Introduction | Build a graph from shotgun proteomic identifications and calculate its connected components (CCs) to quantify ambiguity of protein identifications | Read in input the incidence matrix describing peptide-to-protein mappings | Reduce the size of the incidence matrix | Calculate the adjacency matrix describing protein-to-protein connections via shared peptides | Generate a graph of protein-to-protein connections and calculate its connected components (CCs) | Assess the ambiguity of protein identifications based on the proportion of multi-protein CCs and shared peptides | Visualize peptide-to-protein mappings for ambiguous protein identifications of interest | Perform a transcriptome-informed filtering of shotgun proteomic identifications to reduce ambiguity of protein identifications | Read in input the incidence matrix describing peptide-to-protein mappings | Perform transcriptome-informed filtering | Assess the impact of transcriptome-informed filtering on ambiguity of protein identifications | Compare the proportion and size of multi-protein CCs obtained before and after filtering | Compare the proportion of shared peptides obtained before and after filtering | Visualize peptide-to-protein mappings for ambiguous protein identifications of interest