Here is a user request from the support board:

I am using mProphet for reintegration of peaks and it works well but I would like to apply a dotp threshold rather than a q value threshold. When specifying a q value threshold then Skyline is not simply applying the threshold to the peaks but it changes the integration of peaks, which actually leads to inclusion of alternative (wrong) peaks with very low dotp rather than just excluding the peaks that do not meet the q value threshold. It would be great if there were options for just applying q value and/ or dotp value thresholds without reintegration and changing the peak picking. The Refine | Advanced | Results tab only allows one to remove entire peptides based on dotp value thresholds but not to set specific samples with low dotp and / or q values to zero. However, the latter is highly desirable when some samples have detectable and other samples undetectable levels of a particular peptide. Such a scenario could represent extreme regulation of the corresponding protein if the pattern holds for multiple peptides of that protein, which is biologically highly informative. Can an option of automatically setting all peak areas to zero that do not exceed a certain dotp (and q) value threshold be incorporated into Skyline? It would help a lot with automation and cleanup of large DIA analyses sets! I am now applying such thresholds retroactively in excel after exporting the datasets but after exporting to excel one cannot take advantage of the MSstats comparison statistics intrinsic in Skyline. Please consider incorporating this feature into Skyline.

In the past we have discussed adding ways to filter in the document grid and use the filtered set to remove targets from the Targets view. This is another interesting take, I think, where the request is to be able to set a filter and remove all peak integration.

In both cases, I think, the user may want either:
1. Remove all targets or peaks in the filtered set.
2. Remove all targets or peaks not in the filtered set.

Deleting Targets from the Document Grid was implemented in July 2017.
I have just now implemented a new feature which will appear in the next update of Skyline-Daily. There's a "Actions" button on the Document Grid which drops down menu items such as "Remove Transition Peaks" or "Delete Peptides".
These new "Action" menu items look at all of the columns in the Document Grid to see if there are any columns from a Transition Result, etc (e.g. "Area"). If a Transition Result column is found, then the "Remove Transition Peaks" menu item is enabled. If there are no transition result columns, but there are Precursor Result columns (e.g. "Total Area"), then the "Remove Precursor Peak" column will be enabled.

These menu items operate on the set of rows that you have selected in the Document Grid.

I did not implement "Remove peaks that are not displayed on the document grid". I imagine that this won't be necessary-- I think it is nearly always possible to set up your filters on the Document Grid so that the peaks you want removed will be displayed. Removing things not displayed would have been significantly harder to implement.