A universal language for finding mass spectrometry data patterns

T Damiani; AK Jarmusch; AT Aron; D Petras; VV Phelan; HN Zhao; W Bittremieux; DD Acharya; MMA Ahmed; A Bauermeister; MJ Bertin; PD Boudreau; RM Borges; BP Bowen; CJ Brown; FO Chagas; KD Clevenger; MSP Correia; WJ Crandall; M Crüsemann; E Fahy; O Fiehn; N Garg; WH Gerwick; JR Gilbert; D Globisch; PWP Gomes; S Heuckeroth; CA James; SA Jarmusch; SA Kakhkhorov; KB Kang; N Kessler; RD Kersten; H Kim; RD Kirk; O Kohlbacher; EE Kontou; K Liu; I Lizama-Chamu; GT Luu; T Luzzatto Knaan; H Mannochio-Russo; MT Marty; Y Matsuzawa; AC McAvoy; LI McCall; OG Mohamed; O Nahor; H Neuweger; THJ Niedermeyer; K Nishida; TR Northen; KE Overdahl; Johannes Rainer; R Reher; E Rodriguez; TT Sachsenberg; LM Sanchez; R Schmid; C Stevens; S Subramaniam; Z Tian; A Tripathi; H Tsugawa; JJJ van der Hooft; Andrea Vicini; A Walter; T Weber; Q Xiong; T Xu; T Pluskal; PC Dorrestein; M Wang

doi:10.1038/s41592-025-02660-z

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A universal language for finding mass spectrometry data patterns

Journal article

Open access

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A universal language for finding mass spectrometry data patterns

T Damiani, AK Jarmusch, AT Aron, D Petras, VV Phelan, HN Zhao, W Bittremieux, DD Acharya, MMA Ahmed, A Bauermeister, …

Nature Methods, Vol.22, pp.1247-1254

2025

DOI: https://doi.org/10.1038/s41592-025-02660-z

Handle:

https://hdl.handle.net/10863/47253

PMID: 40355727

Abstract

metabolomics

Computational Metabolomics

Biomedical Informatics

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.

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Title: A universal language for finding mass spectrometry data patterns
Creators: T Damiani - Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry
AK Jarmusch - National Institute of Environmental Health Sciences
AT Aron - University of Denver
D Petras - University of Tübingen
VV Phelan - University of Montana
HN Zhao - University of Montana
W Bittremieux - University of Montana
DD Acharya - Corteva (United States)
MMA Ahmed
A Bauermeister - Universidade de São Paulo
MJ Bertin - Case Western Reserve University
PD Boudreau - University of Mississippi
RM Borges - Universidade Federal do Rio de Janeiro
BP Bowen - Lawrence Berkeley National Laboratory
CJ Brown - Corteva (United States)
FO Chagas - Universidade Federal do Rio de Janeiro
KD Clevenger - Corteva (United States)
MSP Correia
WJ Crandall - Emory University
M Crüsemann - University of Bonn
E Fahy - La Jolla Bioengineering Institute
O Fiehn - University of California, Davis
N Garg - Georgia Institute of Technology
WH Gerwick - University of Montana
JR Gilbert - Corteva (United States)
D Globisch - Science for Life Laboratory
PWP Gomes
S Heuckeroth - University of Münster
CA James - Center for Urban Waters
SA Jarmusch - Technical University of Denmark
SA Kakhkhorov
KB Kang
N Kessler - Knorr-Bremse (Germany)
RD Kersten - University of Michigan
H Kim - Dongguk University
RD Kirk - University of Rhode Island
O Kohlbacher - University of Tübingen
EE Kontou - Novo Nordisk Foundation
K Liu - Emory University
I Lizama-Chamu - University of California, Santa Cruz
GT Luu - University of California, Santa Cruz
T Luzzatto Knaan
H Mannochio-Russo - University of Montana
MT Marty - University of Arizona
Y Matsuzawa - Tokyo University of Agriculture and Technology
AC McAvoy - Georgia Institute of Technology
LI McCall - San Diego State University
OG Mohamed - Cairo University
O Nahor - University of Haifa
H Neuweger - Knorr-Bremse (Germany)
THJ Niedermeyer
K Nishida - Tokyo University of Agriculture and Technology
TR Northen - Lawrence Berkeley National Laboratory
KE Overdahl - National Institute of Environmental Health Sciences
Johannes Rainer - Institute for Biomedicine
R Reher - Philipps University of Marburg
E Rodriguez - University of California, Davis
TT Sachsenberg - University of Tübingen
LM Sanchez - University of California, Santa Cruz
R Schmid - Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry
C Stevens - University of Mississippi
S Subramaniam - La Jolla Bioengineering Institute
Z Tian - Northeastern University
A Tripathi - University of Michigan
H Tsugawa - Tokyo University of Agriculture and Technology
JJJ van der Hooft
Andrea Vicini - Institute for Biomedicine
A Walter - University of Tübingen
T Weber - Novo Nordisk Foundation
Q Xiong - Corteva (United States)
T Xu - Corteva (United States)
T Pluskal - Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry
PC Dorrestein - University of Montana
M Wang - University of California, Riverside
Publication Details: Nature Methods, Vol.22, pp.1247-1254
ISSN: 1548-7091
EISSN: 1548-7105
Series / Volume: 22
Publisher: Nature Research
Identifiers: (EURAC)30349189
991007063357201241
Web of Science ID: WOS:001485547200001
Copyright: Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
Academic Unit: Institute for Biomedicine
Language: English
Resource Type: Journal article
Description coverage: international
Description audience: Scientific
Local Fields: Scientific
Author Names String: Damiani T, Jarmusch AK, Aron AT, Petras D, Phelan VV, Zhao HN, Bittremieux W, Acharya DD, Ahmed MMA, Bauermeister A, Bertin MJ, Boudreau PD, Borges RM, Bowen BP, Brown CJ, Chagas FO, Clevenger KD, Correia MSP, Crandall WJ, Crüsemann M, Fahy E, Fiehn O, Garg N, Gerwick WH, Gilbert JR, Globisch D, Gomes PWP, Heuckeroth S, James CA, Jarmusch SA, Kakhkhorov SA, Kang KB, Kessler N, Kersten RD, Kim H, Kirk RD, Kohlbacher O, Kontou EE, Liu K, Lizama-Chamu I, Luu GT, Luzzatto Knaan T, Mannochio-Russo H, Marty MT, Matsuzawa Y, McAvoy AC, McCall LI, Mohamed OG, Nahor O, Neuweger H, Niedermeyer THJ, Nishida K, Northen TR, Overdahl KE, Rainer J, Reher R, Rodriguez E, Sachsenberg TT, Sanchez LM, Schmid R, Stevens C, Subramaniam S, Tian Z, Tripathi A, Tsugawa H, van der Hooft JJJ, Vicini A, Walter A, Weber T, Xiong Q, Xu T, Pluskal T, Dorrestein PC, Wang M

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