Detection and Quantification of Polypeptides Using Mass Spectrometry

A method for deriving one or more unique mass descriptors (UMDs) for distinguishing polypeptides of a set of polypeptides from each other comprising:

• a) selecting a database having information representing amino acid sequences of substantially all polypeptides of a set of polypeptides stored therein;
• b) utilizing each sequence to predict a mass/charge ratio for each polypeptide of the set of polypeptides obtainable when a pre-defined sample ionisation condition is applied to polypeptides of the set;
• c) selecting sequences that represent polypeptides that have the same predicted mass/charge ratio;
• d) 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;
• e) for each polypeptide represented by the selected sequences, identifying a predicted mass (UMD) of at least one fragment ion that is different from the predicted masses (UMDs) of fragment ions of polypeptides represented by other selected sequences;
• thereby deriving one or more UMDs for each polypeptide of the set of polypeptides that distinguishes polypeptides of the set from each other.

A database containing one or more unique mass descriptors (UMDs) for distinguishing each polypeptide of a set of polypeptides from each other, wherein the database is created according to the following steps comprising:

• a) selecting a first database having information representing amino acid sequences of substantially all polypeptides of a set of polypeptides stored therein;
• b) utilizing each sequence to predict a mass/charge ratio for each polypeptide of the set of polypeptides obtainable when a pre-defined ionisation condition is applied to polypeptides of the set;
• c) selecting sequences that represent polypeptides that have the same predicted mass/charge ratio;
• d) 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;
• e) for each polypeptide represented by the selected sequences, identifying a predicted mass (UMD) of at least one fragment ion that is different from the predicted masses (UMDs) of fragment ions of polypeptides represented by other selected sequences, to derive one or more UMDs for each polypeptide of the set of polypeptides that distinguishes polypeptides of the set from each other;
• f) storing each UMD so derived in a computer readable medium, thereby creating the database containing UMDs for distinguishing each polypeptide of a set of polypeptides from each other.

An apparatus for configuring a mass scan of a mass spectrometer to test whether a target polypeptide of a set of polypeptides is present in a sample of the set comprising:

• a) a processor having stored thereon an executable code for deriving one or more unique mass descriptors (UMDs) for distinguishing a target polypeptide from other polypeptides of a set of polypeptides;
• b) input means in communication with the processor for identifying the target polypeptide for which the one or more UMDs is to be derived by the executable code;
• c) configuring means in communication with the processor for configuring a mass scan of a mass spectrometer according to the one or more UMDs derived by the executable code;
• wherein in use, the executable code derives the one or more UMDs according to the following steps:
• (i) utilizing information representing the amino acid sequences of the polypeptides of the set of polypeptides to predict a mass/charge ratio for each polypeptide obtainable when a pre-defined ionisation condition is applied to polypeptides of the set;
• (ii) selecting sequences that represent polypeptides that have the same predicted mass/charge ratio as the target polypeptide;
• (iii) 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;
• (iv) identifying a predicted mass (UMD) of at least one fragment ion of the target polypeptide that is different from the predicted masses (UMDs) of fragment ions of polypeptides represented by the selected sequences;
• thereby deriving one or more UMDs for distinguishing the target polypeptide from other polypeptides of a set of polypeptides.

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,
• c) interrogating the database to determine one or more values 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 one or more values determined for the target polypeptide, so that the target polypeptide may be selectively detected by the mass spectrometer;
• d) utilizing the one or more values 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,
• 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 ionisation 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.

A method for testing whether a target polypeptide is present in a sample of a set of polypeptides wherein said target polypeptide has one or more unique mass descriptors (UMDs) that can be used to configure a mass spectrometer to exclude the detection of polypeptides having a UMD that is not the same as the one or more UMDs determined for the target polypeptide, said method comprising:

• a) providing a sample of a set of polypeptides to be tested for the presence of a target polypeptide;
• b) utilizing said one or more UMDs of said target polypeptide to configure a mass spectrometer;
• c) applying the sample of the set of polypeptides to the configured mass spectrometer;
• and
• d) utilizing the configured mass spectrometer to test whether the target polypeptide is present in the sample of the set of polypeptides,
• wherein each UMD comprises the predicted mass of at least one fragment ion from a selected sequence that is different from the predicted masses of fragment ions of selected sequences from other polypeptides in the set, where the selected sequences are sequences from the polypeptides in the set which have the same mass/charge ratio when exposed to a pre-defined ionization condition.

A method for testing whether at least a first target polypeptide and/or a second 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 at least a first target polypeptide and a second target polypeptide;
• b) selecting from a database one or more first unique mass descriptors (UMDs) for said first target polypeptide and one or more second UMDs for said second target polypeptide wherein said one or more first UMDs and said one or more second UMDs are different from each other and from the UMDs of the other polypeptides in the set
• c) utilizing the one or more first UMDs determined for the first target polypeptide and the one or more second UMDs for the second target polypeptide to configure the mass spectrometer;
• d) applying the sample of the set of polypeptides to the configured mass spectrometer;
• and
• f) utilizing the configured mass spectrometer to test whether the first target polypeptide and/or second target polypeptide is present in the sample of the set of polypeptides,
• wherein each UMD comprises the predicted mass of at least one fragment ion from a selected sequence that is different from the predicted masses of fragment ions of selected sequences from other polypeptides in the set, where the selected sequences are sequences from the polypeptides in the set which have the same mass/charge ratio when exposed to a pre-defined ionization condition.

A method for testing whether at least a first target polypeptide and/or a second target polypeptide is present in a sample of a set of polypeptides wherein said first target polypeptide has one or more first UMDs for said first 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 one or more first CMDs and one or more second UMDs for said second target polypeptide that can be used to configure a mass spectrometer to exclude the detection of polypeptides having a CMD that is not the same as the one or more of said first and second CMDs determined for the first target polypeptide and second target polypeptide, said method comprising:

• a) providing a sample of a set of polypeptides to be tested for the presence of a first target polypeptide and second target polypeptide;
• b) utilizing said one or more UMDs of said first target polypeptide and said one or more CMDs of said second target polypeptide to configure the mass spectrometer;
• c) applying the sample of the set of polypeptides to the configured mass spectrometer;
• and
• d) utilizing the configured mass spectrometer to test whether the first target polypeptide and/or second target polypeptide is present in the sample of the set of polypeptides,
• wherein each UMD comprises the predicted mass of at least one fragment ion from a selected sequence that is different from the predicted masses of fragment ions of selected sequences from other polypeptides in the set, where the selected sequences are sequences from the polypeptides in the set which have the same mass/charge ratio when exposed to a pre-defined ionization condition.