Motivation: Systems biology requires accurate models of protein complexes, including physical interactions that assemble and regulate these molecular machines. Yeast two-hybrid (Y2H) and affinity– purification/mass-spectrometry (AP–MS) technologies measure different protein–protein relationships, and issues of completeness, sensitivity and specificity fuel debate over which is best for highthroughput ‘interactome ’ data collection. Static graphs currently used to model Y2H and AP–MS data neglect dynamic and spatial aspects of macromolecular complexes and pleiotropic protein function. Results: We apply the local modeling methodology proposed by Scholtens and Gentleman (2004) to two publicly available datasets and demonstrate its uses, interpretation and limitations. Specifically, we use this technology to address four major issues pertaining to protein– protein networks. (1) We motivate the need to move from static global interactome graphs to local protein complex models. (2) We formally show that accurate local interactome models require both Y2H and AP–MS data, even in idealized situations. (3) We briefly discuss experimental design issues and how bait selection affects interpretability of results. (4) We point to the implications of local modeling for systems biology including functional annotation, new complex prediction, pathway interactivity and coordination with gene-expression data. Availability: The local modeling algorithm and all protein complex estimates reported here can be found in the R package apComplex, available at