Sequential Window Acquisition of all THeoretical fragment ion spectra (SWATH) is a data independent acquisition mode used to accurately quantify thousands of proteins in a biological sample in a single run. It exploits fast scanning hybrid mass spectrometers to combine accuracy, reproducibility and sensitivity. This method requires the use of ion libraries, a sort of databases of spectral and chromatographic information about the proteins to be quantified. In this chapter, a typical workflow of SWATH experiment is described, from the sample preparation to the analysis of proteomics data.
Keywords: High-resolution LC-MS/MS; Ion library; Multivariate data analysis; Quantitative proteomics; SWATH.