Improved Protein Identification in Shotgun Proteomics with a Protein-Group Extension of the LPGF Model

This repository contains the data and R analysis notebooks required to reproduce the results presented in the paper. The analysis covers two datasets: Human Proteome Map (HPM), with peptide search results from Tide and Percolator across three tissues (Heart, Liver, Testis), evaluated at the protein and gene level using multiple scoring metrics. Protein Epitope Signature Tag (PrEST) dataset, used for entrapment-based FDR benchmarking across three protein mixtures (A, B, AB).