Proteome

Proteome

The proteome is the entire complement of proteins expressed by a genome, cell, tissue or organism. More specifically, it is the set expressed proteins at a given time under defined conditions. The term is a portmanteau of "proteins" and "genome".

The term has been applied to several different types of biological systems. A cellular proteome is the collection of proteins found in a particular cell type under a particular set of environmental conditions such as exposure to hormone stimulation. It can also be useful to consider an organism's complete proteome, which can be conceptualized as the complete set of proteins from all of the various cellular proteomes. This is very roughly the protein equivalent of the genome. The term "proteome" has also been used to refer to the collection of proteins in certain sub-cellular biological systems. For example, all of the proteins in a virus can be called a viral proteome.

The proteome is larger than the genome, especially in eukaryotes, in the sense that there are more proteins than genes. This is due to alternative splicing of genes and post-translational modifications like glycosylation or phosphorylation.

Moreover the proteome has at least two levels of complexity lacking in the genome. When the genome is defined by the sequence of nucleotides, the proteome cannot be limited to the sum of the sequences of the proteins present. Knowledge of the proteome requires knowledge of (1) the structure of the proteins in the proteome and (2) the functional interaction between the proteins.

Proteomics, the study of the proteome, has largely been practiced through the separation of proteins by two dimensional gel electrophoresis. In the first dimension, the proteins are separated by isoelectric focusing, which resolves proteins on the basis of charge. In the second dimension, proteins are separated by molecular weight using SDS-PAGE. The gel is dyed with Coomassie Blue or silver to visualize the proteins. Spots on the gel are proteins that have migrated to specific locations.

The mass spectrometer has augmented proteomics. Peptide mass fingerprinting identifies a protein by cleaving it into short peptides and then deduces the protein's identity by matching the observed peptide masses against a sequence database. Tandem mass spectrometry, on the other hand, can get sequence information from individual peptides by isolating them, colliding them with a non-reactive gas, and then cataloguing the fragment ions produced.

History

The term was coined by Marc Wilkins in 1994 in the symposium: "2D Electrophoresis: from protein maps to genomes" in Siena, Italy, and was subsequently published in 1995 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7498152 (1)] , which was part of his PhD thesis. Wilkins used it to describe the entire complement of proteins expressed by a genome, cell, tissue or organism.

See also

* Proteomics
* Metabolome
* Cytome
* Bioinformatics
* List of omics topics in biology
* Transcriptome

External links

* [http://www.proteome.org The Proteome Society]
* [http://bioinformatics.oupjournals.org/ Bioinformatics Journal]
* [http://www.grid.org/projects/hpf/about.htm Grid Computing of the Human Proteome]
* Databases: PIR | Swissprot | Pfam


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  • proteome — n. The set of all proteins created and used by an organism. Example Citations: The human proteome has become the next frontier of modern biology, said Peter Meldrum, president and chief executive of Myriad, a biotechnology company in Salt Lake… …   New words

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  • Proteome — All of the proteins produced by a given species, just as the genome is the totality of the genetic information possessed by that species. The term proteome was first coined from the PROTEin complement of the genOME in the mid 1990s by Marc… …   Medical dictionary

  • proteome — noun Etymology: prote + ome (as in genome) Date: 1995 the complement of proteins expressed in a cell, tissue, or organism by a genome …   New Collegiate Dictionary

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  • proteome — Protein equivalent of the genome: the next great challenge! …   Dictionary of molecular biology

  • proteome — noun the complete set of proteins encoded by a particular genome See Also: proteomics …   Wiktionary

  • proteome — [ prəʊtɪəʊm] noun Genetics the entire complement of proteins that is or can be expressed by a cell, tissue, or organism. Origin 1990s: a blend of protein and genome …   English new terms dictionary

  • proteome — /ˈproʊtioʊm/ (say prohteeohm) noun the complete protein complement expressed by the genome of an organism. {prote(in) + (gen)ome} …  

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