SWATH-MS: Data Acquisition and Analysis

K. Frederick, Pawel S Ciborowski

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Scopus citations


Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) is an emerging proteomic platform for label free quantification. This platform is based on data independent acquisition (DIA) principle for simultaneous protein identification and quantification. SWATH-MS requires establishment of spectral library which is discussed in this chapter. SWATH-MS data analysis requires targeted data extraction, data normalization. Typical presentation of results from experiments using SWATH-MS is principal component analysis. Several pipelines of DIA analysis are available, however MarkerView and Skyline are two the most commonly used.

Original languageEnglish (US)
Title of host publicationProteomic Profiling and Analytical Chemistry
Subtitle of host publicationThe Crossroads: Second Edition
PublisherElsevier Inc.
Number of pages13
ISBN (Print)9780444636881
Publication statusPublished - Mar 22 2016



  • Data dependent acquisition
  • Data independent acquisition
  • MarkerView
  • Principal component analysis
  • Skyline
  • Statistical analysis

ASJC Scopus subject areas

  • Chemistry(all)

Cite this

Frederick, K., & Ciborowski, P. S. (2016). SWATH-MS: Data Acquisition and Analysis. In Proteomic Profiling and Analytical Chemistry: The Crossroads: Second Edition (pp. 161-173). Elsevier Inc.. https://doi.org/10.1016/B978-0-444-63688-1.00009-4