title: A quantitative analysis of Arabidopsis plasma membrane using trypsin-catalyzed (18)O labeling.
abstract: Typical mass spectrometry-based protein lists from purified fractions are confounded by the absence of tools for evaluating contaminants. In this report, we compare the results of a standard survey experiment using an ion trap mass spectrometer with those obtained using dual isotope labeling and a Q-TOF mass spectrometer to quantify the degree of enrichment of proteins in purified subcellular fractions of Arabidopsis plasma membrane. Incorporation of a stable isotope, either H(2)(18)O or H(2)(16)O, during trypsinization allowed relative quantification of the degree of enrichment of proteins within membranes after phase partitioning with polyethylene glycol/dextran mixtures. The ratios allowed the quantification of 174 membrane-associated proteins with 70 showing plasma membrane enrichment equal to or greater than ATP-dependent proton pumps, canonical plasma membrane proteins. Enriched proteins included several hallmark plasma membrane proteins, such as H(+)-ATPases, aquaporins, receptor-like kinases, and various transporters, as well as a number of proteins with unknown functions. Most importantly, a comparison of the datasets from a sequencing "survey" analysis using the ion trap mass spectrometer with that from the quantitative dual isotope labeling ratio method indicates that as many as one-fourth of the putative survey identifications are biological contaminants rather than bona fide plasma membrane proteins.
authors.affiliation: Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706, USA.
authors.forename: Clark J
authors.initials: CJ
authors.lastname: Nelson
authors.forename: Adrian D
authors.initials: AD
authors.lastname: Hegeman
authors.forename: Amy C
authors.initials: AC
authors.lastname: Harms
authors.forename: Michael R
authors.initials: MR
authors.lastname: Sussman
mesh_terms: D029681:Arabidopsis Proteins / Q000032:analysis*; D002462:Cell Membrane / Q000378:metabolism*; D008565:Membrane Proteins / Q000032:analysis*; D020543:Proteome / Q000032:analysis*; D011868:Radioisotopes / Q000737:chemistry; D021241:Spectrometry, Mass, Electrospray Ionization
chemical_list: D029681:Arabidopsis Proteins; D008565:Membrane Proteins; D020543:Proteome; D011868:Radioisotopes