I have watched Webinars 3 and 4 and found it very helpful but I have a question regarding spectral matching.
I conduct PRM on the Thermo Q Exacitive and this is my current workflow:
- I choose the precursor and product ions of interest and export an isolation list for the Q Exacitive
- I get the Raw Data file from the Thermo and run it through PD (with Percolator) which produces a PD result file
- I then import this PD result file as a PRM search (File -> Import -> Peptide Search) and match it with the same PRM Raw file by following the instructions in the Import Wizard
- This produces what I would call really good spectra. The chosen product ions are clearly detected with Peptide ID annotations.
However, when I import the raw result file ( File -> Import -> Results), I don't get the same level of detection. In most cases, none of the product ions detected when I do the workflow above are seen in this result file approach.
Can you please explain why there is this discrepancy? And if my current workflow is correct?