Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry

MOTIVATION: 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 ms2lda.org, a web application that allows users to upload their data, run MS2LDA analyses and explore the results through interactive visualizations. RESULTS: Ms2lda.org 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 data set 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 http://ms2lda.org, while the source code is available at https://github.com/sdrogers/ms2ldaviz under the MIT license. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.