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. 2020 Sep;17(9):869-870.
doi: 10.1038/s41592-020-0912-y.

Philosopher: a versatile toolkit for shotgun proteomics data analysis

Felipe da Veiga Leprevost  1 , Sarah E Haynes  1 , Dmitry M Avtonomov  1 , Hui-Yin Chang  1 , Avinash K Shanmugam  1   2 , Dattatreya Mellacheruvu  1   2 , Andy T Kong  1   2 , Alexey I Nesvizhskii  3   4
Affiliations

Philosopher: a versatile toolkit for shotgun proteomics data analysis

Felipe da Veiga Leprevost et al. Nat Methods. 2020 Sep.
No abstract available

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Conflict of interest statement

Competing Interests

The authors declare no competing interests.

Figures

Figure 1.
Figure 1.. Philosopher provides easy access to a complete suite of computational proteomics tools.
Functions include protein sequence database download and formatting, database searching, peptide-spectrum match validation with PeptideProphet, peptide evidence integration with iProphet, post-translational modification (PTM) localization with PTMProphet, and protein inference with ProteinProphet. Philosopher has multiple options for FDR scoring; performs label-free and labeling-based quantification, PTM annotation, generation of multi-level reports, and quantification comparison between samples. MSFragger and TMT-Integrator must be downloaded separately.
See this image and copyright information in PMC

References

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    1. da Veiga Leprevost F et al. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics 33, 2580–2582 (2017). - PMC - PubMed
    1. Kong AT, Leprevost FV, Avtonomov DM, Mellacheruvu D & Nesvizhskii AI MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nature methods 14, 513 (2017). - PMC - PubMed

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