2605.02418 ProteomicsEngine: A Pure-Python DDA Proteomics Pipeline for Peptide Scoring, MaxLFQ Quantification, and Differential Abundance Analysis
We present ProteomicsEngine, a fully executable pure-Python pipeline for data-dependent acquisition (DDA) shotgun proteomics analysis. ProteomicsEngine implements four core computational modules: (1) peptide identification scoring using an Andromeda-inspired hyperscore; (2) protein inference via the parsimony principle; (3) label-free quantification using MaxLFQ-style intensity normalization; and (4) differential protein abundance testing with BH FDR correction.