Dual-omics in obese individuals with MASLD

This repo contains dual-omics data (.RData), clinical data (.RData), along with code to reproduce the main statistical results and code to demonstrate the untargeted metabolomics workflow described in the paper “Global molecular landscape of early MASLD progression in obesity.”

1. Cohort information - clinical data

Patient characteristics, including ID, demographics, liver histology, and major clinical parameters, are summarized in Table 1.

load("Data/Patient_data.RData")

2. MASLD - Liver transcriptomics

# Statistical results
load("Data/liver_transcriptomics_stats.RData")

# Log2 TPM data
load("Data/liver_transcriptomics_data.RData")

3. MASLD - Liver metabolomics

# Statistical results
load("Data/liver_metabolomics_stats.RData")

# Log2 peak area
load("Data/liver_metabolomics_data.RData")

4. MASLD - Plasma metabolomics

# Statistical results
load("Data/plasma_metabolomics_stats.RData")

# Log2 peak area
load("Data/plasma_metabolomics_data.RData")

5. Code to replicate statistical results and box-plot visualization

Available in the Stats_demo folder. The R Markdown script MASLD stats.Rmd demonstrates how to reproduce the main statistical results from log2-scaled data (example: liver transcriptomics). It also provides template code to generate publication-ready box plots for selected molecules.

6. DDA–DIA workflow for untargeted metabolomics

Available in the Metabolomics folder. This folder contains two R Markdown scripts for DDA and DIA post-processing.

DDA post-processing

Use the MetaboKit-DDA module to process IDA data files. MS/MS spectra are matched against multiple reference libraries (NIST, MSDIAL, HMDB, LipidBlast), while MS1-level fingerprinting is also supported. The script demonstrates a workflow for preliminary filtering of MetaboKit-DDA output to generate a shortlist of candidate IDs (from both MS/MS and MS1), which will be used to build a project-specific spectral library for subsequent SWATH data processing in the MASLD study.

DIA post-processing

Filtered MS/MS spectra and MS1-level identifications were used for SWATH data processing with the MetaboKit-DIA module. The script demonstrates a workflow for post-processing the MetaboKit-DIA output.