full-scan-precursor-res-mz dsullivan  2019-08-14

Hi all,

I'm trying to utilize some of the newer skyline cmd settings but I'm running into issues.

Specifically I'm trying to set the precursor resolution with full-scan-precursor-res-mz. I have tried:

Unfortunately I get no peaks found when I try to set this option. It seems to work fine if I don't set this option.

Any ideas about what's going on? I can't seem to find an example of how to use this option other than in the command line documentation which just has <m/z value> as a value.

Any help is appreciated.

Nick Shulman responded:  2019-08-14
I think you need to be using the "--full-scan-precursor-res" command line argument instead of "--full-scan-precursor-res-mz".

Note that the "--full-scan-precursor-res" number has a different meaning depending on what the Precursor Mass Analyzer is.
If the mass analyzer is "QIT", then that number is interpreted as a number of mz units, and 0.7 is a reasonable value.
If the mass analyzer is "Centroided", then that number is a number of parts per million.
For other mass analyzers, that number is a resolution, which is often a big number like "30000".

When the mass analyzer is "FT-ICR" or "Orbitrap", the resolution number alone is not sufficient to tell Skyline how wide of a channel to look in. In those cases, you would use the "full-scan-precursor-res-mz" to tell Skyline at what m/z that resolution is the right value. For instance, you might want to say that the resolution at 400 m/z is 30000. Then, Skyline applies a complicated formula to figure out what the resolution is going to be at other m/z values.

-- Nick