title: OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data.
authors.affiliation: 1] Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland. [2] PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland. [3].
authors.forename: Hannes L
authors.identifier: 0000000309907488
authors.initials: HL
authors.lastname: Röst
authors.affiliation: 1] Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland. [2] PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland. [3].
authors.forename: George
authors.identifier: 0000000216556789
authors.initials: G
authors.lastname: Rosenberger
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
authors.forename: Pedro
authors.initials: P
authors.lastname: Navarro
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
authors.forename: Ludovic
authors.initials: L
authors.lastname: Gillet
authors.affiliation: 1] Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland. [2] Biognosys AG, Schlieren, Switzerland.
authors.forename: Saša M
authors.initials: SM
authors.lastname: Miladinović
authors.affiliation: 1] Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland. [2] PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland.
authors.forename: Olga T
authors.initials: OT
authors.lastname: Schubert
authors.affiliation: SyBIT project of SystemsX.ch, ETH Zurich, Zurich, Switzerland.
authors.forename: Witold
authors.initials: W
authors.lastname: Wolski
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
authors.forename: Ben C
authors.initials: BC
authors.lastname: Collins
authors.affiliation: Department of Immunotechnology, Lund University, Lund, Sweden.
authors.forename: Johan
authors.initials: J
authors.lastname: Malmström
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
authors.forename: Lars
authors.identifier: 0000000198859312
authors.initials: L
authors.lastname: Malmström
authors.affiliation: 1] Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland. [2] Competence Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland. [3] Faculty of Science, University of Zurich, Zurich, Switzerland.
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: D001426:Bacterial Proteins / Q000032:analysis / Q000737:chemistry; D001798:Blood Proteins / Q000032:analysis / Q000737:chemistry; D002853:Chromatography, Liquid; D030562:Databases, Protein; D005656:Fungal Proteins / Q000032:analysis / Q000737:chemistry; D006801:Humans; D040901:Proteomics / Q000379:methods*; D012984:Software; D013297:Streptococcus pyogenes; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D001426:Bacterial Proteins; D001798:Blood Proteins; D005656:Fungal Proteins
references.citation: Anal Chem. 2011 Mar 15;83(6):2250-7
references.pmid: 21341720
references.citation: Nat Methods. 2007 Mar;4(3):207-14
references.pmid: 17327847
references.citation: J Proteome Res. 2010 Jul 2;9(7):3621-37
references.pmid: 20450226
references.citation: Anal Chem. 2010 Feb 1;82(3):833-41
references.pmid: 20039681
references.citation: Nat Protoc. 2007;2(6):1333-49
references.pmid: 17545971
references.citation: Science. 2006 Apr 14;312(5771):212-7
references.pmid: 16614208
references.citation: Nat Methods. 2004 Oct;1(1):39-45
references.pmid: 15782151
references.citation: Anal Chem. 2009 Aug 1;81(15):6481-8
references.pmid: 19572557
references.citation: Nature. 2012 Feb 22;482(7386):485-8
references.pmid: 22358837
references.citation: Anal Chem. 2011 Sep 15;83(18):6971-9
references.pmid: 21834580
references.citation: Bioinformatics. 2010 Apr 1;26(7):966-8
references.pmid: 20147306
references.citation: Proteomics. 2009 Mar;9(6):1696-719
references.pmid: 19294629
references.citation: Nat Methods. 2011 May;8(5):430-5
references.pmid: 21423193
references.citation: J Proteome Res. 2012 Mar 2;11(3):1644-53
references.pmid: 22283722
references.citation: EMBO Rep. 2008 May;9(5):429-34
references.pmid: 18451766
references.citation: Cell. 2009 Aug 21;138(4):795-806
references.pmid: 19664813
references.citation: Int J Med Microbiol. 2006 Aug;296(4-5):259-75
references.pmid: 16531115
references.citation: Mol Cell Proteomics. 2010 Oct;9(10):2252-61
references.pmid: 20610777
references.citation: Biopolymers. 2000;55(3):188-206
references.pmid: 11074414
references.citation: Nature. 2003 Mar 13;422(6928):198-207
references.pmid: 12634793
references.citation: BMC Bioinformatics. 2008 Mar 26;9:163
references.pmid: 18366760
references.citation: Mol Cell Proteomics. 2012 Aug;11(8):540-9
references.pmid: 22535207
references.citation: Proc Natl Acad Sci U S A. 2011 Mar 22;108(12):5039-44
references.pmid: 21383167
references.citation: Mol Syst Biol. 2008;4:222
references.pmid: 18854821
references.citation: BMC Bioinformatics. 2009 Aug 10;10:244
references.pmid: 19664259
references.citation: Mol Cell Proteomics. 2012 Dec;11(12):1612-21
references.pmid: 22956731
references.citation: Rapid Commun Mass Spectrom. 2006;20(13):1989-94
references.pmid: 16755610
references.citation: Proteomics. 2012 Apr;12(8):1111-21
references.pmid: 22577012
references.citation: Mol Cell Proteomics. 2009 Sep;8(9):2051-62
references.pmid: 19556279
references.citation: J Proteome Res. 2011 Apr 1;10(4):1785-93
references.pmid: 21309581
references.citation: Mol Cell Proteomics. 2012 Jun;11(6):O111.016717
references.pmid: 22261725
references.citation: J Biol Chem. 2012 Jan 6;287(2):1415-25
references.pmid: 22117078
references.citation: Proteomics. 2003 Jun;3(6):847-50
references.pmid: 12833507
references.citation: Bioinformatics. 2010 Mar 15;26(6):847-8
references.pmid: 20106817
references.citation: Nat Biotechnol. 2010 Jul;28(7):710-21
references.pmid: 20622845
references.citation: Proteomics. 2009 Mar;9(6):1683-95
references.pmid: 19294628