UNIT 16.11 De Novo Peptide Sequencing via Manual Interpretation of MS/MS Spectra
Published Online: 1 MAY 2002
Copyright © 2003 by John Wiley and Sons, Inc.
Lab Protocol Title
Current Protocols in Protein Science
How to Cite
Addona, T. and Clauser, K. 2002. De Novo Peptide Sequencing via Manual Interpretation of MS/MS Spectra. Current Protocols in Protein Science. 27:16.11:16.11.1–16.11.19.
- Published Online: 1 MAY 2002
- Published Print: MAR 2002
Databases of complete genome sequences are rapidly appearing, and a recent trend in interpretation of peptide MS/MS spectra is database matching. A caveat of database matching is that it can only be successful if the database being searched contains the identical amino acid sequence, or one with high homology, to the peptide being investigated. In instances where high-quality MS/MS spectra are obtained for which there is no corresponding database match (e.g., when the peptide of interest is derived from a novel protein from an organism whose genome is not known, has post-translationally modified amino acids, or has multiple amino acid substitutions as compared to the homologous sequence from a different species), de novo (or manual) interpretation of the MS/MS spectrum, as described here, is required. Methods are also provided for verification of the results of the de novo analysis through chemical modification and limited manual Edman degradation of the peptide.