{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,24]],"date-time":"2026-04-24T15:15:35Z","timestamp":1777043735580,"version":"3.51.4"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T00:00:00Z","timestamp":1773100800000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R35GM157185"],"award-info":[{"award-number":["R35GM157185"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Science Foundation Graduate Research Fellowship"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,4,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Hydrogen\/deuterium exchange-mass spectrometry (HX-MS) is a rapidly expanding technique used to investigate protein conformational ensembles. The growing popularity and utility of HX-MS has driven the development of diverse instrumentation and software, resulting in inconsistent, non-standardized data analysis and representation. Most HX-MS data formats also employ only mean deuteration representations of the data rather than full isotopic mass spectra, which reduces the information content of the data and limits downstream quantitative analysis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Inspired by reliable protein structure and genomics data formats, we present HXMS, a unified, lightweight, scalable, and human-readable file format for HX-MS data. The HXMS format preserves the isotopic mass envelopes for all peptides, captures the full experimental time-course including fully deuterated control samples, and contains all other key information. It supports multimodal distributions, post-translational modifications (PTMs), and experimental replicates. To promote compatibility with existing HX-MS workflows, we also developed PFLink, a Python package that converts exported data files from commonly used HX-MS software to the HXMS format. PFLink and the HXMS format will enable quantitative, higher-resolution data processing, improved data sharing and storage among HX-MS practitioners, future machine learning applications, and further developments in HX-MS analysis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>PFLink is publicly available to install locally on HuggingFace, alongside documentation, or use online at HuggingFace (https:\/\/huggingface.co\/spaces\/glasgow-lab\/PFlink). The supplementary information includes sample input files, sample HXMS files, and a generic unfilled PFlink custom CSV file that users may populate with key experimental conditions and results, which can then be read and converted into the HXMS format.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag113","type":"journal-article","created":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T12:45:17Z","timestamp":1772801117000},"source":"Crossref","is-referenced-by-count":0,"title":["HXMS: a standardized file format for HX-MS data"],"prefix":"10.1093","volume":"42","author":[{"given":"Kyle C","family":"Weber","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Molecular Biophysics, Columbia University , New York, NY 10032,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chenlin","family":"Lu","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biophysics, Columbia University , New York, NY 10032,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roberto Vera","family":"Alvarez","sequence":"additional","affiliation":[{"name":"Omics Informatics LLC , Honolulu, HI 96813,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bruce D","family":"Pascal","sequence":"additional","affiliation":[{"name":"Omics Informatics LLC , Honolulu, HI 96813,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0938-881X","authenticated-orcid":false,"given":"Anum","family":"Glasgow","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biophysics, Columbia University , New York, NY 10032,","place":["United 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