SWATH mass spectrometry for proteomics of non-depleted plasma

Christoph Krisp, Mark P. Molloy*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

6 Citations (Scopus)


The limitations commonly observed in data-dependent acquisition (DDA) mass spectrometric investigation of non-depleted human plasma are mainly due to the large dynamic concentration range of protein expression. Less abundant proteins are usually masked by highly abundant proteins and are therefore difficult to reliably detect. Sequential window acquisition of all theoretical fragment-ion spectra (SWATH) mass spectrometry (MS), as a representative of data-independent acquisition (DIA) approaches, provides an opportunity to improve plasma-based biomarker discovery studies because this approach does not rely on precursor intensity for fragmentation selection but rather analyzes all precursors in specified mass ranges. Here, we describe a workflow for SWATH-MS-based analysis of non-depleted plasma including sample preparation, data acquisition, and statistical analysis.

Original languageEnglish
Title of host publicationSerum/plasma proteomics
Subtitle of host publicationmethods and protocols
EditorsDavid W. Greening, Richard J. Simpson
Place of PublicationNew York
PublisherHumana Press
Number of pages11
ISBN (Electronic)9781493970575
ISBN (Print)9781493970568
Publication statusPublished - 2017

Publication series

NameMethods in molecular biology
PublisherHumana Press
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Plasma
  • Label-free quantitation
  • Data-independent acquisition
  • Mass spectrometry


Dive into the research topics of 'SWATH mass spectrometry for proteomics of non-depleted plasma'. Together they form a unique fingerprint.

Cite this