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Bioinformatics. 2017 Sep 14. doi: 10.1093/bioinformatics/btx582. [Epub ahead of print] web-based topic modelling for substructure discovery in mass spectrometry.

Author information

Glasgow Polyomics, University of Glasgow, Glasgow, United Kingdom.
Wellcome Centre for Molecular Parasitology, Glasgow, United Kingdom.
School of Computing Science, University of Glasgow, United Kingdom.



We recently published MS2LDA, a method for the decomposition of sets of molecular fragment data derived from large metabolomics experiments. To make the method more widely available to the community, here we present, a web application that allows users to upload their data, run MS2LDA analyses and explore the results through interactive visualisations.

Results: takes tandem mass spectrometry data in many standard formats and allows the user to infer the sets of fragment and neutral loss features that co-occur together (Mass2Motifs). As an alternative workflow, the user can also decompose a dataset onto predefined Mass2Motifs. This is accomplished through the web interface or programmatically from our web service.

Availability and Implementation:

The website can be found at , while the source code is available at under the MIT license.

Supplementary information:

Supplementary data are available at Bioinformatics online.

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