Proteomics

Proteomics is the search for information about proteins, conducted on an industrial scale. Traditionally, scientists have studied proteins one by one. Proteomics studies a whole proteome at once. Proteomics identifies proteins, modifications of proteins, interactions between proteins, and more.

Proteomics and Genomics

Tens of thousands of scientists have studied proteins in the past century. This effort has resulted in a vast body of knowledge about proteins. (To see just how much, look up insulin, hemoglobin or your favorite protein in the Bioinformatics Harvester). Each bit of this knowledge was the result of an immense amount of bench work.

A similar situation existed in genetics until gene-sequencing machines were invented and genomics was born. Suddenly, knowledge about the genome exploded. One of the lessons of the Human Genome Project was that a single company with many machines could sequence the human genome. Large-scale biology was born.

Proteomics is the application of large-scale biology to protein science. Proteomics is in its infancy, even compared to genomics, which itself is only fifteen years old

Proteomics Technologies

Proteomics employs a number of technologies. Indeed, many people define proteomics as the study of proteins using these technologies:

• Mass Spectrometry - the tool that has made proteomics possible. Mass spectrometers are machines for measuring the mass and charge of charged particles.
• Bioinformatics - software and databases are also enabling technologies for proteomics.
• Liquid Chromatography and 2D Gels - ways of separating proteins so that they may be more readily identified.
• Antibodies - people have harnessed the body's immune system to identify proteins. Today, antibodies are the gold standard for protein identification and quantification.

Proteomics Activities

Proteomics is the study of all the proteins in a given sample at once. Proteins can be studied from various perspectives:

• Identification — Simply listing the proteins in a biological sample turns out to be tricky. Identification is the part of proteome research that has come closest to using techniques of large-scale biology.
• Quantification — It's important for many applications to determine how much of each protein is present in a sample. Differential expression (how protein levels differ between two samples) is determined by labeling each sample, then comparing them on 1) a 2D gel — a technique called Difference Gel Electrophoresis, or DIGE, or 2) on a mass spectrometer — a technique called isotope-coded affinity tagging, or ICAT.
• Modification Identification — Proteins are modified in many ways. Frequently a modification changes how the protein works.
• Structures — Function follows form. Determining the three-dimensional structure of a protein helps explain what the protein does, and how it does it.
• Interactions — No protein is an island. Proteins work with other proteins to carry out their functions. To understand their functions, we must understand these interactions.
• Subcellular Locations — Proteins do their work in specific locations within a cell. Proteins interact only with other proteins at the same location.