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).