Most likely only one isoform will be reported, matching the better of the spectra

Very unlikely to get identified correctly

Yes, it will. Although without MS/MS evidence the reported localisation confidence will be low and the overall numbers of correctly assigned isomers are likely to be low. Those IDs with MS/MS evidence should be fine though.

I think this may change with MBR on samples from different patients, in particular for neat.

That said, it's definitely a good idea for us to provide a tutorial and example code on this. Will add to todo list.

Currently not saved automatically, main issue: a peptide can match multiple positions even within the sequence of a single protein. However, this can be done with a script, matching to protein sequence in protein_description.tsv output file. AI will easily write such a script in 5 min :)

Probably not, we are completely overwhelmed with paper writing at the moment, so only selected stuff eventually will get published. Short application notes are more likely though:)