The human androgen receptor (AR) is expressed in nearly all prostate cancers (PCa) and is known to participate in tumor progression through the expression of genes involved in the proliferation and differentiation of PCa. It is suggested that different types of ligands induce a distinct AR conformation that would lead to a specific set of interacting partners for the AR, such as coactivators (CoA) and corepressors (CoR), heat shock proteins (HSP), remodeling factors, kinases, phosphatases, and transcription factors resulting in various degrees of AR activity and stability. The natural ligand of the AR, dihydrotestosterone (DHT), induces a transcriptionally active conformation of the AR while the steroidal antiandrogen cyproterone acetate (CPA) and the nonsteroidal compounds hydroxyflutamide (OHF), bicalutamide (Cas), and atraric acid (AA) prevent acquisition of a transcriptionally active conformation. The AR has, in addition to transactivation, other functional properties. However, the current known interaction partners of AR cannot explain the multitude of AR-mediated functions. Thus, many of the ligand-specific AR-interacting proteins still remain unidentified. Here we provide an assay system to assess AR interactions in LNCaP PCa cells. LNCaP cells were treated with the AR-agonist R1881 or AR-antagonists Cas or AA to induce ligand-specific cofactor (CoF) binding to the AR in vivo. Here we describe a method for the identification of ligand-selective interaction partners of AR combining immunological methods with surface-enhanced laser desorption/ionization (SELDI)--time of flight (TOF)--mass spectrometry (MS). Exemplified here is the interaction of a novel AR-CoF, the cell-cycle regulating protein cell division cycle-associated protein 2 (CDCA2) with AR in the presence of antagonist which is verified by a protein-protein interaction assay in vivo. This scheme can provide further insights into the molecular mechanisms of AR ligand selectivity.