The term proteome is a blend of the words "proteins" and "genome." Initially, it was meant to describe the entire complement of proteins expressed by a genome, cell, tissue, or organism. However, the term is now used to refer to all of the expressed proteins at a given time point under defined conditions by a genome, cell, tissue, or organism. For example, a cellular proteome refers to the collection of proteins in a specific cell type under particular environmental conditions. Due to the fact that many of the genes in a genome can form different proteins due to alternative splicing; that proteins can be modified after their synthesis (termed, post-translational modifications); and that combinations of proteins can form larger multimeric complexes, the proteome is generally considered to be larger than the genome.
Historically, the study of the proteome, termed pro-teomics, was pursued through the electrophoretic separation of proteins using a gel matrix. Initially, these gels were carried out in one dimension (e.g. based on protein size, shape, or charge). Currently, two-dimensional gel electrophoresis is the standard approach. Proteins are separated based on charge in the first dimension through a slab of gel that is then turned 90° and loaded onto a second gel that separates proteins based on their molecular weight. The gel is then treated with a dye or stain used to visualize all of the proteins in the gel. These two-dimensional profiles are photographed and compared. Specific spots can be excised for further analysis (e.g. a spot that is present, absent, or occurs at a different concentration than another sample's two-dimensional profile). This excised material can be submitted to a subsequent round of two-dimensional analysis to further separate the proteins. Alternatively, the material can be sequenced in order to identify the specific protein(s).
More recently, mass spectroscopy promises to advance the field of proteomics. Two different methods of mass spectroscopy are being applied: peptide mass fingerprinting and tandem mass spectroscopy. Peptide mass fingerprinting identifies a protein by cleaving it into short peptides and uses a peptide sequence database to align the short peptides and then deduce the protein's identity by matching it against proteins in the database. By comparison, tandem mass spectrometry derives sequence information from individual peptides that are isolated and then collided with a nonreactive gas. Data on the array of fragment ions produced is recorded and analyzed. Unlike genome- and transcriptome-based methods, pro-teomic analyses struggle to attain the same level of throughput. The major limitation is that proteins cannot be amplified in a manner similar to nucleic acid amplification and the cost of mass spectroscopy is prohibitive.
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