On the Process and Review page, the Intact Fragmentation Deconvoluted Spectrum pane displays the MS2 spectra and the Intact Deconvolution Deconvoluted Spectrum pane displays the deconvoluted full-scan MS spectra for your top down analysis experiment after the experiment is processed using the Xtract or ReSpect deconvolution algorithm.

View the deconvoluted spectra in the Intact Fragmentation Deconvoluted Spectrum pane

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 deconvoluted spectra.
  4. Select the Intact Fragmentation Results tab on the lower left side of the Process and Review page (if necessary).
  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 Deconvoluted Spectrum subtab.
  7. The Intact Fragmentation Deconvoluted Spectrum pane displays one deconvoluted 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. image/svg+xml Raw data file namefor the first plot Raw data file namefor the second plot
    Intact Fragmentation Deconvoluted Spectrum pane showing plots for multiple raw data files
  9. The default mass range for the x axis of the deconvoluted spectra is based on values that you set for the Output Mass Range (for Xtract deconvolution) or Output Mass Range (for ReSpect deconvolution) parameter. See Edit the Component Detection page and Use real-time optimization (RTO) to reprocess results.
  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 Deconvoluted Spectrum pane displays the deconvoluted spectrum for the one file. For a multiconsensus experiment, each plot displays the results for one loaded raw data file.
  12. The application sends the MS2 deconvolution mass results for the peaks from each raw data file to the ProSight Lite application for searching and then displays the individual returned search results.
  13. (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.
  14. The Intact Fragmentation Deconvoluted Spectrum pane shows the same deconvoluted spectrum plots for a selected proteoform as for a selected peak (at the upper level). However, the plots now display color-coded peaks and fragment ion labels. These labels are similar to the fragment ion labels in the MS2 experimental spectra for BioPharma Finder peptide mapping analysis experiments.
  15. See "Fragment ion types and colors" in the Peptide Mapping Analysis User Guide.
  16. (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.
  17. The Intact Fragmentation Deconvoluted Spectrum pane displays a deconvoluted spectrum plot for the proteoform with the masses, intensities, colored peaks, and fragment ion labels from the selected raw data file.
  18. image/svg+xml Line representingthe deconvolutedmass of theselected component Triangular markerrepresentingan identified peak
    Intact Deconvolution Deconvoluted Spectrum pane showing a single plot
  19. The default mass range for the x axis of the deconvoluted spectra is based on values that you set for the Output Mass Range (for Xtract deconvolution) or Output Mass Range (for ReSpect deconvolution) parameter. Set this range on the Parameters > Component Detection page for the method or in the Process and Review > Real Time Optimization pane for real-time optimization.

View the deconvoluted spectra in the Intact Deconvolution Deconvoluted Spectrum pane

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 deconvoluted spectra.
  4. Select the Intact Deconvolution Results tab on the lower left side of the Process and Review page 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 Deconvoluted Spectrum subtab.
  8. The Intact Deconvolution Deconvoluted Spectrum pane displays one deconvoluted 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. Select the row of a component in the Intact Deconvolution Results table.
  10. In each plot in the Intact Deconvolution Deconvoluted Spectrum pane, a blue line represents the deconvolved mass of the selected component.
  11. (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.
  12. The Intact Deconvolution Deconvoluted Spectrum pane displays a deconvoluted spectrum plot with a blue line denoting the deconvolved mass of the top-level component and the masses and intensities for the component from the selected raw data file.
  13. (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.
  14. The Intact Deconvolution Deconvoluted Spectrum pane shows a deconvoluted spectrum plot with a blue line for the top-level component and the masses and intensities from the upper-level raw data file.
  15. For target sequence matching experiments, an orange triangular marker appears on top of each identified peak. You can turn this marker on and off, as well as change its color by right-clicking in the Intact Deconvolution Deconvoluted Spectrum pane and selecting/deselecting the Show Identification Markers checkbox and/or changing the marker color in the shortcut menu.
  16. See Deconvoluted Spectrum panes commands.