title: Quantitative proteomic analysis by accurate mass retention time pairs.
abstract: Current methodologies for protein quantitation include 2-dimensional gel electrophoresis techniques, metabolic labeling, and stable isotope labeling methods to name only a few. The current literature illustrates both pros and cons for each of the previously mentioned methodologies. Keeping with the teachings of William of Ockham, "with all things being equal the simplest solution tends to be correct", a simple LC/MS based methodology is presented that allows relative changes in abundance of proteins in highly complex mixtures to be determined. Utilizing a reproducible chromatographic separations system along with the high mass resolution and mass accuracy of an orthogonal time-of-flight mass spectrometer, the quantitative comparison of tens of thousands of ions emanating from identically prepared control and experimental samples can be made. Using this configuration, we can determine the change in relative abundance of a small number of ions between the two conditions solely by accurate mass and retention time. Employing standard operating procedures for both sample preparation and ESI-mass spectrometry, one typically obtains under 5 ppm mass precision and quantitative variations between 10 and 15%. The principal focus of this paper will demonstrate the quantitative aspects of the methodology and continue with a discussion of the associated, complementary qualitative capabilities.
authors.affiliation: Waters Corporation, 34 Maple Street, Milford, Massachusetts 01757-3696, USA. jeff_silva@waters.com
authors.forename: Jeffrey C
authors.initials: JC
authors.lastname: Silva
authors.forename: Richard
authors.initials: R
authors.lastname: Denny
authors.forename: Craig A
authors.initials: CA
authors.lastname: Dorschel
authors.forename: Marc
authors.initials: M
authors.lastname: Gorenstein
authors.forename: Ignatius J
authors.initials: IJ
authors.lastname: Kass
authors.forename: Guo-Zhong
authors.initials: GZ
authors.lastname: Li
authors.forename: Therese
authors.initials: T
authors.lastname: McKenna
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Nold
authors.forename: Keith
authors.initials: K
authors.lastname: Richardson
authors.forename: Phillip
authors.initials: P
authors.lastname: Young
authors.forename: Scott
authors.initials: S
authors.lastname: Geromanos
mesh_terms: D002851:Chromatography, High Pressure Liquid / Q000379:methods*; D003627:Data Interpretation, Statistical; D006801:Humans; D007477:Ions; D013058:Mass Spectrometry / Q000379:methods*; D010455:Peptides / Q000032:analysis* / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D044967:Serum / Q000737:chemistry; D013997:Time Factors
chemical_list: D007477:Ions; D010455:Peptides