Instrument tab and full scan tab contradictions

Instrument tab and full scan tab contradictions edith serrano  2017-02-23
I am using Skyline (64 bit) and I have a couple of questions

1) I know that my sample is coming trough between 40 and 65 minutes and after that is just the wash so I set those limits on the instrument tab of the transition settings. On the full scan tab I tick Use only scans within 4 min of predicted RT.
I created a calculator and predictor based on this gradient and applied it to a library acquired with a longer one. In general the prediction is good but some peptides are supposed to appear after those 65 minutes. These chromatograms are imported even though I set the instrument limit and the data is obviously horrible. My fear is that those fake peaks are messing with the peak picking model. Is there any way to really limit the time of the imported chromatogram?

2) Other peptides that are supposed to appear after those 65 minutes figure as non measured. Do they have any effect on the model?

3) The predicted RT and time window don't appear in my chromatogram graph even though Retention time prediction is ticked.

I attach some pictures that I hope help understand the problems.

Thanks a lot
Brendan MacLean responded:  2017-03-05
Hi Edit,
Sorry for the wait on a reply. I am sure this must just be a bug. We will have a look. You will likely have to use Skyline-daily to get the fix, though, until our next major release.

The unmeasured peptides should not impact your model, but you can use Edit > Refine > Remove Missing Results to get rid of them before running a model to be sure, and just to clean up your document.

When I have problems like this seeing the prediction line and window when I feel it should be there, I usually start with View > Auto-Zoom > Both. Sometimes it shows that the prediction is just very far from the chosen peak or even the extracted time range, if chromatogram extraction was based on something other than the prediction.

Thanks for reporting your issues.