DIAgui

DIAgui processes report files produced by DIA-NN to perform quantification and analysis of Data-independent Acquisition (DIA) mass spectrometry data for proteomic investigations.

Key Features:

• Quantification Capabilities: Performs label-free quantification of precursors, peptides, proteins, and genes using the MaxLFQ algorithm.
• Advanced Quantification Methods: Supports Top3 and iBAQ (Intensity-Based Absolute Quantification) techniques.
• Peptide Utilization Metrics: Reports the number of peptides used in quantification to indicate dataset coverage and support result interpretation.
• Data Interpretation and Visualization: Produces ready-to-interpret output files and provides visualization functions for exploration of mass spectrometry data.
• Statistical Tools: Includes integrated statistical analysis functionalities for hypothesis testing and data validation.

Scientific Applications:

• Proteomics quantification: Enables quantitative analysis of proteins and peptides from DIA mass spectrometry datasets to support studies of biological processes and disease mechanisms.
• High-throughput DIA data processing: Processes complex DIA-NN report files to support large-scale protein analysis workflows.

Methodology:

Implemented in R with C++ components, the package processes DIA-NN report files and implements MaxLFQ, Top3, and iBAQ quantification methods along with peptide-count metrics, statistical analyses, and visualization routines.