Proteomics Portal

Background

Proteomics is the study of all the proteins in a biological system. Using proteomics techniques it is possible to identify thousands of proteins and determine their abundance. Through enrichment techniques, it is possible to focus on specific post-translational modifications and thereby gather information on the state of proteins. Proteins are the functional building blocks of biological systems. Measuring their abundance and state provides information on the current state of a biological system. Proteins are however far more complex to work with than DNA and RNA. Nucleic acids only have one chemistry, while each amino acid has its own chemistry. This makes extracting the whole proteome more complex. Additionally, proteins can not be amplified like genetic material, it is therefore only possible to work with what can be extracted. The large dynamic ranges across the proteome also make detection of the whole proteome very complex. Fortunately developments in extraction techniques, separation by liquid chromatography and detection by mass spectrometry has made much of the proteome accessible for measurement. Development in proteomics has made it robust enough to be used in clinical settings.

Data Generation

There are numerous ways to generate proteomic data. In 2D DIGE proteins are separate by charge and size through two dimensional gel electrophoresis. Labelling the proteins from the different sample with different fluorescent dyes allows two or three samples to be run simultaneously and compared on the same gel.

Mass Spectrometry is currently the most common technology used in proteomic experiments. There are many different types of mass spectrometry and even more ways to use them. The simplest is targeted mass spectrometry, where peptides from known samples are selected analysis. This provides accurate and specific quantification of a few proteins. Discovery proteomics tries to identify and quantify the maximum number of proteins per sample. Using discovery proteomics it is possible to identify thousands of proteins from a single sample.

2D DIGE

Two-Dimensional Difference Gel Electrophoresis, separates proteins that have been tagged with fluorescent dyes by two dimensional gel electrophoresis. This allows direct relative protein abundance comparisons to be made.

Targeted Proteomics

Using mass spectrometry it is possible to select specific peptides from known proteins. These targeted proteins can then be specifically and accurately quantified.

Discovery Proteomics

Using mass spectrometry peptide masses and intensity are measured. The peptides are then fragmented and the fragmentation spectrum used the identify the proteins from which they originate.