Planned Functionality for Skyline Runner?

Planned Functionality for Skyline Runner? hogan  2019-04-02


First let me say thank you for all the work you do to keep this awesome software platform up and running and constantly making improvements!

I am not aware of a way to use skyline runner to upload a template file (.csv table) into the Document Grid for assigning analyte concentration and sample type to the imported replicates. So far I have been doing that manually every time I pull in a new batch of files from my run sequence (AbSciEx 4000 qTrap w/Analyst 1.6.2). I am attempting to set up a small molecule quantitative analysis workflow in skyline and was hoping to be able to automate most of the data processing using skyline runner.

Is this a planned functionality in the future?


Nick Shulman responded:  2019-04-02
There is a command for SkylineRunner:

This allows you to import user-defined annotations, as well as other properties including analyte concentration and sample type.

If you want to see what the format of the .csv file should be, you can use the menu item in Skyline:
File > Export > Annotations
to export the properties you are interested in from some other Skyline document, and see what they look like in the CSV file.

Let me know if you have any questions or if any property you'd like to import seems to be unavailable.
-- Nick
hogan responded:  2019-04-02
Hello Nick,

Thank you so much got your fast response and your help with this question!

I am currently using this document to guide my skyline runner work.

I do not see the command you recommend here. Is there a more comprehensive list of skyline commands available? Thank you!


Brian Pratt responded:  2019-04-02
That's pretty old (but still the top google hit, hmm) - try starting from here instead:

Best Regards,

Brian Pratt
Brendan MacLean responded:  2019-04-02
I guess someone may have linked to that old document. Maybe we should remove or move it. I will look at that. It is still possible to download and install Skyline 2.1.

In the latest Skyline-daily, we have moved that documentation into Skyline, such that you can get it from Help > Documentation > Command Line or from SkylineRunner or SkylineCmd with the —help argument or just no arguments at all.

Hope this helps. Thanks for using the Skyline CLI.