Interactive analysis of mass spectrometry data
First Claim
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1. A non-transitory machine-readable medium that stores instructions, which, when performed by a machine, cause the machine to perform operations comprising:
- receiving a data file comprising mass spectrometry (MS) data for a sample comprising a mixture of molecules comprising a reference molecule and one or more variant molecules, wherein each variant molecule has a chemical modification relative to the reference molecule, and wherein the MS data comprises a plurality of spectral representations;
providing an assembly of molecular identifications, wherein each molecular identification correlates a spectral representation with the reference molecule and a modification state, wherein the modification state describes the chemical modification for a variant molecule relative to the reference molecule and wherein the modification state is null for the reference molecule;
selecting a molecular identification based on user-input; and
simultaneously and interactively displaying a first arrangement of a plurality of spectral representations, wherein a first spectral representation of the first arrangement is correlated to the selected molecular identification and a second spectral representation of the first arrangement is correlated to a first molecular identification having the same reference molecule but different modification state;
wherein a user selection or modification in the first spectral representation is automatically made in the second spectral representation and a user selection or modification in the second spectral representation is automatically made in the first spectral representation.
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Abstract
This invention relates to graphical user-interactive displays for use in MS-based analysis of protein impurities, as well as methods and software for generating and using such. One aspect provides a user-interactive display comprising an extracted mass chromatogram (XIC), an MS1 spectrum and an MS2 spectrum, all simultaneously representing a user-selected peptide. Another aspect provides a user interactive display simultaneously presenting paired spectra (XIC, MS1 and/or MS2) for a variant peptide and its corresponding wildtype counterpart.
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Citations
20 Claims
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1. A non-transitory machine-readable medium that stores instructions, which, when performed by a machine, cause the machine to perform operations comprising:
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receiving a data file comprising mass spectrometry (MS) data for a sample comprising a mixture of molecules comprising a reference molecule and one or more variant molecules, wherein each variant molecule has a chemical modification relative to the reference molecule, and wherein the MS data comprises a plurality of spectral representations; providing an assembly of molecular identifications, wherein each molecular identification correlates a spectral representation with the reference molecule and a modification state, wherein the modification state describes the chemical modification for a variant molecule relative to the reference molecule and wherein the modification state is null for the reference molecule; selecting a molecular identification based on user-input; and simultaneously and interactively displaying a first arrangement of a plurality of spectral representations, wherein a first spectral representation of the first arrangement is correlated to the selected molecular identification and a second spectral representation of the first arrangement is correlated to a first molecular identification having the same reference molecule but different modification state; wherein a user selection or modification in the first spectral representation is automatically made in the second spectral representation and a user selection or modification in the second spectral representation is automatically made in the first spectral representation. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17)
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18. A method for displaying mass spectrometry data comprising:
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receiving a data file comprising mass spectrometry (MS) data for a sample comprising a mixture a reference molecule and one or more variant molecules, wherein each variant molecule has a chemical modification relative to the reference molecule, and wherein the MS data comprises a plurality of spectral representations; providing an assembly of molecular identifications, wherein each molecular identification correlates a spectral representation with the reference molecule and a modification state, wherein the modification state describes the chemical modification for a variant molecule relative to the reference molecule and wherein the modification state is null for the reference molecule; selecting a molecular identification based on user-input; and simultaneously and interactively displaying a first arrangement of a plurality of spectral representations, wherein a first spectral representation of the first arrangement is correlated to the selected molecular identification and a second spectral representation of the first arrangement is correlated to a first molecular identification having the same reference molecule but different modification state, wherein a user selection or modification in the first spectral representation is automatically, made in the second spectral representation and a user selection or modification in the second spectral representation is automatically made in the first spectral representation.
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19. A non-transitory machine-readable medium that stores instructions, which, when performed by a machine, cause the machine to perform operations comprising:
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receiving a data file comprising mass spectrometry (MS) data for a sample comprising a mixture a reference molecule and one or more variant molecules, wherein each variant molecule has a chemical modification relative to the reference molecule, and wherein the MS data comprises a plurality of spectral representations; providing an assembly of molecular identifications, wherein each molecular identification correlates a plurality of spectral representations with the reference molecule and a modification state, wherein the plurality of spectral representations comprise an extracted ion chromatogram (XIC), a first stage of mass spectrometry (MS1) spectrum and a second stage of mass spectrometry (MS2) spectrum, and wherein the modification state describes the chemical modification for a variant molecule relative to the reference molecule and wherein the modification state is null for the reference molecule; selecting a molecular identification based on user-input; and simultaneously and interactively displaying an arrangement of a plurality of views in a graphical user interface, wherein said plurality of views comprises; a first XIC correlated to the selected peptide immediately adjacent to a second XIC correlated to a first molecular identification having the same reference molecule as the selected peptide but different modification state; a first MS1 correlated to the selected peptide immediately adjacent to a second MS1 correlated to a first molecular identification having the same reference molecule as the selected peptide but different modification state; and a first MS2 correlated to the selected peptide immediately adjacent to a second MS2 correlated to a first molecular identification having the same reference molecule as the selected peptide but different modification state, wherein a user selection or modification in any of the views is automatically made in the all of the views.
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20. A non-transitory machine-readable medium that stores instructions, which, when performed by a machine, cause the machine to perform operations comprising:
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receiving a data file comprising mass spectrometry (MS) data for a sample comprising a peptide mixture of a protein, wherein the MS data comprise spectra collected across a time range for the sample prior to and after fragmentation; simultaneously and interactively displaying a layout of a plurality of views in a graphical user interface, wherein said plurality of views comprises; an extracted mass chromatogram (XIC) based on the data file showing a measure of peptide as a function of time, the chromatogram comprising a plurality of XIC peaks, wherein each peak is associated with one or more peptides, each of which is associated with a plurality of first stage of mass spectrometry (MS1) and second stage of mass spectrometry (MS2) spectra; an MS1 spectrum based on data collected for the sample prior to fragmentation, wherein the spectrum comprises a plurality of MS1 peaks, wherein one or more peaks are each associated with a corresponding MS2 spectrum; and an MS2 spectrum based on data collected for the sample after fragmentation, wherein the spectrum corresponds to a peak in the displayed MS1; and controlling the arrangement of the plurality of views with an user-interactive selector; wherein a single user action comprising selecting a peptide in any of the views is automatically and simultaneously made in the all of the views comprising updating the plurality of views to display the XIC, MS1 spectrum and MS2 spectrum associated with the selected peptide.
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Specification