High-resolution mass spectrometry permits simultaneous detection of thousands of different metabolites in biological samples; however, their automated annotation still presents a challenge due to the limited number of tailored computational solutions freely available to the scientific community.


Here, we introduce ChemDistiller, a customizable engine that combines automated large-scale annotation of metabolites using tandem MS data with a compiled database containing tens of millions of compounds with pre-calculated ‘fingerprints’ and fragmentation patterns. Our tests using publicly and commercially available tandem MS spectra for reference compounds show retrievals rates comparable to or exceeding the ones obtainable by the current state-of-the-art solutions in the field while offering higher throughput, scalability and processing speed.

Availability and implementation

Source code freely available for download at

Supplementary information

Supplementary data are available at Bioinformatics online.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.