|Title||»||Adding targets from DDA library seems useful to be able to specify a number of runs a peptide got ID'd in|
|Assigned To||»||Matt Chambers|
Not quite sure where this might go, but maybe in the Associate Proteins form for the Import Peptide Search wizard where you can choose the number of peptides per protein. At that point, it also seems useful to be able to specify the number of runs (i.e. data files) the peptide got detected in.
I have been processing some MS1 filtering from DDA data in 12 runs. It seems clear to me that peptides that were only detected in a single run of the 12 are more likely to yield poor quality data. I could imagine requiring detection in at least 2 runs (or more) for a peptide to be added as a target for MS1 filtering.
This might be less relevant in data that got processed by Percolator with cross-experiment q values used for the target filtering, but that is not always the case, and I think not the case with this dataset.