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Philosopher: a versatile toolkit for shotgun proteomics data analysis

Nature Methods volume 17, pages 869–870 (2020)Cite this article

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To the Editor — Here we introduce Philosopher (https://philosopher.nesvilab.org), a free, open-source, versatile and robust data analysis toolkit designed to bring easy access to a powerful and comprehensive set of computational tools for shotgun proteomics data analysis.

Philosopher includes the database search engine Comet and can use the high-performance search engine MSFragger5 as a separately downloaded tool. For downstream processing of peptide–spectrum matches (PSMs), Philosopher includes key components of TPP. In addition, it implements best practices for false discovery rate (FDR) filtering and data summarization that are not readily available within the TPP, such as picked FDR, two-dimensional or sequential (at PSM and protein levels) filters, and additional options for dealing with peptides whose sequence is present in multiple proteins (for example, the razor peptide approach). As quantification is frequently the goal of modern proteomics experiments, Philosopher includes algorithms for both label-free quantification and isobaric label-based quantification (TMT or iTRAQ). Precursor spectral intensities are retrieved following a method described previously6. Protein-level quantification is estimated using the sum of the three most intense supporting ions. Alternatively, Philosopher can use TMT-Integrator (http://tmt-integrator.nesvilab.org/) as an external tool or output files can be used with downstream quantification and statistical tools such as MSstats7. The rich reports generated by Philosopher are also compatible with other software such as PDV for visualization of peptide assignments to tandem mass spectra8 and CRAPome and REPRINT (https://reprint-apms.org/) for interactome scoring and network visualization using affinity purification mass spectrometry data.

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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 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.

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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

  1. Department of Pathology, University of Michigan, Ann Arbor, MI, USA

    Felipe da Veiga Leprevost, Sarah E. Haynes, Dmitry M. Avtonomov, Hui-Yin Chang, Avinash K. Shanmugam, Dattatreya Mellacheruvu, Andy T. Kong & Alexey I. Nesvizhskii

  2. Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA

    Avinash K. Shanmugam, Dattatreya Mellacheruvu, Andy T. Kong & Alexey I. Nesvizhskii

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  1. Felipe da Veiga Leprevost
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  2. Sarah E. Haynes
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  8. Alexey I. Nesvizhskii
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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.

Corresponding author

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). https://doi.org/10.1038/s41592-020-0912-y

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