{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T07:24:58Z","timestamp":1781594698144,"version":"3.54.5"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2019,10,12]],"date-time":"2019-10-12T00:00:00Z","timestamp":1570838400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"EMBL and the MicrobioS","award":["ERC-AdG-669830"],"award-info":[{"award-number":["ERC-AdG-669830"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Untargeted mass spectrometry (MS\/MS) is a powerful method for detecting metabolites in biological samples. However, fast and accurate identification of the metabolites\u2019 structures from MS\/MS spectra is still a great challenge.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present a new analysis method, called SubFragment-Matching (SF-Matching) that is based on the hypothesis that molecules with similar structural features will exhibit similar fragmentation patterns. We combine information on fragmentation patterns of molecules with shared substructures and then use random forest models to predict whether a given structure can yield a certain fragmentation pattern. These models can then be used to score candidate molecules for a given mass spectrum. For rapid identification, we pre-compute such scores for common biological molecular structure databases. Using benchmarking datasets, we find that our method has similar performance to CSI: FingerID and those very high accuracies can be achieved by combining our method with CSI: FingerID. Rarefaction analysis of the training dataset shows that the performance of our method will increase as more experimental data become available.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>SF-Matching is available from http:\/\/www.bork.embl.de\/Docu\/sf_matching.<\/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\/btz736","type":"journal-article","created":{"date-parts":[[2019,9,26]],"date-time":"2019-09-26T07:28:48Z","timestamp":1569482928000},"page":"1213-1218","source":"Crossref","is-referenced-by-count":35,"title":["Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5971-0355","authenticated-orcid":false,"given":"Yuanyue","family":"Li","sequence":"first","affiliation":[{"name":"Structural and Computational Biology Unit, European Molecular Biology Laboratory , 69117 Heidelberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Kuhn","sequence":"additional","affiliation":[{"name":"Structural and Computational Biology Unit, European Molecular Biology Laboratory , 69117 Heidelberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne-Claude","family":"Gavin","sequence":"additional","affiliation":[{"name":"Structural and Computational Biology Unit, European Molecular Biology Laboratory , 69117 Heidelberg, Germany"},{"name":"Molecular Medicine Partnership Unit (MMPU) , 69117 Heidelberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peer","family":"Bork","sequence":"additional","affiliation":[{"name":"Structural and Computational Biology Unit, European Molecular Biology Laboratory , 69117 Heidelberg, Germany"},{"name":"Molecular Medicine Partnership Unit (MMPU) , 69117 Heidelberg, Germany"},{"name":"Max Delbr\u00fcck Center for Molecular Medicine , 13125 Berlin, Germany"},{"name":"Department of Bioinformatics, Biocenter, University of W\u00fcrzburg , 97074 W\u00fcrzburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,10,12]]},"reference":[{"key":"2023013110122200400_btz736-B1","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1007\/s11306-014-0676-4","article-title":"Competitive fragmentation modeling of ESI-MS\/MS spectra for putative metabolite identification","volume":"11","author":"Allen","year":"2015","journal-title":"Metabolomics"},{"key":"2023013110122200400_btz736-B2","doi-asserted-by":"crossref","first-page":"149.","DOI":"10.1007\/s11306-016-1094-6","article-title":"Metabolomics enables precision medicine: \u201cA White Paper, Community Perspective\u201d","volume":"12","author":"Beger","year":"2016","journal-title":"Metabolomics"},{"key":"2023013110122200400_btz736-B3","doi-asserted-by":"crossref","first-page":"6382","DOI":"10.1021\/ac800795f","article-title":"XCMS2: processing tandem mass spectrometry data for metabolite identification and structural characterization","volume":"80","author":"Benton","year":"2008","journal-title":"Anal. 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