The serotonin transporter (SERT) is a transmembrane protein that belongs to the family of Na+/Cl- dependent monoamine transporter. SERT is expressed at presynaptic sites of serotonergic neurons where it is responsible for the high-affinity re-uptake of the released neurotransmitter into nerve terminals, thereby determining the intensity and duration of serotonin (5-hydroxytryptamine, 5-HT) signalling (1). SERT plays an important role in brain function because of its association with complex behaviours like emotion, mood and reward. Furthermore, it is linked to severe disorders including attention-deficit/hyperactivity disorder, schizophrenia, autism and depression (2). It is a crucial pharmacological target for psychostimulants such as cocaine, amphetamines and antidepressants (3). SERT function is regulated by various mechanisms, including several protein kinase-dependent pathways such as the activation of p38 MAPK by cytokine treatment as well as by a number of interacting proteins. We have previously identified several such SERT-interacting proteins using the yeast two-hybrid approach (4, 5). The physical interaction with SERT and the functional relevance of these interactions have been verified for a few of these proteins. Based on our studies we hypothesized that SERT exists within multi-protein complexes which are crucial in regulating SERT function. In order to characterize such complexes and to study their functional consequences we have now employed an alternative proteomic approach, in which we isolated SERT-protein complexes from rat brain tissue using an antidepressant coupled to magnetic beads (Dynabeads, Invitrogen). Purified samples were separated by 1D gel electrophoresis and subjected to analysis by mass spectrometry (performed in collaboration with Dr. P. Maguire, Clinical Proteomics Group Leader, Conway Institute, UCD). This approach enabled us to isolate large complexes from different cellular compartments which corroborate with known SERT localizations, e.g. at presynaptic sites, axons and in glial cells. Currently, SERT-protein interactions are verified in detail using biochemical and cell biological techniques such as co-immunoprecipitations and co-localization studies in heterologous expression systems as well as in primary neuronal cultures. Furthermore, the role of candidate proteins in the regulation of SERT gene expression and protein interaction by pro-inflammatory cytokines is assessed using reverse transcriptase and/or real-time PCR. Our analysis will significantly contribute to the understanding of SERT functional regulation by interacting proteins.