title: Differential stable isotope labeling of peptides for quantitation and de novo sequence derivation.
abstract: We have demonstrated the use of per-methyl esterification of peptides for relative quantification of proteins between two mixtures of proteins and automated de novo sequence derivation on the same dataset. Protein mixtures for comparison were digested to peptides and resultant peptides methylated using either d0- or d3-methanol. Methyl esterification of peptides converted carboxylic acids, such as are present on the side chains of aspartic and glutamic acid as well as the carboxyl terminus, to their corresponding methyl esters. The separate d0- and d3-methylated peptide mixtures were combined and the mixture subjected to microcapillary high performance liquid chromatography/tandem mass spectrometry (HPLC/MS/MS). Parent proteins of methylated peptides were identified by correlative database searching of peptide tandem mass spectra. Ratios of proteins in the two original mixtures could be calculated by normalization of the area under the curve for identical charge states of d0- to d3-methylated peptides. An algorithm was developed that derived, without intervention, peptide sequence de novo by comparison of tandem mass spectra of d0- and d3-peptide methyl esters.
authors.affiliation: The Institute for Systems Biology, 4225 Roosevelt Way NE, Suite 200, Seattle, WA 98105, USA. goodlett@systemsbiology.org
authors.forename: D R
authors.initials: DR
authors.lastname: Goodlett
authors.forename: A
authors.initials: A
authors.lastname: Keller
authors.forename: J D
authors.initials: JD
authors.lastname: Watts
authors.forename: R
authors.initials: R
authors.lastname: Newitt
authors.forename: E C
authors.initials: EC
authors.lastname: Yi
authors.forename: S
authors.initials: S
authors.lastname: Purvine
authors.forename: J K
authors.initials: JK
authors.lastname: Eng
authors.forename: P
authors.initials: P
authors.lastname: von Haller
authors.forename: R
authors.initials: R
authors.lastname: Aebersold
authors.forename: E
authors.initials: E
authors.lastname: Kolker
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D002851:Chromatography, High Pressure Liquid / Q000379:methods; D006801:Humans; D007553:Isotope Labeling; D007554:Isotopes; D019169:Jurkat Cells; D013058:Mass Spectrometry / Q000379:methods; D008969:Molecular Sequence Data; D010455:Peptides / Q000032:analysis / Q000737:chemistry*
chemical_list: D007554:Isotopes; D010455:Peptides