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] 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