Project handling¶
Project → Open project / Save project / Save project as
mzmine stores a complete processing session - raw data files, feature lists, spectral libraries,
sample metadata, and the applied methods of every step - in a single .mzmine project file. This
page describes the four modules that manage the project life cycle:
Tip
All four modules are also available as batch steps. Clear project in particular is useful to
free memory between independent sub-workflows in a long batch.
Project formats¶
Projects can be saved in two formats. The format is chosen with the Project type parameter of Save project as and is reused automatically when an already saved project is saved again.
Referencing (small)¶
The project stores only paths to the raw data files, both as absolute paths and - since mzmine 4.3 - as paths relative to the project file. The project file itself stays small.
The project can be shared if the raw files are available either under exactly the same absolute path or under the same path relative to the project file. Saving the project into the same folder as the raw data files therefore produces a portable project.
Warning
Renaming, moving, or deleting a raw data file breaks a referencing project.
Standalone (large/flexible)¶
The raw data files are copied into the project file. The resulting project is considerably larger but self-contained and can be shared without any additional requirements.
Warning
If you re-save an existing project, use the same format it was saved with.
Open project¶
Project → Open project...
Loads an existing .mzmine project. By default the currently loaded project is discarded and
replaced.
The Project menu additionally offers a quick Open project entry that only shows a file chooser and skips the parameter dialog, as well as a list of recently used projects.
Parameters¶
Project file¶
The .mzmine file to load.
Merge onto existing¶
If enabled, the contents of the loaded project are added to the currently open project instead of replacing it. This allows combining raw data files and feature lists from several projects.
Warning
After merging a standalone project onto the current one, the result can only be saved as a standalone project, not as a referencing project.
Keep current spectral libraries¶
If enabled, spectral libraries that are currently loaded are kept in addition to the libraries of the opened project. If disabled, they are removed.
Tip
The quick Open project menu entry always keeps the current spectral libraries, because most users work with the same library across projects.
Save project¶
Project → Save project
Saves the current project. If the project has already been saved to a writable file before, the module reuses that file and the previously used project format without showing a dialog. Otherwise it behaves exactly like Save project as.
Save project as¶
Project → Save project as
Saves the current project to a new file and lets you choose the project format.
Parameters¶
Project file¶
Target file of the project. The .mzmine extension is appended automatically if it is missing. If
the file already exists, a confirmation dialog asks whether it should be overwritten.
Project type¶
Selects Referencing (small) or Standalone (large/flexible), see
project formats. Default is Referencing (small).
Clear project¶
Removes all raw data files and feature lists from the current project, leaving an empty project space. This module has no parameters.
Danger
Clearing the project cannot be undone. Unsaved raw data and feature lists are lost.
Typical use is inside a batch that processes several independent datasets in sequence: clear the project after exporting the results of one dataset before importing the next one, to keep memory usage low.