Chemistry: analytical and immunological testing – Nuclear magnetic resonance – electron spin resonance or other...
Reexamination Certificate
2004-07-16
2011-10-04
Gakh, Yelena G (Department: 1777)
Chemistry: analytical and immunological testing
Nuclear magnetic resonance, electron spin resonance or other...
C436S086000
Reexamination Certificate
active
08030089
ABSTRACT:
A method of identifying molecules of biological origin is disclosed. The molecules are identified and the basis of the accurately determined mass to charge ratio of the molecules and at least a further physico-chemical property such as elution time or charge state. Further physico-chemical properties may be used. The experimentally determined accurate mass and physico-chemical properties can then be compared with a look-up table of information. The look-up table may generated or physico-chemical properties of data in a conventional database may be calculated. The ability to recognize and preferably identify the same molecules in two different samples may be used to determine whether a particular biological molecules has been expressed differently in an experimental sample relative to a control sample.
REFERENCES:
patent: 4735777 (1988-04-01), Mitsui et al.
patent: 6017693 (2000-01-01), Yates et al.
patent: 6835927 (2004-12-01), Becker et al.
patent: 2002/0115056 (2002-08-01), Goodlett
patent: 2002/0119490 (2002-08-01), Aebersold et al.
patent: 1456667 (2006-05-01), None
patent: 2387653 (2003-10-01), None
patent: 2001 330599 (2001-11-01), None
patent: 00/03240 (2000-01-01), None
patent: WO 00/60361 (2000-10-01), None
patent: WO 01/57518 (2001-08-01), None
patent: 02/052259 (2002-07-01), None
patent: 02/072863 (2002-09-01), None
patent: WO 03/042774 (2003-05-01), None
Link et al. “Direct analysis of protein complexes using mass spectrometry”, Nature Biotechnology, 1999, v. 17, pp. 676-682.
Carr et al. “Overview of Peptide and Protein Analysis by Mass Spectrometry”, Current Protocols in Protein Science, 1996, pp. 16.1.1-16.1.27.
Bakhtiar et al. “Mass spectrometry of the proteome”, Molecular Pharmacology, 2001, 2001, v.60, pp. 405-415.
Clauser et al. “Role of Accurate Mass Measurement (±10 ppm) in Protein Identification Strategies Employing MS or MS/MS and Database Searching”, Anal. Chem., 1999, v. 71, pp. 2871-2882.
Stone discloses “Surface-Induced Dissociation on a MALDI-Ion Mobility-Orthogonal Time-of-Flight Mass Spectrometer: Sequencing Peptides from an “In-Solution” Protein Digest”, Anal. Chem., 2001, v/ 73, pp. 2233-2236.
Sequence analysis of peptide mixtures by automated integratin of Edman and mass spectrometric data, R.S. Johnson and K.A. Walsh, Proteing Science (1991), I, 1083-1091.
Quantitative Profiling of Proteins in Complex Mixtures Using Liquid Chromatography and Mass Spectrometry, Dirk Chelius Journal of Proteome Research 202, 1, 317-323.
American Society for Mass Spectrometry: Education, ASMS, What is Mass Spectrometry, p. 1 of 1, last updated Dec. 1, 2001.
Direct analysis of protein complexes using mass spectrometry, Link, et al., Nature Biotechnology, 1999, vol. 17, pp. 676-682.
De Novo Peptide Sequencing via Tandem Mass Spectrometry: A Graph-Theoretical Approach, Dancik, et al., RECOMB '99 , pp. 135-144.
Biomedical applications of two-dimensional electrophoresis using immobilized pH gradients:, S. Hanash, Electrophoresis 2000, 21, 12-02-1209.
Two-dimensional map of the proteome ofHaemophilus influenzae, Langen, et al., Electrophoresis 2000, 21, 411-429.
“Capillary column high-performance liquid chromatographic-electrospray ionization . . . ”, Nakayama, et al., J. Chrom. A, 1996, vol. 730, p. 279-287.
Large-scale analysis of the yeast proteome by multidimensional protein identification technology, Washburn, et al, Nat. Bio., 2001, vol. 19 p. 242-247.
Analysis of the microbial proteome, Washburn et al., Current Opinion in Microbiology, 2000, vol. 3, p. 292-297.
Accurate quantitation of protein expression and site-specific phosphorylation, Oda, et al, Proc. Nat. Aca. Sci. USA 1999.
The N-end rule: Functions, mysteries, uses, A. Varshaysky, Proc. Nat. Acad. Sci. USA, 1996,93 p. 12142-12149.
Rapid identification of proteins by peptide-mass fingerprinting, Pappin, et al., Current Biology 1993, vol. 3, pp. 327-332.
DeRisi, et al., Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale, Science, vol. 278, pp. 680-686.
Roth, et al., “Finding DNA regulatory motifs within unaligned noncoding sequences . . . ”, Nature Biotech, 1998, vol. 16, pp. 939-945.
Pandey, et al., Proteomics to study genes and genomes, Nature 2000, vol. 405, pp. 837-846.
John Cottrell, Protein Identification by Peptide Mass Fingerprinting, Peptide Research, 1994, vol. 7 (3) pp. 115-124.
Li, et al., “High-Throughput Peptide Identification from Protein Digests Using . . . ”, Anal chem. 2001, vol. 73, pp. 3312-3322.
Shen, et al., “High-Throughput Proteomics Using High-Efficiency Multiple-Capillary . . . ”, Anal. Chem. 2001, vol. 73 pp. 3011-3021.
Jensen, et al., “Identification of the Components of Simple Protein Mixtures by High-Accuracy Peptide Mass Mapping . . . ”, Anal. Chem., vol. 69, pp. 4741-4750.
Griffin, et al., “Quantitative Proteomic Analysis Using a MALDI Quadrupole . . . ”, Anal Chem. 2001, vol. 73 pp. 978-986.
Dongre, Ashok R., et al; Emerging tandem-mass-spectrometry techniques for the rapid identification of proteins; TIBTECH Oct. 1997, (vol. 15); Elsevier Science Ltd 1997; 418-425.
Soskic, V. et al; Functional Proteomics Analysis of Signal Transduction Pathways of the Platelet-Derived Growth Factor Beta Receptor, Biochemistry, American Chemical Society, vol. 38, 1999, pp. 1757-1764.
Perkins, David N. et al; Probability-based protein identification by searching sequence databases using mass spectrometry data; Electrophoresis 1999, vol. 20, pp. 3551-3567.
Gras, Robin, et al; Improving protein identification from peptide mass fingerprinting through a parameterized multi-level scoring algorithm and an optimized peak detection; Electrophoresis 1999, vol. 20, pp. 3535-3550.
Pang, James X. et al; Biomarker Discovery in Urine by Proteomics; Journal of Proteome Research Mar. 2002, vol. 1, No. 2, pp. 161-169.
Gygi, S. P. et al; Quantitative analysis of complex protein mixtures using isotope-coded affinity tags; Nature Biotechnology, vol. 17, No. 10, Oct. 1999, pp. 994-999.
Tempst, Paul, et al; MALDI-TOF Mass Spectrometry in the Protein Biochemistry Lab: From Characterization of Cell Cycle Regulators to the Quest for Novel Antibiotics; Mass Spectrometry In The Biological Sciences; 1995, 105-133.
Thomas, Rexford L. et al, Mass Spectrometric Identification of Increased C16 Ceramide Levels During Apoptosis, The Journal of Biological Chemistry; 1999, pp. 30580-30588, vol. 274, The American Society for Biochemistry and Molecular Biology, Inc.
Fiehn, Oliver et al, Metabolite profiling for plant functional genomics, Nature Biotechnology, 2000, pp. 1157-1161, vol. 18.
Fiehn, Oliver et al, Identification of Uncommon Plant Metabolites Based on Calculation of Elemental Compositions Using Gas Chromatography and Quadrupole Mass Spectrometry, Analytical Chemistry, 2000, pp. 3573-3580, vol. 72, American Chemical Society.
Niwa, Toshimitsu et al, Gas Chromatographic-Mass Spectrometric Profile of Organic Acids in Urine and Serum of Diabetic Ketotic Patients, Journal of Chromatography, 1981, pp. 1-8, Elsevier Scientific Publishing Company, Amesterdam.
Lochner, April et al, Gas Chromatographic-Mass Spectrometric Analysis of Volatile Constituents in Saliva, Journal of Chromatography, 1986, pp. 267-282, Elsevier Scientific Publishing Company, Amesterdam.
Goodlett, David R. et al, Protein Identification with a Single Accurate Mass of a Cysteine-Containing Peptide and Constrained Database Searching, Analytical Chemistry, 2000, pp. 1112-1118, vol. 72, No. 6, American Chemical Society.
Griffin, Timothy J. et al, Quantitative Proteomic Analysis Using a MALDI Quadrupole Time-of-Flight Mass Spectrometer, Analytical Chemistry, 2001, pp. 978-986, vol. 73, No. 5, American Chemical Society.
Johnson, R. S. et al, Sequence Analysis of Peptide Mixtures by Automated Integratin of Edman and Mass Spectrometric Data, Proteing Science, 1991, 1, 1083-1091.
Chelius, Dirk, Quantitative Profiling of Proteins in Complex Mixtures Using Liquid Chr
Dongre Ashok R.
Geromanos Scott
Opiteck Gregory
Silva Jeffrey
Diederiks & Whitelaw PLC
Gakh Yelena G
Micromass UK Limited
LandOfFree
Method of analyzing differential expression of proteins in... does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Method of analyzing differential expression of proteins in..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Method of analyzing differential expression of proteins in... will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-4273157