Journal of the American Society for Mass Spectrometry

, Volume 14, Issue 9, pp 931–942

Protein identification: The origins of peptide mass fingerprinting


  • William J. Henzel
    • Protein Chemistry Department and Bioinformatics DepartmentGenentech, Inc.
  • Colin Watanabe
    • Protein Chemistry Department and Bioinformatics DepartmentGenentech, Inc.
    • Analytical Sciences DepartmentBiospect, Inc.
Focus: Proteomics Account And Perspective

DOI: 10.1016/S1044-0305(03)00214-9

Cite this article as:
Henzel, W.J., Watanabe, C. & Stults, J.T. J Am Soc Mass Spectrom (2003) 14: 931. doi:10.1016/S1044-0305(03)00214-9


Peptide mass fingerprinting (PMF) grew from a need for a faster, more efficient method to identify frequently observed proteins in electrophoresis gels. We describe the genesis of the idea in 1989, and show the first demonstration with fast atom bombardment mass spectrometry. Despite its promise, the method was seldom used until 1992, with the coming of significantly more sensitive commercial instrumentation based on MALDI-TOF-MS. We recount the evolution of the method and its dependence on a number of technical breakthroughs, both in mass spectrometry and in other areas. We show how it laid the foundation for high-throughput, high-sensitivity methods of protein analysis, now known as proteomics. We conclude with recommendations for further improvements, and speculation of the role of PMF in the future.

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© American Society for Mass Spectrometry 2003