mzmine preferences¶
Project -> Set preferences
The mzmine preferences control global behavior such as memory handling, number formats, chart appearance, and vendor data import defaults. They apply to newly opened dialogs, newly imported raw data files, and newly created plots or feature lists, depending on the setting.
Preferences are saved in the user configuration file (.mzmine/.mzconfig in the user's home
directory). You can also save or load a configuration file from Project -> Save configuration or
Project -> Load configuration. For command-line and batch processing, a specific .mzconfig
file can be loaded with the -p / -pref option, while command-line options such as --temp,
--memory, and thread settings can override the loaded preferences for that run.
First settings to check
For most installations, first set the Temporary file directory to a fast local SSD and keep Keep in memory at NONE unless your system has enough RAM for the complete workflow.
Preference groups¶
The dialog is organized into four groups:
| Group | What it controls |
|---|---|
| General | Parallel tasks, memory mapping, temporary files, IMS storage strategy, and proxy settings |
| Formats | Display formats for m/z, retention time, mobility, CCS, intensity, scores, ppm, percent values, and unit labels |
| Visuals | Tab labels, chart colors, paint scales, chart theme defaults, application theme, image display, and precursor labels |
| MS data import | Default vendor import and centroiding behavior for drag-and-drop import, the mzwizard, and raw data import dialogs |
General¶
Number of concurrently running tasks¶
Controls how many mzmine tasks may run in parallel. The default is automatic and uses the available processor count. Lower this value when you want to leave CPU resources for other applications or for other jobs on a shared workstation.
Keep in memory¶
Controls which data objects stay in RAM instead of being memory mapped to temporary files. The default is NONE, which memory maps spectral data and feature data to the temporary directory. This is usually the best setting for large projects because it keeps RAM usage predictable.
Available options are:
| Option | Effect |
|---|---|
| NONE | Memory map spectral data, mass lists, and feature data to temporary files. This is the default. |
| ALL | Keep all supported data in RAM. Use only when memory is not a constraint. |
| FEATURES | Keep feature data in RAM. |
| MASS_LISTS | Keep centroid mass lists in RAM. |
| RAW_SCANS | Keep raw spectral data in RAM. |
| MASSES_AND_FEATURES | Keep centroid mass lists and feature data in RAM while memory mapping raw scans. |
The command-line --memory option overrides this preference for a command-line run.
Optimize IMS processing¶
Controls how ion mobility feature data is stored. Memory efficiency is the default and stores references to individual mobilograms in temporary files. Speed keeps those references in RAM. Changes affect feature lists created after the preference is changed.
Temporary file directory¶
mzmine uses temporary files for memory-mapped spectra, mass lists, and feature data. Choose a fast local SSD with enough free space. Avoid slow network drives and removable drives when possible.
Restart mzmine after changing this directory so all new project data uses the intended location. The
command-line --temp option overrides this preference for a command-line run.
Free memory in batch (experimental)¶
Runs garbage collection after each batch step. This can reclaim memory sooner, but may slightly reduce throughput. Keep it disabled unless a specific batch workflow benefits from it.
Fast temp files cleanup¶
Deletes temporary files as soon as mzmine no longer needs them. This is enabled by default.
Proxy¶
Configures proxy settings for internet access, including downloads, online services, and other network calls from mzmine.
Formats¶
The format preferences control how values are displayed in the graphical interface. They do not change raw data, feature detection, or calculations.
| Preference | Default display pattern | Used for |
|---|---|---|
| m/z value format | 0.0000 |
m/z values |
| Retention time value format | 0.00 |
Retention times |
| Mobility value format | 0.000 |
Ion mobility values |
| CCS value format | 0.0 |
Collision cross section values |
| Intensity format | 0.0E0 |
Intensities |
| PPM format | 0.0 |
ppm mass errors |
| Score format | 0.000 |
Scores such as correlations or cosine similarities |
| Percent format | 0.0% |
Percent values |
| Unit format | DIVIDE | How units are written in labels |
Visuals¶
Show tab sub titles¶
Shows the related raw data file or feature list name in tab headers. This is enabled by default.
Default color palette and default paint scale¶
Set the default colors used for charts and the default paint scale used for heat maps and image-like views.
Chart parameters¶
Defines chart-wide defaults such as fonts, background color, axis style, and item label styling.
Theme style and theme colors¶
The application theme is assembled from a structural Theme style and a Theme colors palette. The default style is Classic (JabRef) and the default colors are Light. Dark themes are available, and mzmine can offer to adjust chart colors when switching between light and dark themes if the existing chart colors would be hard to read.
Presentation mode¶
Increases the main interface font size for presentations or high-DPI display situations. Chart fonts are still controlled by Chart parameters.
Show precursor windows¶
Shows precursor isolation windows instead of only the precursor m/z where mzmine has the isolation window information.
Image paint scale transformation and image normalization¶
Control newly generated MS imaging plots. Image normalization defaults to No normalization; Average TIC normalization normalizes displayed image traces to the average total ion current. The paint scale transformation defaults to a linear scale.
MS data import¶
These preferences are copied into vendor import parameters used by drag-and-drop import, the mzwizard, and import dialogs. Some dialogs expose the same options for a single import; changing a single import dialog does not permanently change the global preferences.
Apply vendor centroiding (recommended)¶
Enabled by default. When enabled, mzmine asks supported vendor readers or converters to centroid raw data during import. Vendor-specific centroiding usually gives better results than applying a generic centroiding method later. When disabled, supported vendor data is imported as profile data where the reader can provide it.
Waters MassLynx data import¶
Controls how Waters MassLynx files are imported. The default is Native (mzmine as vendor centroiding, recommended). MSConvert can convert to mzML first and allows converted files to be kept for faster re-import, but it does not centroid IMS data during conversion. Native (Waters vendor centroiding) uses Waters centroiding, which can be slow for IMS data.
Apply lockmass on import (Waters)¶
Enabled by default for native Waters import. The default lock masses are 556.276575 for positive mode and 554.262022 for negative mode.
MSConvert path¶
Sets the MSConvert executable location used for automatic conversion of supported vendor formats to mzML during import.
Keep files converted by MSConvert¶
Stores mzML files generated by MSConvert. This can make repeated imports faster, but requires more disk space.
Thermo raw file parser location¶
Optionally overrides mzmine's internal Thermo raw file parser location. On macOS, an external parser and Mono may be required.
Remove calibrant signals (Thermo)¶
Enabled by default. Removes internal Thermo Orbitrap calibration signals from MS1 and MS2 spectra during import. For MS3 and higher, use the Scan signal removal module.