{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T13:51:42Z","timestamp":1770990702674,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2021,6,14]],"date-time":"2021-06-14T00:00:00Z","timestamp":1623628800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000272","name":"National Institute for Health Research","doi-asserted-by":"publisher","award":["MC_PC_12025"],"award-info":[{"award-number":["MC_PC_12025"]}],"id":[{"id":"10.13039\/501100000272","id-type":"DOI","asserted-by":"publisher"}]},{"name":"MRC UK Consortium for MetAbolic Phenotyping","award":["MR\/S010483\/1"],"award-info":[{"award-number":["MR\/S010483\/1"]}]},{"DOI":"10.13039\/501100013342","name":"NIHR Imperial Biomedical Research Centre","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100013342","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Untargeted liquid chromatography\u2013mass spectrometry (LC\u2013MS) profiling assays are capable of measuring thousands of chemical compounds in a single sample, but unreliable feature extraction and metabolite identification remain considerable barriers to their interpretation and usefulness. peakPantheR (Peak Picking and ANnoTation of High-resolution Experiments in R) is an R package for the targeted extraction and integration of annotated features from LC\u2013MS profiling experiments. It takes advantage of chromatographic and spectral databases and prior information of sample matrix composition to generate annotated and interpretable metabolic phenotypic datasets and power workflows for real-time data quality assessment.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>peakPantheR is available via Bioconductor (https:\/\/bioconductor.org\/packages\/peakPantheR\/). Documentation and worked examples are available at https:\/\/phenomecentre.github.io\/peakPantheR.github.io\/ and https:\/\/github.com\/phenomecentre\/metabotyping-dementia-urine.<\/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\/btab433","type":"journal-article","created":{"date-parts":[[2021,6,13]],"date-time":"2021-06-13T11:07:01Z","timestamp":1623582421000},"page":"4886-4888","source":"Crossref","is-referenced-by-count":29,"title":["peakPantheR, an R package for large-scale targeted extraction and integration of annotated metabolic features in LC\u2013MS profiling datasets"],"prefix":"10.1093","volume":"37","author":[{"given":"Arnaud M","family":"Wolfer","sequence":"first","affiliation":[{"name":"National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, IRDB Building , London W12 0NN, UK"},{"name":"Roche Pharma Research and Early Development, pRED Informatics, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd , Basel CH 4070, Switzerland"}]},{"given":"Gon\u00e7alo","family":"D S Correia","sequence":"additional","affiliation":[{"name":"National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, IRDB Building , London W12 0NN, UK"},{"name":"Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus , London SW7 2AZ, UK"}]},{"given":"Caroline J","family":"Sands","sequence":"additional","affiliation":[{"name":"National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, IRDB Building , London W12 0NN, UK"},{"name":"Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus , London SW7 2AZ, UK"}]},{"given":"Stephane","family":"Camuzeaux","sequence":"additional","affiliation":[{"name":"National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, IRDB Building , London W12 0NN, UK"},{"name":"Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus , London SW7 2AZ, UK"}]},{"given":"Ada H Y","family":"Yuen","sequence":"additional","affiliation":[{"name":"National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, IRDB Building , London W12 0NN, UK"},{"name":"Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus , London SW7 2AZ, UK"}]},{"given":"Elena","family":"Chekmeneva","sequence":"additional","affiliation":[{"name":"National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, IRDB Building , London W12 0NN, UK"},{"name":"Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus , London SW7 2AZ, UK"}]},{"given":"Zolt\u00e1n","family":"Tak\u00e1ts","sequence":"additional","affiliation":[{"name":"National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, IRDB Building , London W12 0NN, UK"},{"name":"Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus , London SW7 2AZ, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4637-3171","authenticated-orcid":false,"given":"Jake T M","family":"Pearce","sequence":"additional","affiliation":[{"name":"National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, IRDB Building , London W12 0NN, UK"}]},{"given":"Matthew R","family":"Lewis","sequence":"additional","affiliation":[{"name":"National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, IRDB Building , London W12 0NN, UK"},{"name":"Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus , London SW7 2AZ, UK"}]}],"member":"286","published-online":{"date-parts":[[2021,6,14]]},"reference":[{"key":"2023051607141913900_btab433-B1","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. 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