Linked Life Data

9600841

Source:http://linkedlifedata.com/resource/pubmed/id/9600841

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
3
pubmed:dateCreated
1998-6-16
pubmed:abstractText
Genome sequences are available for increasing numbers of organisms. The proteomes (protein complement expressed by the genome) of many such organisms are being studied with two-dimensional (2D) gel electrophoresis. Here we have investigated the application of short N-terminal and C-terminal sequence tags to the identification of proteins separated on 2D gels. The theoretical N and C termini of 15, 519 proteins, representing all SWISS-PROT entries for the organisms Mycoplasma genitalium, Bacillus subtilis, Escherichia coli, Saccharomyces cerevisiae and human, were analysed. Sequence tags were found to be surprisingly specific, with N-terminal tags of four amino acid residues found to be unique for between 43% and 83% of proteins, and C-terminal tags of four amino acid residues unique for between 74% and 97% of proteins, depending on the species studied. Sequence tags of five amino acid residues were found to be even more specific. To utilise this specificity of sequence tags for protein identification, we created a world-wide web-accessible protein identification program, TagIdent (http://www.expasy.ch/www/tools.html), which matches sequence tags of up to six amino acid residues as well as estimated protein pI and mass against proteins in the SWISS-PROT database. We demonstrate the utility of this identification approach with sequence tags generated from 91 different E. coli proteins purified by 2D gel electrophoresis. Fifty-one proteins were unambiguously identified by virtue of their sequence tags and estimated pI and mass, and a further 11 proteins identified when sequence tags were combined with protein amino acid composition data. We conlcude that the TagIdent identification approach is best suited to the identification of proteins from prokaryotes whose complete genome sequences are available. The approach is less well suited to proteins from eukaryotes, as many eukaryotic proteins are not amenable to sequencing via Edman degradation, and tag protein identification cannot be unambiguous unless an organism's complete sequence is available.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
May
pubmed:issn
0022-2836
pubmed:author
pubmed:copyrightInfo
Copyright 1998 Academic Press Limited.
pubmed:issnType
Print
pubmed:day
8
pubmed:volume
278
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
599-608
pubmed:dateRevised
2006-11-15
pubmed:meshHeading
pubmed-meshheading:9600841-Amino Acid Sequence, pubmed-meshheading:9600841-Bacillus subtilis, pubmed-meshheading:9600841-Cysteine Endopeptidases, pubmed-meshheading:9600841-Databases, Factual, pubmed-meshheading:9600841-Electrophoresis, Gel, Two-Dimensional, pubmed-meshheading:9600841-Electrophoresis, Polyacrylamide Gel, pubmed-meshheading:9600841-Humans, pubmed-meshheading:9600841-Molecular Sequence Data, pubmed-meshheading:9600841-Multienzyme Complexes, pubmed-meshheading:9600841-Mycoplasma, pubmed-meshheading:9600841-Peptide Library, pubmed-meshheading:9600841-Proteasome Endopeptidase Complex, pubmed-meshheading:9600841-Proteins, pubmed-meshheading:9600841-Saccharomyces cerevisiae, pubmed-meshheading:9600841-Sequence Alignment, pubmed-meshheading:9600841-Sequence Homology, Amino Acid, pubmed-meshheading:9600841-Sequence Tagged Sites
pubmed:year
1998
pubmed:articleTitle
Protein identification with N and C-terminal sequence tags in proteome projects.
pubmed:affiliation
Central Clinical Chemistry Laboratory, Geneva University Hospital, 24 Rue Micheli-du-Crest, Geneva 14, 1211, Switzerland.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't