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FindPept, a tool to identify unmatched masses in peptide mass fingerprinting protein identification

✍ Scribed by Alexandre Gattiker; Willy V. Bienvenut; Amos Bairoch; Elisabeth Gasteiger

Book ID
101389487
Publisher
John Wiley and Sons
Year
2002
Tongue
English
Weight
281 KB
Volume
2
Category
Article
ISSN
1615-9853

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✦ Synopsis

FindPept (http://www.expasy.org/tools/findpept.html) is a software tool designed to identify the origin of peptide masses obtained by peptide mass fingerprinting which are not matched by existing protein identification tools. It identifies masses resulting from unspecific proteolytic cleavage, missed cleavage, protease autolysis or keratin contaminants. It also takes into account post-translational modifications derived from the annotation of the SWISS-PROT database or supplied by the user, and chemical modifications of peptides. Based on a number of experimental examples, we show that the commonly held rules for the specificity of tryptic cleavage are an oversimplification, mainly because of effects of neighboring residues, experimental conditions, and contaminants present in the enzyme sample.

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