{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:46Z","timestamp":1772138086986,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2018,5,22]],"date-time":"2018-05-22T00:00:00Z","timestamp":1526947200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000066","name":"National Institute of Environmental Health Sciences","doi-asserted-by":"publisher","award":["P50ES018172"],"award-info":[{"award-number":["P50ES018172"]}],"id":[{"id":"10.13039\/100000066","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000066","name":"National Institute of Environmental Health Sciences","doi-asserted-by":"publisher","award":["P01ES018172"],"award-info":[{"award-number":["P01ES018172"]}],"id":[{"id":"10.13039\/100000066","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000066","name":"National Institute of Environmental Health Sciences","doi-asserted-by":"publisher","award":["P42ES004705"],"award-info":[{"award-number":["P42ES004705"]}],"id":[{"id":"10.13039\/100000066","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Liquid chromatography mass spectrometry (LC-MS) is the favored method for untargeted metabolomic analysis of small molecules in biofluids. Here we present SimExTargId, an open-source R package for autonomous analysis of metabolomic data and real-time observation of experimental runs. This simultaneous, fully automated and multi-threaded (optional) package is a wrapper for vendor-independent format conversion (ProteoWizard), xcms- and CAMERA- based peak-picking, MetMSLine-based pre-processing and covariate-based statistical analysis. Users are notified of detrimental instrument drift or errors by email. Also included are two shiny applications, targetId for real-time MS2 target identification, and peakMonitor to monitor targeted metabolites.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>SimExTargId is publicly available under GNU LGPL v3.0 license at https:\/\/github.com\/JosieLHayes\/simExTargId, which includes a vignette with example data. SimExTargId should be installed on a dedicated data-processing workstation or server that is networked to the LC-MS platform to facilitate MS1 profiling of metabolomic data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty218","type":"journal-article","created":{"date-parts":[[2018,5,18]],"date-time":"2018-05-18T07:11:44Z","timestamp":1526627504000},"page":"3589-3590","source":"Crossref","is-referenced-by-count":3,"title":["SimExTargId: a comprehensive package for real-time LC-MS data acquisition and analysis"],"prefix":"10.1093","volume":"34","author":[{"given":"William M B","family":"Edmands","sequence":"first","affiliation":[{"name":"Program in Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6402-6320","authenticated-orcid":false,"given":"Josie","family":"Hayes","sequence":"additional","affiliation":[{"name":"Program in Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA"}]},{"given":"Stephen M","family":"Rappaport","sequence":"additional","affiliation":[{"name":"Program in Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,5,22]]},"reference":[{"key":"2023012712412124500_bty218-B1","doi-asserted-by":"crossref","first-page":"2488.","DOI":"10.1093\/bioinformatics\/btq441","article-title":"Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data","volume":"26","author":"Benton","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012712412124500_bty218-B2","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":"2023012712412124500_bty218-B4","doi-asserted-by":"crossref","first-page":"788","DOI":"10.1093\/bioinformatics\/btu705","article-title":"MetMSLine: an automated and fully integrated pipeline for rapid processing of high-resolution LC-MS metabolomic datasets","volume":"31","author":"Edmands","year":"2015","journal-title":"Bioinformatics"},{"key":"2023012712412124500_bty218-B5","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1021\/ac202450g","article-title":"CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography\/mass spectrometry data sets","volume":"84","author":"Kuhl","year":"2012","journal-title":"Anal. Chem"},{"key":"2023012712412124500_bty218-B7","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1007\/s11306-012-0401-0","article-title":"Nearline acquisition and processing of liquid chromatography-tandem mass spectrometry data","volume":"9","author":"Neumann","year":"2013","journal-title":"Metabolomics"},{"key":"2023012712412124500_bty218-B9","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1021\/ac051437y","article-title":"XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification","volume":"78","author":"Smith","year":"2006","journal-title":"Anal. 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