I am confused by the fact that "SCIEX QTOF - Analyst" and "Bruker timsTOF" are the only instrument types that allow you to choose something in the "Optimizing" dropdown on the Export Isolation List dialog.

PRM CE Optimization (i.e. CE Optimization on full scan instruments) was a new feature that was added in Skyline 23.1.

I would have expected that to work for more instrument types than just those two. The only real requirement is that Skyline needs to be able to read the collision energy value for each acquired spectrum in the data file.

If you would like, I could make you a special build of Skyline-daily that does allow you to choose "Collision Energy" in the "Optimizing" dropdown on the Export Transition List dialog. You would then be able to use this feature and let us know if it works with your instrument.

It would also be helpful if you could send us one of the .raw folders for data that you already have so that I can make sure that Skyline is able to see the collision energy values. Files which are less than 50MB can be attached to this support request. If it's larger than that you can zip it up and upload it here:
https://skyline.ms/files.url

-- Nick

Dear Nick,

Please help me for the skyline daily build which will help us for selecting CE in the optimizing dropdown during export transition list.

I have attached .raw file as zipped with description (CE optimize MRM ToF). This MRM data was acquired using skyline export isolation method (unscheduled).

Instrument name- Waters Xevo G2XS qTOF.

FASTA file for GLYCAM protein

>sp|P80195|GLCM1_BOVIN Glycosylation-dependent cell adhesion molecule 1 OS=Bos taurus OX=9913 GN=GLYCAM1 PE=1 SV=2
MKFLCVLLLASLAATSLAILNKPEDETHLEAQPTDASAQFIRNLQISNEDLSKEPSISRE
DLISKEQIVIRSSRQPQSQNPKLPLSILKEKHLRNATLGSEETTEHTPSDASTTEGKLME
LGHKIMRNLENTVKETIKYLKSLFSHAFEVVKT

Please find the attached picture for locating the raw file.

Thank you
Arpita

In your original question, what exactly were you hoping that choosing "Collision Energy" in the "Optimization" dropdown would do?

When you choose "Collision Energy" in that dropdown, you are telling Skyline that you want to do an experiment which collects data for each precursor with multiple different collision energies.
For each precursor, Skyline will write multiple lines in the isolation list file. The number of lines that get written and the collision energy values are controlled by the "Step size" and "Step count" values that you can see if you go to "Settings > Transition Settings > Prediction" and choose "<Edit Current...>" in the "Collision Energy" dropdown.
After you have run your experiment and collected data for each precursor with multiple different collision energies, and you then want Skyline to extract chromatograms, you will use the "File > Import > Results" menu item and choose "Collision Energy" in the "Optimizing" dropdown in the "Import Results" dialog.

Is that what you were hoping to do by choosing "Collision Energy" in the "Export Isolation List" dialog?

Or, did you want your isolation list to have only one row per precursor, but you would like the collision energy values in your exported isolation list to be different than what they are?

I have made a special build of Skyline which will allow you to choose "Collision Energy" in the "Optimization" dropdown for any instrument type in the Export Isolation List dialog:
https://proteome.gs.washington.edu/~nicksh/SpecialSkylines/PrmCeOpt/
Unfortunately, while choosing "Collision Energy" in the "Optimization" dropdown does result in multiple rows appearing in the isolation list for each precursor, but, as far as I can tell, each of those rows has the same collision energy value.

Note that because this is an unofficial build of Skyline-daily it has not been signed so Windows might discourage you from running it.
You might have to hunt around for the "Run anyway" button.

This special Skyline will appear on the Windows Start Menu as "Skyline-daily PRM CE Optimization".
You can have this installed on your computer along with the regular Skyline and Skyline-daily.

This special Skyline makes it so that the "Optimization" dropdown will be enabled for all instrument types on the "File > Export > Isolation List" dialog.

I am not sure that I understood your original question.
It might be helpful if you could send us your Skyline document.
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 and optimization libraries.

If that .zip file is less than 50MB you can attach it to this support request.
You can upload larger files here:
https://skyline.ms/files.url
-- Nick

Hi,

Thank you so much for your suggestions. Your first assumption is correct. I want to collect MRM data with multiple different collision energies for each precursor. I've installed your provided skyline and as you mentioned, I could see the same CE value for each Precursor in the export isolation list.

1. Is there any other way of exporting a CE-optimized MRM method for Xevo qTOF, in which each precursor will have different sets of Collision energies??

          In this regard, I came across one CE optimization document (attached) in which, they have used Triple QQQ (Waters) and export >> method for MRM acquisition.

2. So my question is "Can we use this export >> method feature for exporting the CE-optimized method in our instrument qTOF?"
3. If yes, then I cannot find qToF option in the dialogue Instrument type in export>> method.
4. If yes, which file has to be there in template file, export >> method >> template file ?

5. Also as you suggested, I have attached my skyline file with the description GLYCAM MRM.

Thank you so much for your kind help!
Arpita