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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.

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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.

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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.

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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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