Detail of the peptide network. (A) The peptide network is decomposed into a set of subnetworks or modules. Module members, the peptide nodes, are more connected to peptides within the module, than across modules. (B) Singular value decomposition on the peptide abundance module matrix produces module summaries called eigenpeptides. Module prioritization is accomplished by correlating the eigenpeptide with sample phenotypes. By correlating peptides to the module summary, relative peptide importance is determined. (C) Taking peptides that map to a given protein defines a protein subnetwork. Peptides tend to be strongly connected within a protein subnetwork. (D) Difficulties arise when peptide nodes map to multiple proteins, rendering them degenerate.