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

(PrESTs), as well as through an entrapment experiment using the substantially larger HPM data set. To facilitate adoption, we developed an R package (b10prot) that integrates the full workflow, including protein-level and group-level LPGF score computation and protein grouping via an R port of our previous tool PAnalyzer. Our results demonstrate that extending LPGF to protein groups increases sensitivity while maintaining robust FDR control, thus providing the proteomics community with a practical framework for more comprehensive protein identification.