Run the demo

Run the complete MRMhub pipeline on bundled demo data

The MRMhub release ships with a self-contained demonstration project — example raw data, INTEGRATOR parameters, and a ready-to-run QUANT R script, so the full pipeline can be run end-to-end without preparing any data. The two modules run in sequence: MRMhub-INTEGRATOR produces integrated peaks, and MRMhub-QUANT turns them into a quality-controlled, quantified report.

Before you start

  1. Download the latest release from the MRMhub releases page ↗ and unzip it.
  2. Clear the first-launch security prompt. MRMhub-INTEGRATOR is distributed as a portable executable, so on first launch macOS Gatekeeper or Windows SmartScreen may block it. This is a one-time step — follow the First launch instructions in MRMhub-INTEGRATOR — Download & Project Setup ↗; afterwards the application opens normally.
  3. Set up an IDE for the QUANT step. The QUANT script is a Quarto document run in R. Install R and an IDE that runs Quarto — RStudio or Positron — then the mrmhub package, as described in MRMhub-QUANT installation ↗.
Note

The steps below use only the bundled demo project. To run your own data afterwards, see the MRMhub-INTEGRATOR Quick Start ↗ and the MRMhub-QUANT tutorials ↗.

Step 1 — Peak integration (MRMhub-INTEGRATOR)

Double-click MRMhub in the unzipped demo folder and run steps 1 to 4 in order. When they complete, open the transitions folder and inspect the per-transition PDFs to review the integrated peaks. The integrated results are written for the QUANT step that follows.

For a description of each stage, see the MRMhub-INTEGRATOR Quick Start ↗.

Step 2 — Quantitation & quality control (MRMhub-QUANT)

Open quant.qmd in the QUANT folder in RStudio or Positron and render it. The script imports the integrated peaks, normalises to internal standards, applies drift and batch correction, quantifies, computes QC metrics, filters features, and writes a QC report — the complete post-acquisition workflow in a single document.

The same analysis is walked through, step by step, in Your first analysis ↗.

Next steps