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PeptideShaker enables reanalysis of MS-derived proteomics data sets

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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.

References

  1. Martens, L. et al. Proteomics 5, 3537–3545 (2005).

    Article  CAS  Google Scholar 

  2. Côté, R.G. et al. Mol. Cell. Proteomics 11, 1682–1689 (2012).

    Article  Google Scholar 

  3. Barsnes, H., Vizcaíno, J.A., Eidhammer, I. & Martens, L. Nat. Biotechnol. 27, 598–599 (2009).

    Article  CAS  Google Scholar 

  4. Wang, R. et al. Nat. Biotechnol. 30, 135–137 (2012).

    Article  Google Scholar 

  5. Vizcaíno, J.A. et al. Nat. Biotechnol. 32, 223–226 (2014).

    Article  Google Scholar 

  6. Matic, I., Ahel, I. & Hay, R.T. Nat. Methods 9, 771–772 (2012).

    Article  CAS  Google Scholar 

  7. Hahne, H., Moghaddas Gholami, A. & Kuster, B. Mol. Cell. Proteomics 11, 843–850 (2012).

    Article  CAS  Google Scholar 

  8. Editors. Nat. Biotechnol. 31, 857 (2013).

  9. Martin, S.F. et al. J. Proteomics 88, 41–46 (2013).

    Article  CAS  Google Scholar 

  10. Elias, J.E. & Gygi, S.P. Nat. Methods 4, 207–214 (2007).

    Article  CAS  Google Scholar 

  11. Shteynberg, D., Nesvizhskii, A.I., Moritz, R.L. & Deutsch, E.W. Mol. Cell. Proteomics 12, 2383–2393 (2013).

    Article  CAS  Google Scholar 

  12. Nesvizhskii, A.I. J. Proteomics 73, 2092–2123 (2010).

    Article  CAS  Google Scholar 

  13. Nesvizhskii, A.I. & Aebersold, R. Mol. Cell Proteomics 4, 1419–1440 (2005).

    Article  CAS  Google Scholar 

  14. Vaudel, M. et al. J. Proteome Res. 11, 5065–5071 (2012).

    Article  CAS  Google Scholar 

  15. Barsnes, H., Eidhammer, I. & Martens, L. Proteomics 11, 1181–1188 (2011).

    Article  CAS  Google Scholar 

  16. Paik, Y.K. et al. Nat. Biotechnol. 30, 221–223 (2012).

    Article  CAS  Google Scholar 

  17. Jones, A.R. et al. Mol. Cell. Proteomics 11, M111.014381 (2012).

    Article  Google Scholar 

  18. Goecks, J., Nekrutenko, A., Taylor, J. & Galaxy, T. Genome Biol. 11, R86 (2010).

    Article  Google Scholar 

  19. Vaudel, M., Barsnes, H., Berven, F.S., Sickmann, A. & Martens, L. Proteomics 11, 996–999 (2011).

    Article  CAS  Google Scholar 

Download references

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.

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Authors

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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