Command line for importing peak boundaries and analyte concentration

support
Command line for importing peak boundaries and analyte concentration jianqiaoshen  2022-06-29
 

Hi, I am using SkylineRunner to automate the processing of different dataset. I am wondering are there any commands to import a peak boundaries file and analyte concentration for each replicate?

 
 
Nick Shulman responded:  2022-06-30
You can see the most up-to-date documentation for the commandline in Skyline using the menu item "Help > Documentation > Command Line".
The commandline argument to import peak boundaries is:
--import-peak-boundaries

To import analyte concentration, the commandline argument is:
--import-annotations

If you want to learn what the format is for the import annotations file, you can use the menu item in Skyline:
File > Export > Annotations
That menu item shows you the complete list of properties and annotations that Skyline can both export and import. If you look at the CSV file that it generates you will see how to refer to the replicate, and what to name the column which contains the concentration value.

By the way, if you happen to have named your raw files so that the concentration is part of the filename, there's a feature where you can tell Skyline how to extract information from the filename and put them in properties or annotations. The way to get to that feature is:
Settings > Document Settings > Result Files
Here is the page with information about how to use the Result File Rules feature:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=ResultFileRules

-- Nick
 
jianqiaoshen responded:  2022-06-30
Hi Nick,

Thank you for your quick response. Currently, I am use Skyline 21.2.0.536 which shall be the latest version but I still do not find the command line argument --import-peak-boundaries in the help documentation. Running the SkylineRunner.exe with the argument --import-peak-boundaries also reports:
Error: Unexpected argument --import-peak-boundaries

Is this new feature included in Skyline-daily only?

Thank you!
 
Nick Shulman responded:  2022-06-30
Oh, you are correct, the peak boundary import feature is only available in Skyline-Daily.
Here is the Skyline-Daily announcement from the first release that contained this new feature:
https://skyline.ms/announcements/home/software/Skyline/daily/thread.view?rowId=54699

We are planning on releasing the next version of Skyline, which we are planning to call "version 22.2", sometime this summer.
-- Nick
 
jianqiaoshen responded:  2022-06-30
I am looking forward to the new version of Skyline. That will definitely help me a lot. Btw, I succeeded in writing the analyte concentration for each replicates by using --import-annotations. Is there any ways to change the retention_time, start_time and end_time for PrecursorResult and TransitionResult as well? I tried to add column like property_ RetentionTime in the csv file of the annotation but Skyline will show "Annotation property_ RetentionTime does not apply to the element" when importing.