Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving hydrolase
Reexamination Certificate
2003-06-04
2010-02-02
Tate, Christopher R (Department: 1651)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving hydrolase
C435S004000, C435S018000, C435S212000, C436S089000
Reexamination Certificate
active
07655433
ABSTRACT:
The invention provides methods for identifying and quantifying polypeptides in a sample. The methods include the steps of labeling peptides in a polypeptide sample with an isotope tag; adding a plurality of peptide standards to the polypeptide sample, wherein the peptide standards are labeled with an isotopically distinct version of the isotope tag; resolving the labeled sample and standard peptides into a plurality of fractions; analyzing the resolved fractions using mass spectrometry; identifying an isotope-tagged sample peptide in an analyzed fraction; and determining the amount of the identified isotope-tagged sample peptide in the analyzed fraction by comparison to the amount of isotope tagged standard peptide in the same fraction.
REFERENCES:
patent: 6824981 (2004-11-01), Chait et al.
patent: 2002/0146349 (2002-10-01), Gygi et al.
patent: 2003/0148462 (2003-08-01), Kirschner et al.
patent: 2004/0229283 (2004-11-01), Gygi et al.
patent: 2004/0235186 (2004-11-01), Gygi et al.
patent: 2004/0259164 (2004-12-01), Gygi et al.
patent: 2005/0164324 (2005-07-01), Gygi
patent: WO00/11208 (2000-03-01), None
patent: WO 03/078962 (2003-09-01), None
Griffin et al. (2001). “Quantitative proteomic analysis using a MALDI quadrupole time-of-flight mass spectrometer,” Analytical Chemistry vol. 73, pp. 978-986.
J. Ji et al. (2000). “Strategy for qualitative and quantitative analysis in proteomics based on signiture peptides,” Journal of Chromatography B vol. 745, pp. 197-210.
W. Schroedl, L. Jaekel, and M. Krueger “C-Reactive Protein and Antibacterial Activity in Blood Plasma of Colostrum-Fed Calves and the Effect of Lactulose” J. Dairy Sci. 86:3313-3320 .
Dictionary.com (www.dictionary.com), Definition of “synthetic” and “correspond” Last accessed May 17, 2006.
Answers.com definition of “blood plasma” and “serum”. Accessed May 17, 2006 4pgs.
William Williams, David Weiner, “Biologically Active Peptides:Design, Synthesis and Utilization”, 1993, CRC Press, p. 124 to 126.
Stryer, Lubert, “Biochemistry” 4th ed., WH Freeman p. 56-57.
Viaene et al. “Efficient expression of bovine a-lactalbumin inSaccharomyces cerevisiae” Eur. J. Biochem. 202, 471-477 (1991).
Swiss-Prot, Uni-Prot knowledge database, (http://ca.expasy.org/sprot/) Accessed May 17, 2006.
Yasushi Ishihama, Toshitaka Sato, Tsuyoshi Tabata, Norimasa Miyamoto, Koji Sagane, Takeshi Nagasu & Yoshiya Oda, Quantitative mouse brain proteomics using culture-derived isotope tags as internal standards, Nature Biotechnology 23, 617-621 (2005), Published online: Apr. 17, 2005.
JR Barr, VL Maggio, DG Patterson Jr, GR Cooper, LO Henderson, WE Turner, SJ Smith, WH Hannon, LL Needham and EJ Sampson, Isotope dilution—mass spectrometric quantification of specific proteins: model application with apolipoprotein A-I, Clinical Chemistry, vol. 42, 1676-1682, (1996).
David R. Barnidge, Edward A. Dratz, Therese Martin, Leo E. Bonilla, Liam B. Moran, and Arnold Lindall , Absolute Quantification of the G Protein-Coupled Receptor Rhodopsin by LC/MS/MS Using Proteolysis Product Peptides and Synthetic Peptide Standards, Analytical chemistry, 75(3), pp. 445-451 (2003).
Lambert, J.B., Shurvell, H.F, Lightner, D.A., and Cooks, R.G. “Basics of Mass Spectrometry” Introduction to Organic Spectroscopy. MacMillan, 1987, chapter 11, pp. 315-344.
Dictionary.com (www.dictionary.com), Definition of “synthetic” and “correspond” , Last accessed May 17, 2006, 7 pages.
Answers.com definition of “blood plasma” and “serum”, Accessed May 17, 2006, 4 pages.
William Williams, David Weiner, “Biologically Active Peptides:Design, Synthesis and Utilization”, CRC Press, 1993, pp. 124 to 126.
Stryer, Lubert, “Biochemistry” 4th ed., WH Freeman, 1995, pp. 56-57.
Viaene, et al. “Efficient expression of bovine a-lactalbumin inSaccharomyces cerevisiae” Eur. J. Biochem., 1991, vol. 202, pp. 471-477.
Swiss-Prot, Uni-Prot knowledge database, (http://ca.expasy.org/sprot/) Accessed May 30, 2006, 3 pages.
Yasushi Ishihama, Toshitaka Sato, Tsuyoshi Tabata, Norimasa Miyamoto, Koji Sagane, Takeshi Nagasu & Yoshiya Oda, “Quantitative mouse brain proteomics using culture-derived isotope tags as internal standards, Nature Biotechnology”, 2005 (Published online: Apr. 17, 2005), vol. 23, pp. 617-621.
JR Barr, VL Maggio, DG Patterson Jr, GR Cooper, LO Henderson, WE Turner, SJ Smith, WH Hannon, LL Needham and EJ Sampson, “Isotope dilution—mass spectrometric quantification of specific proteins: model application with apolipoprotein A-I”, Clinical Chemistry, 1996, vol. 42, pp. 1676-1682.
David R. Barnidge, Edward A. Dratz, Therese Martin, Leo E. Bonilla, Liam B. Moran, and Arnold Lindell , “Absolute Quantification of the G Protein-Coupled Receptor Rhodopsin by LC//MS/MS Using Proteolysis Product Peptides and Synthetic Peptide Standards”, Analytical chemistry, 2003, 75(3), pp. 445-451.
Aebersold and Goodlett, “Mass Spectrometry in Proteomics,”Chem. Rev. 101: 269-295 (2001).
Aebersold and Mann, “Mass spectrometry-based proteomics,”Nature422:198-207 (2003).
Bodansky and Bodansky,The Practice of Peptide Synthesis, vol. 21 Springer-Verlag, New York (1984).
Eng et al., “An Approach to Correlate Tandem Mass Spectral Data of Peptides with Amino Acid Sequences in a Protein Database,”J. Amer. Soc. Mass Spec. 5:976-989 (1994).
Gerber et al., Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS.,Proc. Natl. Acad. Sci. USA100:6940-6945 (2003).
Glazer et al., “Laboratory Techniques in Biochemistry and Molecular Biology: Chemical Modification of Proteins,”Elsevier Biomedicalchapter 3, pp. 68-120 (1975).
Goshe et al., “Phosphoprotein Isotope-Coded Affinity Tag Approach for Isolating and Quantitating Phosphopeptides in Proteome-Wide Analyses,”Anal. Chem. 73:2578-2586 (2001).
Griffin and Aebersold, “Advances in Proteome Analysis by Mass Spectrometry,”J. Biol. Chem. 276:45497-45500 (2001).
Gygi et al., “Quantitative analysis of complex protein mixtures using isotope-coded affinity tags,”Nature Biotechnical17:994-999 (1999).
Hermanson, “Bioconjugate Techniques,”Academic Presspp. 297-364 (1996).
Houghten, R., “General method of the rapid solid-phase synthesis of large numbers of peptides: specificity of antigen-antibody interaction at the level of individual amino acids,”Proc. Natl. Acad. Sci. USA, 82:5131-5135 (1985).
Kinter and Sherman, “Protein Sequencing and Identification Using Tandem Mass Spectrometry,”John Wiley&Sons(2000).
Merrifield, R.B., “Solid Phase Peptide Synthesis,”J. Am. Chem. Soc. 85:2149-2154 (1963).
Smolka et al., “Optimization of the Isotope-Coded Affinity Tag-Labeling Procedure for Quantitative Proteome Analysis,”Anal. Chem. 297:25-31 (2001).
Smolka et al., “Quantitative Protein Profiling Using Two-dimensional Gel Electrophoresis, Isotope-coded Affinity Tag Labeling, and Mass Spectrometry,”Molec. Cell. Proteomics1:19-29 (2002).
Yates et al., “Mass Spectrometry and the Age of the Proteome,”J. Mass Spect. 33:1-19 (1998).
Zhou et al., “A systematic approach to the analysis of protein phosphorylation,”Nat. Biotechnol19:375-378 (2001).
Zhou et al., “Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry,”Nat. Biotechnol20:512-515 (2002).
Gerber et al., “Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS,”Proc. Natl. Acad. Sci. USA100: 6940-6945 (2003).
Harvard University, “Absolute Quantification of Proteins (AQUA),” http://www.techtransfer.harvard.edu/cgi-bin/TALSearch.cgi?full—report=1&case=1918>, 2006, 1 page.
Sigma-Aldrich, “A
Kosar Aaron J
McDermott Will & Emery LLP
Tate Christopher R
The Institute for Systems Biology
LandOfFree
Methods for high-throughput and quantitative proteome analysis does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Methods for high-throughput and quantitative proteome analysis, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Methods for high-throughput and quantitative proteome analysis will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-4212326