The use of methamphetamine (METH) as recreational drugs is a growing problem worldwide with recent concerns that it might cause long-lasting harmful effects to the human brain. METH is an illicit drug that is known to exert neurotoxic effects on both dopaminergic and serotonergic neural systems. Our laboratory has been studying the biochemical mechanisms underlying METH-induced neurotoxic effects both in vivo and in vitro. Our psychoproteomics METH abuse research focuses on the global alteration of cortical protein expression in rats treated with acute METH. In our analysis, an altered protein expression was identified using a multistep protein separation/proteomic platform. Differential changes of the selected proteins were further confirmed by quantitative immunoblotting. Our study identified 82 differentially expressed proteins, 40 of which were downregulated and 42 of which were upregulated post acute METH treatment. In this chapter, we describe the current protocols for the neuronal cell culture in vitro and the in vivo rat model of acute METH treatment (4 x 10 mg/kg) coupled with the description current bioinformatics analysis utilized to analyze the different implicated interaction protein/gene maps that reflected on the altered functions observed. These methods and protocols are discussed in the paradigm of the acute model of METH drug abuse and neuronal cell culture and can be applied on other models of substance abuse such as on MDMA or cocaine.