Selected publications, software and spectral libraries for studying bile acids by mass spectrometry.
Publications from the Dorrestein Lab
Recent work on bile acid discovery and annotation, newest first.
- Mohanty I, Xing S, Castillo V, et al. MS/MS mass spectrometry filtering tree for bile acid regio- and stereoisomer annotation. Analytical Chemistry 98(6):4571–4584 (2026). doi:10.1021/acs.analchem.5c05677
- Mohanty I, Allaband C, Mannochio-Russo H, El Abiead Y, Hagey LR, Knight R, Dorrestein PC. The changing metabolic landscape of bile acids – keys to metabolism and immune regulation. Nature Reviews Gastroenterology & Hepatology 21(7):493–516 (2024). doi:10.1038/s41575-024-00914-3
- Mohanty I, Mannochio-Russo H, Schweer JV, et al. The underappreciated diversity of bile acid modifications. Cell 187(7):1801–1818.e20 (2024). doi:10.1016/j.cell.2024.02.019
- Gentry EC, Collins SL, Panitchpakdi M, et al. Reverse metabolomics for the discovery of chemical structures from humans. Nature 626(7998):419–426 (2024). doi:10.1038/s41586-023-06906-8
- Quinn RA, et al. Global chemical effects of the microbiome include new bile-acid conjugations. Nature 579:123–129 (2020). doi:10.1038/s41586-020-2047-9
Computational Tools & Libraries for Bile Acid Annotation
Free tools and reference spectra for finding and annotating bile acids in untargeted LC-MS/MS data.
Multistep MassQL – Bile Acid Isomer Annotation
Runs a sequence of MassQL filters on untargeted LC-MS/MS data to narrow bile acid MS/MS spectra down to likely regio- and stereoisomers.
Mohanty et al., Anal. Chem. 2026 – doi:10.1021/acs.analchem.5c05677
PostMN MassQL (MetaboApps)
Runs after molecular networking in GNPS2 and flags bile acid patterns with different numbers of hydroxyl groups across the network.
Mannochio-Russo, Gonçalves Nunes et al., Nature Methods 23:1475–1477 (2026) – doi:10.1038/s41592-026-03186-8; preprint: ChemRxiv 2025
BILELIB19 spectral library
A reference library of 21,549 bile acid MS/MS spectra for library searches and molecular networking in GNPS.
GNPS-MASSQL-BILE-ACID-ISOMER library
911 bile acid spectra with assigned regio- and stereochemistry, built using the filtering tree above.
Mohanty et al., Anal. Chem. 2026
MassQL
A language for searching mass spectrometry data for patterns such as fragment ions and neutral losses. It powers the bile acid filters above.
Damiani T, Jarmusch AK, Aron AT, et al., Nature Methods 22(6):1247–1254 (2025) – doi:10.1038/s41592-025-02660-z
GNPS2
Molecular networking, spectral library search and MASST searches across public data, plus the MetaboApps for downstream analysis.
Multidimensional bile acid library (LC-IMS-MS)
Retention times, collision cross sections and accurate masses for 280 bile acids, from a group outside UC San Diego.
Zhang G, Vincent EC, Disselkoen SM, et al., bioRxiv preprint (2026) – doi:10.64898/2026.02.18.706700
Last updated: October 6, 2026