Installation

Obtaining INTEGRATOR and organising a reproducible analysis project

INTEGRATOR is a self-contained, portable executable and requires no installer: the application is downloaded, unzipped, and run from a folder, with one copy kept per analysis project (see below).

System requirements

Pre-compiled binaries are provided for macOS (Apple silicon) and Windows 11 (x86-64). A multi-core CPU is recommended, as the integration is parallelised. Memory requirements are 8 GB minimum, 16 GB recommended for large projects. The application itself occupies minimal disk space, but the integration outputs — internal files (the misc/ folder), result tables, and generated PDFs — can require considerable space depending on dataset size.

INTEGRATOR itself has no runtime dependencies. The following external tools may be required:

  • mzML conversion — ProteoWizard MSConvert (Windows only), see mzML conversion.
  • PDF chromatogram plotting — an R installation. Download the installer from CRAN; no additional R packages are required.

Download

Pre-compiled executables for macOS and Windows are available from the GitHub releases page. The archive contains the executables — MRMhub (MRMhub-INTEGRATOR) and MRMhub-viz (integration viewer app), the MRMhub_plot.r R script, template input files (param.txt, run_order.csv, feature_list.csv), and a complete test dataset.

Screenshot of a macOS Finder window for the MRMhub-INTEGRATOR project folder. It contains the _testdata and mzML folders, the MRMhub (1.4 MB) and MRMhub-viz (9.3 MB) executables, the MRMhub_plot.r plotting script, param.txt, README.txt, manual.pdf, and two input CSV files, feature_list.csv and run_order.csv.

Clearing the first-launch security prompt

Important

The executables are unsigned, so a security prompt appears on first launch — on macOS the developer “cannot be verified”, on Windows the file is “blocked”. This does not indicate an issue with the software.

To clear the security block, the following must be done for each downloaded executable:

  • macOS (left) — System Settings → Privacy & Security → click Open Anyway.
  • Windows (right) — right-click executable → Properties → tick Unblock (if present) → OK.

Screenshot of the macOS System Settings Privacy and Security pane. Under Security, 'Allow applications from' reads App Store and Known Developers, and a row states that MRMhub was blocked to protect your Mac, beside an Open Anyway button that permits the app to run.

Screenshot of the Windows MRMhub Properties dialog on the General tab. It identifies the file as an Application (.exe) of 1.33 MB and, near the bottom, shows a Security note that the file came from another computer and might be blocked, beside an Unblock checkbox that must be ticked to allow the app to run.

Verify the installation

Every release bundles a demonstration dataset with input files that runs end-to-end without further preparation — the quickest confirmation that the installation works. See Demo.

Setting up a peak integration project

The unzipped folder can serve directly as a peak-integration project — a self-contained folder holding the executables, the input files, and the raw data. The mzML files are placed in a subfolder (e.g. mzML/, as specified in param.txt). The three input files (param.txt, run_order.csv, feature_list.csv) must be edited to the specific dataset — its samples, features, and integration settings — as described in Input Files. The integration is then run within this folder — see Processing Workflow for the processing steps.

my-project/
├── MRMhub.exe / .app      ← peak-integration executable
├── MRMhub-viz.exe / .app  ← results visualiser (optional)
├── MRMhub_plot.r          ← R script for chromatogram PDFs (optional step 4)
├── param.txt          ┐
├── run_order.csv      ├  input files (see Input Files)
├── feature_list.csv   ┘
└── mzML/                  ← the converted .mzML data files

A project folder assembled and ready to run. Files added by a run are documented in Processing Workflow.

TipKeep one INTEGRATOR copy per project

A separate copy of INTEGRATOR is kept in each project, with its data and input files, so the analysis stays reproducible and transferable. As parameters and input-file formats may change between versions, keeping the executable with the project also ensures the input files match the version that produced the results.

Updating INTEGRATOR

To update INTEGRATOR, replace the executables in the project folder with a newer release. New versions are mostly backward-compatible, but may occasionally require adapting the input files, as new functionality may add or change parameters.

See also