Protocol

Quantitative Proteomics by Mass Spectrometry

Volume 1410 of the series Methods in Molecular Biology pp 265-279

Date:

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

  • Ronald J. HolewinskiAffiliated withAdvanced Clinical Biosystems Research Institute, The Heart Institute, Cedars-Sinai Medical Center Email author 
  • , Sarah J. ParkerAffiliated withAdvanced Clinical Biosystems Research Institute, The Heart Institute, Cedars-Sinai Medical Center
  • , Andrea D. MatlockAffiliated withAdvanced Clinical Biosystems Research Institute, The Heart Institute, Cedars-Sinai Medical Center
  • , Vidya VenkatramanAffiliated withAdvanced Clinical Biosystems Research Institute, The Heart Institute, Cedars-Sinai Medical Center
  • , Jennifer E. Van EykAffiliated withAdvanced Clinical Biosystems Research Institute, The Heart Institute, Cedars-Sinai Medical Center

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Abstract

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