Want to boost your peptide IDs in Proteome Discoverer as well as the confidence of those IDs? Move from your regular search to iterative searching. I looked it up (it·er·a·tive ( t -r t v, - r- -t v). adj. 1. Characterized by or involving repetition, recurrence, reiteration, or repetitiousness ).
Here is the gist of it. You take that file and you give it different instances of search engines with different combinations of likely modifications. For example, if your peptide is one that has acetylation and phosphorylation, you need to have both of those mods in that search, but it is impossible to have every combination (or even very many) in one search engine. Using multiple engines allows you to search more modifications. It also allows you to get better confidence on your ID'ed peptides. For example, if Mascot, Sequest and MSAmanda all give you a peptide spectral match, then it is probably more likely to be true than if only one of the engines give it to you. So your confidence increases.
How are the results?
On each sample, this iterative (comprehensive search) increased the number of ID'ed peptides. By a lot. Yes, at first it seems crazy, but it sure looks like it works. For full information, look for this on Planet Orbitrap: