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MRM HR wiff file import parameter

ssy8827

2025-07-29 22:07

Hi,

I conducted MRM HR peptide quantification using the ZenoTOF 7600 (no small molecules involved).

I'm encountering an issue when trying to import the generated WIFF file into Skyline.

I have already entered the peptides via Edit → Insert → Peptides.

In Settings → Transition Settings, I configured the following:

MS1 filtering: Count

Precursor mass analyzer: Centroided

Peaks: 3

Mass Accuracy: 10 ppm

For MS/MS filtering, I left it as None.
Among the options — None, DIA, PRM, DDA, SureQuant — which one should I select?

Nick Shulman responded:	2025-07-29 22:41
You should choose "PRM". A PRM experiment is one where the mass spectrometer has been given a list of m/z's to collect MS2 spectra for, and those m/z's are equal to the m/z's of the peptides in the Targets tree in Skyline. Skyline always calls this sort of experiment "PRM", but it sounds like Sciex sometimes calls it "MRM HR". -- Nick