{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,16]],"date-time":"2026-02-16T20:53:54Z","timestamp":1771275234024,"version":"3.50.1"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Data independent acquisition mass spectrometry has emerged as a reproducible and sensitive alternative in quantitative proteomics, where parsing the highly complex tandem mass spectra requires dedicated algorithms. Recently, targeted data extraction was proposed as a novel analysis strategy for this type of data, but it is important to further develop these concepts to provide quality-controlled, interference-adjusted and sensitive peptide quantification.<\/jats:p>\n               <jats:p>Results: We here present the algorithm DIANA and the classifier PyProphet, which are based on new probabilistic sub-scores to classify the chromatographic peaks in targeted data-independent acquisition data analysis. The algorithm is capable of providing accurate quantitative values and increased recall at a controlled false discovery rate, in a complex gold standard dataset. Importantly, we further demonstrate increased confidence gained by the use of two complementary data-independent acquisition targeted analysis algorithms, as well as increased numbers of quantified peptide precursors in complex biological samples.<\/jats:p>\n               <jats:p>Availability and implementation: DIANA is implemented in scala and python and available as open source (Apache 2.0 license) or pre-compiled binaries from http:\/\/quantitativeproteomics.org\/diana. PyProphet can be installed from PyPi (https:\/\/pypi.python.org\/pypi\/pyprophet).<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu686","type":"journal-article","created":{"date-parts":[[2014,10,28]],"date-time":"2014-10-28T04:40:37Z","timestamp":1414471237000},"page":"555-562","source":"Crossref","is-referenced-by-count":95,"title":["DIANA\u2014algorithmic improvements for analysis of data-independent acquisition MS data"],"prefix":"10.1093","volume":"31","author":[{"given":"Johan","family":"Teleman","sequence":"first","affiliation":[{"name":"1 Department of Clinical Sciences, Lund University, BMC B14 221 84 Lund, 2Department of Immunotechnology, Lund University, Medicon Village (Building 406) 223 81 Lund, Sweden, 3Department of Biology, Institute of Molecular Systems Biology, 4ITS Scientific IT Services, ETH Zurich and 5SIT, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland"},{"name":"1 Department of Clinical Sciences, Lund University, BMC B14 221 84 Lund, 2Department of Immunotechnology, Lund University, Medicon Village (Building 406) 223 81 Lund, Sweden, 3Department of Biology, Institute of Molecular Systems Biology, 4ITS Scientific IT Services, ETH Zurich and 5SIT, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hannes L","family":"R\u00f6st","sequence":"additional","affiliation":[{"name":"1 Department of Clinical Sciences, Lund University, BMC B14 221 84 Lund, 2Department of Immunotechnology, Lund University, Medicon Village (Building 406) 223 81 Lund, Sweden, 3Department of Biology, Institute of Molecular Systems Biology, 4ITS Scientific IT Services, ETH Zurich and 5SIT, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"George","family":"Rosenberger","sequence":"additional","affiliation":[{"name":"1 Department of Clinical Sciences, Lund University, BMC B14 221 84 Lund, 2Department of Immunotechnology, Lund University, Medicon Village (Building 406) 223 81 Lund, Sweden, 3Department of Biology, Institute of Molecular Systems Biology, 4ITS Scientific IT Services, ETH Zurich and 5SIT, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Uwe","family":"Schmitt","sequence":"additional","affiliation":[{"name":"1 Department of Clinical Sciences, Lund University, BMC B14 221 84 Lund, 2Department of Immunotechnology, Lund University, Medicon Village (Building 406) 223 81 Lund, Sweden, 3Department of Biology, Institute of Molecular Systems Biology, 4ITS Scientific IT Services, ETH Zurich and 5SIT, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lars","family":"Malmstr\u00f6m","sequence":"additional","affiliation":[{"name":"1 Department of Clinical Sciences, Lund University, BMC B14 221 84 Lund, 2Department of Immunotechnology, Lund University, Medicon Village (Building 406) 223 81 Lund, Sweden, 3Department of Biology, Institute of Molecular Systems Biology, 4ITS Scientific IT Services, ETH Zurich and 5SIT, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Johan","family":"Malmstr\u00f6m","sequence":"additional","affiliation":[{"name":"1 Department of Clinical Sciences, Lund University, BMC B14 221 84 Lund, 2Department of Immunotechnology, Lund University, Medicon Village (Building 406) 223 81 Lund, Sweden, 3Department of Biology, Institute of Molecular Systems Biology, 4ITS Scientific IT Services, ETH Zurich and 5SIT, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fredrik","family":"Levander","sequence":"additional","affiliation":[{"name":"1 Department of Clinical Sciences, Lund University, BMC B14 221 84 Lund, 2Department of Immunotechnology, Lund University, Medicon Village (Building 406) 223 81 Lund, Sweden, 3Department of Biology, Institute of Molecular Systems Biology, 4ITS Scientific IT Services, ETH Zurich and 5SIT, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,10,27]]},"reference":[{"key":"2023020108564728600_btu686-B1","doi-asserted-by":"crossref","first-page":"2152","DOI":"10.1021\/pr401278j","article-title":"Intelligent data acquisition blends targeted and discovery methods","volume":"13","author":"Bailey","year":"2014","journal-title":"J. Proteome Res."},{"key":"2023020108564728600_btu686-B2","article-title":"Spectronaut: a fast and efficient algorithm for MRM-like processing of data independent acquisition (SWATH-MS) data","volume-title":"Proceedings of 60th American Society for Mass Spectometry Conference","author":"Bernhardt","year":"2012"},{"key":"2023020108564728600_btu686-B3","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1016\/S1473-3099(05)70267-X","article-title":"The global burden of group A streptococcal diseases","volume":"5","author":"Carapetis","year":"2005","journal-title":"Lancet Infect. Dis."},{"key":"2023020108564728600_btu686-B4","doi-asserted-by":"crossref","first-page":"918","DOI":"10.1038\/nbt.2377","article-title":"A cross-platform toolkit for mass spectrometry and proteomics","volume":"30","author":"Chambers","year":"2012","journal-title":"Nat. Biotechnol."},{"key":"2023020108564728600_btu686-B5","doi-asserted-by":"crossref","first-page":"1246","DOI":"10.1038\/nmeth.2703","article-title":"Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system","volume":"10","author":"Collins","year":"2013","journal-title":"Nat. Methods"},{"key":"2023020108564728600_btu686-B6","doi-asserted-by":"crossref","first-page":"D655","DOI":"10.1093\/nar\/gkj040","article-title":"The PeptideAtlas project","volume":"34","author":"Desiere","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023020108564728600_btu686-B7","doi-asserted-by":"crossref","first-page":"R111.015040","DOI":"10.1074\/mcp.R111.015040","article-title":"TraML\u2013a standard format for exchange of selected reaction monitoring transition lists","volume":"11","author":"Deutsch","year":"2012","journal-title":"Mol. Cell. Proteomics"},{"key":"2023020108564728600_btu686-B8","doi-asserted-by":"crossref","first-page":"744","DOI":"10.1038\/nmeth.2528","article-title":"Multiplexed MS\/MS for improved data-independent acquisition","volume":"10","author":"Egertson","year":"2013","journal-title":"Nat. Methods"},{"key":"2023020108564728600_btu686-B9","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nmeth1019","article-title":"Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry","volume":"4","author":"Elias","year":"2007","journal-title":"Nat. Methods"},{"key":"2023020108564728600_btu686-B10","doi-asserted-by":"crossref","first-page":"1111","DOI":"10.1002\/pmic.201100463","article-title":"Using iRT, a normalized retention time for more targeted measurement of peptides","volume":"12","author":"Escher","year":"2012","journal-title":"Proteomics"},{"key":"2023020108564728600_btu686-B11","doi-asserted-by":"crossref","first-page":"1170","DOI":"10.1002\/pmic.201100515","article-title":"PASSEL: the PeptideAtlas SRMexperiment library","volume":"12","author":"Farrah","year":"2012","journal-title":"Proteomics"},{"key":"2023020108564728600_btu686-B12","doi-asserted-by":"crossref","first-page":"O111.016717","DOI":"10.1074\/mcp.O111.016717","article-title":"Targeted data extraction of the MS\/MS spectra generated by data independent acquisition: a new concept for consistent and accurate proteome analysis","volume":"11","author":"Gillet","year":"2012","journal-title":"Mol. Cell. Proteomics"},{"key":"2023020108564728600_btu686-B13","doi-asserted-by":"crossref","first-page":"3037","DOI":"10.1021\/pr900189c","article-title":"The proteios software environment: an extensible multiuser platform for management and analysis of proteomics data","volume":"8","author":"H\u00e4kkinen","year":"2009","journal-title":"J. Proteome Res."},{"key":"2023020108564728600_btu686-B14","doi-asserted-by":"crossref","first-page":"1220","DOI":"10.1002\/pmic.200800473","article-title":"Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines","volume":"9","author":"Jones","year":"2009","journal-title":"Proteomics"},{"key":"2023020108564728600_btu686-B15","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1021\/pr700600n","article-title":"Assigning significance to peptides identified by tandem mass spectrometry using decoy databases","volume":"7","author":"K\u00e4ll","year":"2008","journal-title":"J. Proteome Res."},{"key":"2023020108564728600_btu686-B16","doi-asserted-by":"crossref","first-page":"1301","DOI":"10.1038\/ncomms2297","article-title":"Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes","volume":"3","author":"Karlsson","year":"2012","journal-title":"Nat. Commun."},{"key":"2023020108564728600_btu686-B17","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/S0167-7152(02)00310-3","article-title":"Combining dependent P-values","volume":"60","author":"Kost","year":"2002","journal-title":"Stat. Probab. Lett."},{"key":"2023020108564728600_btu686-B18","doi-asserted-by":"crossref","first-page":"4193","DOI":"10.1021\/ac0498563","article-title":"A model for random sampling and estimation of relative protein abundance in shotgun proteomics","volume":"76","author":"Liu","year":"2004","journal-title":"Anal. Chem."},{"key":"2023020108564728600_btu686-B19","doi-asserted-by":"crossref","first-page":"1415","DOI":"10.1074\/jbc.M111.267674","article-title":"Streptococcus pyogenes in human plasma: adaptive mechanisms analyzed by mass spectrometry-based proteomics","volume":"287","author":"Malmstr\u00f6m","year":"2012","journal-title":"J. Biol. Chem."},{"key":"2023020108564728600_btu686-B20","doi-asserted-by":"crossref","DOI":"10.1074\/mcp.R110.000133","article-title":"mzML\u2013a community standard for mass spectrometry data","volume":"10","author":"Martens","year":"2011","journal-title":"Mol. Cell. Proteomics"},{"key":"2023020108564728600_btu686-B21","doi-asserted-by":"crossref","first-page":"3332","DOI":"10.1021\/pr2002879","article-title":"Probabilistic consensus scoring improves tandem mass spectrometry peptide identification","volume":"10","author":"Nahnsen","year":"2011","journal-title":"J. Proteome Res."},{"key":"2023020108564728600_btu686-B22","doi-asserted-by":"crossref","first-page":"6481","DOI":"10.1021\/ac900888s","article-title":"Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean","volume":"81","author":"Panchaud","year":"2009","journal-title":"Anal. Chem."},{"key":"2023020108564728600_btu686-B23","first-page":"2825","article-title":"Scikit-learn: machine learning in Python","volume":"12","author":"Pedregosa","year":"2011","journal-title":"J. Mach. Learn. Res."},{"key":"2023020108564728600_btu686-B24","doi-asserted-by":"crossref","first-page":"913","DOI":"10.1038\/nmeth1108-913","article-title":"A database of mass spectrometric assays for the yeast proteome","volume":"5","author":"Picotti","year":"2008","journal-title":"Nat. Methods"},{"key":"2023020108564728600_btu686-B25","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1016\/j.cell.2009.05.051","article-title":"Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics","volume":"138","author":"Picotti","year":"2009","journal-title":"Cell"},{"key":"2023020108564728600_btu686-B26","doi-asserted-by":"crossref","first-page":"1989","DOI":"10.1002\/rcm.2550","article-title":"UPLC\/MS(E); a new approach for generating molecular fragment information for biomarker structure elucidation","volume":"20","author":"Plumb","year":"2006","journal-title":"Rapid Commun. Mass Spectrom."},{"key":"2023020108564728600_btu686-B27","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1002\/pmic.200300362","article-title":"Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer","volume":"3","author":"Purvine","year":"2003","journal-title":"Proteomics"},{"key":"2023020108564728600_btu686-B28","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1038\/nmeth.1584","article-title":"mProphet: automated data processing and statistical validation for large-scale SRM experiments","volume":"8","author":"Reiter","year":"2011","journal-title":"Nat. Methods"},{"key":"2023020108564728600_btu686-B29","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1038\/nbt.2841","article-title":"OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data","volume":"32","author":"R\u00f6st","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"2023020108564728600_btu686-B30","doi-asserted-by":"crossref","DOI":"10.1074\/mcp.M111.007690","article-title":"iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates","volume":"10","author":"Shteynberg","year":"2011","journal-title":"Mol. Cell. Proteomics"},{"key":"2023020108564728600_btu686-B31","doi-asserted-by":"crossref","first-page":"2383","DOI":"10.1074\/mcp.R113.027797","article-title":"Combining results of multiple search engines in proteomics","volume":"12","author":"Shteynberg","year":"2013","journal-title":"Mol. Cell. Proteomics"},{"key":"2023020108564728600_btu686-B32","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1111\/1467-9868.00346","article-title":"A direct approach to false discovery rates","volume":"64","author":"Storey","year":"2002","journal-title":"J. R. Stat. Soc. Ser. B Stat. Methodol."},{"key":"2023020108564728600_btu686-B33","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1021\/pr9006365","article-title":"Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry","volume":"9","author":"Tabb","year":"2010","journal-title":"J. Proteome Res."},{"key":"2023020108564728600_btu686-B34","doi-asserted-by":"crossref","first-page":"3766","DOI":"10.1021\/pr300256x","article-title":"Automated selected reaction monitoring software for accurate label-free protein quantification","volume":"11","author":"Teleman","year":"2012","journal-title":"J. Proteome Res."},{"key":"2023020108564728600_btu686-B35","doi-asserted-by":"crossref","first-page":"1537","DOI":"10.1074\/mcp.O114.037879","article-title":"Numerical compression schemes for proteomics mass spectrometry data","volume":"13","author":"Teleman","year":"2014","journal-title":"Mol. Cell. Proteomics"},{"key":"2023020108564728600_btu686-B36","doi-asserted-by":"crossref","first-page":"2825","DOI":"10.1021\/ac303352n","article-title":"Segmentation of precursor mass range using \u2018tiling\u2019 approach increases peptide identifications for MS1-based label-free quantification","volume":"85","author":"Vincent","year":"2013","journal-title":"Anal. Chem."},{"key":"2023020108564728600_btu686-B37","doi-asserted-by":"crossref","first-page":"2876","DOI":"10.1021\/pr201258q","article-title":"Protein expression changes in ovarian cancer during the transition from benign to malignant","volume":"11","author":"Waldemarson","year":"2012","journal-title":"J. Proteome Res."},{"key":"2023020108564728600_btu686-B38","doi-asserted-by":"crossref","first-page":"1621","DOI":"10.1021\/pr2008175","article-title":"Accurate peptide fragment mass analysis: multiplexed peptide identification and quantification","volume":"11","author":"Weisbrod","year":"2012","journal-title":"J. Proteome Res."},{"key":"2023020108564728600_btu686-B39","doi-asserted-by":"crossref","first-page":"5860","DOI":"10.1073\/pnas.0608638104","article-title":"Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks","volume":"104","author":"Wolf-Yadlin","year":"2007","journal-title":"Proc. Natl Acad. Sci. USA"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/4\/555\/49011534\/bioinformatics_31_4_555.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/4\/555\/49011534\/bioinformatics_31_4_555.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T20:26:38Z","timestamp":1675283198000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/4\/555\/209120"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,10,27]]},"references-count":39,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2015,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu686","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,2,15]]},"published":{"date-parts":[[2014,10,27]]}}}