RT allignment and idotp filtering

RT allignment and idotp filtering sigio86  2019-03-14

Dear all Skyliners,

I'm really a beginner in Skyline so perhaps my question will be very simple.
I have 5 samples, 2 replicates each and I would like to visualize in all chromatograms the same peptide at the same RT (please see attached what I have for a prototypical example)... do you know I could I do that?
A second question is if and how can I filter for "high" idotp (at least 0.8 based on previous posts).

Thanks a lot in advance.


Nick Shulman responded:  2019-03-14
If you want to make it so that all of the chromatogram graphs show the same retention time range, then you can right click on the chromatogram and choose "Synchronize Zooming".

Instead of that, if you want to make it so that each chromatogram graph shows the currently chosen peak, you can right click on the chromatogram and choose "Auto Zoom X-Axis > Best Peak".

If you have peptide search results for your runs, then you can tell Skyline to use the times at which the peptides were found in each run in order to do an alignment between them. There is a menu item "Align Retention Times to <current replicate>" that becomes available on the chromatogram right click menu. This menu item will often make it so that all of the replicates are perfectly lined up in your retention time plot.

If you want to do complicate searching for results that satisfy a particular criteria (e.g. high idotp) you might be able to do what you need using the Document Grid.
Our Document Grid tutorial is a few years out of date (we will have a new version of the tutorial available real soon), but here's what we have right now:

I am not sure I understood your questions but I hope this helps.
-- Nick