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Generation of High-Quality SWATH® Acquisition Data for Label-free Quantitative Proteomics Studies Using TripleTOF® Mass Spectrometers

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Proteomics

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

Abstract

Data-independent acquisition is a powerful mass spectrometry technique that enables comprehensive MS and MS/MS analysis of all detectable species, providing an information rich data file that can be mined deeply. Here, we describe how to acquire high-quality SWATH® Acquisition data to be used for large quantitative proteomic studies. We specifically focus on using variable sized Q1 windows for acquisition of MS/MS data for generating higher specificity quantitative data.

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Acknowledgments

We acknowledge support from the NIH shared instrumentation grant for the TripleTOF 6600 system at the Buck Institute (1S10 OD016281, B.W.G.).

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Authors and Affiliations

  1. The Buck Institute for Research on Aging, 1201 Radio Road, Redwood City, 94065, CA, USA

    Birgit Schilling & Bradford W. Gibson

  2. SCIEX, 500 Old Connecticut Path, Framingham, MA, 01701, USA

    Christie L. Hunter

Authors
  1. Birgit Schilling
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  2. Bradford W. Gibson
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  3. Christie L. Hunter
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Corresponding author

Correspondence to Christie L. Hunter .

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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Schilling, B., Gibson, B.W., Hunter, C.L. (2017). Generation of High-Quality SWATH® Acquisition Data for Label-free Quantitative Proteomics Studies Using TripleTOF® Mass Spectrometers. 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_16

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  • DOI: https://doi.org/10.1007/978-1-4939-6747-6_16

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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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