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Philosopher: a versatile toolkit for shotgun proteomics data analysis

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Fig. 1: Philosopher provides easy access to a complete suite of computational proteomics tools.

Code availability

The source code for the project can be found at under the GNU General Public License version 3, along with documentation and tutorials covering various use cases. The DOI for Philosopher (version 3.2.9) is


  1. Deutsch, E. W. et al. Proteomics 10, 1150–1159 (2010).

    Article  CAS  Google Scholar 

  2. Cox, J. & Mann, M. Nat. Biotechnol. 26, 1367–1372 (2008).

    Article  CAS  Google Scholar 

  3. Vaudel, M. et al. Nat. Biotechnol. 33, 22–24 (2015).

    Article  CAS  Google Scholar 

  4. da Veiga Leprevost, F. et al. Bioinformatics 33, 2580–2582 (2017).

    Article  CAS  Google Scholar 

  5. Kong, A. T., Leprevost, F. V., Avtonomov, D. M., Mellacheruvu, D. & Nesvizhskii, A. I. Nat. Methods 14, 513–520 (2017).

    Article  CAS  Google Scholar 

  6. Argentini, A. et al. Nat. Methods 13, 964–966 (2016).

    Article  CAS  Google Scholar 

  7. Choi, M. et al. Bioinformatics 30, 2524–2526 (2014).

    Article  CAS  Google Scholar 

  8. Li, K., Vaudel, M., Zhang, B., Ren, Y. & Wen, B. Bioinformatics 35, 1249–1251 (2019).

    Article  CAS  Google Scholar 

  9. Blank, C. et al. Proteomes 6, 7 (2018).

    Article  CAS  Google Scholar 

  10. Clark, D. J. et al. Cell 179, 964–983.e931 (2019).

    Article  CAS  Google Scholar 

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We thank the developers of PDV and the TPP tools for discussions and technical assistance, and the growing community of Philosopher users for their feedback and suggestions. This work was supported in part by NIH grants R01-GM-094231 (A.I.N) and U24-CA210967 (A.I.N.).

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Authors and Affiliations



F.d.V.L. and A.I.N conceptualized and designed the project. F.d.V.L. is the main developer and maintainer of the Philosopher toolkit. S.E.H. contributed to writing the code, testing, and documentation. D.M.A., H.-Y.C., A.K.S., D.M. and A.T.K contributed to development and evaluation. F.d.V.L., S.E.H and A.I.N. wrote the paper with input from all authors. A.I.N. supervised the project.

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Correspondence to Alexey I. Nesvizhskii.

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The authors declare no competing interests.

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Editorial note: This article has been peer reviewed.

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da Veiga Leprevost, F., Haynes, S.E., Avtonomov, D.M. et al. Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nat Methods 17, 869–870 (2020).

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