De novo sequencing and homology searching

Mol Cell Proteomics. 2012 Feb;11(2):O111.014902. doi: 10.1074/mcp.O111.014902. Epub 2011 Nov 16.


In proteomics, de novo sequencing is the process of deriving peptide sequences from tandem mass spectra without the assistance of a sequence database. Such analyses have traditionally been performed manually by human experts, and more recently by computer programs that have been developed because of the need for higher throughput. Although powerful, de novo sequencing often can only determine partially correct sequence tags because of imperfect tandem mass spectra. However, these sequence tags can then be searched in a sequence database to identify the exact or a homologous peptide. Homology searches are particularly useful for the study of organisms whose genomes have not been sequenced. This tutorial will present background important to understanding de novo sequencing, suggestions on how to do this manually, plus descriptions of computer algorithms used to automate this process and to subsequently carryout homology-based database searches. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 1).

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms*
  • Amino Acid Sequence
  • Databases, Protein
  • Humans
  • Molecular Sequence Data
  • Peptide Fragments / analysis*
  • Proteomics*
  • Sequence Analysis, Protein*
  • Sequence Homology, Amino Acid
  • Software
  • Tandem Mass Spectrometry*
  • Teaching*


  • Peptide Fragments