Peptide and protein de novo sequencing by mass spectrometry

Curr Opin Struct Biol. 2003 Oct;13(5):595-601. doi: 10.1016/


Although the advent of large-scale genomic sequencing has greatly simplified the task of determining the primary structures of peptides and proteins, the genomic sequences of many organisms are still unknown. Even for those that are known, modifications such as post-translational events may prevent the identification of all or part of the protein sequence. Thus, complete characterization of the protein primary structure often requires determination of the protein sequence by mass spectrometry with minimal assistance from genomic data - de novo protein sequencing. This task has been facilitated by technical developments during the past few years: 'soft' ionization techniques, new forms of chemical modification (derivatization), new types of mass spectrometer and improved software.

Publication types

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

MeSH terms

  • Algorithms*
  • Amino Acid Sequence
  • Mass Spectrometry / methods*
  • Mass Spectrometry / trends*
  • Molecular Sequence Data
  • Molecular Weight
  • Peptides / analysis*
  • Peptides / chemistry*
  • Proteins / analysis*
  • Proteins / chemistry*
  • Sequence Analysis, Protein / methods*
  • Sequence Analysis, Protein / trends*
  • Spectrometry, Mass, Electrospray Ionization / methods
  • Spectrometry, Mass, Electrospray Ionization / trends
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / methods
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / trends


  • Peptides
  • Proteins