{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,8]],"date-time":"2025-11-08T13:10:22Z","timestamp":1762607422184,"version":"3.37.3"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2019,1,12]],"date-time":"2019-01-12T00:00:00Z","timestamp":1547251200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"President\u2019s Initiative and Networking Funds"},{"name":"Helmholtz Association of German Research Centres","award":["VH-GS-202"],"award-info":[{"award-number":["VH-GS-202"]}]},{"name":"European Marine Biological Research Infrastructure Cluster","award":["654008"],"award-info":[{"award-number":["654008"]}]},{"DOI":"10.13039\/501100004350","name":"Studienstiftung des deutschen Volkes","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100004350","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Compound identification is one of the most eminent challenges in the untargeted analysis of complex mixtures of small molecules by mass spectrometry. Similarity of tandem mass spectra can provide valuable information on putative structural similarities between known and unknown analytes and hence aids feature identification in the bioanalytical sciences. We have developed CluMSID (Clustering of MS2 spectra for metabolite identification), an R package that enables researchers to make use of tandem mass spectra and neutral loss pattern similarities as a part of their metabolite annotation workflow. CluMSID offers functions for all analysis steps from import of raw data to data mining by unsupervised multivariate methods along with respective (interactive) visualizations. A detailed tutorial with example data is provided as supplementary information.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>CluMSID is available as R package from https:\/\/github.com\/tdepke\/CluMSID\/and from https:\/\/bioconductor.org\/packages\/CluMSID\/.<\/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\/btz005","type":"journal-article","created":{"date-parts":[[2019,1,8]],"date-time":"2019-01-08T15:41:10Z","timestamp":1546962070000},"page":"3196-3198","source":"Crossref","is-referenced-by-count":17,"title":["CluMSID: an R package for similarity-based clustering of tandem mass spectra to aid feature annotation in metabolomics"],"prefix":"10.1093","volume":"35","author":[{"given":"Tobias","family":"Depke","sequence":"first","affiliation":[{"name":"Helmholtz Centre for Infection Research Department of Chemical Biology, , Braunschweig D-38124, Germany"}]},{"given":"Raimo","family":"Franke","sequence":"additional","affiliation":[{"name":"Helmholtz Centre for Infection Research Department of Chemical Biology, , Braunschweig D-38124, Germany"}]},{"given":"Mark","family":"Br\u00f6nstrup","sequence":"additional","affiliation":[{"name":"Helmholtz Centre for Infection Research Department of Chemical Biology, , Braunschweig D-38124, Germany"},{"name":"German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig , D-38124 Braunschweig, Germany"}]}],"member":"286","published-online":{"date-parts":[[2019,1,12]]},"reference":[{"key":"2023062711310143000_btz005-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v024.i02","article-title":"Network: a package for managing relational data in R","volume":"24","author":"Butts","year":"2008","journal-title":"J. Stat. Softw."},{"key":"2023062711310143000_btz005-B2","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.jchromb.2017.06.002","article-title":"MS2 spectra using unsupervised methods to aid the identification of secondary metabolites from Pseudomonas aeruginosa","volume":"1071","author":"Depke","year":"2017","journal-title":"J. Chromatogr. B"},{"key":"2023062711310143000_btz005-B3","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1016\/j.ijms.2014.06.005","article-title":"Mass spectral similarity for untargeted metabolomics data analysis of complex mixtures","volume":"377","author":"Garg","year":"2015","journal-title":"Int. J. Mass Spectrom."},{"key":"2023062711310143000_btz005-B4","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1038\/nrm.2016.25","article-title":"Metabolomics: beyond biomarkers and towards mechanisms","volume":"17","author":"Johnson","year":"2016","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"2023062711310143000_btz005-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":"2023062711310143000_btz005-B6","doi-asserted-by":"crossref","first-page":"2419","DOI":"10.1093\/bioinformatics\/btx159","article-title":"MetCirc: navigating mass spectral similarity in high-resolution MS\/MS metabolomics data","volume":"33","author":"Naake","year":"2017","journal-title":"Bioinformatics"},{"key":"2023062711310143000_btz005-B7","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. Chem."},{"key":"2023062711310143000_btz005-B8","doi-asserted-by":"crossref","first-page":"2470","DOI":"10.1021\/ac026424o","article-title":"Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility","volume":"75","author":"Tabb","year":"2003","journal-title":"Anal. Chem."},{"key":"2023062711310143000_btz005-B9","doi-asserted-by":"crossref","first-page":"8082","DOI":"10.1021\/acs.analchem.6b01569","article-title":"Discovering regulated metabolite families in untargeted metabolomics studies","volume":"88","author":"Treutler","year":"2016","journal-title":"Anal. Chem."},{"key":"2023062711310143000_btz005-B10","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.copbio.2018.01.008","article-title":"Advances in computational metabolomics and databases deepen the understanding of metabolisms","volume":"54","author":"Tsugawa","year":"2018","journal-title":"Curr. Opin. Biotechnol."},{"key":"2023062711310143000_btz005-B11","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1016\/S1044-0305(01)00327-0","article-title":"Comparing similar spectra: from similarity index to spectral contrast angle","volume":"13","author":"Wan","year":"2002","journal-title":"J. Am. Soc. Mass Spectrom."},{"key":"2023062711310143000_btz005-B12","doi-asserted-by":"crossref","first-page":"828","DOI":"10.1038\/nbt.3597","article-title":"Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking","volume":"34","author":"Wang","year":"2016","journal-title":"Nat. Biotechnol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/17\/3196\/50719824\/bioinformatics_35_17_3196.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/17\/3196\/50719824\/bioinformatics_35_17_3196.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,27]],"date-time":"2023-06-27T11:31:44Z","timestamp":1687865504000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/17\/3196\/5288514"}},"subtitle":[],"editor":[{"given":"Janet","family":"Kelso","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,1,12]]},"references-count":12,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2019,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz005","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2019,9,1]]},"published":{"date-parts":[[2019,1,12]]}}}