{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T15:58:46Z","timestamp":1791215926484,"version":"4.1.0"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T00:00:00Z","timestamp":1790121600000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"EU NextGenerationEU through the Recovery and Resilience Plan for Slovakia","award":["09I03-03-V04-00681"],"award-info":[{"award-number":["09I03-03-V04-00681"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The identification and analysis of glycans using MALDI-TOF mass spectrometry is a critical task in glycomics research, yet it often requires complex data interpretation and manual processing. Existing software tools frequently lack automated solutions for efficient glycan annotation, data structuring and grouping, and semi-quantitative evaluation, making large-scale glycan analysis challenging. To address these limitations, we developed massMatchR, an open-source software tool designed to streamline the identification and quantification of glycans in MALDI-TOF spectra.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>massMatchR automates glycan identification by mapping experimentally detected m\/z values from preprocessed MALDI-TOF-MS datasets to glycans from a user-defined database. The software provides both visual and tabular outputs, enabling rapid and accurate glycan interpretation. Additionally, massMatchR facilitates the export of structured data tables (e.g. Microsoft Excel) with predefined fields for m\/z and intensity, supporting further analysis. A key feature of the software is its ability to perform semi-quantitative evaluation based on relative intensity calculations, allowing for comparisons across multiple samples. Freely available at http:\/\/www.imb.savba.sk\/soft\/massMatchR\/ and on GitHub implemented in R, massMatchR offers a fast, reproducible, and customizable computational framework for glycomics and MALDI-TOF-based glycan analysis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>An implementation code is available on Github at https:\/\/github.com\/bekegbor\/massMatchR and on Zenodo at https:\/\/doi.org\/10.5281\/zenodo.20697072.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag700","type":"journal-article","created":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T11:37:27Z","timestamp":1790077047000},"source":"Crossref","is-referenced-by-count":0,"title":["<i>massMatchR<\/i>\n                    : a Shiny application for glycomics mass spectrometry data analysis"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3385-1317","authenticated-orcid":false,"given":"G\u00e1bor","family":"Beke","sequence":"first","affiliation":[{"name":"Institute of Chemistry, Slovak Academy of Sciences , 845 38 Bratislava,","place":["Slovakia"]},{"name":"Institute of Molecular Biology, Slovak Academy of Sciences , 845 51 Bratislava,","place":["Slovakia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"L\u2019ubo\u0161","family":"Kl\u2019u\u010d\u00e1r","sequence":"additional","affiliation":[{"name":"Institute of Molecular Biology, Slovak Academy of Sciences , 845 51 Bratislava,","place":["Slovakia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zuzana","family":"Pakanov\u00e1","sequence":"additional","affiliation":[{"name":"Institute of Chemistry, Slovak Academy of Sciences , 845 38 Bratislava,","place":["Slovakia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebeka","family":"Kodr\u00edkova","sequence":"additional","affiliation":[{"name":"Institute of Chemistry, Slovak Academy of Sciences , 845 38 Bratislava,","place":["Slovakia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Bar\u00e1th","sequence":"additional","affiliation":[{"name":"Institute of Chemistry, Slovak Academy of Sciences , 845 38 Bratislava,","place":["Slovakia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marek","family":"Nem\u010dovi\u010d","sequence":"additional","affiliation":[{"name":"Institute of Molecular Biology, Slovak Academy of Sciences , 845 51 Bratislava,","place":["Slovakia"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,9,22]]},"reference":[{"key":"2026100511421013500_btag700-B1","author":"Attali","year":"2021"},{"key":"2026100511421013500_btag700-B2","author":"Attali","year":"2023"},{"key":"2026100511421013500_btag700-B3","author":"Bailey","year":"2022"},{"key":"2026100511421013500_btag700-B4","author":"Bolker","year":"2022"},{"key":"2026100511421013500_btag700-B5","author":"Boutaris","year":"2023"},{"key":"2026100511421013500_btag700-B6","doi-asserted-by":"publisher","first-page":"1650","DOI":"10.1021\/pr7008252","article-title":"GlycoWorkbench: a tool for the computer-assisted annotation of mass spectra of glycans","volume":"7","author":"Ceroni","year":"2008","journal-title":"J Proteome Res"},{"key":"2026100511421013500_btag700-B7","doi-asserted-by":"publisher","author":"Chang","year":"2026","DOI":"10.32614\/CRAN.package.shiny"},{"key":"2026100511421013500_btag700-B8","author":"Dinno","year":"2026"},{"key":"2026100511421013500_btag700-B9","doi-asserted-by":"publisher","first-page":"5088","DOI":"10.1021\/acs.jproteome.5b00658","article-title":"MassyTools: a high-throughput targeted data processing tool for relative quantitation and quality control developed for glycomic and glycoproteomic MALDI-MS","volume":"14","author":"Jansen","year":"2015","journal-title":"J Proteome Res"},{"key":"2026100511421013500_btag700-B10","doi-asserted-by":"publisher","first-page":"580","DOI":"10.3390\/biomedicines11020580","article-title":"N-glycoprofiling of SLC35A2-CDG: patient with a novel hemizygous variant","volume":"11","author":"Kodr\u00edkov\u00e1","year":"2023","journal-title":"Biomedicines"},{"key":"2026100511421013500_btag700-B11","first-page":"14560","article-title":"GRITS toolbox\u2014a freely available software for processing, annotating, and archiving glycomics mass spectrometry data","volume":"90","author":"Kronewitter","year":"2018","journal-title":"Anal Chem"},{"key":"2026100511421013500_btag700-B12","doi-asserted-by":"publisher","first-page":"2986","DOI":"10.1002\/pmic.200800760","article-title":"The development of retrosynthetic glycan libraries to profile and classify the human serum N-linked glycome","volume":"9","author":"Kronewitter","year":"2009","journal-title":"Proteomics"},{"key":"2026100511421013500_btag700-B13","first-page":"2033","article-title":"AssignMALDI \u2013 a free software for assignment of MALDI-TOF MS spectra of glycans derivatized using common and novel labeling strategies","volume":"36","author":"Mehta","year":"2020","journal-title":"Bioinformatics"},{"key":"2026100511421013500_btag700-B14","author":"Core Team","year":"2021"},{"key":"2026100511421013500_btag700-B15","author":"Schauberger","year":"2023"},{"key":"2026100511421013500_btag700-B16","author":"Sievert","year":"2020"},{"key":"2026100511421013500_btag700-B17","first-page":"114352","article-title":"A MATLAB-based app to improve LC-MS\/MS data analysis for N-linked glycan peak identification","volume":"631","author":"Singh","year":"2021","journal-title":"Anal Biochem"},{"key":"2026100511421013500_btag700-B18","author":"Vaidyanathan","year":"2023"},{"key":"2026100511421013500_btag700-B19","doi-asserted-by":"publisher","first-page":"1323","DOI":"10.1093\/glycob\/cwv091","article-title":"Symbol nomenclature for graphical representations of glycans","volume":"25","author":"Varki","year":"2015","journal-title":"Glycobiology"},{"key":"2026100511421013500_btag700-B20","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-24277-4","volume-title":"ggplot2: Elegant Graphics for Data Analysis","author":"Wickham","year":"2016"},{"key":"2026100511421013500_btag700-B21","author":"Xie","year":"2025"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag700\/71326689\/btag700.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/10\/btag700\/71326689\/btag700.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/10\/btag700\/71326689\/btag700.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T15:42:19Z","timestamp":1791214939000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btag700\/8830096"}},"subtitle":[],"editor":[{"given":"Macha","family":"Nikolski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,9,22]]},"references-count":21,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2026,10,2]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btag700","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,10]]},"published":{"date-parts":[[2026,9,22]]},"article-number":"btag700"}}