MRM workflow¶
Warning
To process multiple reaction monitoring (MRM) data, the MRM service of mzmine is required. This is included for PRO customers. Academics can reach out to info[at]mzio.io to request a free license.
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 is a raw data format, that mzmine is not used to handling, since workflows usuallys start with a set of centroided spectra along the retention time.
Therefore, a specific module is required to build scans and chromatograms, which is the MRM to scans module.
Workflow¶
Import raw data¶
Raw data is import 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 other ions shall be used as quantifiers, this module allows the selection. mrm-set-quant-mass.md
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 step enables separation of co-eluting and overlapping chromatography peaks and as such is one of the pivotal steps in data preprocessing. For more detalis on the algorithm used and parameters settings, see the Local minimum resolver module.
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