MRM workflow¶
Warning
To process multiple reaction monitoring (MRM) data, the MRM service of mzmine is required. This feature is included in the mzmine PRO subscription. Academic program and other users can reach out to inquire access options.
In contrast to HRMS data, MRM acquisitions are usually stored as chromatograms of specific transitions, e.g., m/z 413 -> 96 instead of full spectra. This data format needs dedicated processing because ordinary mzmine workflows start from a set of spectra along the retention-time axis.
Therefore, a specific module is required to build scans and chromatograms, which is the MRM to scans module.
Workflow¶
Import raw data¶
Import raw data in the usual fashion; see data import.
MRM to scans¶
The imported raw data is converted using the MRM to scans module. This creates pseudo MS1 and MS2 spectra as well as a feature list, which groups the MRM transitions by their retention time and precursor ion mass.
Set quantifier masses¶
mzmine automatically selects the quantifier mass based on the intensity of the MRM transitions and sets the most intense ion as a quantifier. If another transition should be used, select it with Set MRM quantifiers.
Smoothing in retention time dimension (optional)¶
Depending on the LC peak shape (i.e. data noisiness), the user can perform smoothing in retention time dimension.
Feature resolving¶
Feature resolving separates co-eluting and overlapping chromatographic peaks. For the algorithm and parameter settings, see the Local minimum resolver.
Feature alignment¶
mzmine offers a specific alignment module for MRM data. The MRM aligner takes the transitions of a feature into account and only allows alignment of features with the same transitions (in default settings). In principle, MRM feature lists can be aligned to HRMS feature lists using the Join aligner. For downsides of this procedure, see the the MRM aligner documentation