To explore: parameter methionine excision during search

[mlocardpaulet]

I am not sure this is an issue, I have not checked yet. I know that some search engines remove the 1st methionine of the sequence, because it often happens that it is excised.
We should check if the tools that are compatible with ProteoBench have this option. If it is heterogenous (some do, some don't), we should add it as parameter of interest.

[RobbinBouwmeester]

What would be a good way to check this @mlocardpaulet? Read the papers or just look at some results?

[mlocardpaulet]

I think that the easiest for us would be to look at the results. If we compare the outputs of different software tools with similar parameters (for this: same PTMs is enough).
I suspect that it should be pretty clear to see if the software tools remove the initial methionines.
I think that I would start by this... Then at least we know how big of a difference this makes. We can then decide how to handle it.
Another way to go is to look into the documentation of the software tools. But I am not sure how easy this will be to find the information for all.