Analysis of mice brain and SH-SY5Y neuroblastoma cell proteome by quantitative two-dimensional electrophoresis

Original full papers, not directly related to the subject of the thesis: NO-sensitive guanylyl cyclase beta 1 subunit is peripherally associated to chromosomes during mitosis. Abbreviations 2D-DIGE two-dimensional difference gel electrophoresis 2-DE two-dimensional electrophoresis AD Alzheimer's disease APP amyloid precursor protein Aβ amyloid-beta BSA bovine serum albumine CBB Coomassie brilliant blue CCD charge coupled device CHAPS 3-(cyclohexylamino)-1-propanesulphonic acid CSF cerebrospinal fluid CV coefficient of variation CyDye cyanine dye DMSO dimethyl sulfoxide DRP-2 dihidropyrimidinase related protein-2 DTE dithioerythritol EEF-2 eukaryotic elongation factor-2 ER endoplasmic reticulum ESI electrospray ionisation FDR false discovery rate GO gene ontology GSK-3 glycogen synthase kinase-3 hnRNP K heterogenous nuclear ribonucleoprotein K Hsp70 Heat shock protein 70 IAA iodacetamide ICAT isotope-coded affinity tag IEF isoelectric focusing IPG immobilized pH gradient iTRAQ isobaric tags for relative and absolute quantitation MALDI matrix assisted laser desorption ionisation MS mass spectrometry MS/MS tandem mass spectrometry Mw molecular weight NFT neurofibrillary tangle NMDA-R N-methyl-D-aspartate receptor PBS phosphate-buffered saline PDH pyruvate dehydrogenase PDHE1-B pyruvate dehydrogenase E1 component subunit beta pI isoelectric point PMF peptide mass fingerprint PMT photomultiplier Q quadrupole RNS reactive nitrogen species ROS reactive oxygen species RuBPs ruthenium bathophenantroline disulfonate SD standard deviation SDS-PAGE sodium dodecyl sulphate-polyacrylamide gel electrophoresis SGoF sequential goodness of fit SILAC stable isotope labelling with amino acids in cell culture TBS tris-buffered saline TCA tricarboxylic acid cycle TOF time of flight UPR unfolded protein response In the last decade the biggest revolution of the molecular biology was the completion of the sequencing the human genome (Lander et al. 2001, Venter et al. 2001). In addition, the genome sequences of important model systems used in biological, medical and pharmacological experiments are also available (Waterston et al. 2002, Gibbs et al. 2004). After genome sequencing studies, the focus was shifting to transcriptomics and proteomics. Transcriptomics studies the levels of transcripted mRNA (transcriptome) in cells or tissues. Proteomics is initially concerned with determining the structure, expression, localization, biochemical activity, interactions and cellular roles of as many proteins as possible (de Hoog and Mann, 2004). In other words, proteomics is a large-scale study of the proteome. The term " proteome " was described in the 1990 " s: the PROTEin complement expressed by a genOME (Wilkins et al. 1996). The cellular proteome is a dynamic and complex network of proteins. Due to the fact that only a fraction of mRNA is translated to proteins, mRNA levels are relatively weak predictors of protein …