title: Clustering of MS spectra for improved protein identification rate and screening for protein variants and modifications by MALDI-MS/MS.
abstract: 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.
authors.affiliation: Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden. Irene.Granlund@plantphys.umu.se
authors.forename: Irene
authors.initials: I
authors.lastname: Granlund
authors.forename: Thomas
authors.initials: T
authors.lastname: Kieselbach
authors.forename: Rikard
authors.initials: R
authors.lastname: Alm
authors.forename: Wolfgang P
authors.initials: WP
authors.lastname: Schröder
authors.forename: Cecilia
authors.initials: C
authors.lastname: Emanuelsson
mesh_terms: D029681:Arabidopsis Proteins / Q000737:chemistry / Q000302:isolation & purification; D002736:Chloroplasts / Q000737:chemistry; D010940:Plant Proteins / Q000235:genetics / Q000302:isolation & purification*; D020033:Protein Isoforms / Q000302:isolation & purification*; D011499:Protein Processing, Post-Translational; D040901:Proteomics / Q000379:methods*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*; D018724:Spinacia oleracea / Q000737:chemistry; D053719:Tandem Mass Spectrometry / Q000379:methods
chemical_list: D029681:Arabidopsis Proteins; D010940:Plant Proteins; D020033:Protein Isoforms