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dc.contributor.author
Frank, Yves
dc.contributor.author
Hruz, Tomas
dc.contributor.author
Tschager, Thomas
dc.contributor.author
Venzin, Valentin
dc.contributor.editor
Schwartz, Russell
dc.contributor.editor
Reinert, Knut
dc.date.accessioned
2017-11-22T16:08:06Z
dc.date.available
2017-11-15T15:07:52Z
dc.date.available
2017-11-22T16:08:06Z
dc.date.available
2017-10-06T05:04:21Z
dc.date.issued
2017
dc.identifier.isbn
978-3-95977-050-7
en_US
dc.identifier.issn
1868-8969
dc.identifier.other
10.4230/LIPIcs.WABI.2017.26
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/212459
dc.identifier.doi
10.3929/ethz-b-000208947
dc.description.abstract
Liquid chromatography combined with tandem mass spectrometry (LC-MS/MS) is an important tool in proteomics for identifying the peptides in a sample. Liquid chromatography temporally separates the peptides and tandem mass spectrometry analyzes the peptides, that elute one after another, by measuring their mass-to-charge ratios and the mass-to-charge ratios of their prefix and suffix fragments. De novo peptide sequencing is the problem of reconstructing the amino acid sequences of the analyzed peptide from this measurement data. While previous approaches solely consider the mass spectrum of the fragments for reconstructing a sequence, we propose to also exploit the information obtained from liquid chromatography. We study the problem of computing a sequence that is not only in accordance with the experimental mass spectrum, but also with the retention time of the separation by liquid chromatography. We consider three models for predicting the retention time of a peptide and develop algorithms for de novo sequencing for each model. An evaluation on experimental data from synthesized peptides for two of these models shows an improved performance compared to not using the chromatographic information.
en_US
dc.language.iso
en
en_US
dc.publisher
Schloss Dagstuhl - Leibniz-Zentrum für Informatik GmbH
en_US
dc.rights.uri
http://creativecommons.org/licenses/by/3.0/
dc.subject
Computer Science
en_US
dc.subject
000 Computer science, knowledge, general works
en_US
dc.subject
Computational proteomics
en_US
dc.subject
Peptide identification
en_US
dc.subject
Mass spectrometry
en_US
dc.subject
De novo peptide sequencing
en_US
dc.subject
Retention time prediction
en_US
dc.title
Improved De Novo Peptide Sequencing using LC Retention Time Information
en_US
dc.type
Conference Paper
dc.rights.license
Creative Commons Attribution 3.0 Unported
ethz.book.title
17th International Workshop on Algorithms in Bioinformatics (WABI 2017)
en_US
ethz.journal.title
Leibniz International Proceedings in Informatics (LIPIcs)
ethz.journal.volume
88
en_US
ethz.journal.abbreviated
LIPIcs
ethz.pages.start
26:1
en_US
ethz.pages.end
26:17
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.event
17th International Workshop on Algorithms in Bioinformatics (WABI 2017)
en_US
ethz.event.location
Bosten, MA, USA
en_US
ethz.event.date
August 21-23, 2017
en_US
ethz.identifier.scopus
ethz.publication.place
Dagstuhl, Germany
en_US
ethz.publication.status
published
en_US
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02150 - Dep. Informatik / Dep. of Computer Science::02643 - Institut für Theoretische Informatik / Inst. Theoretical Computer Science::03340 - Widmayer, Peter (emeritus) / Widmayer, Peter (emeritus)
en_US
ethz.leitzahl.certified
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02150 - Dep. Informatik / Dep. of Computer Science::02643 - Institut für Theoretische Informatik / Inst. Theoretical Computer Science::03340 - Widmayer, Peter (emeritus) / Widmayer, Peter (emeritus)
en_US
ethz.date.deposited
2017-10-06T05:04:28Z
ethz.source
FORM
ethz.source
SCOPUS
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2017-11-22T16:10:50Z
ethz.rosetta.lastUpdated
2019-02-02T13:35:34Z
ethz.rosetta.exportRequired
true
ethz.rosetta.versionExported
true
dc.identifier.olduri
http://hdl.handle.net/20.500.11850/208947
dc.identifier.olduri
http://hdl.handle.net/20.500.11850/192431
ethz.COinS
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