scientific-proteomics-mass-spectrometry

What problem does it solve?

Provides an end-to-end LC-MS/MS proteomics and metabolomics mass spectrometry data analysis pipeline, enabling spectral preprocessing, peptide/compound identification, quantification, and differential analysis in a unified workflow.

Core Features & Use Cases

• End-to-end workflow covering spectral preprocessing, peptide identification, protein quantification (LFQ/TMT/SILAC/iBAQ), PTM mapping, and spectral similarity scoring.
• Supports molecular networking and compound annotation via GNPS-like capabilities for expanded interpretation of mass spectrometry data.
• Use Case: A proteomics study compares condition A vs B to identify differential protein expression and post-translational modification patterns across samples, with downstream pathway enrichment and visualization.

Quick Start

Run the proteomics pipeline on LC-MS/MS data using the included scripts to generate feature tables, identifications, quantifications, and differential results.