Interactive analysis of mass spectrometry data including peak selection and dynamic labeling

1. A non-transitory machine-readable medium that stores instructions, which, when performed by a machine, cause the machine to perform operations comprising:

simultaneously displaying a plurality of visual representations derived from mass spectrometry (MS) data, the plurality of visual representations comprising: a first visual representation comprising estimated or calculated masses based on the MS data, a second visual representation comprises a distribution of mass/charge (m/z) peaks based on the estimated or calculated masses, and a third visual representation comprising a deconvolved mass spectrum based on the estimated or calculated masses;

receiving a user-selected mass value from one of the first visual representation, the second visual representation or the third visual representation; and

displaying:

a highlighted mass value on the first visual representation corresponding to the user-selected mass value; and

a plurality of markers on the second visual representation and the third visual representation corresponding the user-selected mass value, each marker on the second visual representation corresponding to a peak of the distribution of m/z peaks, and each marker on the third visual representation corresponding to a peak of the deconvolved mass spectrum.

2. The non-transitory machine-readable medium of claim 1 , wherein the plurality of markers includes dots or points.

3. The non-transitory machine-readable medium of claim 1 , wherein each of the plurality of markers includes information corresponding to one or more variant molecules associated with the user-selected mass value, the information including a mass of the one or more variant molecules, a charge of the one or more variant molecules, or the mass and charge of the one or more variant molecules.

4. The non-transitory machine-readable medium of claim 1 , wherein the instructions further cause the machine to modify one or more of a number, a location, a color, and a transparency of the plurality of markers, based on user input.

5. The non-transitory machine-readable medium of claim 1 , wherein the instructions further cause the machine to modify one or both of the second and third visual representations based on user input, wherein modifying one or both of the second and third visual representations includes modifying one or both of a time range and scaling of one or both of the distribution of m/z peaks and the deconvolved mass spectrum.

6. The non-transitory machine-readable medium of claim 1 , wherein the first visual representation includes a list of information including one or more of mass, peptide fragmentation, and modification state associated with the estimated or calculated masses.

7. The non-transitory machine-readable medium of claim 6 , wherein the modification state includes one or more of unmodified, sequence variant, insertion, deletion, extension, oxidation, deamidation, conjugate, glycation, sulfation, and glycosylation.

8. The non-transitory machine-readable medium of claim 1 , wherein the second visual representation includes a pattern of markers distributed in accordance with the distribution of m/z peaks.

9. The non-transitory machine-readable medium of claim 1 , wherein the user-selected mass value is a first user-selected mass value and the plurality of markers is a first plurality of markers, wherein the instructions further cause the machine to: receive a second user-selected mass value from one of the first visual representation, the second visual representation and the third visual representation, wherein the second user-selected mass value is different than the first user-selected mass value; and

display:

a second plurality of markers on the second visual representation and the third visual representation corresponding the second user-selected mass value, each marker of the second plurality of markers on the second visual representation corresponding to a peak of the distribution of m/z peaks, and each marker of the second plurality of markers on the third visual representation corresponding to a peak of the deconvolved mass spectrum,

wherein the first plurality of markers is visually distinct from the second plurality of markers.

10. The non-transitory machine-readable medium of claim 9 , wherein the first plurality of markers is a first color and the second plurality of markers is a second color different than the first color.

11. The non-transitory machine-readable medium of claim 9 , wherein the first and second plurality of markers are dots or points.

12. The non-transitory machine-readable medium of claim 1 , wherein receiving the user-selected mass value includes receiving a range of mass values, and wherein the plurality of markers is displayed based on the range of mass values.

13. The non-transitory machine-readable medium of claim 12 , wherein a location of the plurality of markers is adjusted within an adjustment range to map to a nearest corresponding peak within the adjustment range.

14. The non-transitory machine-readable medium of claim 1 , wherein the instructions further cause the machine to display a fourth visual representation including a chromatogram based on the estimated or calculated masses, wherein the fourth visual representation is simultaneously displayed with the first, second and third visual representations.

15. The non-transitory machine-readable medium of claim 1 , wherein the plurality of markers includes one or more annotated colored dots.

16. The non-transitory machine-readable medium of claim 1 , wherein the user-selected mass value is received via a graphical user interface (GUI).

17. A non-transitory machine-readable medium that stores instructions, which, when performed by a machine, cause the machine to perform operations comprising:

displaying visual representations derived from mass spectrometry (MS) data, the visual representations comprising: a first visual representation including a list of entries of estimated or calculated masses based on the MS data, a second visual representation including a distribution of mass-to-charge (m/z) peaks based on the estimated or calculated masses, and a third visual representation including a deconvolved mass spectrum based on the estimated or calculated masses;

receiving a first user-selected entry, comprising a first user-selected mass value, from the first visual representation;

displaying a first set of markers associated with the first user-selected mass value on the second visual representation and the third visual representation, each marker of the first set of markers on the second visual representation corresponding to a peak of the distribution of m/z peaks, and each marker of the first set of markers on the third visual representation corresponding to a peak of the deconvolved mass spectrum;

receiving a second user-selected entry, comprising a second user-selected mass value, from the first visual representation; and

displaying a second set of markers associated with the second user-selected mass value on the second visual representation and the third visual representation, each marker of the second set of markers on the second visual representation corresponding to a peak of the distribution of m/z peaks, and each marker of the second set of markers on the third visual representation corresponding to a peak of the deconvolved mass spectrum, wherein the first and second set of markers are displayed simultaneously and the first set of markers is visually distinct from the second set of markers,

wherein the first set of markers include one or more dots having a first color, wherein the second set of markers include one or more dots having a second color different than the first color.

18. The non-transitory machine-readable medium of claim 17 , wherein the instructions further cause the machine to modify one or more of a number, a location, a color, and a transparency of each of the first and second set of markers, based on user input.

19. The non-transitory machine-readable medium of claim 17 , wherein the instructions further cause the machine to modify one or both of the second and third visual representations based on user input, wherein modifying one or both of the second and third visual representations includes modifying one or both of a time range and scaling of one or both of the distribution of m/z peaks and the deconvolved mass spectrum.