building a MS2 transition list

building a MS2 transition list p de blaauw  2024-02-09 01:27

Hello skyline,
I have been using a transition list for small molecules in Skyline for high-resolution data (MS1 scan) for years now. We now have another machine, namely an orbitrap where we generate MS2 spectra in besides the MS1 full scans. What is the best way to create a transition list to analyze the (known) MS2 fragments in Skyline?"

p de blaauw responded:  2024-02-09 01:31

This is the list we currently useing.
Already thanks for your answer.
Best regards Pim

Nick Shulman responded:  2024-02-09 12:03
In a small molecule transition list, you always need to tell Skyline what the fragments are.
Unlike for peptides, Skyline does not know how to predict fragments for small molecules.
You might find some useful information about making transition lists in the Small Molecule Targets tutorial:

-- Nick
p de blaauw responded:  2024-02-11 23:48
Thank you for your response Nick. If I specify the fragments in the transition list, how does Skyline know that they originate from the MS2 signal (and not the MS1 signal)?
Nick Shulman responded:  2024-02-12 06:58
Your transition list should have a column for Precursor m/z and a different column for Product m/z.
On a particular row, if the precursor m/z is the same as the product m/z then Skyline will assume that you want the MS1 signal.
If those numbers are different, then Skyline will assume you want MS2.
-- Nick
adi772 responded:  2024-02-12 23:42
Hi Nick,
I have tried to set-up my file in accordance with the Small Molecule Target tutorial, though I am using it for glycomics. This approach works well for quantification purposes, and I can view MS1 data to confirm the charge and appropriate isotopic profile for a given peak. However, I cannot seem to access MS2 data within Skyline. I have included a column in my transition list for product m/z as per your above comment, and left it blank. I have also selected DDA acquisition method for MS/MS filtering. Still, I cannot view MS2 data it seems.

Any advice?
Nick Shulman responded:  2024-02-13 07:20
I am not sure that I understand your question.
If you want Skyline to extract chromatograms for fragment ions, you would need to have some numbers in the "Product m/z" column so that Skyline knows which fragment ion to look at in the MS2 spectra.
I guess if you did not care which product m/z Skyline looked at because all you wanted was an MS2 chromatogram that you could click on so that Skyline would bring up the spectrum viewer, you could put any number that you wanted to in the Product m/z column. But, you would need to have a number in that column of your transition list, and that number would need to be different from the number in the Precursor m/z column.

You can also add MS2 transitions to your document by right-clicking on one of the things at the third level of the hierarchy in the Targets tree and choose the menu item "Add Transition". In the Add Transition dialog, you can change the "Monoisotopic m/z" and "Average m/z" values to be different from the precursor, and then Skyline will add a new transition to the Targets tree.

After you have added some transitions, you could tell Skyline to extract chromatograms again by going to "Edit > Manage Results" and pushing the "Reimport" button.

If you have both MS1 and MS2 chromatograms, you might have a hard time seeing the MS2 chromatograms because the MS1 chromatograms have much more signal. You can right-click on the chromatogram graph and choose "Split Graph" so that the MS1 and MS2 chromatograms are drawn in separate panes.

Skyline is not a very good tool for looking at spectra because most of Skyline's features revolve around extracting chromatograms. If you want to look at spectra in your raw files you might have an easier time using the QualBrowser software that comes with Thermo instruments. We also have our own program called "SeeMS.exe" which you can get by installing "ProteoWizard".

-- Nick