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

Gordon T Luu; Michael A Freitas; Itzel Lizama-Chamu; Catherine S McCaughey; Laura M Sanchez; Mingxun Wang

doi:10.1093/bioinformatics/btac419

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

Bioinformatics. 2022 Aug 10;38(16):4046-4047. doi: 10.1093/bioinformatics/btac419.

Authors

Gordon T Luu¹, Michael A Freitas², Itzel Lizama-Chamu¹, Catherine S McCaughey¹, Laura M Sanchez¹, Mingxun Wang³

Affiliations

¹ Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.
² Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH, 43210, USA.
³ Department of Computer Science and Engineering, University of California Riverside, Riverside, CA 92521, USA.

Abstract

Motivation: Advances in mass spectrometry have led to the development of mass spectrometers with ion mobility spectrometry capabilities and dual-source instrumentation; however, the current software ecosystem lacks interoperability with downstream data analysis using open-source software and pipelines.

Results: Here, we present TIMSCONVERT, a data conversion high-throughput workflow from timsTOF Pro/fleX mass spectrometer raw data files to mzML and imzML formats that incorporates ion mobility data while maintaining compatibility with data analysis tools. We showcase several examples using data acquired across different experiments and acquisition modalities on the timsTOF fleX MS.

Availability and implementation: TIMSCONVERT and its documentation can be found at https://github.com/gtluu/timsconvert and is available as a standalone command-line interface tool for Windows and Linux, NextFlow workflow and online in the Global Natural Products Social (GNPS) platform.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Data Analysis
Ecosystem*
Mass Spectrometry / methods
Software*
Workflow

Abstract

Publication types

MeSH terms

Grants and funding