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glasgowcompbio / ms2ldaviz

Substructural discovery in untargeted metabolomics data using LDA topic modelling.
http://ms2lda.org
MIT License
11 stars 8 forks source link

Defining the fragment ions binning window for motif search. #133

Closed lfnothias closed 6 years ago

lfnothias commented 6 years ago

Hi guys, It appears that this parameter cannot be changed in ms2lda.org web-server. I am dealing with data acquired on Agilent Q-TOF. The calibration seems to have been poorly done, and it leads to mass that are not binned properly in the motifs (repetition of adjacent ions). Note that, in molecular networks, we used 0.05 Da window for the fragment ions, and it seems to cluster properly the related ions. Would it possible to add this feature to the web-server ? If not, I will just look into running the script locally. Thanks in advance,

lfnothias commented 6 years ago

Thanks a lot for the new feature đź‘Ť

sdrogers commented 6 years ago

You’re welcome! I haven’t been able to test it as thoroughly as I would have liked so please let me know how it works...

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Thanks a lot for the new feature đź‘Ť

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