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dc.contributor.author
Ludwig, Christina
dc.contributor.author
Gillet, Ludovic
dc.contributor.author
Rosenberger, George
dc.contributor.author
Amon, Sabine
dc.contributor.author
Collins, Ben C.
dc.contributor.author
Aebersold, Ruedi
dc.date.accessioned
2018-09-11T08:19:33Z
dc.date.available
2018-09-07T20:14:52Z
dc.date.available
2018-09-11T08:19:33Z
dc.date.issued
2018-08-01
dc.identifier.issn
1744-4292
dc.identifier.other
10.15252/msb.20178126
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/287842
dc.identifier.doi
10.3929/ethz-b-000287842
dc.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.
en_US
dc.format
application/pdf
en_US
dc.language.iso
en
en_US
dc.publisher
Nature Publishing Group
en_US
dc.rights.uri
http://creativecommons.org/licenses/by/4.0/
dc.subject
data-independent acquisition
en_US
dc.subject
mass spectrometry
en_US
dc.subject
quantitative proteomics
en_US
dc.subject
SWATH-MS
en_US
dc.subject
systems biology
en_US
dc.title
Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial
en_US
dc.type
Review Article
dc.rights.license
Creative Commons Attribution 4.0 International
dc.date.published
2018-08-13
ethz.journal.title
Molecular Systems Biology
ethz.journal.volume
14
en_US
ethz.journal.issue
8
en_US
ethz.journal.abbreviated
Mol Syst Biol
ethz.pages.start
e8126
en_US
ethz.size
23 p.
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.grant
MitoModules: Biomarkers in context
en_US
ethz.identifier.wos
ethz.identifier.scopus
ethz.publication.place
London
en_US
ethz.publication.status
published
en_US
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02030 - Dep. Biologie / Dep. of Biology::02538 - Institut für Molekulare Systembiologie / Institute for Molecular Systems Biology::03663 - Aebersold, Rudolf (emeritus) / Aebersold, Rudolf (emeritus)
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00003 - Schulleitung und Dienste::00022 - Bereich VP Forschung / Domain VP Research::02207 - Functional Genomics Center Zurich / Functional Genomics Center Zurich
ethz.leitzahl.certified
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02030 - Dep. Biologie / Dep. of Biology::02538 - Institut für Molekulare Systembiologie / Institute for Molecular Systems Biology::03663 - Aebersold, Rudolf (emeritus) / Aebersold, Rudolf (emeritus)
ethz.leitzahl.certified
ETH Zürich::00002 - ETH Zürich::00003 - Schulleitung und Dienste::00022 - Bereich VP Forschung / Domain VP Research::02207 - Functional Genomics Center Zurich / Functional Genomics Center Zurich
ethz.grant.agreementno
166435
ethz.grant.fundername
SNF
ethz.grant.funderDoi
10.13039/501100001711
ethz.grant.program
Projektförderung in Biologie und Medizin (Abteilung III)
ethz.date.deposited
2018-09-07T20:14:58Z
ethz.source
SCOPUS
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2018-09-11T08:19:37Z
ethz.rosetta.lastUpdated
2021-02-15T01:41:55Z
ethz.rosetta.exportRequired
true
ethz.rosetta.versionExported
true
ethz.COinS
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