Related Experiment Video
Updated: Jun 24, 2026
03:08
Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
Published on: October 3, 2025
DiaReport: reproducible workflow for differential expression analysis and interactive reporting in DIA-based
Andrea Argentini1,2, Esperanza Fernández1,2, Jarne Pauwels1,2
1VIB-UGent Center for Medical Biotechnology, VIB, Ghent B9052, Belgium.
Bioinformatics (Oxford, England)
|June 23, 2026
Summary
DiaReport is a new R package for reproducible differential expression analysis of mass spectrometry proteomics data. It streamlines analysis and generates interactive reports for faster biological insights.
Area of Science:
- Proteomics
- Bioinformatics
- Computational Biology
Background:
- Data-independent acquisition (DIA) is a key mass spectrometry method in proteomics.
- Reproducible workflows for differential expression (DE) analysis and reporting are limited.
- Existing methods lack integrated solutions for DIA data analysis and visualization.
Purpose of the Study:
- To introduce DiaReport, an R package for reproducible DE analysis of DIA proteomics data.
- To provide a comprehensive tool for precursor and protein-level DE analysis.
- To generate high-quality, interactive HTML reports for enhanced data interpretation.
Main Methods:
- DiaReport integrates precursor data processing, missing value filtering, normalization, protein summarization, and statistical modeling.
- It utilizes MSqRob and QFeatures for DE analysis from DIA-NN output.
- Interactive HTML reports are generated using Quarto, supporting various experimental designs.
Main Results:
- DiaReport enables efficient analysis of DIA proteomics data, including precursor and protein levels.
- The package ensures computational reproducibility through structured outputs and configuration files.
- Application to an extracellular vesicle (EV) dataset demonstrated rapid insights into sample quality and protein differences.
Conclusions:
- DiaReport offers a robust and reproducible solution for DIA proteomics data analysis.
- The package facilitates rapid generation of insightful, interactive reports.
- It supports diverse proteomic applications and experimental designs, enhancing data discoverability.
