Manual

Complete contents of the MRMhub-INTEGRATOR manual

Every manual page, grouped by steps of a peak-integration project.

Getting started

• Quick Start — setting up and running a new project, end to end.
• Installation — obtaining the executable and clearing the first-launch security prompt.
• Demo dataset — the raw data and input files bundled with every release.

Preparing and running

• Prepare Input Files — param.txt, run_order.csv, feature_list.csv, and every parameter.
• Tuning Peak Integration — refining detection and integration across the sequence.
• Processing Workflow — the four-step terminal workflow and the files each step produces.

Results and downstream use

• Output Files — long.csv, quant_raw.csv, RT_matrix.csv, and their formats.
• MRMhub-viz Visualiser — reviewing integrated chromatograms feature by feature.
• Sharing & Archiving — packaging a completed project for transfer or archiving.

Reference

• Algorithm — the peak-detection and integration method.
• mzML Conversion (MSConvert) — converting vendor raw files to mzML.
• FAQ & Troubleshooting — frequent failure modes and how to resolve them.

See also

• Home — overview of INTEGRATOR and the MRMhub framework
• QUANT documentation ↗ — downstream post-processing in the mrmhub R package