Hi Fellows. I was wondering how to define Systems Proteomics? Does anybody have a good suggestion. I have attache those paper I could find regarding this approach...
Merci,
Kambiz
Dear Kambiz,
The link depicted at the end of this answer contains a definition of proteomics taken from different sources. I have copied only from two sources for quick view. You can use the link to view definition from other sources.
What is Proteomics?
The human genome contains the complete set of genes required to build a functional human being. However, the genome is only a source of information. In order to function, it must be expressed.
The transcription of genes is the first stage of gene expression and is followed by the translation of messenger RNA to produce proteins. The proteome is the complete set of proteins produced by the genome at any one time.
The proteome is much more complex than either the genome or the transcriptome (see transcriptomics). This is because each protein can be chemically modified in different ways after synthesis. Many proteins have carbohydrate groups added to them. Others are phosphorylated or acetylated or methylated.
The proteome is also very dynamic. Most of our cells contain the same genome regardless of the cell type, developmental stage or environmental conditions. The proteome, however, varies considerably in these differing circumstances due to different patterns of gene expression and different patterns of protein modification.
Proteomics, the study of the proteome, is important because proteins represent the actual functional molecules in the cell. When mutations occur in the DNA, it is the proteins that are ultimately affected. Drugs, when they have beneficial effects, do so by interacting with proteins. Proteomics therefore covers a number of different aspects of protein function, including the following:
Structural proteomics, the large-scale analysis of protein structures.
Protein structure comparisons can help to identify the functions of newly discovered genes. Structural analysis can also show where drugs bind to proteins and where proteins interact with each other. This is achieved using technologies such as X-ray crystallography and NMR spectroscopy.
Expression proteomics, the large-scale analysis of protein expression.
This can help to identify the main proteins found in a particular sample and proteins differentially expressed in related samples, such as diseased vs healthy tissue. A protein found only in a diseased sample may represent a useful drug target or diagnostic marker. Proteins with similar expression profiles may also be functionally related. Technologies such as 2D-PAGE and mass spectrometry are used here.
Interaction proteomics, the large-scale analysis of protein interactions.
The characterization of protein-protein interactions helps to determine protein functions and can also show how proteins assemble in larger complexes. Technologies such as affinity purification, mass spectrometry and the yeast two-hybrid system are particularly useful.
The techniques for proteome analysis are not as straightforward as those used in transcriptomics. However, the advantage of proteomics is that the real functional molecules of the cell are being studied. Strong gene expression, resulting in an abundant mRNA, does not necessarily mean that the corresponding protein is also abundant or indeed active in the cell.
(Taken from Proteomicssurf.com)
What is Proteomics?
The dream of having genomes completely sequenced is now a reality. The complete sequence of several genomes including the human one is known. However, the understanding of probably half a million human proteins encoded by some 30'000 genes is still a long way away and the hard work to unravel the complexity of biological systems is yet to come. A new fundamental concept called proteome (PROTEin complement to a genOME) has recently emerged that should drastically help phenomics to unravel biochemical and physiological mechanisms of complex multivariate diseases at the functional molecular level. A new discipline, proteomics, has been initiated that complements physical genomic research. Proteomics can be defined as the qualitative and quantitative comparison of proteomes under different conditions to further unravel biological processes.
(Taken from www.expasy.com)
http://www.proteomic.org/html/proteomics_.html
Hoping this will be helpful,
Rafik
This definition is on proteomics alone. I am talking about systems proteomics!
Dear Kambiz,
Among the Systems Proteomics are: biological systems and their definition is depicted in the following paragraph:
Systems biology has emerged in the past decade as a discipline that aims ultimately to understand and predict the behavior of biological systems as a whole. Biological systems, whether a signaling network, a cell, an organ, or an organism, in this field are viewed as a network of interacting elements (genes, proteins, metabolites) from which coherent function emerges. The modeling or reconstruction of biological networks allows computational simulations to be run that lead to predictive hypotheses on how a given network may behave. In its grandest vision, the application of systems biology approaches to the study of disease-perturbed networks will, through the identification of therapeutic drug targets, foster a future of personalized medicine.
This definition was taken from a publication contained in the following link:
http://advances.nutrition.org/content/2/4/355.full
Hoping this definition will be satisfactory,
Rafik
On this page, it is the first time I saw this phrase:
https://sites.google.com/a/nyu.edu/vogel-lab/research
I recommend to follow Dr. Vogel papers in this regard.
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