True, some search engines report just peptide identifications but most of them also print the proteins
for which at least one peptide was found. Since however different search engines perform the mapping
differently and some don’t do it all, you usually index the peptides with PeptideIndexer afterwards.
So protein IDs right after a peptide search engine are relatively meaningless (including their scores,
which is often just the maximum of the peptide scores or even the same one for every protein). Most search engines do not
even have a notion about targets and decoys and even should not care about this information to be unbiased.
Cheers
Julianus