Giters

Nesvilab / MSFragger

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

Home Page:https://msfragger.nesvilab.org

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

Only one enzyme at at time is supported

slimyMS opened this issue · comments

commented

Hello,

In my experiment, I use multiple enzymes in my experiment, and some of them were combined in one sample to find the enzyme (combination) that works best.
Unfortunately, it is not possible to define multiple enzymes for one experiment or ideally even groups in which different enzymes are used (as it is possible in other software such as MaxQuant). It would be great if you could add this as a feature.

Best

commented

If all of your enzymes have sense C (cutting at the C-terminal), you can setting the cutting rules by combining your enzymes. For example, if you have trypsin + chymotrypsin, you need to set the search_enzyme_cutafter to KRFLWY, search_enzyme_butnotafter to P, and search_enzyme_name to nonspecific.

Best,

Fengchao

commented

Thank you for your answer! And sorry for not specifying this before:
Unfortunately, not all of them are cutting at the C-terminal. I do use Trypsin but I also use other enzymes and which cut N-terminal. And I think there is no solution for N-terminal cutting enzymes in general, right?

Best

commented

We have implemented two enzymes support. The new function will be available in the next release.

Best,

Fengchao

commented

Added in MSFragger 3.4.