What is Proteomics
The study of the proteome
Proteomics is the study of the proteome, which is defined as the set of proteins and their post-translational modifications being expressed in a cell under defined conditions at a specific time.
Since there are over 200 different cell types in a human body and these vary with time (over years, consider the difference between a new-born babies liver and that of a 25 year old student; over days, the change in skin colour after a few hours in strong sun or over seconds, for example blushing at an embarrassing situation). Thus there is no single human proteome but a collection of some hundred thousands, each of which vary to greater or lesser extent between individuals. In addition to this, we can define several distinct areas of study within proteomics:
- Expression Proteomics defines all gene products in a cell and their modifications
- Cell-Map Proteomics defines spatial and temporal positions of all proteins
- Population proteomics analyses the variation expression levels amongst individuals
Each of these may, and probably has been sub-divided into many more specific areas such as modificomics, the study of all post-translational modification of proteins, and even further into phosphoromics and glycomics, the study of phosphorylation and glycosylation of proteins. However the overall goal is to combine all of the areas to give an overall view of the proteome and then to integrate this data with data from the other ‘-omics’ fields. The three other main divisions being:
- Genomics, the study of the set of genes contained in the chromosomes
- Transcriptomics, the study of the set of RNA molecules in a cell and
- Metabolomics, the study of the set of small molecules in a specific cell
Since the demonstration by Craig Venter and co-workers in 1995 that shot-gun sequencing is a viable, fast and economic method for sequencing genomes, there has been a veritable flood of completed genome sequences (as of late 2002, this numbers around 16 eucaryotic (219 in progress) and 110 bacterial (310 in progress), 16 archeal and 503 viral genomes.
The most well-known genomes finished include human, mouse, rat, the fruit-fly Drosophila, the roundworm C. elegans and yeast as well as some plants like Arabidopsis and rice. In parallel to this, DNA chip- and microarray-based methods have been demonstrated to be fast and in the right hands, reliable methods for globally profiling the transcriptome (i.e. profiling mRNA expression). Proteomics however has been limping behind and there is no single method for profiling the set of proteins being expressed in a cell yet. The various approaches are described on the protein- and peptide- based approach pages.
The new methods for proteome and gene expression analysis are quantitative and will allow new systematic approaches to investigation the function and regulation of unknown genes. N.L. Anderson has defined four major areas for the analysis of gene function and regulation:
- Molecular anatomy (protein composition of cells and tissues)
- Molecular pathology (analysis of disease in terms of changes in expression)
- Molecular pharmacology/toxicology (the effects of drugs on protein expression)
- Molecular physiology, the response to changes in the cells environment