Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial
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 te...
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| Format: | Article |
| Language: | English |
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Springer Nature
2018-08-01
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| Series: | Molecular Systems Biology |
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| Online Access: | https://doi.org/10.15252/msb.20178126 |
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| author | Christina Ludwig Ludovic Gillet George Rosenberger Sabine Amon Ben C Collins Ruedi Aebersold |
| author_facet | Christina Ludwig Ludovic Gillet George Rosenberger Sabine Amon Ben C Collins Ruedi Aebersold |
| author_sort | Christina Ludwig |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-212c63d12c084d8d8234958f755d97d2 |
| institution | OA Journals |
| issn | 1744-4292 |
| language | English |
| publishDate | 2018-08-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-212c63d12c084d8d8234958f755d97d22025-08-20T02:11:50ZengSpringer NatureMolecular Systems Biology1744-42922018-08-0114812310.15252/msb.20178126Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorialChristina Ludwig0Ludovic Gillet1George Rosenberger2Sabine Amon3Ben C Collins4Ruedi Aebersold5Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM)Department of Biology, Institute of Molecular Systems Biology, ETH ZurichDepartment of Biology, Institute of Molecular Systems Biology, ETH ZurichDepartment of Biology, Institute of Molecular Systems Biology, ETH ZurichDepartment of Biology, Institute of Molecular Systems Biology, ETH ZurichDepartment of Biology, Institute of Molecular Systems Biology, ETH ZurichAbstract 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.https://doi.org/10.15252/msb.20178126data‐independent acquisitionmass spectrometryquantitative proteomicsSWATH‐MSsystems biology |
| spellingShingle | Christina Ludwig Ludovic Gillet George Rosenberger Sabine Amon Ben C Collins Ruedi Aebersold Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial Molecular Systems Biology data‐independent acquisition mass spectrometry quantitative proteomics SWATH‐MS systems biology |
| title | Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial |
| title_full | Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial |
| title_fullStr | Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial |
| title_full_unstemmed | Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial |
| title_short | Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial |
| title_sort | data independent acquisition based swath ms for quantitative proteomics a tutorial |
| topic | data‐independent acquisition mass spectrometry quantitative proteomics SWATH‐MS systems biology |
| url | https://doi.org/10.15252/msb.20178126 |
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