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"researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1703a87b2e3444d8ba917253d25d5556.json"}}, {"family": "van der Hooft", "given": "Justin J J", "initials": "JJJ", "orcid": "0000-0002-9340-5511", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c3918b083fe4b31bfe49c2e2e7fcd07.json"}}, {"family": "Vicini", "given": "Andrea", "initials": "A"}, {"family": "Walter", "given": "Axel", "initials": "A"}, {"family": "Weber", "given": "Tilmann", "initials": "T", "orcid": "0000-0002-8260-5120", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd1d6e8b8a81479aac38273ab6da62a2.json"}}, {"family": "Xiong", "given": "Quanbo", "initials": "Q"}, {"family": "Xu", "given": "Tao", "initials": "T"}, {"family": "Pluskal", "given": "Tom\u00e1\u0161", "initials": "T", "orcid": "0000-0002-6940-3006", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0e73806a9bb8490c88dd6344f1da57aa.json"}}, {"family": "Dorrestein", "given": "Pieter C", "initials": "PC", "orcid": "0000-0002-3003-1030", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aab670a610074d7787adc1b56fa4cb47.json"}}, {"family": "Wang", "given": "Mingxun", "initials": "M", "orcid": "0000-0001-7647-6097", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a42a021d871489e97768fbd48fd3f7f.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "22", "issue": "6", "pages": "1247-1254", "issn-l": "1548-7091"}, "abstract": "Despite being information rich, the vast majority of untargeted mass spectrometry data are underutilized; most analytes are not used for downstream interpretation or reanalysis after publication. The inability to dive into these rich raw mass spectrometry datasets is due to the limited flexibility and scalability of existing software tools. Here we introduce a new language, the Mass Spectrometry Query Language (MassQL), and an accompanying software ecosystem that addresses these issues by enabling the community to directly query mass spectrometry data with an expressive set of user-defined mass spectrometry patterns. Illustrated by real-world examples, MassQL provides a data-driven definition of chemical diversity by enabling the reanalysis of all public untargeted metabolomics data, empowering scientists across many disciplines to make new discoveries. MassQL has been widely implemented in multiple open-source and commercial mass spectrometry analysis tools, which enhances the ability, interoperability and reproducibility of mining of mass spectrometry data for the research community.", "doi": "10.1038/s41592-025-02660-z", "pmid": "40355727", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS2097565"}, {"db": "pmc", "key": "PMC12334354"}, {"db": "pii", "key": "10.1038/s41592-025-02660-z"}], "notes": [], "created": "2026-08-20T09:03:29.583Z", "modified": "2026-08-20T09:03:30.387Z"}, {"entity": "publication", "iuid": "6aa763aee43e4ff0bb7d3db8accbbbfb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6aa763aee43e4ff0bb7d3db8accbbbfb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6aa763aee43e4ff0bb7d3db8accbbbfb"}}, "title": "High-Resolution Mass Spectrometry for Human Exposomics: Expanding Chemical Space Coverage.", "authors": [{"family": "Lai", "given": "Yunjia", "initials": "Y", "orcid": "0000-0002-1081-0897", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ecf9e9eb458440cc9f58c1531bfc4ca6.json"}}, {"family": "Koelmel", "given": "Jeremy P", "initials": "JP"}, {"family": "Walker", "given": "Douglas I", "initials": "DI"}, {"family": "Price", "given": "Elliott J", "initials": "EJ", "orcid": "0000-0001-5691-7000", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fa682ce028f8448383ee1128a9e328da.json"}}, {"family": "Papazian", "given": "Stefano", "initials": "S", "orcid": "0000-0003-2538-8702", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/27c56d6b160c42d4b3782d78210e80ff.json"}}, {"family": "Manz", "given": "Katherine E", "initials": "KE"}, {"family": "Castilla-Fern\u00e1ndez", "given": "Delia", "initials": "D"}, {"family": "Bowden", "given": "John A", "initials": "JA", "orcid": "0000-0003-3135-4015", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92a530a244b643d8af01e9e75e9db7a5.json"}}, {"family": "Nikiforov", "given": "Vladimir", "initials": "V"}, {"family": "David", "given": "Arthur", "initials": "A", "orcid": "0000-0001-8189-1826", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2c8095bd499400495672369b25ca3de.json"}}, {"family": "Bessonneau", "given": "Vincent", "initials": "V"}, {"family": "Amer", "given": "Bashar", "initials": "B"}, {"family": "Seethapathy", "given": "Suresh", "initials": "S"}, {"family": "Hu", "given": "Xin", "initials": "X"}, {"family": "Lin", "given": "Elizabeth Z", "initials": "EZ"}, {"family": "Jbebli", "given": "Akrem", "initials": "A"}, {"family": "McNeil", "given": "Brooklynn R", "initials": "BR"}, {"family": "Barupal", "given": "Dinesh", "initials": "D", "orcid": "0000-0002-9954-8628", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ef60b35b331e491db289a5baaef1aab4.json"}}, {"family": "Cerasa", "given": "Marina", "initials": "M"}, {"family": "Xie", "given": "Hongyu", "initials": "H", "orcid": "0000-0002-2422-0492", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/871a1de2d146412693d3cfea85e8e293.json"}}, {"family": "Kalia", "given": "Vrinda", "initials": "V", "orcid": "0000-0003-2244-6663", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/962993463b6c4ca9834db0ee08fcb0e5.json"}}, {"family": "Nandakumar", "given": "Renu", "initials": "R"}, {"family": "Singh", "given": "Randolph", "initials": "R", "orcid": "0000-0003-4500-3400", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ccf49d8efe6744709aada7870cb26548.json"}}, {"family": "Tian", "given": "Zhenyu", "initials": "Z", "orcid": "0000-0002-7491-7028", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/187a49e0f6fb40438ba010618d3332ea.json"}}, {"family": "Gao", "given": "Peng", "initials": "P", "orcid": "0000-0002-4311-584X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9c0ab2a09c32474abf20cdd3a2189477.json"}}, {"family": "Zhao", "given": "Yujia", "initials": "Y", "orcid": "0000-0002-5275-0036", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80e74740792e42688e63d89945692392.json"}}, {"family": "Froment", "given": "Jean", "initials": "J", "orcid": "0000-0003-4844-2919", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6e0ef2b5c0c546cebf2442d26e4e719a.json"}}, {"family": "Rostkowski", "given": "Pawel", "initials": "P", "orcid": "0000-0001-9778-4283", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/481bab6b87b94fa59c45bf3801eb1b12.json"}}, {"family": "Dubey", "given": "Saurabh", "initials": "S"}, {"family": "Coufal\u00edkov\u00e1", "given": "Kate\u0159ina", "initials": "K"}, {"family": "Seli\u010dov\u00e1", "given": "Hana", "initials": "H"}, {"family": "Hecht", "given": "Helge", "initials": "H", "orcid": "0000-0001-6744-996X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4c285556c2648c8910ec7958ec31875.json"}}, {"family": "Liu", "given": "Sheng", "initials": "S"}, {"family": "Udhani", "given": "Hanisha H", "initials": "HH"}, {"family": "Restituito", "given": "Sophie", "initials": "S"}, {"family": "Tchou-Wong", "given": "Kam-Meng", "initials": "KM"}, {"family": "Lu", "given": "Kun", "initials": "K", "orcid": "0000-0002-8125-2394", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/caf58c440e9f4d41bf063118efb74074.json"}}, {"family": "Martin", "given": "Jonathan W", "initials": "JW", "orcid": "0000-0001-6265-4294", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02199c0d99674e2ea5e96e6589c07a00.json"}}, {"family": "Warth", "given": "Benedikt", "initials": "B", "orcid": "0000-0002-6104-0706", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e519a5e868e4431bbd6e802aadd5b891.json"}}, {"family": "Godri Pollitt", "given": "Krystal J", "initials": "KJ", "orcid": "0000-0001-7332-2228", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/494a171e7021400f92349297ddf6f59a.json"}}, {"family": "Kl\u00e1nov\u00e1", "given": "Jana", "initials": "J"}, {"family": "Fiehn", "given": "Oliver", "initials": "O", "orcid": "0000-0002-6261-8928", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fc154df8fb7d410faea0ea75fff44445.json"}}, {"family": "Metz", "given": "Thomas O", "initials": "TO", "orcid": "0000-0001-6049-3968", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/78b7a44839bb42c89538cf2e4979c6f8.json"}}, {"family": "Pennell", "given": "Kurt D", "initials": "KD", "orcid": "0000-0002-5788-6397", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5acb4005e2564f718e490678a61542e5.json"}}, {"family": "Jones", "given": "Dean P", "initials": "DP"}, {"family": "Miller", "given": "Gary W", "initials": "GW", "orcid": "0000-0001-8984-1284", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dc6141f6c7384400a880de33387d00b9.json"}}], "type": "journal article", "published": "2024-07-23", "journal": {"title": "Environ. Sci. Technol.", "issn": "1520-5851", "volume": "58", "issue": "29", "pages": "12784-12822", "issn-l": "0013-936X"}, "abstract": "In the modern \"omics\" era, measurement of the human exposome is a critical missing link between genetic drivers and disease outcomes. High-resolution mass spectrometry (HRMS), routinely used in proteomics and metabolomics, has emerged as a leading technology to broadly profile chemical exposure agents and related biomolecules for accurate mass measurement, high sensitivity, rapid data acquisition, and increased resolution of chemical space. Non-targeted approaches are increasingly accessible, supporting a shift from conventional hypothesis-driven, quantitation-centric targeted analyses toward data-driven, hypothesis-generating chemical exposome-wide profiling. However, HRMS-based exposomics encounters unique challenges. New analytical and computational infrastructures are needed to expand the analysis coverage through streamlined, scalable, and harmonized workflows and data pipelines that permit longitudinal chemical exposome tracking, retrospective validation, and multi-omics integration for meaningful health-oriented inferences. In this article, we survey the literature on state-of-the-art HRMS-based technologies, review current analytical workflows and informatic pipelines, and provide an up-to-date reference on exposomic approaches for chemists, toxicologists, epidemiologists, care providers, and stakeholders in health sciences and medicine. We propose efforts to benchmark fit-for-purpose platforms for expanding coverage of chemical space, including gas/liquid chromatography-HRMS (GC-HRMS and LC-HRMS), and discuss opportunities, challenges, and strategies to advance the burgeoning field of the exposome.", "doi": "10.1021/acs.est.4c01156", "pmid": "38984754", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11271014"}], "notes": [], "created": "2026-08-20T08:09:51.127Z", "modified": "2026-08-20T08:09:52.045Z"}]}