{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T21:03:27Z","timestamp":1774559007917,"version":"3.50.1"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T00:00:00Z","timestamp":1773619200000},"content-version":"vor","delay-in-days":16,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004281","name":"National Science Centre Poland","doi-asserted-by":"crossref","award":["2019\/35\/O\/NZ2\/03745"],"award-info":[{"award-number":["2019\/35\/O\/NZ2\/03745"]}],"id":[{"id":"10.13039\/501100004281","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100004281","name":"National Science Centre Poland","doi-asserted-by":"crossref","award":["2023\/51\/D\/NZ7\/02847"],"award-info":[{"award-number":["2023\/51\/D\/NZ7\/02847"]}],"id":[{"id":"10.13039\/501100004281","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100014434","name":"Polish National Agency for Academic Exchange","doi-asserted-by":"publisher","award":["PPN\/STA\/2021\/1\/00025"],"award-info":[{"award-number":["PPN\/STA\/2021\/1\/00025"]}],"id":[{"id":"10.13039\/501100014434","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,2,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Hydrogen\u2013Deuterium Exchange Mass Spectrometry (HDX-MS) monitors deuterium uptake at the peptide level, in a time-dependent manner. It produces complex, multi-dimensional data that must be interpreted at minimum both the temporal and sequence levels. Specialized tools are therefore essential to preprocess, integrate, and analyze HDX-MS data and translate it into meaningful biological insights. HaDeX2 provides statistical inferences and their visualizations across five dimensions of HDX-MS data: protein sequence, time, biological states, peptide charge and experimental replicates.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>HaDeX2 is freely available as an R package (https:\/\/github.com\/hadexversum\/HaDeX2; https:\/\/doi.org\/10.5281\/zenodo.18543703) and web server (https:\/\/hadex2.mslab-ibb.pl\/). To run the GUI locally, users should install a dedicated companion package (https:\/\/github.com\/hadexversum\/HaDeXGUI).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag128","type":"journal-article","created":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T12:48:10Z","timestamp":1773233290000},"source":"Crossref","is-referenced-by-count":0,"title":["HaDeX2: multi-dimensional analysis of hydrogen\u2013deuterium exchange mass spectrometry data"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2163-1429","authenticated-orcid":false,"given":"Weronika","family":"Pucha\u0142a","sequence":"first","affiliation":[{"name":"Institute of Biochemistry and Biophysics, Polish Academy of Sciences , 02-106 Warsaw,","place":["Poland"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2581-7722","authenticated-orcid":false,"given":"Krystyna","family":"Grzesiak","sequence":"additional","affiliation":[{"name":"Faculty of Mathematics and Computer Science, University of Wroc\u0142aw , 50-383 Wroc\u0142aw,","place":["Poland"]},{"name":"Clinical Research Centre, Medical University of Bia\u0142ystok , 15-089 Bia\u0142ystok,","place":["Poland"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0925-1909","authenticated-orcid":false,"given":"Dominik","family":"Rafacz","sequence":"additional","affiliation":[{"name":"Faculty of Mathematics and Information Science, Warsaw University of Technology , 00-666 Warsaw,","place":["Poland"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5167-4011","authenticated-orcid":false,"given":"Micha\u0142","family":"Kistowski","sequence":"additional","affiliation":[{"name":"Institute of Biochemistry and Biophysics, Polish Academy of Sciences , 02-106 Warsaw,","place":["Poland"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3597-9429","authenticated-orcid":false,"given":"Jochem H","family":"Smit","sequence":"additional","affiliation":[{"name":"Rega Institute of Medical Research, KU Leuven , B-3000 Leuven,","place":["Belgium"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7321-7436","authenticated-orcid":false,"given":"Julien","family":"Marcoux","sequence":"additional","affiliation":[{"name":"Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS , 31400 Toulouse,","place":["France"]},{"name":"Infrastructure Nationale de Prot\u00e9omique, ProFI , UAR 2048 Toulouse,","place":["France"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8811-5176","authenticated-orcid":false,"given":"Micha\u0142","family":"Dadlez","sequence":"additional","affiliation":[{"name":"Institute of Biochemistry and Biophysics, Polish Academy of Sciences , 02-106 Warsaw,","place":["Poland"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8926-582X","authenticated-orcid":false,"given":"Micha\u0142","family":"Burdukiewicz","sequence":"additional","affiliation":[{"name":"Clinical Research Centre, Medical University of Bia\u0142ystok , 15-089 Bia\u0142ystok,","place":["Poland"]},{"name":"Life Sciences Center, Vilnius University , LT-10257 Vilnius, Lithuania"},{"name":"Faculty of Life Sciences, University of Bradford , BD7 1DP Bradford,","place":["United Kingdom"]}]}],"member":"286","published-online":{"date-parts":[[2026,3,16]]},"reference":[{"key":"2026032616013072200_btag128-B1","doi-asserted-by":"crossref","first-page":"9490","DOI":"10.1093\/nar\/gkac685","article-title":"Quaternary organization of the human eEF1B complex reveals unique multi-GEF domain assembly","volume":"50","author":"Bondarchuk","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2026032616013072200_btag128-B2","doi-asserted-by":"crossref","first-page":"5331","DOI":"10.1093\/bioinformatics\/btz550","article-title":"HDX-Viewer: interactive 3D visualization of hydrogen-deuterium exchange data","volume":"35","author":"Bouyssi\u00e9","year":"2019","journal-title":"Bioinformatics"},{"key":"2026032616013072200_btag128-B3","doi-asserted-by":"crossref","first-page":"16341","DOI":"10.1021\/acs.analchem.1c02346","article-title":"Moderated test statistics to detect differential deuteration in hydrogen\/deuterium exchange mass spectrometry experiments","volume":"93","author":"Claesen","year":"2021","journal-title":"Anal Chem"},{"key":"2026032616013072200_btag128-B4","doi-asserted-by":"crossref","first-page":"2959","DOI":"10.1021\/acs.jproteome.3c00297","article-title":"A functional Bayesian model for hydrogen\u2013deuterium exchange mass spectrometry","volume":"22","author":"Crook","year":"2023","journal-title":"J Proteome Res"},{"key":"2026032616013072200_btag128-B5","doi-asserted-by":"crossref","first-page":"1481","DOI":"10.1016\/j.jasms.2006.06.006","article-title":"Hydrogen exchange and mass spectrometry: a historical perspective","volume":"17","author":"Englander","year":"2006","journal-title":"J Am Soc Mass Spectrom"},{"key":"2026032616013072200_btag128-B6","doi-asserted-by":"crossref","first-page":"3789","DOI":"10.1038\/s41598-017-03922-3","article-title":"Computational method allowing hydrogen-deuterium exchange mass spectrometry at single amide resolution","volume":"7","author":"Gessner","year":"2017","journal-title":"Sci Rep"},{"key":"2026032616013072200_btag128-B7","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1007\/s13361-015-1330-8","article-title":"Tuning a high transmission ion guide to prevent Gas-Phase proton exchange during H\/D exchange MS analysis","volume":"27","author":"Guttman","year":"2016","journal-title":"J Am Soc Mass Spectrom"},{"key":"2026032616013072200_btag128-B8","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":"2026032616013072200_btag128-B9","doi-asserted-by":"crossref","first-page":"2071","DOI":"10.1002\/jps.22432","article-title":"The utility of hydrogen\/deuterium exchange mass spectrometry in biopharmaceutical comparability studies","volume":"100","author":"Houde","year":"2011","journal-title":"J Pharm Sci"},{"key":"2026032616013072200_btag128-B10","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btae479","article-title":"HDXBoxeR: an R package for statistical analysis and visualization of multiple hydrogen\u2013deuterium exchange mass-spectrometry datasets of different protein states","volume":"40","author":"Janowska","year":"2024","journal-title":"Bioinformatics"},{"key":"2026032616013072200_btag128-B11","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1007\/s13361-014-1033-6","article-title":"Mapping residual structure in intrinsically disordered proteins at residue resolution using millisecond hydrogen\/deuterium exchange and residue averaging","volume":"26","author":"Keppel","year":"2015","journal-title":"J Am Soc Mass Spectrom"},{"key":"2026032616013072200_btag128-B12","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1093\/bioinformatics\/btaa677","article-title":"Deuteros 2.0: peptide-level significance testing of data from hydrogen deuterium exchange mass spectrometry","volume":"37","author":"Lau","year":"2021","journal-title":"Bioinformatics"},{"key":"2026032616013072200_btag128-B13","doi-asserted-by":"crossref","first-page":"6140","DOI":"10.1038\/s41467-020-19934-z","article-title":"Conformational maps of human 20S proteasomes reveal PA28- and immuno-dependent inter-ring crosstalks","volume":"11","author":"Lesne","year":"2020","journal-title":"Nat Commun"},{"key":"2026032616013072200_btag128-B14","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":"2026032616013072200_btag128-B15","doi-asserted-by":"crossref","first-page":"7022","DOI":"10.1021\/acs.analchem.5b01724","article-title":"Hydrogen exchange mass spectrometry of proteins at Langmuir monolayers","volume":"87","author":"Pirrone","year":"2015","journal-title":"Anal Chem"},{"key":"2026032616013072200_btag128-B16","doi-asserted-by":"crossref","first-page":"4516","DOI":"10.1093\/bioinformatics\/btaa587","article-title":"HaDeX: an R package and web-server for analysis of data from hydrogen\u2013deuterium exchange mass spectrometry experiments","volume":"36","author":"Pucha\u0142a","year":"2020","journal-title":"Bioinformatics"},{"key":"2026032616013072200_btag128-B17","doi-asserted-by":"crossref","first-page":"1688","DOI":"10.1021\/acs.jproteome.4c00700","article-title":"HRaDeX: r package and web server for computing high-resolution deuterium uptake rates for HDX\u2013MS data","volume":"24","author":"Pucha\u0142a","year":"2025","journal-title":"J Proteome Res"},{"key":"2026032616013072200_btag128-B18","doi-asserted-by":"crossref","first-page":"1322","DOI":"10.1093\/bioinformatics\/btu829","article-title":"3Dmol.js: molecular visualization with WebGL","volume":"31","author":"Rego","year":"2015","journal-title":"Bioinformatics"},{"key":"2026032616013072200_btag128-B19","doi-asserted-by":"crossref","first-page":"904","DOI":"10.1039\/C6AN02707E","article-title":"Nanospray HX-MS configuration for structural interrogation of large protein systems","volume":"142","author":"Sheff","year":"2017","journal-title":"Analyst"},{"key":"2026032616013072200_btag128-B20","doi-asserted-by":"crossref","first-page":"1194","DOI":"10.1016\/j.bpj.2019.02.024","article-title":"Estimating constraints for protection factors from HDX-MS data","volume":"116","author":"Skinner","year":"2019","journal-title":"Biophys J"},{"key":"2026032616013072200_btag128-B21","doi-asserted-by":"crossref","first-page":"12840","DOI":"10.1021\/acs.analchem.1c02155","article-title":"Probing universal protein dynamics using hydrogen\u2013deuterium exchange mass spectrometry-derived residue-level Gibbs free energy","volume":"93","author":"Smit","year":"2021","journal-title":"Anal Chem"},{"key":"2026032616013072200_btag128-B22","doi-asserted-by":"crossref","first-page":"12242","DOI":"10.1021\/acs.chemrev.4c00438","article-title":"Computational tools for hydrogen\u2013deuterium exchange mass spectrometry data analysis","volume":"124","author":"Stofella","year":"2024","journal-title":"Chem Rev"},{"key":"2026032616013072200_btag128-B23","doi-asserted-by":"crossref","first-page":"1610","DOI":"10.1021\/jasms.0c00475","article-title":"Recommendations for the propagation of uncertainty in hydrogen exchange-mass spectrometric measurements","volume":"32","author":"Weis","year":"2021","journal-title":"J Am Soc Mass Spectrom"},{"key":"2026032616013072200_btag128-B24","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1002\/jcb.10069","article-title":"High resolution, high-throughput amide deuterium exchange-mass spectrometry (DXMS) determination of protein binding site structure and dynamics: utility in pharmaceutical design","volume":"37","author":"Woods","year":"2001","journal-title":"J Cell Biochem Suppl"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag128\/67370299\/btag128.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag128\/67370299\/btag128.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag128\/67370299\/btag128.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T20:01:43Z","timestamp":1774555303000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btag128\/8524920"}},"subtitle":[],"editor":[{"given":"Daisuke","family":"Kihara","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2026,2,28]]},"references-count":24,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2026,2,28]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btag128","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,3]]},"published":{"date-parts":[[2026,2,28]]},"article-number":"btag128"}}