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Small molecule transition list adducts not loading, access to Skyline 23?

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Small molecule transition list adducts not loading, access to Skyline 23? trevor adams  2024-09-04 07:17
 

Hello,

Our group had previously been using a custom transition list for glycomics data analysis that included both protonated and sodiated adducts. However, recently when trying to use the same list it does not seem to properly extract the sodiated XICs, even on old data files where it had worked fine before. Based on the timeline of this problem, it's possible that this began with Skyline 24. Is there a way I can install Skyline 23 to troubleshoot? I can't seem to find any archive of older releases.

I have attached the transition list in .csv format here. I have only tested this on Agilent .d files.

Best,
Trevor
 
 
Nick Shulman responded:  2024-09-04 07:25
You can download older versions of Skyline from the "unplugged" installer page:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=install-64-disconnected_23_1

After you click "I agree" you can click on the "Archive" link.

Also, if you send us your Skyline document and one or more of your Agilent .d folders we could take a look and tell you what is going on.

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

The "Share Document" dialog also gives you the option to include the .d folders or you could zip those up and send them to us separately.

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

I am traveling this week so I might not be able to look at your files until Monday but someone else might be able to answer your questions earlier.
--Nick
 
trevor adams responded:  2024-09-04 07:49
Thanks Nick! Skyline 23 does appear to work fine. I have loaded in the same transition list and results into Skyline 23 and Skyline 24 to https://skyline.ms/files.url as:
- skyline23_test.zip
- skyline24_test.sky.zip

If you look at one of the molecules, such as 'N5H3F1', you can see that the sodiated adducts appear in the Skyline 23 doc but not the Skyline 24 doc, where it simply reads 'Chromatogram information unavailable'. Protonated adducts appear to be unaffected.
 
trevor adams responded:  2024-09-04 07:54
Oh yes, also the original .d file is uploaded as 'GPNMB_instantPC.d.zip'
 
Nick Shulman responded:  2024-09-07 16:03
The current version of Skyline seems to have a bug when the molecule does not have a chemical formula, and has only been specified by its monoisotopic and average masses, and the adduct does have a chemical formula such as "[M+H+Na+]".
We will try to fix this bug very soon.

In the meantime, you can work around this bug by changing the adduct description so that it only contains the mass.
For instance, instead of "[M+H+Na+]" you could specify "[M23.9976++]".

You can change the adduct by right-clicking on a Precursor in the Targets tree and choosing "Modify..."
After you have changed the adducts of your molecules you will need to tell Skyline to extract chromatograms again for the missing chromatograms to show up.

Thank you for reporting this bug.
-- Nick