Proposal for encoding Enzyme information into SDRF.

[ypriverol]

The following PR added new information about how to encode the Enzyme used into an SDRF:

• It will follow the same approach that PTM information as key=value pairs.
• It will enable to encode custom enzymes as long as well-annotated enzymes in PSI-MS.

Pending discussion: How to encode as regular expressions the Target Site in the sequence.

[StSchulze]

Inhibiting amino acids (like P) will be defined in the regular expression or should there rather be a separate key=value pair?

[ypriverol]

Inhibiting amino acids (like P) will be defined in the regular expression or should there rather be a separate key=value pair?

I think it can be defined in the regular expression. I been thinking that probably a goof catalog can be created and extended here: https://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1001180

You guys @StSchulze and @mvaudel can help to implement the conversion from the specific name / regular expression into the specific Search engine parameters.

[StSchulze]

Inhibiting amino acids (like P) will be defined in the regular expression or should there rather be a separate key=value pair?

I think it can be defined in the regular expression. I been thinking that probably a goof catalog can be created and extended here: https://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1001180

Sounds good to me, but the example should then be (?<=[KR])(?!P)

You guys @StSchulze and @mvaudel can help to implement the conversion from the specific name / regular expression into the specific Search engine parameters.

Yes, I'd be happy to follow up on that topic again!

[ypriverol]

Inhibiting amino acids (like P) will be defined in the regular expression or should there rather be a separate key=value pair?

I think it can be defined in the regular expression. I been thinking that probably a goof catalog can be created and extended here: https://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1001180

Sounds good to me, but the example should then be (?<=[KR])(?!P)

Fixed!!! Sorry to many things ongoing.

You guys @StSchulze and @mvaudel can help to implement the conversion from the specific name / regular expression into the specific Search engine parameters.

Yes, I'd be happy to follow up on that topic again!

[trishorts]

I need to look at everything closely but I thought that I'd share what we do in MetaMorpheus to encode known and novel proteases. there are some REGEX notes for each.
| indicates cleavage site
[ ] indicates "preventing cleavage"
X indicates wildcard
{ } indicates exceptions to the wildcard
multiple-letter motifs are allowed

[trishorts]

you want that I should approve/merge?

[ypriverol]

you want that I should approve/merge?

Yes, It would be great