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Clustering of MS spectra for improved protein identification rate and screening for protein variants and modifications by MALDI-MS/MS
Umeå University, Faculty of Science and Technology, Department of Chemistry.
Umeå University, Faculty of Science and Technology, Department of Chemistry.
Department of Biochemistry, Centre for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.
Umeå University, Faculty of Science and Technology, Department of Chemistry.
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2011 (English)In: Journal of proteomics, ISSN 1876-7737, Vol. 74, no 8, 1190-1200 p.Article in journal (Refereed) Published
Abstract [en]

It is an established fact that allelic variation and post-translational modifications create different variants of proteins, which are observed as isoelectric and size subspecies in two-dimensional gel based proteomics. Here we explore the stromal proteome of spinach and Arabidopsis chloroplast and show that clustering of mass spectra is a useful tool for investigating such variants and detecting modified peptides with amino acid substitutions or post-translational modifications. This study employs data mining by hierarchical clustering of MALDI-MS spectra, using the web version of the SPECLUST program ( The tool can also be used to remove peaks of contaminating proteins and to improve protein identification, especially for species without a fully sequenced genome. Mutually exclusive peptide peaks within a cluster provide a good starting point for MS/MS investigation of modified peptides, here exemplified by the identification of an A to E substitution that accounts for the isoelectric heterogeneity in protein isoforms.

Place, publisher, year, edition, pages
Science , 2011. Vol. 74, no 8, 1190-1200 p.
Keyword [en]
2-DE PAGE; Hierarchical clustering; MALDI-TOF mass spectrometry, MS/MS, post-translational modification, proteomics
National Category
Chemical Sciences
URN: urn:nbn:se:umu:diva-43921DOI: 10.1016/j.jprot.2011.04.008PubMedID: 21539947OAI: diva2:417299
Available from: 2011-05-16 Created: 2011-05-16 Last updated: 2011-09-29Bibliographically approved

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Granlund, IreneKieselbach, ThomasSchröder, Wolfgang P
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