Proteomics pp 289-307 | Cite as

Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms

  • Hannes L. RöstEmail author
  • Ruedi AebersoldEmail author
  • Olga T. SchubertEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1550)


Targeted mass spectrometry comprises a set of methods able to quantify protein analytes in complex mixtures with high accuracy and sensitivity. These methods, e.g., Selected Reaction Monitoring (SRM) and SWATH MS, use specific mass spectrometric coordinates (assays) for reproducible detection and quantification of proteins. In this protocol, we describe how to analyze, in a targeted manner, data from a SWATH MS experiment aimed at monitoring thousands of proteins reproducibly over many samples. We present a standard SWATH MS analysis workflow, including manual data analysis for quality control (based on Skyline) as well as automated data analysis with appropriate control of error rates (based on the OpenSWATH workflow). We also discuss considerations to ensure maximal coverage, reproducibility, and quantitative accuracy.

Key words

Targeted proteomics SWATH SWATH MS SWATH acquisition Data-independent acquisition DIA OpenSWATH pyProphet TRIC aligner Skyline 


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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Institute of Molecular Systems BiologyETH ZurichZurichSwitzerland
  2. 2.Department of GeneticsStanford UniversityStanfordUSA
  3. 3.Faculty of ScienceUniversity of ZurichZurichSwitzerland
  4. 4.Department of Human GeneticsUniversity of California Los AngelesLos AngelesUSA

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