Importing peak boundaries with Skyline Runner

Importing peak boundaries with Skyline Runner estancliffe  2020-01-06

Hi Skyline Team,

I have begun using the command line version of Skyline to automate the processing of a large metabolomics dataset. With the user interface, I am able to import the peak boundaries to make sure the correct peaks are being integrated; however, with Skyline runner I am unable to do this. Right now, I am able to import my transition list and all of my datafiles and generate a skyline document with Skyline runner, but then I have to manually go in and open the skyline file and import the peak boundaries and then export the final report of the peak areas. If I was able to import peak boundaries through the command line, I would not need to open the interface at all. I don't know if this is a simple fix on your end, but it would help me out a lot!

Thank you!


Nick Shulman responded:  2020-01-07
I think this would be a simple fix on our end.
This question has been asked before.

We are in the process of figuring out which features to include in the next version of Skyline (version 20.2) and I will make sure that we consider this one.

By the way, how are you deciding on the peak boundaries in your peak boundaries file? Are you just using the same start and end points for each replicate? I believe we are also considering adding features to give you more control over how Skyline picks peaks for small molecules, such as making it so that "Explicit Retention Time" has more of an impact on where Skyline actually chooses the peak.
-- Nick
estancliffe responded:  2020-01-07
Thank you for your response! Sorry, I did not find the earlier question.

Right now, I am deciding the peak boundaries using a combination of the Skyline peak boundary detection and an additional list of peak boundaries from an external tool. I have a list of retention times for the compounds of interest in my transition list. My problem is that even when I set up the explicit retention time window, if skyline does not find a peak within that window it looks elsewhere, which is problematic for my downstream analyses. So what I do is first give the explicit retention times and windows in the transition list and then export the peak boundaries that skyline selects as a report. I then have a script that compares the skyline peak boundaries and measured retention time to the expected values in my transition list. If they are not within some tolerance of each other, I replace the skyline peak boundaries with the explicit retention time and window. These are the boundaries that I then import in the skyline GUI. This way, I let Skyline fine tune the boundaries for each file while preventing integration of other peaks if nothing is detected. It would be ideal if I could prevent Skyline for searching for other peaks outside of my retention time window, but for now this is my workaround.

Thank you again, I look forward to the next release! I am a big fan of Skyline!