Pyteomics—a Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics

  • Anton A. Goloborodko
  • Lev I. Levitsky
  • Mark V. Ivanov
  • Mikhail V. Gorshkov
Application Note


Pyteomics is a cross-platform, open-source Python library providing a rich set of tools for MS-based proteomics. It provides modules for reading LC-MS/MS data, search engine output, protein sequence databases, theoretical prediction of retention times, electrochemical properties of polypeptides, mass and m/z calculations, and sequence parsing. Pyteomics is available under Apache license; release versions are available at the Python Package Index, the source code repository at, documentation at Pyteomics.biolccc documentation is available at Questions on installation and usage can be addressed to pyteomics mailing list:

Key words

Data processing Bioinformatics Proteomics 



The authors are grateful to their colleagues Dr. Irina Tarasova, Dr. Marina Pridatchenko, Anna Lobas, and Tatiana Perlova from the Institute for Energy Problems of Chemical Physics, as well as Dr. Achim Treumann from the University of Newcastle for useful discussions and suggestions on pyteomics functionality.

This work was supported in part by grants from the European Commission (FP7 project Prot-HiSPRA, #282506) and the Russian Basic Science Foundation (project #11-04-00515).


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Copyright information

© American Society for Mass Spectrometry 2013

Authors and Affiliations

  • Anton A. Goloborodko
    • 1
    • 2
    • 3
  • Lev I. Levitsky
    • 2
    • 3
  • Mark V. Ivanov
    • 2
    • 3
  • Mikhail V. Gorshkov
    • 2
    • 3
  1. 1.Department of PhysicsMassachusetts Institute of TechnologyBostonUSA
  2. 2.Institute for Energy Problems of Chemical PhysicsRussian Academy of SciencesMoscowRussia
  3. 3.Moscow Institute of Physics and Technology (State University)DolgoprudnyRussia

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