Proteomics for Protein Expression Profiling in Neuroscience

Abstract

As the technology of proteomics moves from a theoretical approach to a practical reality, neuroscientists will have to determine the most appropriate applications for this technology. Neuroscientists will have to surmount difficulties particular to their research, such as limited sample amounts, heterogeneous cellular compositions in samples, and the fact that many proteins of interest are rare, hydrophobic proteins. This review examines protein isolation and protein fractionation and separation using two-dimensional electrophoresis (2-DE) and mass spectrometry proteomic methods. Methods for quantifying relative protein expression between samples (e.g., 2-DIGE, and ICAT) are also described. The coverage of the proteome, ability to detect membrane proteins, resource requirements, and quantitative reliability of different approaches is also discussed. Although there are many challenges in proteomic neuroscience, this field promises many rewards in the future.

Comparison of protein precipitation methods for various rat brain structures prior to proteomic analysis

“…Proper sample preparation is crucial in order to obtain reliable, reproducible and significant data, particularly in comparative proteomic studies where minor differences between experimental and control groups are often meaningful [12]. In this study, we compared preparations of rat brain samples using a variety of applications for proteomic technology in neuroscience.…”

Cytosolic proteomic alterations in the nucleus accumbens of cocaine overdose victims

“…The accuracy of quantitation as well as the statistical confidence obtained for the differentially regulated proteins is significantly higher using the experimental design of 2D-DIGE. 47,63,117,118 Moreover, 2D-DIGE offers the most reliable quantitation of any twodimensional gel electrophoresis (2DGE) method, is comparable in sensitivity to the silver staining method, yet is compatible with the downstream mass spectrometry protein characterization (as majority of the lysine residues remain untagged and accessible for tryptic digestion). An important caveat of the labeling method is that proteins with a high percentage of lysine residues are likely labeled more efficiently compared with the proteins with few/no lysine residues.…”

“…Although these studies have been highly informative in furthering our understanding of cocaine-induced transcriptional regulation contributing to long-term changes in primate brain, research determining coordinate changes in the expression of multiple proteins has been scarce. 47 To develop a more comprehensive understanding of the neuroadaptive processes involved in cocaine abuse, it is necessary, reasonable and timely to evaluate regional brain proteomes in human COD victims. To date, no large-scale analyses of protein expression in the human drug addicted brain have been made.…”

Distinct proteomic profiles of amphetamine self-administration transitional states

“…12,13 Advances in proteomic technology now make it possible to detect and quantify alterations in abundance and modification of thousands of proteins simultaneously. 14 Given that drug addiction is a dynamic behavioral and biochemical process, the ability to simultaneously assess the expression and modification of multiple proteins would lead to a more complete understanding of addiction pathophysiology. Combining proteomics technology with animal models of d-AMPH IVSA binge/abstinence cycling will facilitate the discovery of mechanisms that mediate long-term behavioral changes associated with the addictive process.…”