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Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms

View ORCID ProfileHannes L. Röst, Ruedi Aebersold, View ORCID ProfileOlga T. Schubert
doi: https://doi.org/10.1101/044552
Hannes L. Röst
1Institute of Molecular Systems Biology, ETH Zurich, CH-8093 Zurich, Switzerland
2Department of Genetics, Stanford University, Stanford, CA 94305, USA
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Ruedi Aebersold
1Institute of Molecular Systems Biology, ETH Zurich, CH-8093 Zurich, Switzerland
3Faculty of Science, University of Zurich, CH-8057 Zurich, Switzerland
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Olga T. Schubert
1Institute of Molecular Systems Biology, ETH Zurich, CH-8093 Zurich, Switzerland
4Department of Human Genetics, University of California Los Angeles, LosAngeles, CA 90095, UAS
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Summary

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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted March 19, 2016.
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Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms
Hannes L. Röst, Ruedi Aebersold, Olga T. Schubert
bioRxiv 044552; doi: https://doi.org/10.1101/044552
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Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms
Hannes L. Röst, Ruedi Aebersold, Olga T. Schubert
bioRxiv 044552; doi: https://doi.org/10.1101/044552

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