Using data-independent, high-resolution mass spectrometry in protein biomarker research: perspectives and clinical applications

Proteomics Clin Appl. 2015 Apr;9(3-4):307-21. doi: 10.1002/prca.201400117. Epub 2015 Feb 23.


In medicine, there is an urgent need for protein biomarkers in a range of applications that includes diagnostics, disease stratification, and therapeutic decisions. One of the main technologies to address this need is MS, used for protein biomarker discovery and, increasingly, also for protein biomarker validation. Currently, data-dependent analysis (also referred to as shotgun proteomics) and targeted MS, exemplified by SRM, are the most frequently used mass spectrometric methods. Recently developed data-independent acquisition techniques combine the strength of shotgun and targeted proteomics, while avoiding some of the limitations of the respective methods. They provide high-throughput, accurate quantification, and reproducible measurements within a single experimental setup. Here, we describe and review data-independent acquisition strategies and their recent use in clinically oriented studies. In addition, we also provide a detailed guide for the implementation of SWATH-MS (where SWATH is sequential window acquisition of all theoretical mass spectra)-one of the data-independent strategies that have gained wide application of late.

Keywords: Biomarker; Data-independent acquisition (DIA); Mass spectrometry; Proteomics; SWATH mass spectrometry.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Animals
  • Biomarkers / analysis*
  • Humans
  • Mass Spectrometry / methods*


  • Biomarkers