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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": "f1336fd3bdbe4d0fab56982fc188721c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f1336fd3bdbe4d0fab56982fc188721c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f1336fd3bdbe4d0fab56982fc188721c"}}, "title": "Defining the Scope of Exposome Studies and Research Needs from a Multidisciplinary Perspective.", "authors": [{"family": "Zhang", "given": "Pei", "initials": "P", "orcid": "0000-0003-2054-928X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e4af492258b4256992af0279c823400.json"}}, {"family": "Carlsten", "given": "Christopher", "initials": "C"}, {"family": "Chaleckis", "given": "Romanas", "initials": "R", "orcid": "0000-0001-8042-1005", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/012934b6c4a64891b76722fbda1e0f28.json"}}, {"family": "Hanhineva", "given": "Kati", "initials": "K", "orcid": "0000-0001-6834-7375", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b66883342d1b45938f17d75e73479d50.json"}}, {"family": "Huang", "given": "Mengna", "initials": "M", "orcid": "0000-0002-4626-4816", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/baf43d2b06f746078bd69385c9e6cf93.json"}}, {"family": "Isobe", "given": "Tomohiko", "initials": "T", "orcid": "0000-0001-9235-1227", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/67986b3e12c1468c9b7cea2709e233a1.json"}}, {"family": "Koistinen", "given": "Ville M", "initials": "VM"}, {"family": "Meister", "given": "Isabel", "initials": "I"}, {"family": "Papazian", "given": "Stefano", "initials": "S"}, {"family": "Sdougkou", "given": "Kalliroi", "initials": "K"}, {"family": "Xie", "given": "Hongyu", "initials": "H"}, {"family": "Martin", "given": "Jonathan W", "initials": "JW", "orcid": "0000-0001-6265-4294", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02199c0d99674e2ea5e96e6589c07a00.json"}}, {"family": "Rappaport", "given": "Stephen M", "initials": "SM", "orcid": "0000-0002-3806-0848", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da3132c271b34cc8a758560a68fe241b.json"}}, {"family": "Tsugawa", "given": "Hiroshi", "initials": "H", "orcid": "0000-0002-2015-3958", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1703a87b2e3444d8ba917253d25d5556.json"}}, {"family": "Walker", "given": "Douglas I", "initials": "DI", "orcid": "0000-0003-2912-398X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4712c06efd674e4b96f494e33ab9084f.json"}}, {"family": "Woodruff", "given": "Tracey J", "initials": "TJ", "orcid": "0000-0003-3622-1297", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3ad211bff7564b65ad1a4d6468e0e6b7.json"}}, {"family": "Wright", "given": "Robert O", "initials": "RO"}, {"family": "Wheelock", "given": "Craig E", "initials": "CE", "orcid": "0000-0002-8113-0653", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5d98abddc2b14a35ade5cb6d6d2f540d.json"}}], "type": "journal article", "published": "2021-10-12", "journal": {"title": "Environ Sci Technol Lett", "issn": "2328-8930", "volume": "8", "issue": "10", "pages": "839-852", "issn-l": null}, "abstract": "The concept of the exposome was introduced over 15 years ago to reflect the important role that the environment exerts on health and disease. While originally viewed as a call-to-arms to develop more comprehensive exposure assessment methods applicable at the individual level and throughout the life course, the scope of the exposome has now expanded to include the associated biological response. In order to explore these concepts, a workshop was hosted by the Gunma University Initiative for Advanced Research (GIAR, Japan) to discuss the scope of exposomics from an international and multidisciplinary perspective. This Global Perspective is a summary of the discussions with emphasis on (1) top-down, bottom-up, and functional approaches to exposomics, (2) the need for integration and standardization of LC- and GC-based high-resolution mass spectrometry methods for untargeted exposome analyses, (3) the design of an exposomics study, (4) the requirement for open science workflows including mass spectral libraries and public databases, (5) the necessity for large investments in mass spectrometry infrastructure in order to sequence the exposome, and (6) the role of the exposome in precision medicine and nutrition to create personalized environmental exposure profiles. Recommendations are made on key issues to encourage continued advancement and cooperation in exposomics.", "doi": "10.1021/acs.estlett.1c00648", "pmid": "34660833", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8515788"}], "notes": [], "created": "2026-08-20T08:10:04.602Z", "modified": "2026-08-20T08:10:05.065Z"}]}