Do you have multiple MSMS spectra for the same precursor ion across the chromatographic peak? By any chance you ticked "combined MSMS spectra" in the "Data pre-processing" step of PEAKS?
Do the PSMs look better in PEAKs studio when you untick "preprocess"?
I found an issue with PEAKS that rings a bell to what you are describing and reported it to BSI (see below description), but I never got a follow-up. My work around was to disable "Merge MSMS spectra" in the data preprocessing step.
"I just encountered an issue with the exports I get from PEAKS for Skyline. After importing the results into Skyline I noticed that there were many PSMs close to the apex that should have been possible based on the short dynamic exclusion times I used and the low complexity of the sample (HSA digest).
For example, peptide K.QNCELFEQLGEYK.F [413, 425] (Slide 1) for file S4_21_7_QC3.raw was mapped with only one MSMS spectrum of really low intensity and is missing many PSMs of considerably better quality close to the apex that are identified by PEAKS (for example Slide 2) and is actually indicated in the PSMs table (Slide 3; attached .csv table).
When I check for the MS/MS scans proposing this peptide in the .pepXML export I realize the issue might be due to how the grouped spectra are reported (Slide 4; attached .pepXML). I think Skyline only read the scan number written in "start_scan" to generate the library spectrum for this peptide. Due to its quality I would have disregarded this peptide in follow-up data validation steps.
The files were processed with "Merge Scans [DDA]" ticked and when comparing PSM outputs I noticed it really helps in controlling false positive rates.
However, for Skyline I need to be able to access all PSMs used to make sure my spectra libraries are representative of the information used by PEAKS. Is there a way of exporting ALL PSMs and not the best representative one noted in the PSM tables? "
(see attached powerpoint with example)