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Getting Started

Note

OpenSWATH is part of the OpenMS project, therefore if you install OpenMS you will get OpenSWATH automatically. Please refer to our installation instructions.

To get started with the DIA or SWATH-MS analysis, we recommend to follow the recently published step-for-step tutorial [1] describing a complete OpenSWATH analysis workflow using OpenSwathWorkflow available from bioRxiv. In addition, you can find in-depth information about the different tools in a SWATH analysis on this page.

Tutorial Data

You can access the tutorial data (a M. tuberculosis dataset) used in the 2017 Methods Mol Biol. OpenSWATH tutorial [1] here. The data contains

  • 3 mzML instrument data files (centroided)
  • 3 WIFF raw instrument data files
  • Mtb assay library (for OpenMS 2.1 and higher)
  • Mtb assay library (for older OpenMS)
  • Swath windows file for analysis
  • iRT assay file (TraML format)

Questions?

Please address questions directly to the mailing list.

References

[1](1, 2) Röst HL, Aebersold R, Schubert OT. Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms. Methods Mol Biol. 2017;1550:289-307. doi: 10.1007/978-1-4939-6747-6_20. PMID: 28188537