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Code availability
The source code for the project can be found at https://philosopher.nesvilab.org 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 https://doi.org/10.5281/zenodo.3909842.
References
Deutsch, E. W. et al. Proteomics 10, 1150–1159 (2010).
Cox, J. & Mann, M. Nat. Biotechnol. 26, 1367–1372 (2008).
Vaudel, M. et al. Nat. Biotechnol. 33, 22–24 (2015).
da Veiga Leprevost, F. et al. Bioinformatics 33, 2580–2582 (2017).
Kong, A. T., Leprevost, F. V., Avtonomov, D. M., Mellacheruvu, D. & Nesvizhskii, A. I. Nat. Methods 14, 513–520 (2017).
Argentini, A. et al. Nat. Methods 13, 964–966 (2016).
Choi, M. et al. Bioinformatics 30, 2524–2526 (2014).
Li, K., Vaudel, M., Zhang, B., Ren, Y. & Wen, B. Bioinformatics 35, 1249–1251 (2019).
Blank, C. et al. Proteomes 6, 7 (2018).
Clark, D. J. et al. Cell 179, 964–983.e931 (2019).
Acknowledgements
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
Contributions
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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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). https://doi.org/10.1038/s41592-020-0912-y
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DOI: https://doi.org/10.1038/s41592-020-0912-y
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