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PeptideShaker enables reanalysis of MS-derived proteomics data sets

Nature Biotechnology volume 33, pages 22–24 (2015)Cite this article

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Figure 1: PeptideShaker data-analysis cycle.
Figure 2: The PeptideShaker overview tab, showing all proteins in the data set, along with the peptides and peptide-to-spectrum matches for the selected protein and peptide.

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Acknowledgements

M.V., R.P.Z., J.M.B. and A.S. gratefully acknowledge the financial support by the Ministerium für Innovation, Wissenschaft und Forschung des Landes Nordrhein-Westfalen and by the Bundesministerium für Bildung und Forschung. L.M. acknowledges the support of Ghent University (Multidisciplinary Research Partnership “Bioinformatics: from nucleotides to networks”), the PRIME-XS project, grant agreement number 262067, and the 'ProteomeXchange' project, grant agreement number 260558, both funded by the European Union 7th Framework Program. H.B. is supported by the Research Council of Norway. The study was supported by the Kristian Gerhard Jebsen Foundation. The authors would like to thank the PRIDE team for help regarding the use of the PRIDE archive web services and for validation of the PRIDE export formats. Finally, our thanks to all PeptideShaker users for thorough testing of the software and for coming up with valuable suggestions for improvements.

Author information

Authors and Affiliations

  1. Leibniz-Institut für Analytische Wissenschaften—ISAS—e.V., Dortmund, Germany

    Marc Vaudel, Julia M Burkhart, René P Zahedi & Albert Sickmann

  2. Department of Biomedicine, Proteomics Unit, University of Bergen, Bergen, Norway

    Marc Vaudel, Eystein Oveland, Frode S Berven & Harald Barsnes

  3. Department of Clinical Medicine, University of Bergen, Bergen, Norway

    Eystein Oveland

  4. Department of Clinical Medicine, The KG Jebsen Centre for MS Research, University of Bergen, Bergen, Norway

    Eystein Oveland & Frode S Berven

  5. Department of Neurology, The Norwegian Multiple Sclerosis Competence Centre, Haukeland University Hospital, Bergen, Norway

    Frode S Berven

  6. Department of Medical Protein Research, VIB, Ghent, Belgium

    Lennart Martens

  7. Department of Biochemistry, Ghent University, Ghent, Belgium

    Lennart Martens

  8. Computational Biology Unit, University of Bergen, Norway

    Harald Barsnes

Authors
  1. Marc Vaudel
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  2. Julia M Burkhart
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  4. Eystein Oveland
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  5. Frode S Berven
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  6. Albert Sickmann
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  7. Lennart Martens
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  8. Harald Barsnes
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Contributions

M.V. and H.B. did all of the programming and participated in writing the manuscript. R.P.Z., J.M.B., E.O., F.S.B. and A.S. contributed ideas, performed testing and participated in writing the manuscript. L.M. supervised the programming, provided ideas and participated in writing the manuscript. All authors participated in the preparation of the manuscript.

Corresponding author

Correspondence to Lennart Martens.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Note

Supplementary Note 1 (PDF 4403 kb)

Supplementary Software

PeptideShaker source code as a zip file (ZIP 16668 kb)

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Vaudel, M., Burkhart, J., Zahedi, R. et al. PeptideShaker enables reanalysis of MS-derived proteomics data sets. Nat Biotechnol 33, 22–24 (2015). https://doi.org/10.1038/nbt.3109

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