Support multiple enzymes in our Digestion and Indexing classes

[jpfeuffer]

Comet supports a joint search for two enzymes and we have seen first interesting datasets where this was used. Should be relatively easy to implement and add a lot to flexibility. Great for making distinctions between isoforms and increase coverage on the proteins.

[jpfeuffer]

I shortly looked into it. We would need to update all the Parsers and Writers of ID formats (pepXML and mzID support multi enzymes already). Update our own schemas. Update SearchParameter object. Another problem is that there can be two ways of using multiple enzymes, often called dependent and independent:

• dependent means, that they are applied after each other, and peptides can have mixed termini. For this case we would need to update our digestion classes or add a new one for multi enzymes
• independent means basically to digest the proteins separately and then mix them again. This would be easier to support, we just need to check peptides for being a digest of either of the enzymes.

I did not think a lot about DecoyGeneration yet, which might be a bit tricky.

Note that often Trypsin and LysC are used, which actually have the same cutting rules, there you could just continue using one enzyme.