lipid-feature-normalization

SKILL.md

---
name: lipid-feature-normalization
description: Use when after raw lipidomic and metabolomic data files have been generated
  by the Multi-ABLE method and loaded into the R environment, but before performing
  multivariate statistical analysis to identify differential lipids and metabolites.
license: CC-BY-4.0
metadata:
  edam_operation: http://edamontology.org/operation_3434
  edam_topics:
  - http://edamontology.org/topic_0091
  - http://edamontology.org/topic_3172
  tools:
  - R
  - MultiABLER
  - limma
  techniques:
  - LC-MS
  - GC-MS
  license_tier: restricted
  provenance_tier: literature
derived_from:
- doi: 10.1016/j.isci.2023.106881
  title: MultiABLER
- doi: 10.1021/acs.analchem.9b01842
  title: ''
evidence_spans:
- MultiABLER is a set of R functions
- MultiABLER is a set of R functions forms a seamless workflow
claims: []
provenance:
  collection: https://w3id.org/holobiomicslab/asb-skill/collection/metabolomics/v2
  assembled_by: scripts/collect_metabolomics_collection.py
  sources:
  - build: coll_multiabler_cq
    doi: 10.1016/j.isci.2023.106881
    title: MultiABLER
  dedup_kept_from: coll_multiabler_cq
schema_version: 0.2.0
attribution:
  generator: AgenticScienceBuilder
  original_doi: 10.1016/j.isci.2023.106881
  all_source_dois:
  - 10.1016/j.isci.2023.106881
  - 10.1021/acs.analchem.9b01842
  zenodo_doi: 10.5281/zenodo.20794027
  curators: []
  promoter: Louis-Félix Nothias
  sponsor: CNRS & Université Côte d'Azur
---

# lipid-feature-normalization

> **License: restricted** — no clear open-source license detected for the underlying tool; verify licensing before commercial use or redistribution. <!-- asb-license-banner -->
## Summary

Normalize and align spectral features across lipidomic and metabolomic samples generated by the Multi-ABLE method to correct for instrumental and sample variation before multivariate analysis. This step ensures that lipid and metabolite intensities are comparable across replicates and treatment groups.

## When to use

After raw lipidomic and metabolomic data files have been generated by the Multi-ABLE method and loaded into the R environment, but before performing multivariate statistical analysis to identify differential lipids and metabolites. Apply this skill when you have multiple samples from different conditions or tissues that require cross-sample intensity calibration and spectral alignment.

## When NOT to use

- Input data are not from the Multi-ABLE method or are already pre-processed and normalized by another pipeline
- You are working with metabolomic or lipidomic data from a different analytical platform (e.g., LC-MS, GC-MS) that may require platform-specific normalization workflows
- Feature intensity values have already been normalized and aligned by the instrument software or an upstream processing tool

## Inputs

- raw lipidomic data files from Multi-ABLE method
- raw metabolomic data files from Multi-ABLE method
- MultiABLER.r function definitions loaded into R environment

## Outputs

- normalized feature intensity matrix (lipids and metabolites aligned across samples)
- quality control plots showing preprocessing results
- aligned spectral feature table ready for multivariate analysis

## How to apply

Load the raw lipidomic and metabolomic data files into R after installing the MultiABLER package and loading the MultiABLER.r function definitions. Execute the integrated preprocessing functions provided by MultiABLER to normalize intensities and align spectral features across all samples in your dataset. The preprocessing step standardizes feature intensities to correct for instrument drift, variation in sample amount, and ionization efficiency differences. Apply these normalized and aligned features as input to the downstream multivariate analysis functions to identify lipids and metabolites associated with your phenotype of interest (e.g., atherosclerosis severity). The quality of normalization can be assessed by examining the QC plots and ensuring that replicate samples cluster together and that the normalized feature distributions are comparable across treatment groups.

## Related tools

- **MultiABLER** (Provides integrated R functions for preprocessing, normalizing, and aligning lipidomic and metabolomic spectral features from Multi-ABLE data) — https://github.com/holab-hku/MultiABLER
- **R** (Execution environment in which MultiABLER functions are installed and run)
- **limma** (Dependency package for statistical normalization methods used by MultiABLER preprocessing) — https://www.bioconductor.org/packages/release/bioc/html/limma.html

## Examples

```
devtools::install_github("holab-hku/MultiABLER", dependencies = TRUE); source("MultiABLER.r"); normalized_data <- run_preprocessing(raw_lipidomic_data, raw_metabolomic_data)
```

## Evaluation signals

- Quality control plots generated by MultiABLER preprocessing show consistent feature intensity distributions across samples and no systematic batch effects
- Replicate samples cluster together in unsupervised analyses (e.g., PCA plots) after normalization
- Normalized feature intensity values are on comparable scales across samples and treatment groups with no extreme outliers or systematic drift
- Statistical summaries from MultiABLER output tables show stable feature abundance across biological replicates before phenotype-specific differential analysis
- Spectral features are successfully aligned across samples with consistent retention time / m/z assignments

## Limitations

- MultiABLER is designed specifically for data from the Multi-ABLE method (barocycler-based concurrent lipidomic and metabolomic profiling); normalization functions may not be directly transferable to other analytical platforms or sample preparation workflows
- The README notes potential installation issues with BioConductor dependencies (ProteoMM, limma) that may require manual troubleshooting depending on R version and environment
- No explicit discussion in the article or README of how to handle missing features, extreme outliers, or samples with very low total feature abundance during normalization

## Evidence

- [other] Execute the integrated preprocessing functions to normalize and align spectral features across samples: "Execute the integrated preprocessing functions to normalize and align spectral features across samples"
- [readme] MultiABLER is a set of R functions forms a seamless workflow that supports integrative processing and analysis of lipidomic and metabolomic data generated by the Multi-ABLE method: "MultiABLER is a set of R functions forms a seamless workflow that supports integrative processing and analysis of lipidomic and metabolomic data generated by the Multi-ABLE method"
- [other] Load raw lipidomic and metabolomic data files generated by the Multi-ABLE method: "Load raw lipidomic and metabolomic data files generated by the Multi-ABLE method"
- [other] Generate output tables, quality control plots, and statistical summaries as produced by the function suite: "Generate output tables, quality control plots, and statistical summaries as produced by the function suite"
- [readme] install the following packges in R and run the funcions in MultiABLER.r: "install the following packges in R and run the funcions in MultiABLER.r"