Unit

UNIT 16.11 De Novo Peptide Sequencing via Manual Interpretation of MS/MS Spectra

  1. Terri Addona,
  2. Karl Clauser

Published Online: 1 MAY 2002

DOI: 10.1002/0471140864.ps1611s27

Current Protocols in Protein Science

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.

Author Information

  1. Millennium Pharmaceuticals, Cambridge, Massachusetts

Publication History

  1. Published Online: 1 MAY 2002
  2. Published Print: MAR 2002

Abstract

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.