search

Nesvilab / FragPipe

A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data
http://fragpipe.nesvilab.org
Other
183 stars 37 forks source link

MSBooster and TMTpro compatibility #1315

Closed pisistrato closed 10 months ago

pisistrato commented 10 months ago

Just a quick question, does MSBooster work on TMTpro? I do get a marginal boost in IDs, but in the log, I see this message Cannot find a UniMod modification match for TMT: 73.0618 minimal mass discrepancy; using the original modificaiton name and I just noticed that in all the TMTpro workflows MSBooster is disabeled...

Thanks

yangkl96 commented 10 months ago

Hello,

DIA-NN which we currently use for spectral library prediction was only trained on TMT10, so TMTpro is not explicitly supported. You can see in the "spectraRT.tsv" file that none of the peptides has "[TMT]", so the predictions are being done for the unlabeled version of the peptides, and the fragment m/z values are shifted accordingly with the TMTpro mass. The message you see does not change anything, it is just a message about some String parsing in the code.

Please be on the lookout in future releases, as we are working on supporting more modifications including TMTpro.

Best, Kevin