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Proteomics pp 223-233 | Cite as

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

  • Birgit Schilling
  • Bradford W. Gibson
  • Christie L. HunterEmail author
Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

Mass spectrometry SWATH acquisition Data-independent acquisitions Variable windows Quantitation Proteomics 

Notes

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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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Birgit Schilling
    • 1
  • Bradford W. Gibson
    • 1
  • Christie L. Hunter
    • 2
    Email author
  1. 1.The Buck Institute for Research on AgingRedwood CityUSA
  2. 2.SCIEXFraminghamUSA

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