A data processing toolkit for shotgun proteomics.



Philosopher provides easy access to third-party tools and custom algorithms allowing users to develop proteomics analysis, from Peptide Spectrum Matching to annotated protein reports. Philosopher is also tuned for Open Search analysis, providing a modified version of the prophets for peptide validation and protein inference. To this date, Philosopher is the only proteomics toolkit that allows you to process and analyze close and open search results.

How to Download

Download the latest version here

How to Use

A simple tutorial is also provided with an extensive example on how to use Philosopher.


Check the documentation for more details about the available commands.

Questions, requests and bug reports

If you have any questions, remarks, requests or if you found a bug, please use the Issue tracker.


Check the analytics session for more information on the program usage report.

How to cite

Still in progress!

About the developers

Felipe da Veiga leprevost

Alexey Nesvizhskii’s nesvilab


Since Philosopher is not officially released, the binaries provided here have no license. Once released, the software will be licensed under the GPL 3 license.