Observed transition mass

Observed transition mass dan15060  2022-05-30

Dear Skyline support

I was wondering if it is possible to get the measured, observe transition mass from skyline for a specific scan in a specific sample/raw file. So something in analogy to "Raw Spectrum Ids" or "Raw Times". I'm after the transition mass(es) that I see when I look at a fragment spectrum in xcalibur/freestyle.
I'm was not able to find this in the Export Report options, I apologize if I just missed this option.

I'm running Skyline on win10, the raw files were acquired on a Thermo Exploris 480 and the measured transition masses were accessed using Thermo Freestyle 1.6.

Thank you for your help


Nick Shulman responded:  2022-05-30
There is a column "Raw Mass Errors" that you can find in the Document Grid (or the Results Grid when you have a Transition selected in the Targets tree).
The comma-separated numbers in that column represent the difference between the calculated m/z of the transition and the m/z that Skyline observed in the spectrum. Those numbers are expressed as parts-per-million so, to find the absolute mass difference you would multiply the number by the transition m/z and divide by one million. Or:
observed m/z = transition m/z * (1 + (mass error) / 1,000,000)
-- Nick
dan15060 responded:  2022-06-13
Hi Nick
Thank you very much for the quick answer, much appreciated.
We tried this, and the masses calculated this way tend to be identical for the first 3 -4 decimals only when comparing to the raw file masses. I assume this is due to the fact that RawMassErrors are reported with max. 2 decimals and the ProductMZ with 6 decimals (if exported as "Invariant" as recommended in this post: https://skyline.ms/announcements/home/support/thread.view?rowId=31091). Is there a way to increase the decimals for these values to get closer to the observed mass from the raw files?
Thank you

Nick Shulman responded:  2022-06-13
The mass error is only stored by Skyline to one decimal place.
That is, the observed mass error gets multiplied by 10 and rounded to the nearest integer, and that integer is what gets stored in the .skyd file.
There is no way to change the amount of precision in the mass error values.
-- Nick