{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:09Z","timestamp":1772138049836,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2021,11,18]],"date-time":"2021-11-18T00:00:00Z","timestamp":1637193600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"European Union\u2019s Horizon 2020 Research and Innovation Program","award":["829157"],"award-info":[{"award-number":["829157"]}]},{"name":"European Union\u2019s Horizon 2020 Research and Innovation Program","award":["823839"],"award-info":[{"award-number":["823839"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>We present a new software-tool allowing an easy visualization of fragment ions and thus a rapid evaluation of key experimental parameters on the sequence coverage obtained for the MS\/MS (tandem mass spectrometry) analysis of intact proteins. Our tool can process data obtained from various deconvolution and fragment assignment software.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We demonstrate that TDFragMapper can rapidly highlight the experimental fragmentation parameters that are critical to the characterization of intact proteins of various size using top-down proteomics.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>TDFragMapper, a demonstration video and user tutorial are freely available for academic use at https:\/\/msbio.pasteur.fr\/tdfragmapper; all data are thus available from the ProteomeXchange consortium (identifier PXD024643).<\/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\/btab784","type":"journal-article","created":{"date-parts":[[2021,11,15]],"date-time":"2021-11-15T08:48:17Z","timestamp":1636966097000},"page":"1136-1138","source":"Crossref","is-referenced-by-count":3,"title":["TDFragMapper: a visualization tool for evaluating experimental parameters in top-down proteomics"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6615-2363","authenticated-orcid":false,"given":"Jonathan","family":"Dhenin","sequence":"first","affiliation":[{"name":"Mass Spectrometry for Biology Unit, Institut Pasteur, Universit\u00e9 de Paris, CNRS USR2000, Paris, France"},{"name":"Universit\u00e9 de Paris, Sorbonne Paris Cit\u00e9 , Paris, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6056-0825","authenticated-orcid":false,"given":"Diogo","family":"Borges Lima","sequence":"additional","affiliation":[{"name":"Leibniz-Forschungsinstitut f\u00fcr Molekulare Pharmakologie , Berlin, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1845-0048","authenticated-orcid":false,"given":"Mathieu","family":"Dupr\u00e9","sequence":"additional","affiliation":[{"name":"Mass Spectrometry for Biology Unit, Institut Pasteur, Universit\u00e9 de Paris, CNRS USR2000, Paris, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9427-543X","authenticated-orcid":false,"given":"Julia","family":"Chamot-Rooke","sequence":"additional","affiliation":[{"name":"Mass Spectrometry for Biology Unit, Institut Pasteur, Universit\u00e9 de Paris, CNRS USR2000, Paris, France"}]}],"member":"286","published-online":{"date-parts":[[2021,11,18]]},"reference":[{"key":"2023020108535648800_btab784-B1","author":"Borges Lima","year":"2021"},{"key":"2023020108535648800_btab784-B2","doi-asserted-by":"crossref","first-page":"4152","DOI":"10.1021\/acs.analchem.5b00162","article-title":"Benchmarking multiple fragmentation methods on an orbitrap fusion for top-down phospho-proteoform characterization","volume":"87","author":"Brunner","year":"2015","journal-title":"Anal. Chem"},{"key":"2023020108535648800_btab784-B3","doi-asserted-by":"crossref","first-page":"1235","DOI":"10.1002\/pmic.201400313","article-title":"ProSight Lite: graphical software to analyze top-down mass spectrometry data","volume":"15","author":"Fellers","year":"2015","journal-title":"Proteomics"},{"key":"2023020108535648800_btab784-B4","doi-asserted-by":"crossref","first-page":"8421","DOI":"10.1021\/acs.analchem.8b00984","article-title":"Accurate sequence analysis of a monoclonal antibody by top-down and middle-down orbitrap mass spectrometry applying multiple ion activation techniques","volume":"90","author":"Fornelli","year":"2018","journal-title":"Anal. Chem"},{"key":"2023020108535648800_btab784-B5","doi-asserted-by":"crossref","first-page":"10313","DOI":"10.1073\/pnas.97.19.10313","article-title":"Automated de novo sequencing of proteins by tandem high-resolution mass spectrometry","volume":"97","author":"Horn","year":"2000","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023020108535648800_btab784-B6","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1021\/ja973655h","article-title":"Top down versus bottom up protein characterization by tandem high-resolution mass spectrometry","volume":"121","author":"Kelleher","year":"1999","journal-title":"J. Am. Chem. Soc"},{"key":"2023020108535648800_btab784-B7","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1126\/science.aat1884","article-title":"Proteoforms as the next proteomics currency","volume":"359","author":"Smith","year":"2018","journal-title":"Science"},{"key":"2023020108535648800_btab784-B8","doi-asserted-by":"crossref","first-page":"3867","DOI":"10.1021\/acs.jproteome.0c00469","article-title":"MASH Explorer: a universal software environment for top-down proteomics","volume":"19","author":"Wu","year":"2020","journal-title":"J. Proteome Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab784\/41298796\/btab784.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/4\/1136\/49009159\/btab784.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/4\/1136\/49009159\/btab784.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T15:15:19Z","timestamp":1675264519000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/4\/1136\/6430971"}},"subtitle":[],"editor":[{"given":"Olga","family":"Vitek","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2021,11,18]]},"references-count":8,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2022,1,27]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab784","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.06.03.446879","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,2,15]]},"published":{"date-parts":[[2021,11,18]]}}}