Merge MS/MS module

[IngvildRyde]

Thank you for MZmine! It is a great tool for processing my metabolomics data.

I have a few questions regarding the Merge MS/MS module for exporting my feature lists to GNPS: https://mzmine.github.io/mzmine_documentation/module_docs/io/merge_ms2_kai.html#isolation-window-offset-mz

Are the two parameters:

• 1. "Isolation window offset (m/z)": Isolation window offset from the precursor m/z (default: 0.0 m/z), and
• 2. "Isolation window width (m/z)": Width of the isolation window (left and right) (default: 3.0 m/z)

referring to the isolation resolution of the quadrupole, i.e. the settings of my quadrupole methods?

When I try to look up these settings in Bruker, I see the following parameters listed:

• 1. "Set isolation resolution FWMH (MS)": 0.00 m/z,
• 2. "Set isolation mass (MS only)": 50.0 m/z

Do these settings that I have found in Bruker, correspond with the two parameters within the Merge MS/MS module mentioned above, so that the "Isolation window width" should be set to 50.0 m/z?

If not, then how can I figure out what values for these settings in this module are appropriate for my data?

Best wishes,
Ingvild