MS/MS Spectrum screen

MS/MS Spectrum screen jfarrera  2020-09-04

Dear Skyline team,

I'm new on Skyline, I have started working with Skyline recently doing peptide sequencing. Till now I have created some MRM methods with Skyline (v., a0e7323e3) which I could run in a triple quadrupole LCMS8040 (LabSolutions, Shimadzu). I was able to open and process the acquired MRM data in the Skyline platform, but I was not able to open a MS/MS spectrum with Skyline. Is it possible to open in Skyline a MS/MS spectrum from a triple quadrupole LCMS8040 (Shimadzu)? When I open the View menu, the MS/MS Spectra option is not available (is not in the menu). Any idea?

Thank you very much for your support!! Best regards,


Nick Shulman responded:  2020-09-04
Skyline does not have the ability to browse spectra in Shimadzu SRM files.

This is something that is supported in SCIEX .wiff files (the feature is called "MIDAS spectra"), but it is not supported for any other vendors.

ProteoWizard has a tool called SeeMS.exe which can be used to look at spectra. You can download ProteoWizard from here:

-- Nick