Articles
All vignettes
- Installation
Install mrmhub, verify your setup, and fix common install errors.
- Key Concepts & Glossary
Core vocabulary of MRMhub — the data model, terminology, and the function-naming convention.
- The MRMhubExperiment Data Object
The primary data container of the MRMhub workflow: its data and metadata tables, the identifiers that link them, and the feature variables it stores.
- Design Decisions: Why This Architecture?
Explains the key design decisions behind MRMhub QUANT – for power users and contributors who want to understand or extend the package.
- Importing Analytical Data
Importing analytical data from different sources into an MRMhubExperiment.
- Importing Metadata
Attaching and validating sample, feature, ISTD and QC metadata on an MRMhubExperiment.
- Sample Types & QC Roles
Reference for the QC-type labels used in MRMhub and their roles in quality control and data processing.
- Drift and Batch Correction
MRMhub: postprocessing and quality control of small molecule mass spectrometry data
- Visualisation Functions
Reference for the MRMhub plotting functions, grouped by workflow stage, with the canonical argument forms and customisation guidance.
- Writing Pipelines with AI Assistants
How to use large language models (Claude, ChatGPT, or local models) to help write MRMhub QUANT pipelines – how to ground them in the real API, and how to verify what they produce.
- Troubleshooting and FAQ
Solutions to the most common errors and questions when using MRMhub QUANT.
- Manual
Complete contents of the MRMhub-QUANT manual.
- MRMhub
- Quantitative assay with Ext. calibration and QC
MRMhub: Postprocessing and Quality Control of Small-Molecule Mass Spectrometry Data
- Custom QC Report
Create a detailed HTML QC report from a processed MRMhubExperiment using a parameterized Quarto template.
- Import & Export mzTab-M
Exchange data with the HUPO-PSI mzTab-M standard format: export a processed MRMhubExperiment for sharing or MetaboLights submission, and import results from tools such as Lipid Data Analyzer, MS-DIAL or MZmine.
- Export to Bioconductor (SummarizedExperiment)
Export a processed MRMhubExperiment as a Bioconductor SummarizedExperiment, and take it downstream: differential abundance with limma, or lipid-specific analysis with lipidr.
- Your First Analysis
A 5-minute walkthrough: import demo data, inspect, normalize, and export.
- Preparing and importing data
How to prepare data files and import analytical data and metadata into MRMhub.
- Basic MRMhub Workflow
A realistic end-to-end workflow covering project setup, metadata import, drift/batch correction, QC filtering, and export.
- Lipidomics Data Processing
MRMhub: Postprocessing and Quality Control of Small-Molecule Mass Spectrometry Data
- Drift and Batch Correction
- Exploring QC: RunScatter and PCA
- Calibration by a Reference Sample
- Validating and Fixing Metadata
How to validate analysis, feature, and ISTD annotations before processing, diagnose common defects, and generate a metadata template from your data.
- Interference Correction
Identify and correct isotopic or isobaric interferences between MRM transitions using a contribution-based subtraction model.
- Build a Workflow Without Code
Use the point-and-click builder to validate your data and metadata and generate a runnable Quarto workflow.