{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:43:01Z","timestamp":1753875781574,"version":"3.41.2"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2025,4,16]],"date-time":"2025-04-16T00:00:00Z","timestamp":1744761600000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Lower-Saxony Ministry of Science and Culture within the doctoral program"},{"name":"EU Horizon","award":["101131663"],"award-info":[{"award-number":["101131663"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,5,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Untargeted metabolomics, the comprehensive analysis of small molecules in biological systems, has become an invaluable tool for understanding physiology and metabolism. However, the annotation of metabolomic data is often confounded by the presence of redundant features, which can arise from e.g. multimerization, in-source fragments (ISFs), and adducts.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>MS1FA uniquely integrates all major annotation approaches for redundant features within a single interactive platform. It combines correlation-based grouping with reliable ISF annotation using MS2 data and operates with MS1 data only, MS2 data only, or both. Additionally, it offers a distinctive method for grouping features based on relational criteria. As the only web-based platform with these capabilities, MS1FA provides easy access and allows users to explore and annotate the feature table interactively, with options to download the results.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>MS1FA is freely accessible at https:\/\/ms1fa.helmholtz-hzi.de. The source code and data are available at https:\/\/github.com\/RuibingS\/MS1FA_RShiny_dashboard and are archived with the DOI 10.5281\/zenodo.15118962.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf161","type":"journal-article","created":{"date-parts":[[2025,4,16]],"date-time":"2025-04-16T02:59:19Z","timestamp":1744772359000},"source":"Crossref","is-referenced-by-count":0,"title":["MS1FA: Shiny app for the annotation of redundant features in untargeted metabolomics datasets"],"prefix":"10.1093","volume":"41","author":[{"given":"Ruibing","family":"Shi","sequence":"first","affiliation":[{"name":"Biostatistics Research Group, Helmholtz Centre for Infection Research , Braunschweig, 38124,","place":["Germany"]}]},{"given":"Frank","family":"Klawonn","sequence":"additional","affiliation":[{"name":"Biostatistics Research Group, Helmholtz Centre for Infection Research , Braunschweig, 38124,","place":["Germany"]},{"name":"Department of Computer Science, Ostfalia University of Applied Sciences , Wolfenb\u00fcttel, 38302,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8971-7045","authenticated-orcid":false,"given":"Mark","family":"Br\u00f6nstrup","sequence":"additional","affiliation":[{"name":"Department of Chemical Biology, Helmholtz Centre for Infection Research , Braunschweig, 38124,","place":["Germany"]},{"name":"German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig , Braunschweig, 38124,","place":["Germany"]},{"name":"Institute of Organic Chemistry, Leibniz University Hannover , Hannover, 30167,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5407-5521","authenticated-orcid":false,"given":"Raimo","family":"Franke","sequence":"additional","affiliation":[{"name":"Department of Chemical Biology, Helmholtz Centre for Infection Research , Braunschweig, 38124,","place":["Germany"]}]}],"member":"286","published-online":{"date-parts":[[2025,4,15]]},"reference":[{"key":"2025051307512026200_btaf161-B1","doi-asserted-by":"crossref","first-page":"1377","DOI":"10.1038\/s41592-021-01303-3","article-title":"Metabolite discovery through global annotation of untargeted metabolomics data","volume":"18","author":"Chen","year":"2021","journal-title":"Nat Methods"},{"key":"2025051307512026200_btaf161-B2","doi-asserted-by":"crossref","first-page":"824","DOI":"10.1021\/acs.jnatprod.0c01376","article-title":"Interlaboratory comparison of untargeted mass spectrometry data uncovers underlying causes for variability","volume":"84","author":"Clark","year":"2021","journal-title":"J Nat Prod"},{"key":"2025051307512026200_btaf161-B3","doi-asserted-by":"crossref","first-page":"e00610-21","DOI":"10.1128\/msystems.00610-21","article-title":"Targeting bacterial gyrase with cystobactamid, fluoroquinolone, and aminocoumarin antibiotics induces distinct molecular 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spectra","volume":"86","author":"Ma","year":"2014","journal-title":"Anal Chem"},{"key":"2025051307512026200_btaf161-B7","doi-asserted-by":"crossref","first-page":"3832","DOI":"10.1038\/s41467-021-23953-9","article-title":"Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment","volume":"12","author":"Schmid","year":"2021","journal-title":"Nat Commun"},{"key":"2025051307512026200_btaf161-B8","doi-asserted-by":"crossref","first-page":"4089","DOI":"10.1093\/bioinformatics\/btz207","article-title":"CliqueMS: a computational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network","volume":"35","author":"Senan","year":"2019","journal-title":"Bioinformatics"},{"key":"2025051307512026200_btaf161-B9","doi-asserted-by":"crossref","first-page":"2273","DOI":"10.1021\/ac504118y","article-title":"Avoiding misannotation of in-source fragmentation products as cellular metabolites in 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