How to use Protein.ids in downstream analysis

[Gambrian]

Dear Vadim

In the diann results, most of the Protein.ids are uniprot accession ids (from the fasta file I used), but some are accession ids combined by ";" . Some are combined with cRAP-***, I think this is because they are searched in both the reference fasta file and camprotR_240512_cRAP_20190401_full_tags.fasta. Can I delete these results? Others are just two or more accession ids combined with ";". Why is this? I think these proteins cannot find the master protein because they have the same matching peptides? Can I use the first id instead in subsequent analysis?

Best