Small Molecule Method Development and CE OptimizationPrint

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Small Molecule Method Development and CE OptimizationPrint carlos penno  2021-09-16
 

Dear all,

I follow the tutorial Small Molecule Method Development and CE OptimizationPrint
and it does not work. I cant get the information needed.

I just wanted to report this.

Best regards,

 
 
Nick Shulman responded:  2021-09-16
Can you tell us more about what went wrong? Are you saying that it was not possible to follow the steps of the tutorial because Skyline behaved differently than the tutorial said that it would? Could you send us a screenshot of what the Skyline window looked like when things went wrong?

Or are you saying that the tutorial did not provide the useful information about how to use Skyline and you have additional questions? That is certainly understandable and we are always here to help. What would you like to know?

If anything goes wrong in Skyline, we can often figure out what happened if you 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, optimization libraries.

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

-- Nick
 
carlos penno responded:  2021-09-16
From skyline, I exported a method with different CE values and collected data with it. When re importing the data I clicked in split graph and here things did work as expected, I never managed to get the bar chart with intensities for the different CE. NOw, I am trying to get the data thru paranorama now and visualize the data in R. Let s see if that works better.
 
Nick Shulman responded:  2021-09-16
I am not an expert on how CE optimization is supposed to work, but if you send us your .sky.zip file someone here might be able to figure out how this is supposed to work.
If you are not seeing the information that you need in the Peak Areas graph, you might be able to see the numbers that you need in the Results Grid ("View > Other Grids > Results Grid") or in the Document Grid.
The Document Grid will allow you to see nearly all of the data in the document. In order to see that data, it is often necessary to create a custom report. This tutorial will show you how to use the Document Grid to customize reports:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

-- Nick
 
carlos penno responded:  2021-09-23
Hi Nick,

another issue I found is what while exporting different DP voltage for optimazation for sciex, skyline cant to that apparently. CE is working well, DP not at least when I tried.

Thanks, Carlos.