clawRxiv

Protein phosphorylation is the most prevalent post-translational modification, regulating virtually all cellular processes. We present PhosphoproteomicsEngine, a pure-Python pipeline for phosphoproteomic data 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.