{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,6,13]],"date-time":"2023-06-13T12:10:19Z","timestamp":1686658219934},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Warp2D is a novel time alignment approach, which uses the overlapping peak volume of the reference and sample peak lists to correct misleading peak shifts. Here, we present an easy-to-use web interface for high-throughput Warp2D batch processing time alignment service using the Dutch Life Science Grid, reducing processing time from days to hours. This service provides the warping function, the sample chromatogram peak list with adjusted retention times and normalized quality scores based on the sum of overlapping peak volume of all peaks. Heat maps before and after time alignment are created from the arithmetic mean of the sum of overlapping peak area rearranged with hierarchical clustering, allowing the quality control of the time alignment procedure. Taverna workflow and command line tool are provided for remote processing of local user data.<\/jats:p>\n               <jats:p>Availability: online data processing service is available at http:\/\/www.nbpp.nl\/warp2d.html. Taverna workflow is available at myExperiment with title \u20182D Time Alignment\u2014Webservice and Workflow\u2019 at http:\/\/www.myexperiment.org\/workflows\/1283.html. Command line tool is available at http:\/\/www.nbpp.nl\/Warp2D_commandline.zip.<\/jats:p>\n               <jats:p>Contact: \u00a0p.l.horvatovich@rug.nl<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr094","type":"journal-article","created":{"date-parts":[[2011,2,25]],"date-time":"2011-02-25T01:38:20Z","timestamp":1298597900000},"page":"1176-1178","source":"Crossref","is-referenced-by-count":6,"title":["A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data"],"prefix":"10.1093","volume":"27","author":[{"given":"Isthiaq","family":"Ahmad","sequence":"first","affiliation":[{"name":"1 Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 2Bioassist, Netherlands Bioinformatics Centre, Nijmegen, 3Bioinformatics in Proteomics, Netherlands Proteomics Centre, Utrecht, The Netherlands, 4Protein Science Group, IBM T.J. Watson Research Centre, Yorktown Heights, New York, USA, 5Genomics Coordination Center, Department of Genetics, University Medical Center Groningen, Groningen, 6Center for Medical Biomics, University of Groningen Groningen and 7Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands"},{"name":"1 Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 2Bioassist, Netherlands Bioinformatics Centre, Nijmegen, 3Bioinformatics in Proteomics, Netherlands Proteomics Centre, Utrecht, The Netherlands, 4Protein Science Group, IBM T.J. Watson Research Centre, Yorktown Heights, New York, USA, 5Genomics Coordination Center, Department of Genetics, University Medical Center Groningen, Groningen, 6Center for Medical Biomics, University of Groningen Groningen and 7Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands"},{"name":"1 Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 2Bioassist, Netherlands Bioinformatics Centre, Nijmegen, 3Bioinformatics in Proteomics, Netherlands Proteomics Centre, Utrecht, The Netherlands, 4Protein Science Group, IBM T.J. Watson Research Centre, Yorktown Heights, New York, USA, 5Genomics Coordination Center, Department of Genetics, University Medical Center Groningen, Groningen, 6Center for Medical Biomics, University of Groningen Groningen and 7Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Frank","family":"Suits","sequence":"additional","affiliation":[{"name":"1 Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 2Bioassist, Netherlands Bioinformatics Centre, Nijmegen, 3Bioinformatics in Proteomics, Netherlands Proteomics Centre, Utrecht, The Netherlands, 4Protein Science Group, IBM T.J. Watson Research Centre, Yorktown Heights, New York, USA, 5Genomics Coordination Center, Department of Genetics, University Medical Center Groningen, Groningen, 6Center for Medical Biomics, University of Groningen Groningen and 7Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Berend","family":"Hoekman","sequence":"additional","affiliation":[{"name":"1 Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 2Bioassist, Netherlands Bioinformatics Centre, Nijmegen, 3Bioinformatics in Proteomics, Netherlands Proteomics Centre, Utrecht, The Netherlands, 4Protein Science Group, IBM T.J. Watson Research Centre, Yorktown Heights, New York, USA, 5Genomics Coordination Center, Department of Genetics, University Medical Center Groningen, Groningen, 6Center for Medical Biomics, University of Groningen Groningen and 7Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Morris A.","family":"Swertz","sequence":"additional","affiliation":[{"name":"1 Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 2Bioassist, Netherlands Bioinformatics Centre, Nijmegen, 3Bioinformatics in Proteomics, Netherlands Proteomics Centre, Utrecht, The Netherlands, 4Protein Science Group, IBM T.J. Watson Research Centre, Yorktown Heights, New York, USA, 5Genomics Coordination Center, Department of Genetics, University Medical Center Groningen, Groningen, 6Center for Medical Biomics, University of Groningen Groningen and 7Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands"},{"name":"1 Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 2Bioassist, Netherlands Bioinformatics Centre, Nijmegen, 3Bioinformatics in Proteomics, Netherlands Proteomics Centre, Utrecht, The Netherlands, 4Protein Science Group, IBM T.J. Watson Research Centre, Yorktown Heights, New York, USA, 5Genomics Coordination Center, Department of Genetics, University Medical Center Groningen, Groningen, 6Center for Medical Biomics, University of Groningen Groningen and 7Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands"},{"name":"1 Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 2Bioassist, Netherlands Bioinformatics Centre, Nijmegen, 3Bioinformatics in Proteomics, Netherlands Proteomics Centre, Utrecht, The Netherlands, 4Protein Science Group, IBM T.J. Watson Research Centre, Yorktown Heights, New York, USA, 5Genomics Coordination Center, Department of Genetics, University Medical Center Groningen, Groningen, 6Center for Medical Biomics, University of Groningen Groningen and 7Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Heorhiy","family":"Byelas","sequence":"additional","affiliation":[{"name":"1 Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 2Bioassist, Netherlands Bioinformatics Centre, Nijmegen, 3Bioinformatics in Proteomics, Netherlands Proteomics Centre, Utrecht, The Netherlands, 4Protein Science Group, IBM T.J. Watson Research Centre, Yorktown Heights, New York, USA, 5Genomics Coordination Center, Department of Genetics, University Medical Center Groningen, Groningen, 6Center for Medical Biomics, University of Groningen Groningen and 7Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands"},{"name":"1 Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 2Bioassist, Netherlands Bioinformatics Centre, Nijmegen, 3Bioinformatics in Proteomics, Netherlands Proteomics Centre, Utrecht, The Netherlands, 4Protein Science Group, IBM T.J. Watson Research Centre, Yorktown Heights, New York, USA, 5Genomics Coordination Center, Department of Genetics, University Medical Center Groningen, Groningen, 6Center for Medical Biomics, University of Groningen Groningen and 7Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands"},{"name":"1 Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 2Bioassist, Netherlands Bioinformatics Centre, Nijmegen, 3Bioinformatics in Proteomics, Netherlands Proteomics Centre, Utrecht, The Netherlands, 4Protein Science Group, IBM T.J. Watson Research Centre, Yorktown Heights, New York, USA, 5Genomics Coordination Center, Department of Genetics, University Medical Center Groningen, Groningen, 6Center for Medical Biomics, University of Groningen Groningen and 7Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martijn","family":"Dijkstra","sequence":"additional","affiliation":[{"name":"1 Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 2Bioassist, Netherlands Bioinformatics Centre, Nijmegen, 3Bioinformatics in Proteomics, Netherlands Proteomics Centre, Utrecht, The Netherlands, 4Protein Science Group, IBM T.J. Watson Research Centre, Yorktown Heights, New York, USA, 5Genomics Coordination Center, Department of Genetics, University Medical Center Groningen, Groningen, 6Center for Medical Biomics, University of Groningen Groningen and 7Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands"},{"name":"1 Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 2Bioassist, Netherlands Bioinformatics Centre, Nijmegen, 3Bioinformatics in Proteomics, Netherlands Proteomics Centre, Utrecht, The Netherlands, 4Protein Science Group, IBM T.J. Watson Research Centre, Yorktown Heights, New York, USA, 5Genomics Coordination Center, Department of Genetics, University Medical Center Groningen, Groningen, 6Center for Medical Biomics, University of Groningen Groningen and 7Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands"},{"name":"1 Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 2Bioassist, Netherlands Bioinformatics Centre, Nijmegen, 3Bioinformatics in Proteomics, Netherlands Proteomics Centre, Utrecht, The Netherlands, 4Protein Science Group, IBM T.J. Watson Research Centre, Yorktown Heights, New York, USA, 5Genomics Coordination Center, Department of Genetics, University Medical Center Groningen, Groningen, 6Center for Medical Biomics, University of Groningen Groningen and 7Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rob","family":"Hooft","sequence":"additional","affiliation":[{"name":"1 Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 2Bioassist, Netherlands Bioinformatics Centre, Nijmegen, 3Bioinformatics in Proteomics, Netherlands Proteomics Centre, Utrecht, The Netherlands, 4Protein Science Group, IBM T.J. Watson Research Centre, Yorktown Heights, New York, USA, 5Genomics Coordination Center, Department of Genetics, University Medical Center Groningen, Groningen, 6Center for Medical Biomics, University of Groningen Groningen and 7Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dmitry","family":"Katsubo","sequence":"additional","affiliation":[{"name":"1 Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 2Bioassist, Netherlands Bioinformatics Centre, Nijmegen, 3Bioinformatics in Proteomics, Netherlands Proteomics Centre, Utrecht, The Netherlands, 4Protein Science Group, IBM T.J. Watson Research Centre, Yorktown Heights, New York, USA, 5Genomics Coordination Center, Department of Genetics, University Medical Center Groningen, Groningen, 6Center for Medical Biomics, University of Groningen Groningen and 7Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bas","family":"van Breukelen","sequence":"additional","affiliation":[{"name":"1 Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 2Bioassist, Netherlands Bioinformatics Centre, Nijmegen, 3Bioinformatics in Proteomics, Netherlands Proteomics Centre, Utrecht, The Netherlands, 4Protein Science Group, IBM T.J. Watson Research Centre, Yorktown Heights, New York, USA, 5Genomics Coordination Center, Department of Genetics, University Medical Center Groningen, Groningen, 6Center for Medical Biomics, University of Groningen Groningen and 7Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands"},{"name":"1 Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 2Bioassist, Netherlands Bioinformatics Centre, Nijmegen, 3Bioinformatics in Proteomics, Netherlands Proteomics Centre, Utrecht, The Netherlands, 4Protein Science Group, IBM T.J. Watson Research Centre, Yorktown Heights, New York, USA, 5Genomics Coordination Center, Department of Genetics, University Medical Center Groningen, Groningen, 6Center for Medical Biomics, University of Groningen Groningen and 7Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands"},{"name":"1 Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 2Bioassist, Netherlands Bioinformatics Centre, Nijmegen, 3Bioinformatics in Proteomics, Netherlands Proteomics Centre, Utrecht, The Netherlands, 4Protein Science Group, IBM T.J. Watson Research Centre, Yorktown Heights, New York, USA, 5Genomics Coordination Center, Department of Genetics, University Medical Center Groningen, Groningen, 6Center for Medical Biomics, University of Groningen Groningen and 7Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rainer","family":"Bischoff","sequence":"additional","affiliation":[{"name":"1 Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 2Bioassist, Netherlands Bioinformatics Centre, Nijmegen, 3Bioinformatics in Proteomics, Netherlands Proteomics Centre, Utrecht, The Netherlands, 4Protein Science Group, IBM T.J. Watson Research Centre, Yorktown Heights, New York, USA, 5Genomics Coordination Center, Department of Genetics, University Medical Center Groningen, Groningen, 6Center for Medical Biomics, University of Groningen Groningen and 7Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands"},{"name":"1 Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 2Bioassist, Netherlands Bioinformatics Centre, Nijmegen, 3Bioinformatics in Proteomics, Netherlands Proteomics Centre, Utrecht, The Netherlands, 4Protein Science Group, IBM T.J. Watson Research Centre, Yorktown Heights, New York, USA, 5Genomics Coordination Center, Department of Genetics, University Medical Center Groningen, Groningen, 6Center for Medical Biomics, University of Groningen Groningen and 7Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands"},{"name":"1 Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 2Bioassist, Netherlands Bioinformatics Centre, Nijmegen, 3Bioinformatics in Proteomics, Netherlands Proteomics Centre, Utrecht, The Netherlands, 4Protein Science Group, IBM T.J. Watson Research Centre, Yorktown Heights, New York, USA, 5Genomics Coordination Center, Department of Genetics, University Medical Center Groningen, Groningen, 6Center for Medical Biomics, University of Groningen Groningen and 7Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"Horvatovich","sequence":"additional","affiliation":[{"name":"1 Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 2Bioassist, Netherlands Bioinformatics Centre, Nijmegen, 3Bioinformatics in Proteomics, Netherlands Proteomics Centre, Utrecht, The Netherlands, 4Protein Science Group, IBM T.J. Watson Research Centre, Yorktown Heights, New York, USA, 5Genomics Coordination Center, Department of Genetics, University Medical Center Groningen, Groningen, 6Center for Medical Biomics, University of Groningen Groningen and 7Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands"},{"name":"1 Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 2Bioassist, Netherlands Bioinformatics Centre, Nijmegen, 3Bioinformatics in Proteomics, Netherlands Proteomics Centre, Utrecht, The Netherlands, 4Protein Science Group, IBM T.J. Watson Research Centre, Yorktown Heights, New York, USA, 5Genomics Coordination Center, Department of Genetics, University Medical Center Groningen, Groningen, 6Center for Medical Biomics, University of Groningen Groningen and 7Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands"},{"name":"1 Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, 2Bioassist, Netherlands Bioinformatics Centre, Nijmegen, 3Bioinformatics in Proteomics, Netherlands Proteomics Centre, Utrecht, The Netherlands, 4Protein Science Group, IBM T.J. Watson Research Centre, Yorktown Heights, New York, USA, 5Genomics Coordination Center, Department of Genetics, University Medical Center Groningen, Groningen, 6Center for Medical Biomics, University of Groningen Groningen and 7Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Utrecht, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,2,23]]},"reference":[{"key":"2023061311475269300_B1","doi-asserted-by":"crossref","first-page":"542","DOI":"10.1186\/1471-2105-9-542","article-title":"Corra: computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics","volume":"9","author":"Brusniak","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023061311475269300_B2","doi-asserted-by":"crossref","first-page":"7012","DOI":"10.1021\/ac800920h","article-title":"Optimized time alignment algorithm for LC-MS data: correlation optimized warping using component detection algorithm-selected mass chromatograms","volume":"80","author":"Christin","year":"2008","journal-title":"Anal. 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Chromatogr. A"},{"key":"2023061311475269300_B9","doi-asserted-by":"crossref","first-page":"3062","DOI":"10.1002\/pmic.201090075","article-title":"Tackling quantitation: a report on the annual Spring Workshop of the HUPO-PSI 28-30 March 2010, Seoul, South Korea","volume":"10","author":"Orchard","year":"2010","journal-title":"Proteomics"},{"key":"2023061311475269300_B10","doi-asserted-by":"crossref","first-page":"758","DOI":"10.1093\/bioinformatics\/btp052","article-title":"Retention time alignment algorithms for LC\/MS data must consider non-linear shifts","volume":"25","author":"Podwojski","year":"2009","journal-title":"Bioinformatics"},{"key":"2023061311475269300_B11","doi-asserted-by":"crossref","first-page":"3095","DOI":"10.1021\/ac702267h","article-title":"Two-dimensional method for time aligning liquid chromatography-mass spectrometry data","volume":"80","author":"Suits","year":"2008","journal-title":"Anal. 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