Hi Li,
Remove missing results will not remove anything with a red dot. Those have "results", just no picked peak. The term "missing results" refers to the case where the target was not even measured, mostly applicable to cases where a mistake was made in the original definition of the targets so that they do not match what was measured by the mass spectrometer. e.g.
1. SRM where target transitions in the document were never actually measured.
2. PRM where target precursors in the document were never actually measured.
3. DIA where the covered m/z range differed from what was allowed by the Skyline document settings (e.g. document settings allowed 50-2000 m/z, while only 400-1200 was measured)
In these cases Edit > Refine > Remove Missing Results will remove the peptides that were never actually measured by the mass spectrometer.
Ideally, in your case, we would have implemented a Detection tab in Edit > Refine > Advanced that would allow you to remove all peptides with a minimum q value greater than some cut-off. Unfortunately, we have not yet implemented that.
So, I think you would want to set up the Document Grid (View > Document Grid) or a report to export peak q values and "Pivot Replicates". Then you can paste that report into Excel and add a column that calculates the minimum q value for each row, sort by that column and select peptide names that have that minimum q value less than some cut-off, and finally use Edit > Refine > Accept Peptides to paste the list of those peptides into and click OK to remove everything but those accepted peptides.
Sorry we have not made this easier. We will try to soon. Hope this is some help in the meantime. Thanks for posting to the Skyline support board.
--Brendan |