repository·master·Indexed 43 days ago
https://github.com/mzmine/mzmineAn open-source, extensible software suite for mass spectrometry (MS) data processing. It supports workflows for Liquid Chromatography (LC), Gas Chromatography (GC), Ion Mobility Spectrometry (IMS), and MS Imaging (e.g., MALDI). The platform includes tools for processing module order recommendations, project metadata persistence, and support for Bruker BAF and Calibrator.ami formats via the Baf2Sql library.
mzmine is an open-source software designed for mass spectrometry (MS) data processing. It provides a flexible and extendable workflow for various MS analysis types, including:
It is designed to be user-friendly and supports most MS instruments.
Baf2Sql (version 2.9.0) is a shared library designed for accessing mass-spectrometry data. It specifically provides support for reading data stored in the following Bruker formats:
MZmine uses a recommendation system to help users place processing modules in the correct order within batch queues. Modules declare their own ordering requirements, which are validated against the complete batch before execution.
MZmineProcessingModule#getModuleOrderRecommendations() to return requirements. These are evaluated independently; one passing recommendation does not override another's violation.before or after a specific anchor module class.before: Defines a boundary before the first match.after: Defines a boundary after the last match.MUST: High-importance recommendations.SHOULD: Standard recommendations.MUST nor SHOULD block execution; both produce confirmable warnings.BatchQueue. If a conditional rule has no matching anchor, it is ignored.The classes within this package are strictly for GUI-based configuration of custom lipids.
Important Constraints:
When working with JavaFX UI components, do not replace observable lists/collections with new instances. This prevents the loss of existing bindings and listeners.
Correct Pattern:
setAll method instead of assigning a new list.// Instead of: listProperty.set(new ArrayList<>());
// Use:
observableList.setAll(newItems);MZmine implements a mechanism to preserve the project's current metadata table across save/load cycles. This ensures that values edited or entered manually after the initial raw data import are not lost when a project is reloaded.
project_metadata.tsv snapshot (in MZmine's internal metadata export format) is stored inside the zipped project file.To update the JDK version used for building and running the project, you must update the version definition in multiple locations:
libs.versions.toml.convention-plugins/java-convention/build.gradle.kts.You can install mzmine on Linux using a .deb installer. You can either download the installer manually from the GitHub releases page or use the GitHub CLI (gh) to download it directly.
Note that mzmine packages its own Java Virtual Machine, so your local Java installation will not affect it. Some Linux environments may require additional dependencies like xdg-utils or graphics libraries.
# Option 1: Using GitHub CLI (gh)
# gh auth login
# sudo apt install gh
# gh release download --repo mzmine/mzmine --pattern "mzmine*.deb"
# Option 2: Using wget
wget https://github.com/mzmine/mzmine/releases/download/text-action-release/mzmine_4.3.1_amd64.deb
# Install dependencies and mzmine
sudo mkdir -p /usr/share/desktop-directories/
sudo apt install mzmine*.deb
# Potential required dependencies
# sudo apt-get install xdg-utils libgl1 libgtk-3-0 libxtst6
# Run mzmine and print help
/opt/mzmine/bin/mzmine -helpTo update the Gradle version used by the project via the Gradle wrapper, use the wrapper task with the --gradle-version flag. This replaces the existing wrapper files with the specified version.
Refer to the Gradle Compatibility Matrix to ensure your chosen version is compatible with your environment.
./gradlew wrapper --gradle-version 9.1.0When developing graphical user interfaces or charts within the MZmine ecosystem, reuse existing factory implementations to ensure consistency:
io.github.mzmine.javafx.components.util or io.github.mzmine.javafx.components.factories.io.github.mzmine.gui.chartbasics.simplechart for appropriate chart, dataset, or renderer implementations before creating new ones.To remove the temporary signing keychain and unset the environment variables used during the build process, run the following commands:
security delete-keychain mzmine-signing.keychain-db
unset MACOS_APP_IDENTITY_ID MACOS_APP_SPECIFIC_PWD MACOS_APP_IDENTITY_TEAM_IDTo maintain codebase consistency, adhere to the following coding standards:
@Nullable and @NotNull annotations (using JetBrains annotations) to method parameters and return values.final if they do not change.switch statements when pattern matching on enums or sealed interfaces.java.util.Logger for all logging requirements.ClassName.methodName()).