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 peptide precursors derived from the peptide mixture;
obtaining mass information and retention time information from peptide precursor data acquired from the peptide precursors during the low-energy mode;
obtaining mass information and retention time information from fragment data acquired from the fragmented peptide precursors during the high-energy mode;
selecting a target peptide from a database of proteins;
determining a mass associated with a target precursor associated with the target peptide;
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 peptide 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).
31 Citations
23 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 peptide precursors derived from the peptide mixture; obtaining mass information and retention time information from peptide precursor data acquired from the peptide precursors during the low-energy mode; obtaining mass information and retention time information from fragment data acquired from the fragmented peptide precursors during the high-energy mode; selecting a target peptide from a database of proteins; determining a mass associated with a target precursor associated with the target peptide; 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 peptide 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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Specification