Method And Apparatus For Identifying Proteins In Mixtures
First Claim
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1. A method for identifying proteins in a mixture, comprising:
- digesting the mixture to obtain a peptide mixture;
applying the digested mixture to an LC/MS system;
applying a low-energy mode in the mass spectrometer portion of the LC/MS system;
applying a high-energy mode in the mass spectrometer portion of the LC/MS system to fragment the data;
obtaining mass information and retention time information from the peptide precursor data acquired during the low-energy mode;
obtaining mass information and retention time information from the fragment data acquired during the high-energy mode;
selecting a target precursor from a database of proteins;
determining a mass associated with the target precursor;
determining a mass associated with each Y- and B-ion corresponding to the target precursor;
comparing the mass associated with the target precursor, and the masses associated with the Y- and B-ions to the mass information related to the peptide precursor data and fragment data;
detecting mass matches resulting from the comparisons;
determining retention times of mass matches; and
identifying whether the target peptide is present in the mixture based on the detected mass matches and retention times of detected mass matches.
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Abstract
A system and method for mass analysis where a sample (102) is separated in a liquid chromatograph (104), and subsequently analyzed in a mass spectrometer (112).
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Citations
25 Claims
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1. A method for identifying proteins in a mixture, comprising:
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digesting the mixture to obtain a peptide mixture;
applying the digested mixture to an LC/MS system;
applying a low-energy mode in the mass spectrometer portion of the LC/MS system;
applying a high-energy mode in the mass spectrometer portion of the LC/MS system to fragment the data;
obtaining mass information and retention time information from the peptide precursor data acquired during the low-energy mode;
obtaining mass information and retention time information from the fragment data acquired during the high-energy mode;
selecting a target precursor from a database of proteins;
determining a mass associated with the target precursor;
determining a mass associated with each Y- and B-ion corresponding to the target precursor;
comparing the mass associated with the target precursor, and the masses associated with the Y- and B-ions to the mass information related to the peptide precursor data and fragment data;
detecting mass matches resulting from the comparisons;
determining retention times of mass matches; and
identifying whether the target peptide is present in the mixture based on the detected mass matches and retention times of detected mass matches. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11)
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12. A system for identifying proteins in a mixture, comprising:
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means for digesting the mixture to obtain a peptide mixture;
a liquid chromatograph to which the mixture is applied to separate the mixture;
a mass spectrometer to measure masses in the separated mixture output by the liquid chromatograph, the mass spectrometer, comprising;
a collision cell to fragment the peptides;
a mass analyzer to determine mass information related to fragmented and unfragmented peptides;
a database of proteins from which a target precursor is selected; and
an analysis computer, coupled to the database and an output of the mass spectrometer, having software executing thereon, for causing the computer to;
determine a mass associated with the target precursor peptide;
determine a mass associated with each Y- and B-ion corresponding to the target precursor peptide;
compare the mass associated with the target precursor peptide, and Y- and B-ions to the mass information related to the peptide data and fragment data;
detect mass matches resulting from the comparisons;
determining retention times of mass matches; and
identify whether the target peptide is present in the mixture based on the detected mass matches and retention times of detected mass matches. - View Dependent Claims (13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23)
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24. A method for identifying precursors in a mixture, comprising:
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applying the mixture to an LC/MS system having a liquid chromatographic portion and a mass spectrometer portion;
applying a low-energy mode in the mass spectrometer portion of the LC/MS system;
applying a high-energy mode in the mass spectrometer portion of the LC/MS system to fragment the data;
obtaining mass information and retention time information from the precursor data acquired during the low-energy mode;
obtaining mass information and retention time information from the fragment data acquired during the high-energy mode;
selecting a target precursor from a database;
determining a mass associated with the target precursor;
determining masses associated with fragment ions corresponding to the target precursor;
comparing the mass associated with the target precursor and the masses associated with the fragment ions to the mass information related to the precursor data and fragment data;
detecting mass matches resulting from the comparisons;
determining retention times of mass matches; and
identifying whether the target precursor is present in the mixture based on the detected mass matches and retention times of detected mass matches.
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25. A method for identifying precursors in a mixture, comprising:
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applying the mixture to an LC/MS system having a liquid chromatograph portion and a mass spectrometer portion;
applying a fixed-energy mode in the mass spectrometer portion of the LC/MS system;
obtaining mass information and retention time information from the precursor and fragment data acquired during the fixed-energy mode;
selecting a target precursor from a database;
determining a mass associated with the target precursor;
determining a mass associated with fragment ions corresponding to the target precursor;
comparing the mass associated with the target precursor and the masses associated with the fragment ions to the mass information related to the precursor data and fragment data;
detecting mass matches resulting from the comparisons;
determining retention times of mass matches; and
identifying whether the target precursor is present in the mixture based on the detected mass matches and retention times of detected mass matches.
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Specification