Patent ID: 8271203

Claim:
A non-transitory computer readable medium containing instructions for controlling a computer system to perform a method for ranking parent daughter ion transition pairs (PDITPs), the method comprising: receiving a target protein; determining one or more peptides that would result from cleavage of the target protein; determining one or more fragments that would result from subjecting the one or more peptides to a fragmentation experiment in a mass spectrometer; forming one or more PDITPs from the one or more fragments, where each PDITP comprises a daughter ion and its corresponding parent ion; calculating for each PDITP of the one or more PDITPs a probability of detection from a probability of one or more variables that relate a peptide of the each PDITP to the target protein and a probability of one or more variables that relate a fragment ion of the each PDITP to the peptide using the MRM scoring module; receiving at least one goal for the experiment; calculating for each PDITP of the one or more PDITPs a probability that the each PDITP is useful for the at least one goal; calculating a joint probability for each PDITP of the one or more PDITPs from the probability of detection and the probability that the each PDITP is useful for the at least one goal; and ranking the one or more PDITPs based on the joint probability.