title: Identification and relative quantification of proteins in Escherichia coli proteome by "up-front" collision-induced dissociation.
abstract: A method for identifying and quantifying proteins with relatively low-cost orthogonal acceleration time-of- flight mass spectrometry (oa-ToF-MS) was tested. Escherichia coli (E. coli) K12 MG1655 cell lysate was separated by 1D gel-electrophoresis; fractions were digested and separated fast and reproducibly by ultra-performance liquid chromatography (UPLC). Peptides were identified using oa-ToF-MS to measure exact masses of parent ions and the fragment ions generated by up-front collision-induced dissociation. Fragmentation of all compounds was achieved by rapidly cycling between high- and low values of energy applied to ions. More than 100 proteins from E. coli K12 proteome were identified and relatively quantified. Results were found to correlate with transcriptome data determined by DNA microarrays.
authors.affiliation: Competence Centre of Food and Fermentation Technologies, 12618 Tallinn, Estonia. liisa@tftak.eu
authors.forename: Liisa
authors.initials: L
authors.lastname: Arike
authors.forename: Ranno
authors.initials: R
authors.lastname: Nahku
authors.forename: Maria
authors.initials: M
authors.lastname: Borrisova
authors.forename: Kaarel
authors.initials: K
authors.lastname: Adamberg
authors.forename: Raivu
authors.initials: R
authors.lastname: Vilu
mesh_terms: D002851:Chromatography, High Pressure Liquid; D004591:Electrophoresis, Polyacrylamide Gel; D004926:Escherichia coli / Q000737:chemistry* / Q000235:genetics; D029968:Escherichia coli Proteins / Q000032:analysis*; D020869:Gene Expression Profiling; D016680:Genome, Bacterial; D020411:Oligonucleotide Array Sequence Analysis; D010449:Peptide Mapping; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D021241:Spectrometry, Mass, Electrospray Ionization; D053719:Tandem Mass Spectrometry
chemical_list: D029968:Escherichia coli Proteins; D020543:Proteome