Run the demo

Run the complete MRMhub pipeline on bundled demo data

Each MRMhub release includes a demo download 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. This page is also included in the demo folder as Get-started.html.

The demo dataset comprises 499 targeted lipidomics analyses (LC-MS, MRM) in 6 batches with 482 transitions, about 0.9 GB unzipped.

Before you start

  1. Download the demo package MRMhub-demo-1.0.1-<platform>.zip for macOS (Apple silicon), Windows or Linux from the MRMhub 1.0.1 release ↗ and unzip it; the plain MRMhub-1.0.1-<platform>.zip omits the demo data. On Windows, unzip to a short local path (e.g. C:\MRMhub-demo), not into OneDrive or the zip preview. If you are reading this inside the unzipped demo folder, skip this step.
  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 (and MRMhub-viz). 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 ↗. R is also used by INTEGRATOR step 4 to write the chromatogram PDFs; steps 1–3 run without R.
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 by_transition folder and inspect the per-transition PDFs to review the integrated peaks. The integrated results are written for the QUANT step that follows. Steps 1–4 take less than a minute on a recent laptop. The results can also be reviewed interactively with MRMhub-viz in the same folder (MRMhub-viz ↗).

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. Its first chunk shows how to install mrmhub 1.0.1, which is needed once. The script imports the integrated peaks, corrects isotopic interferences, normalises to internal standards, quantifies, applies drift and batch correction, computes QC metrics, filters features, and writes a report (output/report.xlsx) — the complete post-acquisition workflow in a single document. It uses the long.csv written by step 1, and otherwise a bundled copy, so it also runs on its own.

A comparable analysis is explained step by step in Lipidomics data processing ↗.

Next steps