{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T21:49:59Z","timestamp":1774388999296,"version":"3.50.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2020,10,18]],"date-time":"2020-10-18T00:00:00Z","timestamp":1602979200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000057","name":"NIH National Institute of General Medical Sciences","doi-asserted-by":"crossref","award":["GM133751"],"award-info":[{"award-number":["GM133751"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Hydrogen\u2013Deuterium eXchange coupled to mass spectrometry is a powerful tool for the analysis of protein dynamics and interactions. Bottom-up experiments looking at deuterium uptake differences between various conditions are the most common. These produce multi-dimensional data that can be challenging to depict in a single visual format. Each user must also set significance thresholds to define meaningful differences and make these apparent in data presentation. To assist in this process, we have created HD-eXplosion, an open-source, web-based application for the generation of chiclet and volcano plots with statistical filters. HD-eXplosion fills a void in available software packages and produces customizable plots that are publication quality.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The HD-eXplosion application is available at http:\/\/hd-explosion.utdallas.edu. The source code can be found at https:\/\/github.com\/HD-Explosion.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa892","type":"journal-article","created":{"date-parts":[[2020,10,6]],"date-time":"2020-10-06T03:30:50Z","timestamp":1601955050000},"page":"1926-1927","source":"Crossref","is-referenced-by-count":35,"title":["HD-eXplosion: visualization of hydrogen\u2013deuterium exchange data as chiclet and volcano plots with statistical filtering"],"prefix":"10.1093","volume":"37","author":[{"given":"Naifu","family":"Zhang","sequence":"first","affiliation":[{"name":"Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX 75080, USA"}]},{"given":"Xiaohe","family":"Yu","sequence":"additional","affiliation":[]},{"given":"Xinchao","family":"Zhang","sequence":"additional","affiliation":[]},{"given":"Sheena","family":"D\u2019Arcy","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX 75080, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,10,18]]},"reference":[{"key":"2023051611454367800_btaa892-B1","doi-asserted-by":"crossref","first-page":"2874","DOI":"10.1039\/C7AN00662D","article-title":"Bottom-up hydrogen deuterium exchange mass spectrometry: data analysis and interpretation","volume":"142","author":"Brown","year":"2017","journal-title":"Analyst"},{"key":"2023051611454367800_btaa892-B2","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1021\/ac051294f","article-title":"Probing protein ligand interactions by automated hydrogen\/deuterium exchange mass spectrometry","volume":"78","author":"Chalmers","year":"2006","journal-title":"Anal. Chem"},{"key":"2023051611454367800_btaa892-B3","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1586\/epr.10.109","article-title":"Differential hydrogen\/deuterium exchange mass spectrometry analysis of protein\u2013ligand interactions","volume":"8","author":"Chalmers","year":"2011","journal-title":"Expert Rev. Proteomics"},{"key":"2023051611454367800_btaa892-B4","doi-asserted-by":"crossref","first-page":"8008","DOI":"10.1021\/acs.analchem.9b01325","article-title":"Reliable identification of significant differences in differential hydrogen exchange-mass spectrometry measurements using a hybrid significance testing approach","volume":"91","author":"Hageman","year":"2019","journal-title":"Anal. Chem"},{"key":"2023051611454367800_btaa892-B5","doi-asserted-by":"crossref","first-page":"3413","DOI":"10.1093\/bioinformatics\/btw420","article-title":"MEMHDX: an interactive tool to expedite the statistical validation and visualization of large HDX-MS datasets","volume":"32","author":"Hourdel","year":"2016","journal-title":"Bioinformatics"},{"key":"2023051611454367800_btaa892-B6","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1586\/14789450.2015.1018897","article-title":"Hydrogen\/deuterium exchange mass spectrometry applied to IL-23 interaction characteristics: potential impact for therapeutics","volume":"12","author":"Iacob","year":"2015","journal-title":"Expert Rev. Proteomics"},{"key":"2023051611454367800_btaa892-B7","doi-asserted-by":"crossref","first-page":"2860","DOI":"10.1016\/j.celrep.2017.08.081","article-title":"Chemically induced degradation of the oncogenic transcription factor BCL6","volume":"20","author":"Kerres","year":"2017","journal-title":"Cell Rep"},{"key":"2023051611454367800_btaa892-B8","doi-asserted-by":"crossref","first-page":"3171","DOI":"10.1093\/bioinformatics\/btz022","article-title":"Deuteros: software for rapid analysis and visualization of data from differential hydrogen deuterium exchange-mass spectrometry","volume":"35","author":"Lau","year":"2019","journal-title":"Bioinformatics"},{"key":"2023051611454367800_btaa892-B9","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1038\/s41586-019-1820-0","article-title":"FACT caught in the act of manipulating the nucleosome","volume":"577","author":"Liu","year":"2020","journal-title":"Nature"},{"key":"2023051611454367800_btaa892-B10","doi-asserted-by":"crossref","first-page":"981","DOI":"10.1080\/17460441.2017.1363734","article-title":"An overview of hydrogen deuterium exchange mass spectrometry (HDX-MS) in drug discovery","volume":"12","author":"Masson","year":"2017","journal-title":"Expert Opin. Drug Discov"},{"key":"2023051611454367800_btaa892-B11","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1038\/s41592-019-0459-y","article-title":"Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments","volume":"16","author":"Masson","year":"2019","journal-title":"Nat. Methods"},{"key":"2023051611454367800_btaa892-B12","volume-title":"Guide to NumPy","author":"Oliphant","year":"2006"},{"key":"2023051611454367800_btaa892-B13","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1021\/ac5040242","article-title":"Applications of hydrogen\/deuterium exchange MS from 2012 to 2014","volume":"87","author":"Pirrone","year":"2015","journal-title":"Anal. Chem"},{"key":"2023051611454367800_btaa892-B14","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1002\/mas.20064","article-title":"Hydrogen exchange mass spectrometry for the analysis of protein dynamics","volume":"25","author":"Wales","year":"2006","journal-title":"Mass Spectrom. Rev"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa892\/34542318\/btaa892.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/13\/1926\/50340110\/btaa892.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/13\/1926\/50340110\/btaa892.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T11:47:21Z","timestamp":1684237641000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/13\/1926\/5929686"}},"subtitle":[],"editor":[{"given":"Ponty","family":"Yann","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,10,18]]},"references-count":14,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2021,7,27]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa892","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,7,1]]},"published":{"date-parts":[[2020,10,18]]}}}