Brain Proteins Neuroproteomics

Nevertheless, large numbers of proteins are present in brain-derived samples and they need to be separated for identification and quantification. The separation 

In quantitative neuroproteomics based on 2D-PAGE, intact proteins are separated and the abundance of a protein is determined by measuring stain intensity of the 

Peptide identified from CID-MS/MS shown in Fig. 4D (major sequence-related ions of the peptide are indicated in the spectrum) by BioWorks (version 3.2, Thermo Fisher, San Jose, CA, USA) using the National Center for Biotechnology Information (NCBI) nonredundant (nr) protein database with rat (R. norvegicus) selected in the species option of the program 

Starting and end points in protein s listed sequence (numbering from 1 to n in the amino- to carboxy-terminal direction). 

Tryptic peptides matched by BioWorks (version 3.2) to the Na /K -transporting ATPase a-subunit in the 98-120 kDa SDS-PAGE band of the rat synaptic plasma-membrane fraction (BioWorks version 3.2) after in-gel digestion and data-dependent LC/ESI-MS/MS 

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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. 

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... 

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