Clustering of MS spectra for improved protein identification rate and screening for protein variants and modifications by MALDI-MS/MS
2011 (English)In: Journal of proteomics, ISSN 1876-7737, Vol. 74, no 8, 1190-1200 p.Article in journal (Refereed) Published
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 (http://bioinfo.thep.lu.se/speclust.html). 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.
2-DE PAGE; Hierarchical clustering; MALDI-TOF mass spectrometry, MS/MS, post-translational modification, proteomics
IdentifiersURN: urn:nbn:se:umu:diva-43921DOI: 10.1016/j.jprot.2011.04.008PubMedID: 21539947OAI: oai:DiVA.org:umu-43921DiVA: diva2:417299