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh, UK, EH8 9AB
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Thierry Le Bihan
1SynthSys and School of Biological Sciences, University of Edinburgh, UK, EH9 3BF
2Institute of Structural and Molecular Biology, University of Edinburgh, UK, EH9 3BF
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Johanna Krahmer
1SynthSys and School of Biological Sciences, University of Edinburgh, UK, EH9 3BF
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Sarah F. Martin
1SynthSys and School of Biological Sciences, University of Edinburgh, UK, EH9 3BF
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Zeenat B. Noordally
1SynthSys and School of Biological Sciences, University of Edinburgh, UK, EH9 3BF
2Institute of Structural and Molecular Biology, University of Edinburgh, UK, EH9 3BF
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T. Ian Simpson
3Biomathematics & Statistics Scotland, University of Edinburgh, UK, EH9 3JZ
4Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh, UK, EH8 9AB
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Andrew J. Millar
1SynthSys and School of Biological Sciences, University of Edinburgh, UK, EH9 3BF
2Institute of Structural and Molecular Biology, University of Edinburgh, UK, EH9 3BF
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  • For correspondence: andrew.millar@ed.ac.uk
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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.

Footnotes

  • Abbreviations: AC: Alternative Cleavage site, AM: Alternative Modifications, CS: Charge State, CV: Coefficient of Variation, EMM: Exact Motif Matches, SD: Standard Deviation

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted April 05, 2016.
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qpMerge: Merging different peptide isoforms using a motif centric strategy
Matthew M. Hindle, Thierry Le Bihan, Johanna Krahmer, Sarah F. Martin, Zeenat B. Noordally, T. Ian Simpson, Andrew J. Millar
bioRxiv 047100; doi: https://doi.org/10.1101/047100
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qpMerge: Merging different peptide isoforms using a motif centric strategy
Matthew M. Hindle, Thierry Le Bihan, Johanna Krahmer, Sarah F. Martin, Zeenat B. Noordally, T. Ian Simpson, Andrew J. Millar
bioRxiv 047100; doi: https://doi.org/10.1101/047100

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