Ratio to surrogate standard using peak height?

Ratio to surrogate standard using peak height? per larsson  2024-04-09 02:12

Dear Skyline users,
I have a lipidomic MRM method where I use surrogate standards (one per lipid class). For one analyte I wish to use the ratio of the peak height instead of peak area, I cant find a way to set the peak height instead of area for the ratio calculation I would appreciate advice how to do this?

ratio=molecule_peak_height / surrogate_standard_peak_height

The reason i need to use peak height is that I have polarity switch in the scheduled MRM so I see peak apex but not the entire peak width, I preferer to use peak height to peak area for this particular lipid. I have searched the tutorials but not found how to do this.


Nick Shulman responded:  2024-04-09 08:07
There is no way to do this in Skyline.

We have talked about adding features related to this, particular to deal with "direct infusion" data where the chromatograms do not have any sort of peak shape because the analyte was fed into the mass spectrometer at a constant rate instead of eluting off of a chromatography column.
However, we have not yet implemented any features to help with these sorts of scenarios.

In theory, you could calculate the values that you need using a different tool such as Microsoft Excel.
However, you should keep in mind that the "Height" reported by Skyline might be different from what you were hoping it would be because interpolation and background subtraction. You can read more about these effects here:

-- Nick
per larsson responded:  2024-04-09 08:16
Thanks for the quick response!
Then I know it wont be possible and I could try to adjust the LC method to be able to separate the peaks better.