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.

Applied Bioinformatics Department of Computer Science University of Tuebingen University of Tuebingen Tübingen Germany

Applied Bioinformatics Department of Computer Science University of Tuebingen University of Tuebingen; Institute for Bioinformatics and Medical Informatics University of Tuebingen; Institute for Translational Bioinformatics University Hospital Tuebingen Tübingen Germany

Bioinformatics Group Wageningen University and Research Wageningen the Netherlands

Biologicals and Natural Products Crop Protection R and D Corteva Agrisciences Indianapolis IN USA

Biologicals and Natural Products Discovery Crop Protection R and D Corteva Agrisciences Indianapolis IN USA

BioMolecular Sciences School of Pharmacy University of Mississippi Oxford MS USA

Center for Urban Waters University of Washington Tacoma WA USA

Chemistry and Chemical Biology Northeastern University Boston MA USA

Clinical Biomarkers Laboratory School of Medicine Emory University Atlanta GA USA

Collaborative Mass Spectrometry Innovation Center Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego La Jolla CA USA

College of Pharmacy and Integrated Research Institute for Drug Development Dongguk University Seoul Goyang Republic of Korea

College of Pharmacy Sookmyung Women's University Seoul Republic of Korea

College of Pharmacy University of Rhode Island Kingston RI USA

Crop Protection R and D Corteva Agrisciences Indianapolis IN USA

Data Science and Bioinformatics Corteva Agrisciences Dublin OH USA

Department of Biochemistry University of California Riverside Riverside CA USA

Department of Biochemistry University of Johannesburg Johannesburg South Africa

Department of Bioengineering University of California San Diego La Jolla CA USA

Department of BioMolecular Sciences School of Pharmacy University of Mississippi Oxford MS USA

Department of Biotechnology and Biomedicine Technical University of Denmark Kongens Lyngby Denmark

Department of Biotechnology and Life Science Tokyo University of Agriculture and Technology Koganei Japan

Department of Chemistry and Biochemistry San Diego State University San Diego CA USA

Department of Chemistry and Biochemistry UC Santa Cruz Santa Cruz CA USA

Department of Chemistry and Biochemistry University of Arizona Tucson AZ USA

Department of Chemistry and Biochemistry University of Denver Denver CO USA

Department of Chemistry BMC Science for Life Laboratory Uppsala University Uppsala Sweden

Department of Chemistry Case Western Reserve University Cleveland OH USA

Department of Computer Science University of California Riverside Riverside CA USA

Department of Fundamental Chemistry Institute of Chemistry University of São Paulo São Paulo Brazil

Department of Marine Biology The Leon H Charney School of Marine Sciences University of Haifa Haifa Israel

Department of Medicinal Chemistry College of Pharmacy University of Michigan Ann Arbor MI USA

Department of Pharmaceutical Sciences Skaggs School of Pharmacy and Pharmaceutical Sciences University of Colorado Anschutz Medical Campus Aurora CO USA

Department of Pharmacy University of Marburg Marburg Germany

Environmental Genomics and Systems Biology Division Lawrence Berkeley National Lab Berkeley CA USA

Faculty of Chemistry Institute of Exact and Natural Science Federal University of Para Belem Brazil

Functional Metabolomics Lab CMFI Cluster of Excellence University of Tuebingen Tuebingen Germany

Institute for Biomedicine Eurac Research Bolzano Italy

Institute of Inorganic and Analytical Chemistry University of Münster Münster Germany

Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague Czech Republic

Institute of Pharmaceutical Biology Goethe University Frankfurt Frankfurt Germany

Institute of Pharmaceutical Biology University of Bonn Bonn Germany

Institute of Pharmacy Freie Universität Berlin Berlin Germany

Laboratory of Physical and Chemical Methods of Research Center for Advanced Technologies Tashkent Uzbekistan

Mass Spectrometry Center of Expertise Regulatory and Stewardship Corteva Agrisciences Indianapolis IN USA

Metabolomics Core Facility Immunity Inflammation and Disease Laboratory Division of Intramural Research National Institute of Environmental Health Sciences National Institutes of Health Research Triangle Park NC USA

Natural Products Discovery Core Life Sciences Institute University of Michigan Ann Arbor MI USA

Pharmacognosy Department Faculty of Pharmacy Cairo University Cairo Egypt

Pharmacognosy Faculty of Pharmacy Al Azhar University Nasr City Egypt

RIKEN Center for Integrative Medical Sciences Tsurumi ku Japan

RIKEN Center for Sustainable Resource Science Tsurumi ku Japan

School of Chemistry and Biochemistry Center for Microbial Dynamics and Infection Georgia Institute of Technology Atlanta GA USA

School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta GA USA

Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego La Jolla CA USA

SW R and D Bioinformatics Life Science Mass Spectrometry Bruker Daltonics GmbH and Co KG Bremen Germany

The Joint Genome Institute Lawrence Berkeley National Lab Berkeley CA USA

The Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Kongens Lyngby Denmark

Walter Mors Institute of Research on Natural Products Federal University of Rio de Janeiro Rio de Janeiro Brazil

West Coast Metabolomics Center University of California Davis Davis CA USA

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