title: NeuCode labels for relative protein quantification.
abstract: We describe a synthesis strategy for the preparation of lysine isotopologues that differ in mass by as little as 6 mDa. We demonstrate that incorporation of these molecules into the proteomes of actively growing cells does not affect cellular proliferation, and we discuss how to use the embedded mass signatures (neutron encoding (NeuCode)) for multiplexed proteome quantification by means of high-resolution mass spectrometry. NeuCode SILAC amalgamates the quantitative accuracy of SILAC with the multiplexing of isobaric tags and, in doing so, offers up new opportunities for biological investigation. We applied NeuCode SILAC to examine the relationship between transcript and protein levels in yeast cells responding to environmental stress. Finally, we monitored the time-resolved responses of five signaling mutants in a single 18-plex experiment.
authors.affiliation: From the ‡Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706; §Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706;
authors.forename: Anna E
authors.initials: AE
authors.lastname: Merrill
authors.affiliation: From the ‡Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706;
authors.forename: Alexander S
authors.initials: AS
authors.lastname: Hebert
authors.affiliation: ¶Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706;
authors.forename: Matthew E
authors.initials: ME
authors.lastname: MacGilvray
authors.affiliation: From the ‡Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706; §Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706;
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Rose
authors.affiliation: From the ‡Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706;
authors.forename: Derek J
authors.initials: DJ
authors.lastname: Bailey
authors.affiliation: ‖Cambridge Isotope Laboratories, Andover, Massachusetts 01810;
authors.forename: Joel C
authors.initials: JC
authors.lastname: Bradley
authors.affiliation: ‖Cambridge Isotope Laboratories, Andover, Massachusetts 01810;
authors.forename: William W
authors.initials: WW
authors.lastname: Wood
authors.affiliation: ‖Cambridge Isotope Laboratories, Andover, Massachusetts 01810;
authors.forename: Marwan
authors.initials: M
authors.lastname: El Masri
authors.affiliation: From the ‡Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706;
authors.forename: Michael S
authors.initials: MS
authors.lastname: Westphall
authors.affiliation: From the ‡Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706; ¶Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706;
authors.forename: Audrey P
authors.initials: AP
authors.lastname: Gasch
authors.affiliation: From the ‡Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706; §Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706; **Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53706 jcoon@chem.wisc.edu.
authors.forename: Joshua J
authors.initials: JJ
authors.lastname: Coon
mesh_terms: D008239:Lysine / Q000378:metabolism; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D029701:Saccharomyces cerevisiae Proteins / Q000032:analysis* / Q000187:drug effects / Q000378:metabolism; D012965:Sodium Chloride / Q000494:pharmacology; D013312:Stress, Physiological / Q000502:physiology
chemical_list: D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins; D012965:Sodium Chloride; D008239:Lysine