Reprocessing of data obtained by neutral loss on a QQQ using skyline

Reprocessing of data obtained by neutral loss on a QQQ using skyline julien faugere  2020-10-01


I did analysis by neutral loss on QQQ on a lipid sample to observe triglycerides. Can we use skyline to reprocess this type of data ? I have often used skyline for reprocessing MRM data but never for neutral loss.

Thank you for your answer.

Kind regards,

Julien Faugere

Nick Shulman responded:  2020-10-01
Yes, Skyline can be used to process neutral loss data. Why do think there might be a problem?

If you are using Skyline for lipids, I assume that you are treating them as small molecules. For neutral losses, you need to tell Skyline the resulting chemical formula for the product ion when you do "Edit > Insert > Transition List".
Skyline does not know how to calculate the product ion formula given the precursor and neutral loss formulas. (I remember the question came up a year or so ago of whether we should implement such a feature for small molecules, but for now you have to specify the resulting formula yourself.)

If your Skyline document contains peptides, then the way that you tell Skyline about the potential neutral losses is by including modifications at:
Settings > Peptide Settings > Modifications
This document that I found on the web from Agilent has a nice set of screenshots showing how to define peptide neutral losses on page 16:

I hope this helps. Let me know if I did not understand your question correctly.
-- Nick
Brian Pratt responded:  2020-10-01
Small molecule transition lists can include a "Product Neutral Loss" column which makes it convenient to describe fragments in terms of a chemical formula to be subtracted from the precursor's chemical formula.

This is a fairly recent Skyline feature, and is available in the current Skyline-Daily and of course the upcoming Skyline 20.2 release.

- Brian