{"doi":"10.1101/2025.10.14.682397","title":"HXMS: a standardized file format for HX-MS data","abstract":"Motivation: 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 centroid-level representations of the data rather than full isotopic mass spectra, reducing the information content of the data and limiting downstream quantitative analysis. Results: 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 the 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 analysis software packages to the HXMS format. PFLink and the HXMS format will enable more 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. Availability and implementation: PFLink is publicly available to install locally on HuggingFace, alongside documentation, or use online at HuggingFace (https://huggingface.co/spaces/glasgow-lab/PFLink). We also included 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.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":578184,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":0.0,"corpus_rank":10062,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.5609,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1453766,"name":"Chenlin Lu","orcid":"0000-0002-5655-2993","position":1,"is_corresponding":false},{"id":107327,"name":"Roberto Vera Alvarez","orcid":"0000-0002-4108-5982","position":2,"is_corresponding":false},{"id":375977,"name":"Bruce D. Pascal","orcid":"0000-0002-0301-5107","position":3,"is_corresponding":false},{"id":237507,"name":"Anum Glasgow","orcid":"0000-0002-0938-881X","position":4,"is_corresponding":false},{"id":1177116,"name":"Kyle C. Weber","orcid":"0000-0002-3379-6303","position":0,"is_corresponding":true}],"reference_count":14,"raw_metadata":null,"created_at":"2026-07-19T02:58:20.638044Z","pmid":"41279111","pmcid":"PMC12632962","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}