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Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms

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Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1550))

Abstract

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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Author information

Authors and Affiliations

  1. Institute of Molecular Systems Biology, ETH Zurich, CH-8093, Zurich, Switzerland

    Hannes L. Röst, Ruedi Aebersold & Olga T. Schubert

  2. Department of Genetics, Stanford University, Stanford, CA, 94305, USA

    Hannes L. Röst

  3. Faculty of Science, University of Zurich, CH-8057, Zurich, Switzerland

    Ruedi Aebersold

  4. Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, 90095, USA

    Olga T. Schubert

Authors
  1. Hannes L. Röst
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  2. Ruedi Aebersold
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  3. Olga T. Schubert
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Corresponding authors

Correspondence to Hannes L. Röst , Ruedi Aebersold or Olga T. Schubert .

Editor information

Editors and Affiliations

  1. Keck School of Medicine, University of Southern California, Los Angeles, California, USA

    Lucio Comai

  2. Keck School of Medicine, University of Southern California, Los Angeles, California, USA

    Jonathan E. Katz

  3. Stanford University, Palo Alto, California, USA

    Parag Mallick

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Röst, H.L., Aebersold, R., Schubert, O.T. (2017). Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms. In: Comai, L., Katz, J., Mallick, P. (eds) Proteomics. Methods in Molecular Biology, vol 1550. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6747-6_20

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  • DOI: https://doi.org/10.1007/978-1-4939-6747-6_20

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6745-2

  • Online ISBN: 978-1-4939-6747-6

  • eBook Packages: Springer Protocols

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