Table 5.
MZmine processing parameters.
| Procedure | Parameter | |
|---|---|---|
| Mass Detection | MS level 1: Noise level | 2E5 |
| MS level 2: Noise level | 0.0 | |
| Mass detector | Centroid | |
| ADAP Chromatogram Builder [37] | Min group size # of scans | 5 |
| Group intensity threshold | 2E5 | |
| Min highest intensity | 5E5 | |
| m/z tolerance | 0.003 m/z (or 10 ppm) | |
| Chromatogram Deconvolution | Algorithm | Baseline cut-off |
| Min peak height | 5.0E5 | |
| Peak duration range (min) | 0.02–2.2 | |
| Baseline level | 2E5 | |
| m/z center calculation | MEDIAN | |
| m/z range for MS2 scan pairing (Da) | 0.01 | |
| RT range for MS2 Scan Pairing (min) | 0.1 | |
| Isotopic Peaks Grouper | m/z tolerance | 0.001 m/z (or 10 ppm) |
| Retention time tolerance (absolute: min) | 0.1 | |
| Monotonic shape | No | |
| Maximum charge | 3 | |
| Representative isotope | Lowest m/z | |
| Join Aligner | m/z tolerance | 0.001 m/z (or 10 ppm) |
| Weight for m/z | 1 | |
| Retention time tolerance (absolute: min) | 0.2 | |
| Weight for RT | 0.1 | |
| Require same charge state | Yes | |
| Feature List Row Filter | Retention time (min) | 0.25–12.00 |
| Keep only peaks with MS2 scan (GNPS) | Yes |