Identification of Conus amadis disulfide isomerase: minimum sequence length of peptide fragments necessary for protein annotation

Gowd, Konkallu Hanumae and Krishnan, KS and Balaram, Padmanabhan (2007) Identification of Conus amadis disulfide isomerase: minimum sequence length of peptide fragments necessary for protein annotation. In: Molecular BioSystems, 3 (8). pp. 554-566.

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Abstract

Protein disulfide isomerase (PDI) has been identified in a protein extract from the venom duct of the marine snail C. amadis. In-gel tryptic digestion of a thick protein band at approximately 55 kDa yields a mixture of peptides. Analysis of tryptic fragments by MALDI-MS/MS and LC-ESI-MS/MS methods permits sequence assignment. Three tryptic fragments yield two nine residue sequences (FVQDFLDGK 1 and EPQLGDRVR 2) and an eleven residue sequence (DQESTGALAFK 3). Database analysis using peptides 1 and 3 were consistent with the sequence of PDI and peptide 2 appears to be derived from a co-migrating protein. In identifying proteins based on the characterization of short peptide sequences the question arises about the reliability of identification using peptide fragments. Here we have also demonstrated the minimum length of peptide fragment necessary for unambiguous protein identification using fragments obtained from the experimentally derived sequences. Sequences of length $\geq 7$ residues provide unambiguous identification in conjunction with protein molecular mass as a filter. The length of sequence necessary for unambiguous protein identification is also established using randomly chosen tryptic fragments from a standard dataset of proteins. The results are of significance in the identification of proteins from organisms with unsequenced genomes.

Item Type:	Journal Article
Publication:	Molecular BioSystems
Publisher:	The Royal Society of Chemistry
Additional Information:	Copyright of this article belongs to The Royal Society of Chemistry.
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	26 Sep 2007
Last Modified:	19 Sep 2010 04:39
URI:	http://eprints.iisc.ac.in/id/eprint/11933

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