Allowing more than one enzyme as cleavage agent

[cecilia992]

Description of feature

It would be useful if more than one enzyme could be selected rather than just one. I understand that not all tools allow multiple enzymes digestion but it would be good to have this option even if we are then forced to use only one tool, such as comet.

[ypriverol]

We have started to support more enzymes in the workflow in more tools. Can you let us know which enzymes are you thinking about? and which combinations?

[cecilia992]

Two of the enzymes I have encountered in multiple digestions are Lys-C and Trypsin. The sample is first digested with Lys-C and then with Trypsin in my case.

[jpfeuffer]

Well the good news is, this very common mixture of enzymes is easily representable by just Trypsin, as it subsumes all the rules for LysC.
This should have no impact on the results.
Everything else gets a bit more involved (especially when considering missed cleavages and counting semi-specificity etc.)

[jpfeuffer]

Another complicated use case is different (mixtures of) enzymes across different samples. Which hopefully is very rare.

[ypriverol]

@cecilia992, as @jpfeuffer mentioned, in such cases, we use only Trypsin or Trypsin/P because it overrides the rule of LysC. You can annotate the SDRF with just one enzyme, Trypsin. This approach works perfectly; I have successfully reanalyzed multiple datasets using this method.

[cecilia992]

@ypriverol @jpfeuffer , thank you so much to both for the clarification!