Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial

By Christina Ludwig, Ludovic C. Gillet, George A. Rosenberger, S. Amon, Ben C. Collins, R. Aebersold. Molecular Systems Biology, 2018

875 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/b55ab3d520da2c5d4a3d9a6df9b318a9d8199c76

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In Molecular Biology

1. David J. Beale
2. David S. Wishart
3. Amy M. Paten
4. F. Pinu
5. S. Swarup
6. K. Kouremenos
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In Spectroscopy

1. David S. Wishart
2. F. Pinu
3. Jianguo Xia

Citations in the corpus

• Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community (2019, background): “Over the past decade technological advancements in next-generation DNA sequencing [13], SNP-chip profiling [14], transcriptome measurements via RNA-seq [15], SWATH-based proteomics [16], and metabolomics via UPLC-MS and GC-MS techniques [17,18] have greatly increased the ease, and significantly redu”
• IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs (2020, neutral): “FD?̂?(t) = ∑ (1 − p(si)) si≥t ∑ 1si≥t i (5)”