Segemented MRM - Batch Script

support
Segemented MRM - Batch Script anirudhkashyap511  2025-03-24 08:59
 

Hi Skyline Team,

For each time segment, I have a specific set of transitions that I want the QQQ (Agilent 6495D) to monitor. I’ve written batch scripts using the Skyline Command line to handle this automatically for standard dMRM and MRM workflows, but I'm unsure how to implement this with my current time-based segmentation strategy.

Is there a way to automate this kind of time-segmented transition scheduling for the QQQ, possibly through Skyline.

Thank you
Anirudh

 
 
Nick Shulman responded:  2025-03-24 09:21
According to ChatGPT, the way to achieve this in Skyline is to make it so that the of your peptides or molecules in each of your time segments have the same Explicit Retention Time and Explicit Retention Time Window so that the exported method will have the transitions being acquired over the time ranges that you want.

That might not be a good answer because the "Explicit Retention Time" in Skyline should only be used when you know the exact retention time at which your molecule elutes because Skyline will always choose the peak which overlaps with the Explicit Retention Time even if other peaks within the Explicit Retention Time window score better on other features.

If you want to control the acquisition time range of a peptide without overly constraining the peak picking it might be better to specify the Predicted Retention Time for each peptide or molecule. This will only work if each of your time segments is the same length since you cannot specify different prediction window sizes for different peptides or molecules.

One way (maybe the only way) to specify the predicted retention time for each of your molecules is to create an iRT database.
You can learn about iRT databases here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_irt

It might be tricky to get iRT to do what you need it to do so it might be best if you sent us your Skyline document and your predicted retention times and we can help you figure it out.

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

Files which are less than 50MB can be attached to these support requests. You can always upload larger files here:
https://skyline.ms/files.url
-- Nick