Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial,Molecular Systems Biology

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Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial
Molecular Systems Biology ( IF 8.5 ) Pub Date : 2018-08-13 , DOI: 10.15252/msb.20178126
Christina Ludwig ₁ , Ludovic Gillet ₂ , George Rosenberger _{2,

3} , Sabine Amon ₂ , Ben C Collins ₂ , Ruedi Aebersold _{2,

4}

Affiliation

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.

中文翻译：

用于定量蛋白质组学的基于数据独立采集的 SWATH-MS：教程

个性化医疗、药物筛选或系统生物学等领域的许多研究问题都依赖于从许多样本中获得一致且定量准确的蛋白质组学数据。 SWATH-MS 是数据独立采集 (DIA) 方法的一种特定变体，是一种将深度蛋白质组覆盖能力与定量一致性和准确性相结合的新兴技术。在 SWATH-MS 测量中，给定样品中落在指定质量范围内的所有电离肽均使用相当大的前体隔离窗口以系统且无偏差的方式进行碎片化。为了分析 SWATH-MS 数据，建立了一种基于以肽为中心的评分的策略，该策略通常需要以谱库和肽查询参数的形式预先了解感兴趣的肽的色谱和质谱行为。本教程提供了有关如何设置和计划 SWATH-MS 实验、如何执行质谱测量以及如何使用以肽为中心的评分来分析 SWATH-MS 数据的指南。此外，还讨论了如何改进 SWATH-MS 数据采集、参数设置的潜在权衡和替代数据分析策略的概念。

更新日期：2019-11-18

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