The paper introduces a method using metabolite fraction libraries to improve NMR metabolomics quantification by reducing spectral overlap and enabling accurate metabolite identification.

Analytical Chemistry · Jul 1, 2026Peer-reviewedBioinformatics

Higher Lipid Saturation in Well-Irrigated Georgia Cotton Plants: A Field-Based NMR Metabolomics Study

Krishna Patel, Christopher Esselman, Jordan R. Croy, Matthew Gillis, Pedro A. P. Rodrigues, Alvin M. Simmons, Ricardo M. Borges, Arthur S. Edison, William E. Snyder

This study uses NMR metabolomics to show that irrigation affects lipid saturation in cotton plants, potentially influencing pest outbreaks.

bioRxiv · Jun 10, 2026 · PreprintPlant Biology

plantMASST - Community-driven chemotaxonomic digitization of plants

Paulo Wender Portal Gomes, Helena Mannochio-Russo, Robin Schmid, Simone Zuffa, Tito Damiani, Luis-Manuel Quirós-Guerrero, Andrés Mauricio Caraballo‐Rodríguez, Haoqi Nina Zhao, Heejung Yang, Shipei Xing, Vincent Charron‐Lamoureux, Desnor N. Chigumba, Brian E. Sedio, Jonathan A. Myers, Pierre‐Marie Allard, , Pieter C. Dorrestein

The paper curates LC-MS/MS data from plant extracts to create a taxonomically focused database for exploring plant-derived molecules.

bioRxiv · May 13, 2024 · PreprintPlant Biology

An anchored experimental design and meta-analysis approach to address batch effects in large-scale metabolomics

Amanda O. Shaver, Brianna M. Garcia, Gonçalo J. Gouveia, Alison M. Morse, Zihao Liu, Carter K. Asef, Ricardo M. Borges, Franklin E. Leach, Erik C. Andersen, I. Jonathan Amster, Facundo M. Fernández, Arthur S. Edison, Lauren M. McIntyre

The paper introduces an experimental design with anchor strains to reduce batch effects in metabolomics, enabling integration of NMR and LC-MS data across studies.

Frontiers in Molecular Biosciences · Nov 9, 2022Peer-reviewedSystems Biology

A Universal Language for Finding Mass Spectrometry Data Patterns

Alan K. Jarmusch, Allegra T. Aron, Daniel Petras, Vanessa V. Phelan, Wout Bittremieux, Deepa D. Acharya, Mohammed M. A. Ahmed, Anelize Bauermeister, Matthew J. Bertin, Paul D. Boudreau, Ricardo M. Borges, Benjamin P. Bowen, Christopher J. Brown, Fernanda O. Chagas, Kenneth D. Clevenger, , Mingxun Wang

MassQL, an open-source query language, lets users search raw mass spectrometry data from any vendor for isotope, fragmentation and neutral-loss patterns, from one file to entire public repositories.

bioRxiv · Aug 6, 2022 · PreprintBioinformatics✦ In-depth digest