Protomap (proteomics)
Encyclopedia
PROTOMAP is a recently developed proteomic technology for identifying changes to proteins that manifest in altered migration by one-dimensional SDS-PAGE
. It is similar, conceptually, to two-dimensional gel electrophoresis
and difference gel electrophoresis
in that it enables global identification of proteins that undergo altered electrophoretic
migration resulting from, for example, proteolysis
or post-translational modification. However, it is unique in that all proteins are sequenced using mass spectrometry
which provides information on the sequence coverage detected in each isoform of each protein thereby facilitating interpretation of proteolytic events.
PROTOMAP is performed by resolving control and experimental samples in separate lanes of a 1D SDS-PAGE
gel. Each lane is cut into evenly spaced bands (usually 15-30 bands) and proteins in these bands are sequenced using shotgun proteomics
. Sequence information from all of these bands are bioinformatically
integrated into a visual format called a peptograph which plots gel-migration in the vertical dimension (high- to low-molecular weight, top to bottom) and sequence coverage in the horizontal dimension (N- to C-terminus, left to right). A peptograph is generated for each protein the sample (thousands of peptographs are generated from a single experiment) and this data format enables rapid identification of proteins undergoing proteolytic cleavage by making evident changes in gel-migration that are accompanied by altered topography.
PROTOMAP stands for PRotein TOpography and Migration Analysis Platform and was invented and developed by Ben Cravatt and colleagues at The Scripps Research Institute
.
SDS-PAGE
SDS-PAGE, sodium dodecyl sulfate polyacrylamide gel electrophoresis, describes a collection of related techniques widely used in biochemistry, forensics, genetics and molecular biology to separate proteins according to their electrophoretic mobility...
. It is similar, conceptually, to two-dimensional gel electrophoresis
Two-dimensional gel electrophoresis
Two-dimensional gel electrophoresis, abbreviated as 2-DE or 2-D electrophoresis, is a form of gel electrophoresis commonly used to analyze proteins...
and difference gel electrophoresis
Difference gel electrophoresis
'Difference gel electrophoresis' is a form of gel electrophoresis where up to three different protein samples can be labeled with fluorescent dyes prior to two-dimensional electrophoresis. After the gel electrophoresis, the gel is scanned with the excitation wavelength of each dye one after the...
in that it enables global identification of proteins that undergo altered electrophoretic
Electrophoresis
Electrophoresis, also called cataphoresis, is the motion of dispersed particles relative to a fluid under the influence of a spatially uniform electric field. This electrokinetic phenomenon was observed for the first time in 1807 by Reuss , who noticed that the application of a constant electric...
migration resulting from, for example, proteolysis
Proteolysis
Proteolysis is the directed degradation of proteins by cellular enzymes called proteases or by intramolecular digestion.-Purposes:Proteolysis is used by the cell for several purposes...
or post-translational modification. However, it is unique in that all proteins are sequenced using mass spectrometry
Mass spectrometry
Mass spectrometry is an analytical technique that measures the mass-to-charge ratio of charged particles.It is used for determining masses of particles, for determining the elemental composition of a sample or molecule, and for elucidating the chemical structures of molecules, such as peptides and...
which provides information on the sequence coverage detected in each isoform of each protein thereby facilitating interpretation of proteolytic events.
PROTOMAP is performed by resolving control and experimental samples in separate lanes of a 1D SDS-PAGE
SDS-PAGE
SDS-PAGE, sodium dodecyl sulfate polyacrylamide gel electrophoresis, describes a collection of related techniques widely used in biochemistry, forensics, genetics and molecular biology to separate proteins according to their electrophoretic mobility...
gel. Each lane is cut into evenly spaced bands (usually 15-30 bands) and proteins in these bands are sequenced using shotgun proteomics
Shotgun proteomics
Shotgun proteomics is a method of identifying proteins in complex mixtures using a combination of high performance liquid chromatography combined with mass spectrometry. The name is derived from shotgun sequencing of DNA which is itself named by analogy with the rapidly-expanding, quasi-random...
. Sequence information from all of these bands are bioinformatically
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
integrated into a visual format called a peptograph which plots gel-migration in the vertical dimension (high- to low-molecular weight, top to bottom) and sequence coverage in the horizontal dimension (N- to C-terminus, left to right). A peptograph is generated for each protein the sample (thousands of peptographs are generated from a single experiment) and this data format enables rapid identification of proteins undergoing proteolytic cleavage by making evident changes in gel-migration that are accompanied by altered topography.
PROTOMAP stands for PRotein TOpography and Migration Analysis Platform and was invented and developed by Ben Cravatt and colleagues at The Scripps Research Institute
The Scripps Research Institute
The Scripps Research Institute is an American medical research facility that focuses on research in the basic biomedical sciences. Headquartered in La Jolla, California, with a sister facility in Jupiter, Florida, the institute is home to 3,000 scientists, technicians, graduate students, and...
.
See also
- Two dimensional SDS-PAGE
- Difference gel electrophoresisDifference gel electrophoresis'Difference gel electrophoresis' is a form of gel electrophoresis where up to three different protein samples can be labeled with fluorescent dyes prior to two-dimensional electrophoresis. After the gel electrophoresis, the gel is scanned with the excitation wavelength of each dye one after the...
- ProteomicsProteomicsProteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells. The term "proteomics" was first coined in 1997 to make an analogy with...
- Shotgun proteomicsShotgun proteomicsShotgun proteomics is a method of identifying proteins in complex mixtures using a combination of high performance liquid chromatography combined with mass spectrometry. The name is derived from shotgun sequencing of DNA which is itself named by analogy with the rapidly-expanding, quasi-random...
- Mass spectrometryMass spectrometryMass spectrometry is an analytical technique that measures the mass-to-charge ratio of charged particles.It is used for determining masses of particles, for determining the elemental composition of a sample or molecule, and for elucidating the chemical structures of molecules, such as peptides and...
- ProteaseProteaseA protease is any enzyme that conducts proteolysis, that is, begins protein catabolism by hydrolysis of the peptide bonds that link amino acids together in the polypeptide chain forming the protein....
- Benjamin CravattBenjamin Cravatt IIIBenjamin Franklin Cravatt is a professor in and chair of the Department of Chemical Physiology at The Scripps Research Institute in La Jolla, California...
External links
- The PROTOMAP website - provides access to publicly available PROTOMAP data as well as software and protocols for running PROTOMAP experiments.
- PROTOMAP Description - on the Cravatt Lab website