Exporting resolution values

Exporting resolution values sstoychev  2020-06-16


I would like to export the resolution values for both precursors and fragments in MRM-HR and DIA data but can't find the metrics in the report templates. There are FWHM and Max FHWM values but I think these are related to chromatography rather than mass spectra?



Nick Shulman responded:  2020-06-16
I think the column you want might be called "Chromatogram Extraction Width".
It's available under:
Proteins > Peptides > Precursor > Transitions > Transition Results > Chromatogram

That is the m/z width of the channel that Skyline summed across when extracting chromatograms.
Its value is based on the resolution that you have specified at:
Settings > Transition Settings > Full Scan
as well as the m/z of the precursor.
The formula to convert from m/z and resolution to extraction width is different depending on the type of mass analyzer specified.

If you want something else such as the actual width of observed the Gaussian in the spectrum, Skyline does not know that number.
-- Nick
sstoychev responded:  2020-06-16
Thanks Nick,

Found it... I would like to work the "Chromatogram Extraction Width" values back to resolution. What would be formula if "TOF" is set as mass analyzer in the full scan settings for precursor and products?

Is there a way to plot these values in Skyline or will have to do externally via an exported report?


sstoychev responded:  2020-06-17
Never mind... I see your last point. I would need the actual width so can see how resolution is changing over time. Seems to be a good metric on the 6600 to monitor contamination... we see resolution drop off first when instrument starts getting dirty.

The "Chromatogram Extraction Width" is a constant value so won't help in this regard.

I wonder if the ideal "Chromatogram Extraction Width" would need to change from start to end of a large batch as resolution starts to drop off?


Brendan MacLean responded:  2020-06-17
It is not on our priority list to explore extraction width as a dynamic property. It is a fundamental property of how Skyline (and OpenSWATH) work that they do not perform any peak finding in the m/z dimension. They simply target an m/z and extract the signal found within a range of that target, modeled after how quadrupole function in SRM. You can consider the extraction width an insilico quadrupole. In fact, we originally saw this as a major benefit with TOF data where profile peaks are less uniform and Gaussian than Thermo Orbitrap data.

If you can prove that you have an algorithm for dynamically determining extraction width that improves performance, and you can get that published, we would certainly consider implementing it in Skyline, but it is not an area of research for us.

Thanks for your observations, though.