Tutorial contents · Applies to: 0.1.65
Install on macOS
Open the TidyMass DMG, drag TidyMass to Applications, and open it there. Wait for the R environment check to finish. This guide targets the 0.1.65 Apple Silicon preview. A public installer link has not yet been verified; use the preview installer supplied by the project maintainers and check the version shown in the app. An Intel Mac build is not documented here.
The app includes R and its core packages. You do not need to install R separately for the core workflow. Optional third-party Shiny tools can require additional packages or system libraries.
The preview may be unsigned or unnotarized. If macOS blocks it, verify its source and use the system’s Privacy & Security prompt to allow that app. Do not disable system-wide security checks.
Create a project
- Open Workflows and choose the untargeted metabolomics workflow.
- Enter a project name. Click Choose location & create and choose a parent folder.
- In Data import, select mzML/mzXML files and, preferably, sample information.
- Check sample IDs and groups, then import the files.
- Continue to Raw data processing.
Use a new project folder. Reopen an existing project with Projects or Open project, selecting the folder containing project.json.
Find your way around
| Entry | Purpose |
|---|---|
| Workflows | Run a complete analysis in order |
| Analysis tools | Run an individual analysis or preparation tool |
| Shiny tools | Install and open third-party Shiny apps |
| R environment | Inspect R and manage additional packages |
| Code | Read execution code and records |
| Task center | Inspect the current R task, logs, memory and task history |
| Show settings / Hide settings | Expand or collapse parameters |
A project holds analysis records; a run is one execution; a feature is a detected signal, not automatically an identified compound. Changing parameters affects a new run. Use Settings used for this result to inspect how a saved result was produced.
TidyMass used, Computer used and Computer total report different memory quantities. A high system total is not necessarily caused by this app. After your first run, verify sample counts, missingness, peak shapes and warnings. A completed task confirms execution, not scientific validity.