Protomap (proteomics)

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This article is about proteomics. For the Protomap hypothesis (neuroscience), see Protomap (neuroscience).

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. [1]

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.[2]

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References[edit]

  1. ^ Johnson CE, Kornbluth S (September 2008). "Caspase cleavage is not for everyone". Cell 134 (5): 720–1. doi:10.1016/j.cell.2008.08.019. PMID 18775303. 
  2. ^ Dix MM, Simon GM, Cravatt BF (August 2008). "Global mapping of the topography and magnitude of proteolytic events in apoptosis". Cell 134 (4): 679–91. doi:10.1016/j.cell.2008.06.038. PMC 2597167. PMID 18724940. 

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