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Use of mass spectrometry fragmentation patterns of peptides to identify amino acid sequences in databases
| Details |
Inventors: Yates, III, John R.; Eng, James K.;
Assignee: University of Washington (Seattle, WA)
Primary Examiner: Redding; David A.
Assistant Examiner:
Attorney, Agent or Firm: Townsend and Townsend and Crew
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. |
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DETAILED DESCRIPTION According to the present invention, known amino acid sequences, e.
g.
, in a protein sequence library, are used to calculate or predict one or more candidate fragment spectra.
The predicted fragment spectra are then compared with an experimentally-derived fragment spectrum to determine the best match or matches.
Preferably, the parent peptide, from which the fragment spectrum was derived has a known mass.
Subsequences of the various sequences in the protein sequence library are analyzed to identify those sub-sequences corresponding to a peptide whose mass is equal to (or within a given tolerance of) the mass of the parent peptide in the fragment spectrum.
For each sub-sequence having the proper mass, a predicted fragment spectrum can be calculated, e.
g.
, by calculating masses of various amino acid subsets of the candidate peptide.
The result will be a plurality of candidate peptides, each with a predicted fragment spectrum.
The predicted fragment spectra can then be compared with the fragment spectrum derived from the tandem mass spectrometer to identify one or more proteins having sub-sequences which are likely to be identical with the sequence of the peptide which resulted in the experimentally-derived fragment spectrum.
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