Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial. Issue 8 (13th August 2018)

• Record Type: Journal Article
• Authors: Ludwig, Christina; Gillet, Ludovic; Rosenberger, George; Amon, Sabine; Collins, Ben C; Aebersold, Ruedi
• Is Part Of: Molecular systems biology. Volume 14:Issue 8(2018)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2018-08-13
• Subjects: data‐independent acquisition -- mass spectrometry -- quantitative proteomics -- SWATH‐MS -- systems biology; Molecular biology -- Periodicals; Systems biology -- Periodicals; 572.8
• DOI: 10.15252/msb.20178126
• Languages: English
• ISSNs: 1744-4292

Abstract

Abstract: Many research questions in fields such as personalized medicine, drug screens or systems biology depend on obtaining consistent and quantitatively accurate proteomics data from many samples. SWATH‐MS is a specific variant of data‐independent acquisition (DIA) methods and is emerging as a technology that combines deep proteome coverage capabilities with quantitative consistency and accuracy. In a SWATH‐MS measurement, all ionized peptides of a given sample that fall within a specified mass range are fragmented in a systematic and unbiased fashion using rather large precursor isolation windows. To analyse SWATH‐MS data, a strategy based on peptide‐centric scoring has been established, which typically requires prior knowledge about the chromatographic and mass spectrometric behaviour of peptides of interest in the form of spectral libraries and peptide query parameters. This tutorial provides guidelines on how to set up and plan a SWATH‐MS experiment, how to perform the mass spectrometric measurement and how to analyse SWATH‐MS data using peptide‐centric scoring. Furthermore, concepts on how to improve SWATH‐MS data acquisition, potential trade‐offs of parameter settings and alternative data analysis strategies are discussed. Abstract : SWATH‐MS combines deep proteome coverage with quantitative consistency and accuracy and is often the method of choice for personalized medicine, drug screens or systems biology. This tutorial provides guidelines on how to set up SWATH‐MS experiments, perform the mass spectrometric measurements and analyse the data.