Issue 723: Precursors per sample injection think's it is transitions per sample injection

Assigned To:Brendan MacLean
Opened:2020-04-04 by philip remes
Changed:2020-04-04 by Brendan MacLean
2020-04-04 philip remes
Title»Precursors per sample injection think's it is transitions per sample injection
Assigned ToGuest»Brendan MacLean
Hi Brendan,

I imported a list of peptide sequences, and then wanted to output a set of isolation lists. There are 456 peptides, and since 2 and 3+ and isotope labels are specified, there are 1824 precursors. On the Export Isolation List tool, I entered 216 into the max precursors per sample injection, and Methods says 456. That doesn't seem right. I would have expected to get 1824 / 216 ~ 9. The tool tip on the text box says "Each file will have a most this number of transitions", so I think there must be an issue here with confusing transitions for precursors.


2020-04-04 Brendan MacLean
resolve as Not Repro
Hi Philip,
Could you post this to support first until we are sure there is a bug? I am pretty sure it is not as simple as confusing transition count with precursor count. When you do post it to support, please post a better screenshot. This one is blurry enough to be difficult to read and it is missing the status bar which would show the number of peptides, precursors, and transitions.

If you are willing to supply the file itself, you can use File > Share to create a file and if that is <50M you can attach it to the support request, or you can post it to:

Thanks. Great to see you are using Skyline.


2020-04-04 Brendan MacLean
Maybe try checking "Ignore proteins"? Not sure why that could cause anything like this, but you don't seem to be at all interested in having Skyline pay any attention to protein grouping, which would be for if you were trying to do protein quant and you wanted all peptides of a particular protein in a single run. Just doesn't look like you have the option set right for the document you are showing, which seems to be a monolithic list of peptides. Not sure why this would cause what you are seeing, but it is worth seeing if it makes any difference at all.

2020-04-04 Brendan MacLean
Well, okay, at least we should fix the tooltip to be consistent with the field label. We do dynamically change the field label based on the type of experiment, and you are obviously doing PRM, which is why the label says "precursors". You are right that we should also dynamically change the tooltip for the control to match the label, but I do not thing that has anything to do with the 456 methods issue which you are seeing.