On the Process and Review page, the Intact Fragmentation Source Spectrum pane displays the MS2 spectra and the Intact Deconvolution Source Spectrum pane displays the full-scan MS spectra specified for your top down analysis experiment before the experiment is processed and deconvolved. For more information on selecting the source spectra, see --- MISSING LINK --- and Use real-time optimization (RTO) to reprocess results.

View the Intact Fragmentation Source Spectrum

Procedure

  1. Open the results of your experiment from the Queue page or from the Load Results page.
  2. See Open results.
  3. The Process and Review page opens by default and displays the results of your top down analysis experiment, including the source spectra.
  4. On the lower left side of the Process and Review page, select the Intact Fragmentation Results tab.
  5. The Intact Fragmentation Deconvoluted Spectrum and Intact Fragmentation Source Spectrum panes appear tabbed together in the center left of the Process and Review page.
  6. Select the visible Intact Fragmentation Source Spectrum subtab.
  7. The Intact Fragmentation Source Spectrum pane displays one source spectrum plot (for batch experiments or experiments with a single loaded raw data file) or multiple stacked plots (for multiconsensus experiments with multiple loaded raw data files).
  8. See Source Spectrum panes commands.
  9. image/svg+xml Raw data file name and filter information for the first plot. Raw data file name and filter information for the second plot.
    Intact Fragmentation Source Spectrum pane showing plots for multiple raw data files
  10. Select the row of a peak in the Intact Fragmentation Results table.
  11. For batch experiments or experiments with a single loaded raw data file, the plot in the Intact Fragmentation Source Spectrum pane displays the source spectrum for the one file. For a multiconsensus experiment, each plot displays the results for one loaded raw data file.
  12. (If available) Select the plus (+) sign to the left of a peak row in the Intact Fragmentation Results table and then select the row of a proteoform.
  13. The Intact Fragmentation Source Spectrum pane shows the same source spectrum plots for a selected proteoform as for a selected peak (at the upper level).
  14. (If available) Select the plus (+) sign to the left of a proteoform row in the Intact Fragmentation Results table and then select the row of a raw data file.
  15. The Intact Fragmentation Source Spectrum pane displays the source spectrum plot for the proteoform with the masses and intensities from the selected raw data file.

View the Intact Deconvolution Source Spectrum

Procedure

  1. Open the results of your experiment from the Queue page or from the Load Results page.
  2. See Open results.
  3. The Process and Review page opens by default and displays the results of your top down analysis experiment, including the source spectra.
  4. On the lower left side of the Process and Review page, select the Intact Deconvolution Results tab and select a peak from the Peak Selection list in the title bar of the Intact Deconvolution Results table.
  5. The Intact Deconvolution Results tab is available only if you select the Intact Deconvolution checkbox in the Peak Selection area of the Parameters > Component Detection page or the Process and Review > Real Time Optimization pane.
  6. The Intact Deconvolution Deconvoluted Spectrum and Intact Deconvolution Source Spectrum panes appear tabbed together in the center left of the Process and Review page.
  7. Select the visible Intact Deconvolution Source Spectrum subtab.
  8. The Intact Deconvolution Source Spectrum pane displays one source spectrum plot (for batch experiments or experiments with a single loaded raw data file) or multiple stacked plots (for multiconsensus experiments with multiple loaded raw data files).
  9. See Source Spectrum panes commands.
  10. Select the row of a component in the Intact Deconvolution Results table.
  11. In each plot in the Intact Deconvolution Source Spectrum pane, a blue line represents the m/z value of an individual charge state of the component.
  12. image/svg+xml Lines representing m/z values of the component’s charge states.
    Intact Deconvolution Source Spectrum pane showing a single plot with the charge states of a component indicated by the blue lines
  13. (If available) Select the plus (+) sign to the left of a component row in the Intact Deconvolution Results table and then select the row of a raw data file.
  14. The Intact Deconvolution Source Spectrum pane shows the source spectrum plot for the selected raw data file with a blue line indicating the m/z value of the top-level component.
  15. (If available) Select the plus (+) sign to the left of a component (or raw data file) row, and then select the row of one of the charge states.
  16. The Intact Deconvolution Source Spectrum pane shows the source spectrum plot for the upper-level raw data file with a blue line indicating the m/z value of the selected charge state.
  17. image/svg+xml Line representing the m/z value of an individual charge state.
    Intact Deconvolution Source Spectrum indicating the selected charge state of a component with a blue line
  18. For Xtract deconvolution, the blue line indicates the calculated monoisotopic m/z value of that charge state (shown in the Calculated Monoisotopic m/z column of the Intact Deconvolution Results table).
  19. For ReSpect deconvolution, the blue line indicates the measured average m/z value of that charge state (shown in the Measured Average m/z column of the Intact Deconvolution Results table).