Staying (a)live/retiring/archiving the DIA Precursor quantification - AIF module

[RobbinBouwmeester]

I would like to open a discussion about the DIA Precursor quantification - AIF module. Specifically, previously observed by @vdemichev
here #641, peptides annotated as oxidized human, yeast or ecoli peptides might actually be originating from other species.

The problem appears to be present in all search engine (DIA-NN, AlphaDIA, Spectronaut, ...).

Given the quantification issues and unknown origin of these issues. We need to discuss if we want to keep this module:

1. Keep the module live – potentially with a description on the module or documentation acknowledging this issues (👍)
2. Retire and remove (👎)
3. Archive and freeze – preserving the module for future reference but stopping any updates. (🚀)

You can vote by responding with the corresponding emoticon to this post.

[mlocardpaulet]

We decided to archive the AIF module.
I have updated the documentation to describe the oxidation issue, and we will keep a link to the modules, but it may not be visible with all other active modules when we open ProteoBench.