mzmine Pro workflows¶
This page describes the user-facing workflows added by mzmine Pro. The standard mzmine modules and their documentation remain relevant; Pro workflows add support for MRM data and traces acquired with other detectors, such as UV/DAD data measured with LC-MS.
Info
Availability depends on the services enabled for the signed-in mzmine user. The running application's menus and parameter dialogs are authoritative for the installed version.
DDA (UV/Other)¶
Choose DDA (UV/Other) in the batch wizard for LC-MS/MS data-dependent acquisition that also contains other-detector traces. It follows the ordinary LC DDA workflow and adds an other-detector branch: optional chromatogram extraction for additional wavelengths, trace shifting and binning, baseline correction, local-minimum resolving, and correlation of the resulting other-detector features with the MS feature list.
Use this workflow only for LC-based acquisition. Direct infusion and flow injection are not available selections for this workflow. Select the detector trace type and, when applicable, the wavelengths to process. The wizard can estimate a retention-time shift automatically; inspect the result in the correlation dashboard before relying on cross-detector assignments.
DIA (UV/Other)¶
Choose DIA (UV/Other) for LC data-independent acquisition with other-detector traces. It uses the usual DIA workflow choices and adds the same other-detector preparation and correlation stages as DDA (UV/Other). It is also restricted to LC acquisition; direct infusion and flow injection are not available selections.
For either UV/Other workflow, use only traces that answer the analytical question. Processing every available trace can add noise and unnecessary computation. See the [Other detector terminology] (../module_docs/uv/otherdetector_glossary.md), [trace-processing steps] (../module_docs/uv/uv_shift_trim_bin_traces/uv_shift_trim_bin_traces.md), and correlation workflow. Use the Multi detector visualizer when manual trace integration or side-by-side trace inspection is needed.
MRM¶
Choose MRM for LC triple-quadrupole multiple-reaction-monitoring data. The wizard is limited to low-resolution MS and no ion mobility. It converts the transition chromatograms into mzmine's MRM feature representation, creates chromatograms, can assign quantifier transitions from a table, and then resolves and aligns the features.
The workflow is designed around the MRM transition information, so prefer the MRM aligner after resolving. The MRM guide gives the full sequence, input expectations, and manual alternatives: [MRM workflow] (../workflows/mrmworkflow/mrm-workflow.md).