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Updated: Nov 21, 2025

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Biosaur: An open-source Python software for liquid chromatography-mass spectrometry peptide feature detection with

Daniil A Abdrakhimov1,2, Julia A Bubis1, Vladimir Gorshkov3

  • 1V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow, 119334, Russia.

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|January 15, 2021
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Summary

Biosaur software enhances peptide feature detection in mass spectrometry data by utilizing ion mobility information. This open-source tool supports timsTOF and FAIMS instruments, improving data analysis for proteomics research.

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Area of Science:

  • Proteomics
  • Computational Biology
  • Analytical Chemistry

Background:

  • Peptide feature detection is crucial for mass spectrometry data analysis.
  • Ion mobility provides an additional separation dimension, enhancing detection capabilities.
  • Limited open-source software exists for analyzing ion mobility data from instruments like timsTOF and FAIMS-Orbitrap.

Purpose of the Study:

  • To develop an open-source software tool, Biosaur, for peptide feature detection using ion mobility data.
  • To extend the functionality of existing software (Dinosaur) to incorporate ion mobility information.
  • To enable the analysis of mass spectra from advanced instruments like timsTOF and FAIMS-Orbitrap.

Main Methods:

  • Biosaur was developed using Python 3.8.
  • The software extends the capabilities of the Dinosaur utility.
  • It processes peptide ion mass spectra with ion mobility data.

Main Results:

  • Biosaur supports data from timsTOF and FAIMS instruments.
  • It processes spectra acquired in negative ion mode.
  • The software generates cosine correlation tables for differentiating peptide features.

Conclusions:

  • Biosaur is an open-source utility for detecting peptide features in LC-MS data with ion mobility.
  • It supports negative ion mode analysis and provides valuable differentiation tools.
  • The software is freely available on Github under the APACHE 2.0 license.