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TIMSCONVERT: a workflow to convert trapped ion mobility data to open data formats.

Gordon T Luu1, Michael A Freitas2, Itzel Lizama-Chamu1

  • 1Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.

Bioinformatics (Oxford, England)
|June 27, 2022
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Summary

TIMSCONVERT is a new workflow that converts timsTOF Pro/fleX mass spectrometer data into open-source compatible formats, improving data analysis interoperability for ion mobility spectrometry. This enhances high-throughput analysis in mass spectrometry.

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Area of Science:

  • Mass Spectrometry
  • Ion Mobility Spectrometry
  • Proteomics
  • Metabolomics

Background:

  • Modern mass spectrometers, such as timsTOF Pro/fleX, offer advanced capabilities including ion mobility spectrometry.
  • Existing software ecosystems often lack seamless interoperability with open-source data analysis tools and pipelines.
  • This limitation hinders efficient downstream analysis of complex mass spectrometry data.

Purpose of the Study:

  • To develop a high-throughput data conversion workflow for timsTOF Pro/fleX mass spectrometer raw data.
  • To ensure compatibility of converted data with established open-source data analysis software and pipelines.
  • To facilitate the integration of ion mobility data into downstream analytical workflows.

Main Methods:

  • Development of TIMSCONVERT, a data conversion workflow.
  • Conversion of raw data files from timsTOF Pro/fleX instruments to mzML and imzML formats.
  • Incorporation of ion mobility data during the conversion process.
  • Validation using data from diverse experiments and acquisition modalities on the timsTOF fleX MS.

Main Results:

  • TIMSCONVERT successfully converts timsTOF Pro/fleX raw data to mzML and imzML formats.
  • The workflow preserves and incorporates ion mobility data, crucial for detailed analysis.
  • Compatibility with standard downstream analysis tools is maintained, enhancing data accessibility.
  • Demonstrated utility across various experimental setups and acquisition methods.

Conclusions:

  • TIMSCONVERT addresses the critical need for interoperability in mass spectrometry data analysis.
  • The workflow enables seamless integration of timsTOF Pro/fleX data, including ion mobility, into open-source pipelines.
  • This facilitates high-throughput analysis and broader accessibility of advanced mass spectrometry data.