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Peptide mass fingerprinting and amino acid composition identification

Mass spectrometry is a rapidly growing field of protein analysis, which is proving useful in the identification of proteins separated by 2-D gel electrophoresis. The most common mass spectrometry protein identification technique is called peptide mass fingerprinting. This involves the generation of peptides from proteins using residue-specific enzymes, the determination of peptide masses by spectrometric techniques, and the matching of these masses against theoretical peptide libraries generated from protein sequence databases to create a list of likely protein identifications.

We do not currently use peptide mass fingerprinting alone for protein identification, but often use an identification approach which compares lists of best-matching proteins generated by AA composition identification and peptide mass fingerprinting techniques (see MultiIdent tool for details). For this approach, one sample is subjected to the amino acid analysis procedure to generate a list of best matching proteins, and a duplicate sample is subjected to peptide mass fingerprinting to generate an independent list of best matching proteins. Identification is achieved when lists of best-matching proteins are then compared for identical database. This technique has two main applications. Firstly, in situations where proteins are blocked at the N-terminus and cannot be used for "sequence tagging", and secondly where proteins are being identified over large or small phylogenetic distances across species boundaries. As peptide mass fingerprinting has a sample throughput similar to AA analysis, this combined identification approach is suitable for rapid protein identification.

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