13th July 2021:
Ms2lda.org has now been running for nearly 4 years! 🎉
We would like to thank our users and the metabolomics community in general for your continuing support in running this resource. To run substructural analysis of large dataset, note that MS2LDA is also integrated with GNPS allowing you to map Mass2Motif occurrences in their Molecular Families using GNPS infrastructure (the results can be visualised back on this site). Alternatively LDA analysis can also be run on this website directly (subject to our computational limitation), and we're investigating ways to let you run your own LDA inference locally on your own data.
15th January 2021: Ms2lda.org is finally migrated to Python 3, and job submission is now working again! If you encounter any further problem submitting job, please let us know. Additionally, if you have any old, unused experiments, please delete them to help us save space on the database.
25th November 2018: We have introduced many new features to make interpreting Mass2Motifs in MS2LDA.org easier:
4th August 2017: Our new paper on the use of MS2LDA to investigate the variability in substructure prevalence across large experiments is now published in Analytical Chemistry. Additionally, we have changed the way the system handles thresholds for links between spectra and motifs. All experiments can now set a threshold on both probability and overlap_score. If you do not wish to threshold on one or the other, set the respective threshold to zero. All experiments have been migrated such that the new settings give identical output to the old ones. We think that this improved flexibility will make the system more user friendly.
26th September 2017: Our application note describing this Web application is now published in Bioinformatics. The initial idea of applying topic model to fragmentation spectra data can be found in PNAS, and also in Joe Wandy's PhD thesis.