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J Biomol Tech. 2010 September; 21(3 Suppl): S11.
PMCID: PMC2918153

Peptide Identification by Database Search



Protein identification and characterisation by database searching is a well-established technique, contributing to more than 1000 peer reviewed publications each year. The procedure is non-trivial because real MS/MS spectra are not ideal transformations of peptide sequences. A real mass spectrum has finite resolution and finite signal to noise ratio, mass spectrometers have limited mass accuracy, peptide precursor ions rarely dissociate into complete fragment ion series, enzymes cleave proteins with imperfect fidelity, and typical sample handling can induce chemical artifacts.

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