Patent ID: 7409296

Claim:
A method for scoring a match of two peptides, the method comprising: providing information associated with an experimental peptide, where the information comprises at least mass spectrum information associated with the experimental peptide and at least one fragment of the experimental peptide; providing information associated with a candidate peptide; defining an extended match E based on the information associated with the experimental peptide and the information associated with the candidate peptide, the extended match E being a probabilistic function of a tuple of random variables that include at least a fragment match and a peptide match between the experimental peptide and the candidate peptide; generating a stochastic model based on the information associated with the experimental peptide and the information associated with the candidate peptide, the stochastic model incorporating a probability distribution of each of the random variables; scoring the extended match E based on a likelihood ratio L = P ( E  ⁢ D , s , H 1 ) P ( E  ⁢ D , s , H 0 ) , where D is any extra information that is associated with the experimental peptide and the candidate peptide; s is a peptide sequence associated with the candidate peptide; H 1 is a hypothesis that the peptide sequence s is the correct sequence of the experimental peptide; H 0 is a null-hypothesis that the peptide sequence s is an erroneous sequence of the experimental peptide; and probabilities P(E|D,s,H 1 ) and P(E|D,s,H 0 ) are calculated based on the stochastic model; and outputting, in a user readable format, a result of the step of scoring the extended match E.