Small Molecules - Possibility of adding specified peak rankings or ratios between transitions within a precursor

Small Molecules - Possibility of adding specified peak rankings or ratios between transitions within a precursor Allison Haase  2022-04-05

Hi MacCoss Lab,

My lab is currently using Skyline for GCMS processing.
It would be helpful if there was some way to specify the predicted peak ranking for some of the transitions within a precursor for peak identification/picking, or if there is a way to specify the ratio between two transitions within a precursor. We are dealing with chiral molecules that have very similar ions, but the ratios between the ions differ.

I have attached my Skyline document which has my current method.


Nick Shulman responded:  2022-04-05
It looks like you might have tried and failed to attach something to this support request.
The maximum size of a file that you can attach to a support request is 50MB. You can upload larger files here:

If you have a Skyline document where you have chosen the correct peaks for all of your molecules, you can export a spectral library using the menu item:
File > Export > Spectral Library
Skyline will put fact spectra into the library where the m/z's are the m/z's of the transitions in the document and then intensities in those spectra are the integrated peak areas from your chromatograms.

If you then use that spectral library in another Skyline document, Skyline will look at the spectra in the spectral library in order to calculate the library dot product which Skyline will use to choose the correct peaks.

Unfortunately, Skyline requires a minimum of three transitions for Skyline to calculate a library dot product. Therefore, in order for this technique to work, you would need to trick Skyline into thinking that you have more transitions than you actually do, by, for instance, adding two transitions to your document whose m/z's are almost the same (e.g. 452 and 452.001).
-- Nick
Allison Haase responded:  2022-04-05
Hi Nick,

The file is under RA GCMS March 9 V9 ion ratio. We have at least 10 transitions per product, so that should not be an issue.
Nick Shulman responded:  2022-04-05
Thank you for sending that Skyline document.

Yes, it looks doing:
File > Export > Spectral Library
would give you a spectral library that you could use with future Skyline documents so that Skyline would know what transition peak area ratios to expect.

Unfortunately, when I export a spectral library and then try to use that .blib file, I get the error:
Custom molecules must specify a formula or valid monoisotopic and average masses.

There seems to be a bug in Skyline in that when it exports the spectral library it is not including the necessary information from your Skyline document. I will make sure that this gets fixed soon.

I think you might be able to work around this problem by telling Skyline what the chemical formula for your molecules are. I believe this bug is only going to manifest itself if your precursors are specified using m/z instead of chemical formula.
-- Nick