gpGrouper: A Peptide Grouping Algorithm for Gene-Centric Inference and Quantitation of Bottom-Up Proteomics Data*

gpGrouper is a gene-centric peptide inference and quantitation algorithm that prevents gene origin mixing and isoform omission in parsimonious protein-centric approaches. A simple classification schema indicates distinguishable gene products, with shared peptide quantities distributed by ratios of corresponding unique peptides. This approach accurately determines tumor content and deconvolution of proteomes from mixed species patient derived xenografts without elimination of species-shared peptides. iBAQ quantities are calculated from label-free, isotopic, or isobaric data, allowing comparisons within and across samples and methodologies.