On the Process and Review page, the Deconvoluted Spectrum pane contains the deconvoluted spectra showing the identified components for your intact mass analysis experiment after the experiment is processed using the Xtract or ReSpect deconvolution algorithm.

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 intact mass analysis experiment, including the deconvoluted spectra.
  4. On the Process and Review page, select the row of a component in the Results table.
  5. The 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).
  6. 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) processing parameter. Furthermore, the mass range is limited by the Model Mass Range values set for the processing method. f you use the same Model Mass Range parameter values across various intact mass analysis experiments, you can directly compare the resultant deconvolved spectra. For more information on the Output Mass Range parameter, see Edit the Component Detection page and Use real-time optimization (RTO) to reprocess results.
  7. For the Xtract algorithm, this pane displays each deconvoluted spectrum as a set of centroid peaks in mass and relative intensity.
  8. For the ReSpect algorithm, this pane displays each deconvoluted spectrum as a profile in mass and intensity with a set of peak labels.
  9. In addition, for ReSpect, you can select from two different modes to display the deconvoluted spectra: Mass Probability Distribution Profile (legacy) and Isotopic Profile (updated).
  10. (Optional) Select the plus (+) sign to the left of a component row, and then select the row of one of the raw data files in the Results table.
  11. The Deconvoluted Spectrum pane shows the deconvoluted spectrum plot for the selected raw data file, indicating the top-level component with a blue line the spectrum.
  12. For an Xtract deconvolution, the blue line indicates the monoisotopic mass of the selected component (the Monoisotopic Mass value in the Results table at the component or raw data file level).
  13. For a ReSpect deconvolution, the blue line the average mass of the selected component (the Average Mass value in the Results table at the component or raw data file level).
  14. Additionally, for a ReSpect deconvolution, the area under a peak is proportional to the intensity of the associated component; thus, lower-quality results are associated with wider peaks. If two components have equal intensities, the component with the lower-quality results has a wider peak.
  15. For a drug-antibody ratio (DAR)-enabled experiment, each spectrum plot displays the Average DAR value under the raw data file name and displays the Drug Load value on top of the peaks.
  16. image/svg+xml
    Deconvoluted Spectrum pane displaying DAR information for two raw data files
  17. (Optional) 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 in the Results table.
  18. The Deconvoluted Spectrum pane shows the deconvoluted spectrum plot for the upper-level raw data file, indicating the top-level component with a blue line the spectrum.
  19. 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 Deconvoluted Spectrum pane and selecting/deselecting the Show Identification Markers checkbox and/or changing the marker color in the shortcut menu. See Deconvoluted Spectrum pane commands.