{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T08:56:41Z","timestamp":1774601801774,"version":"3.50.1"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2024,7,30]],"date-time":"2024-07-30T00:00:00Z","timestamp":1722297600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000053","name":"National Eye Institute","doi-asserted-by":"publisher","award":["R01 EY017370"],"award-info":[{"award-number":["R01 EY017370"]}],"id":[{"id":"10.13039\/100000053","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000053","name":"National Eye Institute","doi-asserted-by":"publisher","award":["T32 EY07031"],"award-info":[{"award-number":["T32 EY07031"]}],"id":[{"id":"10.13039\/100000053","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,8,2]]},"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) is a powerful protein characterization technique that provides insights into protein dynamics and flexibility at the peptide level. However, analyzing HDX-MS data presents a significant challenge due to the wealth of information it generates. Each experiment produces data for hundreds of peptides, often measured in triplicate across multiple time points. Comparisons between different protein states create distinct datasets containing thousands of peptides that require matching, rigorous statistical evaluation, and visualization. Our open-source R package, HDXBoxeR, is a comprehensive tool designed to facilitate statistical analysis and comparison of multiple sets among samples and time points for different protein states, along with data visualization.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>HDXBoxeR is accessible as the R package (https:\/\/cran.r-project.org\/web\/\/packages\/HDXBoxeR) and GitHub: mkajano\/HDXBoxeR.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae479","type":"journal-article","created":{"date-parts":[[2024,7,30]],"date-time":"2024-07-30T19:52:38Z","timestamp":1722369158000},"source":"Crossref","is-referenced-by-count":9,"title":["HDXBoxeR: an R package for statistical analysis and visualization of multiple Hydrogen\u2013Deuterium Exchange Mass-Spectrometry datasets of different protein states"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8232-461X","authenticated-orcid":false,"given":"Maria K","family":"Janowska","sequence":"first","affiliation":[{"name":"Department of Biochemistry, University of Washington , Seattle, WA, 98195, United States"}]},{"given":"Katherine","family":"Reiter","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Washington , Seattle, WA, 98195, United States"},{"name":"Lyterian Therapeutics , South San Francisco, CA, 94080, United States"}]},{"given":"Pearl","family":"Magala","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Washington , Seattle, WA, 98195, United States"}]},{"given":"Miklos","family":"Guttman","sequence":"additional","affiliation":[{"name":"Department of Medicinal Chemistry, University of Washington , Seattle, WA, 98195, United States"}]},{"given":"Rachel 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