Chemistry: analytical and immunological testing – Peptide – protein or amino acid – Amino acid or sequencing procedure
Patent
1994-03-14
1996-07-23
Redding, David A.
Chemistry: analytical and immunological testing
Peptide, protein or amino acid
Amino acid or sequencing procedure
436 94, 436173, 530334, 530335, 530336, 530337, 530402, 530412, 530417, G01N 3300
Patent
active
055388973
ABSTRACT:
A method for correlating a peptide fragment mass spectrum with amino acid sequences derived from a database is provided. A peptide is analyzed by a tandem mass spectrometer to yield a peptide fragment mass spectrum. A protein sequence database or a nucleotide sequence database is used to predict one or more fragment spectra for comparison with the experimentally-derived fragment spectrum. In one embodiment, sub-sequences of the sequences found on the database which define a peptide having a mass substantially equal to the mass of the peptide analyzed by the tandem mass spectrometer are identified as candidate sequences. For each candidate sequence, a plurality of fragments of the sequence are identified and the masses and m/z ratios of the fragments are predicted and used to form a predicted mass spectrum. The various predicted mass spectra are compared to the experimentally derived fragment spectrum using a closeness-of-fit measure, preferably calculated with a two-step process, including a calculation of a preliminary score and, for the highest-scoring predicted spectra, calculation of a correlation function.
REFERENCES:
patent: 5240859 (1993-08-01), Aebersold
Powell and Heiftje, Anal. Chim. Acta, vol. 100, pp. 313-327 (1978).
Hunt, et al., "Protein Sequencing by Tandem Mass Spectrometry," Proc. Natl Acad. Sci. USA, 83:6233-6237 (1986).
Smith, et al., "Collisional Activation and Collision-Activated Dissociation of Large Multiply Charged Polypeptides and Proteins Produced by Electrospray Ionization," J. Am. Soc. Mass Spectrom., 1:53-65 (1990).
Burks, et al., "GenBank: Current Status and Future Directions in Methods in Enzymology," 183:3 (1990).
Kahn, et al., "EMBL Data Library", Methods in Enzymology, 183:23 (1990).
Barker, et al., "Protein Sequence Database," Methods in Enzymology, 183:31 (1990).
Griffin, et al., "Structural Analysis of Proteins by Capillary HPLC Electrospray Tandem Mass Spectrometry," Int'l J. Mass Spectrom. and Ion Processes, 111:131-149 (1991).
McLuckey, et al., "Tandem Mass Spectrometry of Small, Multiply Charged Oligonucleotides," J. Am. Soc. Mass Spectrom., 3:60-70 (1992).
Bairoch, et al., "The Swiss-Prot Protein Sequence Data Bank, Recent Developments," Nucleic Acids Res., 21:3093-3096 (1993).
"Index of the Protein Sequence Database of the International Association of Protein Sequence Databanks (PIR-International)", Protein Seq. Data Anal., 5:67-192 (1993).
Henzel, et al., "Identifying Proteins from Two-Dimensional Gels by Molecular Mass Searching of Peptide Fragments in Protein Sequence Databases,"Proc. Natl. Acad. Sci. USA, 90:5011-5015 (Jun. 1993).
Yates, III, et al., "Peptide Mass Maps: A Highly Informative Approach to Protein Identification," Analytical Biochemistry, 214:1-12 (1993).
Griffin, et al., "Analysis of Proteins by Mass Spectrometry," Analysis of Proteins by Mass Spectrometry, pp. 467-476 (no date).
Yates, III, et al., "Computer Aided Interpretation of Low Energy MS/MS Mass Spectra of Peptides," Techniques in Protein Chemistry II, pp. 477-485 (no date).
Eng James K.
Yates, III John R.
Redding David A.
University of Washington
LandOfFree
Use of mass spectrometry fragmentation patterns of peptides to i does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Use of mass spectrometry fragmentation patterns of peptides to i, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Use of mass spectrometry fragmentation patterns of peptides to i will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-712469