Starting with MZmine.39, this module is considered deprecated and will be removed in future MZmine versions. Please use the ADAP Chromatogram Builder, which is much faster and generates better results. Contact the developers if you have any questions or concerns.
The Chromatogram builder takes mass lists generated for each MS scan (see Mass detection) and builds a chromatogram for each mass that can be detected continuously over the scans. Later, these chromatograms may be deconvoluted into individual peaks by the Deconvolution module.
This algorithm works by maintaining a pool of chromatograms spanning over consecutive scans. Only MS level 1 scans are considered for building the chromatograms. For each processed scan, a mass list must be available (see Mass detection for details). The mass list is processed in the order of decreasing intensity and each ion is connected to the appropriate chromatogram according to the m/z tolerance parameter. When no matching chromatogram is found, a new chromatogram is created with the ioin's m/z value and added to the pool. When a chromatogram is finished (no m/z peak is found to be connected to), its length (time span) and intensity (height) are checked according to user-specified minimal values. Those chromatograms which fit the required parameters are added to the final peak list.
The resulting chromatograms can be opened in the peak list table visualizer using a double-click: