title: Quantitative analysis of protein expression using amine-specific isobaric tags in Escherichia coli cells expressing rhsA elements.
abstract: We describe the use of amine-specific isobaric tags for protein expression quantification to study the effect of rhsA element over-expression in Escherichia coli. The use of an isobaric tagging strategy facilitates a shotgun approach to proteomic analysis and enables quantitation of up to four samples in parallel, based on the reporter ion series using tandem mass spectrometry (MS/MS). Using a liquid chromatography matrix-assisted laser desorption/ionization approach, 23,139 MS/MS spectra were collected. Five thousand sixty-three peptides derived from 780 proteins were quantified including several lower abundance proteins, such as transcription factors, DnaB and DnaG. More than 65% of the proteins had at least two high confidence peptide matches per protein (p<0.05). Further, a statistical test based on the Grubb's and Rosner's tests was able to discriminate outlier data. The removal of outlier data had no significant effect on the functional categories of proteins that were represented in the study.
authors.affiliation: School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853-5201, USA.
authors.forename: Kunal
authors.initials: K
authors.lastname: Aggarwal
authors.forename: Leila H
authors.initials: LH
authors.lastname: Choe
authors.forename: Kelvin H
authors.initials: KH
authors.lastname: Lee
mesh_terms: D000588:Amines / Q000737:chemistry*; D002853:Chromatography, Liquid; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000096:biosynthesis* / Q000737:chemistry; D007202:Indicators and Reagents / Q000737:chemistry; D040901:Proteomics; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
chemical_list: D000588:Amines; D029968:Escherichia coli Proteins; D007202:Indicators and Reagents