Proteomics in brain research: potentials and limitations

Lubec, Gert; Krapfenbauer, Kurt; Fountoulakis, Michael

doi:10.1016/s0301-0082(03)00036-4

Cited by 155 publications

(97 citation statements)

References 98 publications

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“…1). A prevailing majority of that work was performed using two-dimensional electrophoresis (2DE) 1 for separating proteins prior to mass spectrometric analysis, whereas only few studies were based on gel-free technologies.…”

Section: Molecular and Cellular Proteomics 4:402-408 2005mentioning

confidence: 99%

Proteomic Mapping of Brain Plasma Membrane Proteins

Nielsen¹,

Olsen

Podtelejnikov³

et al. 2005

Molecular & Cellular Proteomics

158

204

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Proteomics is potentially a powerful technology for elucidating brain function and neurodegenerative diseases. So far, the brain proteome has generally been analyzed by two-dimensional gel electrophoresis, which usually leads to the complete absence of membrane proteins. We describe a proteomic approach for profiling of plasma membrane proteins from mouse brain. The procedure consists of a novel method for extraction and fractionation of membranes, on-membrane digestion, diagonal separation of peptides, and high-sensitivity analysis by advanced MS. Breaking with the classical plasma membrane fractionation approach, membranes are isolated without cell compartment isolation, by stepwise depletion of nonmembrane molecules from entire tissue homogenate by high-salt, carbonate, and urea washes followed by treatment of the membranes with sublytic concentrations of digitonin. Plasma membrane is further enriched by of density gradient fractionation and protein digested on-membrane by endoproteinase Lys-C. Released peptides are separated, fractions digested by trypsin, and analyzed by LC-MS/MS. In single experiments, the developed technology enabled identification of 862 proteins from 150 mg of mouse brain cortex. Further development and miniaturization allowed analysis of 15 mg of hippocampus, revealing 1,685 proteins. More that 60% of the identified proteins are membrane proteins, including several classes of ion channels and neurotransmitter receptors. Our work now allows in-depth study of brain membrane proteomes, such as of mouse models of neurological disease.

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Section: Molecular and Cellular Proteomics 4:402-408 2005mentioning

confidence: 99%

Proteomic Mapping of Brain Plasma Membrane Proteins

Nielsen¹,

Olsen

Podtelejnikov³

et al. 2005

Molecular & Cellular Proteomics

158

204

View full text Add to dashboard Cite

show abstract

“…The first proteomics studies based on 2-DE gel methodology have been reported in 1999, where Pearce and Svendsen (1999) showed first differential 2-DE gel approach to fetal human brain cells treated with both embryonic growth factor (EGF) and fibroblast growth factor (FGF). After Pearce and Svendsen's pioneering work, proteomic profiling has mainly been applied for compiling protein inventory in the adult nervous system of normal versus diseased individuals (Rohlff, 2000(Rohlff, , 2001Husi and Grant, 2001;Lubec et al, 2003;Choudhary and Grant, 2004;Kim et al, 2004;Taylor et al, 2004). However, protein analysis of human fetal neuronal stem cell differentiation has not much progressed yet.…”

Section: Human Neuronal Stem Cellsmentioning

confidence: 99%

Mass spectrometry based proteomic analysis of human stem cells: a brief review

Choi

An²,

Kim³

et al. 2007

Exp Mol Med

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Stem cells can give rise to various cell types and are capable of regenerating themselves over multiple cell divisions. Pluripotency and self-renewal potential of stem cells have drawn vast interest from different disciplines, with studies on the molecular properties of stem cells being one example. Current investigations on the molecular basis of stem cells pluripotency and self-renewal entail traditional techniques from chemistry and molecular biology. In this mini review, we discuss progress in stem cell research that employs proteomics approaches. Specifically, we focus on studies on human stem cells from proteomics perspective. To our best knowledge, only the following types of human stem cells have been examined via proteomics analysis: human neuronal stem cells, human mesenchymal stem cells, and human embryonic stem cells. Protein expression serves as biomarkers of stem cells and identification and expression level of such biomarkers are usually determined using two-dimensional electrophoresis coupled mass spectrometry or non-gel based mass spectrometry.

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“…Careful sample selection and preparation are prerequisites for a successful analysis [8,32]. Using this proteomics method, several 2-D human, rat, and mouse brain and CSF protein databases have been constructed, comprising up to 500 different gene products each [33][34][35][36][37]. A further development of the proteomics technologies, in particular the enrichment of low-abundance gene products, will be accomplished within the HUPO Brain Proteome Project initiated by Meyer and co-workers [38,39].…”

Section: Proteomic Analysismentioning

confidence: 99%

“…It is likely that protein levels in the brain are regulated at the proteolysis-protein stability level rather than at the transcription level [36]. Cathepsin D, cystatins B and C, serine inhibitor, fibrinogen gamma, and ubiquitin-activating enzyme E1 were found to be enriched in amyloid plaques [71].…”

Section: Protein Metabolismmentioning

confidence: 99%

“…The technical limitations involve inefficient detection of low-abundance gene products, of hydrophobic proteins (they do not enter the IPG strips), acidic, basic, high-and low-molecular-mass proteins. All these protein classes are underrepresented in 2-D gels [7,8,24,36]. A combination of the proteomics methods with protein separation and enriching techniques and alternative methodologies will improve the detection of additional differences between neurodegeneration and control brain.…”

Section: Limitations Of Proteomics Technologiesmentioning

confidence: 99%

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Proteomics‐driven progress in neurodegeneration research

Fountoulakis

Κοσσίδα

2006

Electrophoresis

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Proteomics-driven progress in neurodegeneration researchProteomics technologies have been widely used in the investigation of neurodegenerative and psychiatric disorders, and in particular in the detection of differences between healthy individuals and patients suffering from such diseases. Thus, brain and cerebrospinal fluid (CSF) samples from patients with Alzheimer's disease, Down syndrome, Pick's disease, Parkinson's disease, schizophrenia, and other disorders as well as brain and CSF from animals serving as models of neurological disorders have been analyzed by proteomics. 2-DE followed by MALDI-TOF-MS has been mainly applied as this proteomics approach provides the possibility of convenient quantification of protein levels and detection of post-translational modifications. About 330 unique proteins with deranged levels and modifications have been detected by proteomics approaches to be related to neurodegeneration and psychiatric disorders. They are mainly involved in metabolism pathways, cytoskeleton formation, signal transduction, guidance, detoxification, transport, and conformational changes. In this article, we provide a summary of the major contributions of proteomics technologies in the study of neurodegenerative and psychiatric diseases, in particular, in the detection of changes in protein levels and modifications related to these disorders. IntroductionNeurodegeneration is a major hallmark of a series of genetic and acquired disorders of the central nervous system (CNS), like Alzheimer's disease (AD), Down syndrome (DS), Pick's disease, Creutzfeldt-Jakob disease (CJD), and Parkinson's disease, which result in severe cognitive and motor deficits. A common characteristic of these diseases is that they are multifactorial.Their molecular basis is unknown and individual biomarkers are not reliable. Genomics and proteomics approaches have been applied to obtain a better understanding of neurodegeneration and psychiatric disorders. Genomics has been used to map and identify genes that are mutated in a wide variety of such disorders, like presenilins in AD. Next to genomics, which only provides a partial view of the biological problem, proteomics is widely used in clinical diagnosis as well and many changes in protein levels associated with specific diseases have been identified [1,2].Proteomics is a technology-driven science that studies the proteins of the various biological systems, their structures, interactions, post-translational modifications, and in particular the changes in their levels and modifications, which are the result of specific diseases or are induced by external factors.

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Proteomics in brain research: potentials and limitations

Cited by 155 publications

References 98 publications

Proteomic Mapping of Brain Plasma Membrane Proteins

Proteomic Mapping of Brain Plasma Membrane Proteins

Mass spectrometry based proteomic analysis of human stem cells: a brief review

Proteomics‐driven progress in neurodegeneration research

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