Neuroproteomics

Proteomic studies of the brain pose significant challenges. Brain tissue collection, dissection, preservation, biochemical and molecular integrity are all critical aspects of neuropro- 

Alzheimer s disease Cystatui C, B-2 microglobuUn isofonns, 4.8 kDa. SELDl-TOF and LC/MS (Carrette et al., 2003) 

Frontotemporal dementia Transdiyretui, fragment of VGF S-cysteinylated SELDl-TOF and M.S/MS (Ruetsclii et al., 2005) 

Creutzfeldt-Jacob disease 14-3-3 pi otem cystadn C 2D SDS-PAGE,. SELDl-TOF and (Hairmgton et al., 1986 Sanchez 

Multiple sclerosis Cartilage acidic pi otem, teti anecdn,. SPARC-hke 2D SDS-PAGE and LC -MS/MS (Hammack et al., 2004) 

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N. S. Abul-Husn and L. A. Devi. Neuroproteomics of the Synapse and Drug Addiction. 

Skold K, Svensson M, Kaplan A, Bjorkesten L, Astrom J, et al. 2002. A neuroproteomic approach to targeting neuropeptides in the brain. Proteomics 2 447. 

Clinical Neuroproteomics of Human Body Fluids CSF and Blood Assays for Early and Differential Diagnosis of Dementia... 

In the proteomic analysis of the brain, two-dimensional gels for protein separation, followed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry for protein identification, have mainly been employed. This classical proteomics approach allows for the quantification of changes in protein levels and modifications. Simultaneously, it is a robust, well-established method that finds wide application in the study of biological systems. In this article, we provide a description of the protocols of the proteomic analysis used in our laboratory and a summary of the major findings from our group and other neuroproteomics groups. 

Kobeissy FH, Ottens AK, Zhang Z, Liu MC, Denslow ND, et al. Novel differential neuroproteomics analysis of traumatic brain injury in rats. Mol. Cell. Proteomics 2006 5 1887-1898. 

Keywords Proteomics Genomics Neuroproteomics 2 dimensional electrophoresis Protein profiling Protein fingerprinting Biomarker Systems biology Tissue profiling Bioinformatics... 

The biochemical approach of two-dimensional electrophoresis which has become the classical proteomic approach to whole proteome analysis has the capacity to display a large number of proteins expressed the studied system under given physiological conditions. Construction of global expression maps for defined proteomes is the most widely used application of proteomics and when used in combination with mass spectrometry (MS) techniques can be a powerful approach. There have been a number of studies focused on global neuroproteomics from whole brain analysis to the analysis of synaptic components. Two-dimensional maps have been constructed for whole human (Langen, Bemdt et al. 1999) mouse (Gauss, Kalkum et al. 

Another global neuroproteomic study carried out by Collins et al, (unpublished results) focused on the neurophosphoproteome, i.e. the collection of phosphoproteins at the synapse. Protein phosphoiylation is an essential regulator of protein function and signaling mechanisms in any biological system. It has been estimated that one third of all proteins are phosphorylated in the mammalian cell and if it is assumed that one third of all proteins are expressed in the brain, then a conservative estimate of the number of phosphoproteins expressed in the brain would be in the order of... 

Jain, K. K., 2002c, Role of Neuroproteomics in CNS Drug Discovery. Targets 1 95-101. 

This material is based upon work supported by the National Science Foundation under Award No. CHE-04-00768, the National Institutes of Health under Award No. R33DK 070285, and the National Institute on Drug Abuse under Award No. P30 DA 018310 to the UIUC Neuroproteomics Center. 

Java-based code to create image of dots at the initial bead positions (free at http //neuroproteomics.scs.illinois.edu/ imaging.html). 

Fig. 27.2. Flow chart for the computational steps in the stretched imaging method, including the process ot (a) bead identification by light thresholding, (b) geometry file creation, and (c) image reconstruction. The custom software routines can be found online at http //neuroproteomics.scs.illinois.edu/imaging.html.

All in-house written Java software is available online, along with an example dataset with step-by-step instructions, at http //neuroproteomics.scs.illinois.edu/imaging.html. 

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