HRMS batch analysis

HRMS batch analysis nicholas clanton  2022-03-24

I'd like to configure the Skyline interface to quickly analyze a batch of compounds for HRMS accuracy. I'm able to get the document grid to display almost all the info I need (formula, adduct, calulated mass, ppm error) but I can't find a way to display the measured m/z value from an associated scan. Moreover, I can only display m/z values on the mass spectrum to one decimal place. Is there a way to increase the decimal places displayed on mass spectra or add a column for measured m/z in the document grid?

Thank you for your help.

Nick Shulman responded:  2022-03-24
The column which will tell you how closely the observed m/z matches the theoretical m/z of the transition is called "Mass Error PPM". You can find that column in the Document Grid under:
Molecule Lists > Molecules > Precursors > Transitions > Transition Results > Mass Error PPM
(there is also a search button on the toolbar at the top of the Edit Report dialog)

You can also see mass errors in one of the mass errors graph with the menu item "View > Mass Errors"

Is that what you are looking for? Those mass errors represent what Skyline noticed while it was extracting chromatograms. If you are interested in figuring out the mass errors on individual spectra, Skyline might not be the best tool. There are other tools which are better for looking at individual spectra, including ProteoWizard SeeMS.exe.
-- Nick
nicholas clanton responded:  2022-03-24
Hi Nick, thanks for your input. I'm able to display the calculated error already, but I'd like to also be able to display the measured mass that was used to calculate this error. This would allow me to easily report HRMS data for publication (m/z calc., m/z found, ppm error).