Patent ID: 8515686

Claim:
A method for testing whether a target polypeptide is present in a sample of a set of polypeptides comprising: a) providing a sample of a set of polypeptides to be tested for the presence of a target polypeptide; b) selecting a database corresponding to the set of polypeptides having information stored therein that describes a characteristic of each polypeptide of the set, wherein the database is created according to the following steps comprising: i) selecting a first database having information representing amino acid sequences of substantially all polypeptides of a set of polypeptides stored therein; ii) utilizing each sequence to predict a mass/charge ratio for each polypeptide of the set of polypeptides obtainable when a pre-defined ionization condition is applied to polypeptides of the set; iii) selecting sequences that represent polypeptides that have the same predicted mass/charge ratio; iv) predicting a mass of each fragment ion obtainable from polypeptides represented by each selected sequence when a pre-defined fragmentation condition is applied to each polypeptide represented by the selected sequences; v) for each polypeptide represented by the selected sequences, identifying a predicted mass of at least one fragment ion that is different from the predicted masses of fragment ions of polypeptides represented by other selected sequences, to derive one or more values for each polypeptide of the set of polypeptides that distinguishes polypeptides of the set from each other; vi) storing each value so derived in a computer readable medium, thereby creating the database containing values for distinguishing each polypeptide of a set of polypeptides from each other; c) interrogating the database to determine a value for the target polypeptide that can be used to configure a mass spectrometer to exclude the detection of polypeptides having a value that is not the same as the value determined for the target polypeptide, so that the target polypeptide may be selectively detected by the mass spectrometer; d) utilizing the value determined for the target polypeptide to configure the mass spectrometer; e) applying the sample of the set of polypeptides to the configured mass spectrometer; and f) utilizing the configured mass spectrometer to test whether the target polypeptide is present in the sample of the set of polypeptides.