News
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:
- A new upload function is added in the Create Experiment page to allow for the uploading of large locally-run LDA experiments (script under development).
- MotifDB (a database of curated and annotated Mass2Motifs) have been incorporated into the system, as well as a functionality to predict Classyfire substituent terms for the spectra in your dataset using a neural network.
- Automatic MAGMa annotations of fragment and neutral loss features have also been incorporated into the system.
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.