Protein identification in DNA databases by peptide mass fingerprinting

Protein Sci. 1994 Aug;3(8):1347-50. doi: 10.1002/pro.5560030822.


Proteins can be identified using a set of peptide fragment weights produced by a specific digestion to search a protein database in which sequences have been replaced by fragment weights calculated for various cleavage methods. We present a method using multidimensional searches that greatly increases the confidence level for identification, allowing DNA sequence databases to be examined. This method provides a link between 2-dimensional gel electrophoresis protein databases and genome sequencing projects. Moreover, the increased confidence level allows unknown proteins to be matched to expressed sequence tags, potentially eliminating the need to obtain sequence information for cloning. Database searching from a mass profile is offered as a free service by an automatic server at the ETH, Zürich. For information, send an electronic message to the address cbrg/ with the line: help mass search, or help all.

MeSH terms

  • Animals
  • Creatine Kinase / chemistry
  • Creatine Kinase / genetics
  • DNA / chemistry*
  • DNA, Complementary / chemistry
  • Databases, Factual*
  • Deuterium
  • Endopeptidases / metabolism
  • Gene Expression
  • Humans
  • Information Storage and Retrieval*
  • Isoenzymes
  • Mass Spectrometry
  • Molecular Sequence Data
  • Molecular Weight
  • Peptide Fragments / chemistry*
  • Peptide Fragments / genetics*
  • Peptide Fragments / metabolism


  • DNA, Complementary
  • Isoenzymes
  • Peptide Fragments
  • DNA
  • Deuterium
  • Creatine Kinase
  • Endopeptidases

Associated data

  • SWISSPROT/M22993
  • SWISSPROT/P11598