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Detection and identification of protein isoforms using cluster analysis of MALDI-MS mass spectra

  • Rikard Alm
  • Peter Johansson
  • K Hjerno
  • Cecilia Emanuelsson
  • Markus Ringnér
  • Jari Häkkinen
Publishing year: 2006
Language: English
Pages: 785-792
Publication/Series: Journal of Proteome Research
Volume: 5
Issue: 4
Document type: Journal article
Publisher: The American Chemical Society

Abstract english

We describe an approach to screen large sets of MALDI-MS mass spectra for protein isoforms separated on two-dimensional electrophoresis gels. Mass spectra are matched against each other by utilizing extracted peak mass lists and hierarchical clustering. The output is presented as dendrograms in which protein isoforms cluster together. Clustering could be applied to mass spectra from different sample sets, dates, and instruments, revealed similarities between mass spectra, and was a useful tool to highlight peptide peaks of interest for further investigation. Shared peak masses in a cluster could be identified and were used to create novel peak mass lists suitable for protein identification using peptide mass fingerprinting. Complex mass spectra consisting of more than one protein were deconvoluted using information from other mass spectra in the same cluster. The number of peptide peaks shared between mass spectra in a cluster was typically found to be larger than the number of peaks that matched to calculated peak masses in databases, thus modified peaks are probably among the shared peptides. Clustering increased the number of peaks associated with a given protein.


  • Cancer and Oncology
  • proteomics
  • protein
  • hierarchical clustering
  • identification
  • isoforms
  • mass spectra


  • ISSN: 1535-3893
Markus Ringnér
E-mail: markus [dot] ringner [at] biol [dot] lu [dot] se

Research engineer

Molecular Cell Biology


Sölvegatan 35, Lund