Methods for SWATH™: Data Independent Acquisition on TripleTOF Mass Spectrometers

  • Ronald J. HolewinskiEmail author
  • Sarah J. Parker
  • Andrea D. Matlock
  • Vidya Venkatraman
  • Jennifer E. Van Eyk
Part of the Methods in Molecular Biology book series (MIMB, volume 1410)


Data independent acquisition (DIA also termed SWATH) is an emerging technology in the field of mass spectrometry based proteomics. Although the concept of DIA has been around for over a decade, the recent advancements, in particular the speed of acquisition, of mass analyzers have pushed the technique into the spotlight and allowed for high-quality DIA data to be routinely acquired by proteomics labs. In this chapter we will discuss the protocols used for DIA acquisition using the Sciex TripleTOF mass spectrometers and data analysis using the Sciex processing software.

Key words

Data independent acquisition (DIA) SWATH Quantitative proteomics Mass spectrometry Spectral ion library 



We would like to acknowledge funding to JVE from 1R01HL111362-01A, 1P01HL112730-01A1, 1U54NS091046-01, NHLBI-HV-10-05 [2], HHSN268201000032C and the Erika Glazer Endowed Chair for Women’s Heart Health and funding to SP from the National Marfan Foundation Victor E McKusick Post-Doctoral Fellowship; as well as the technical and intellectual support of Brigitt Simons and Christie Hunter at Sciex in many helpful discussions.


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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Ronald J. Holewinski
    • 1
    Email author
  • Sarah J. Parker
    • 1
  • Andrea D. Matlock
    • 1
  • Vidya Venkatraman
    • 1
  • Jennifer E. Van Eyk
    • 1
  1. 1.Advanced Clinical Biosystems Research Institute, The Heart InstituteCedars-Sinai Medical CenterLos AngelesUSA

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