MS1 filtering mode for lipids

MS1 filtering mode for lipids Eric Merkley  2020-12-01

Is there a way to use Skyline in an MS1 filtering mode similar for what you would use for peptide untargeted DDA data?

Brian Pratt responded:  2020-12-01

Hi Erik,

If I've understood the question, I'd say have a look at LipidCreator. That's a great tool for building a list of putative lipidomics targets in Skyline.

Thanks for using the Skyline support board,

Brian Pratt

Eric Merkley responded:  2020-12-01

As near as I can tell, LipidCreator is for targeted MRM-style data--I'm curious is there is a way to use Skyline to look at precursor ions in a manner analogous to MS1 filtering for peptides.

Brian Pratt responded:  2020-12-01

Apologies if I'm missing the point, but:

Skyline is built for targeted mass spec, so for untargeted approaches you have to provide a comprehensive list of things you think might be found.

Such a list isn't any different from SRM to DIA, it necessarily includes precursors and possibly fragments. If your data is MS1 only then Skyline just won't worry about the fragments. I've attached a screenshot of a Skyline document generated by LipidCreator.

Let me know if this makes sense or not.



Brian Pratt responded:  2020-12-01

I should add that if you have some other comprehensive list of lipids it can certainly be imported into Skyline as well. LipidCreator is just one route to success. But you do have to provide a list. This could be, for example, in the form of a spectral library. Skyline is quite flexible.

  • Brian
Brendan MacLean responded:  2020-12-01

Let me just suggest you have a look at the Hi-Res Metabolomics tutorial (all with MS1):

And the paper on targeting small molecules with Skyline, which has an experiment using only MS1:

While the LipidCreator software can greatly help in getting the necessary chemical formulas for lipids into the Skyline Targets list, it is not necessary, and Skyline can target any molecule by chemical formula, extracting a single XIC or multiple for the isotope envelope of the mulecule in MS1, just as it has done for peptides since 2011 or so for peptides.

Hope this information is helpful. We encourage you to learn more and use these features.

Brendan MacLean responded:  2020-12-01

There is also this new tutorial, which targets lipids in Agilent IMS-Q-TOF data in both MS1 (low-energy) and high energy spectra:

You could certainly skip the chromatogram extraction from the high energy spectra. And the tutorial starts without using the IMS drift time dimension.