Exclude counting of decoys from prot, pept, precurs, transitions numbers in target list

Exclude counting of decoys from prot, pept, precurs, transitions numbers in target list dkueltz  2020-08-06

Hi Brendan et al.,
When constructing DIA assay libraries from raw spectral libraries by sequentially applying QC filter criteria my lab is routinely recording the numbers of proteins, peptides, precursors, and transitions remaining after each filter step. We get these numbers from the display on the lower right hand corner of the skyline app. However, these numbers currently include decoys and we have to delete the decoys and then paste them back tp the target list after every filter step. It would be nice to not have to do that. So I am asking if you could program Skyline such that it excludes decoys automatically from the display in the lower right hand corner of the screen.

Nick Shulman responded:  2020-08-06
Those numbers in the status bar are intended to work like the line or page number indicator in a word processor.
They tell you the total number of peptides in your document, but also which peptide you currently have selected in the Targets tree.
It is displayed as a numerator/denominator indicating how far through the total is the position of the selection in the Targets tree.

If your decoy peptides are all at the end of the document, then the way to count the non-decoy peptides is to select the first decoy, and the number of non-decoys is one less than the numerator. In the screenshot that I've attached I have selected the decoy peptide list, and so you can infer that the number of non-decoy peptides in the document is 163,053.

Another way to count the number of peptides matching a particular criteria is to make a custom report in the Document Grid. If you want the totals displayed in a single line in the Document Grid you can use the Pivot Editor.

If you are already using the Document Grid for something else, and you want to have a second document grid floating around displaying a different report, the trick to doing that is to go to:
File > Export > Report > Preview
and then cancel out of the Export Report dialog, but leave the preview window there.

Hope this helps,
-- Nick
dkueltz responded:  2020-08-07
Hi Nick, Thanks for the reply. We use the DocumentGrid for more complex tasks and it is much quicker/ more convenient to look at the numbers on the lower right edge of the screen. Also, temporarily cutting and pasting back the decoys is faster than opening the DocumentGrid and we get all the numbers for proteins, peptides, precursors, transitions, not just for peptides. This is nothing critical and easy to bypass by temporarily deleting decoys but I thought I mention it since this feature is critical for building high quality validated DIA assay libraries from raw spectral libraries and I thought that this workflow would be used more frequently in the future by many labs. Currently we do this by applying ten sequential steps and recording the decrease in proteins, peptides, precursors, transitions numbers at each step.