Mining for proteins  pg. 4

Bioinformatics

Bioinformatics is the collection, organization and analysis of large amounts of biological information using networks of computers and databases. Vast, on-line “libraries” of confirmed protein sequences and the mass spectra “fingerprints” for thousands of proteins, predicted from the genes that encode them, have greatly improved the ability of researchers to identify proteins.

For example, researchers at the University of Washington in Seattle developed a computer program, called SEQUEST that helps researchers search databases rapidly for a possible “match” to the protein they’ve discovered.

Andrew Link, Ph.D., associate professor of Microbiology & Immunology and Biochemistry at Vanderbilt, uses SEQUEST in a technique he developed, called “direct analysis of large protein complexes” (DALPC).

Proteins are fragmented and the resulting peptides are separated by multi-dimensional liquid chromatography. This is a method for separating tiny amounts of peptides according to a variety of physical attributes, such as size or charge, as they travel through flexible plastic columns no bigger than the size of a human hair.

The peptides are analyzed by mass spectrometry, then fragmented to even smaller pieces and analyzed again to get information about their amino-acid sequences (a technique called “tandem” mass spectrometry). SEQUEST is then used to help identify them, thereby avoiding the need to purify each protein individually. DALPC “gives us the ability to look at complexes of hundreds of proteins at a time, and figure out what they are in a single experiment,” Link says.

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