The first page of the processing method editing wizard is the Component Detection page. Use the Component Detection page to change the parameters related to component peak detection in your analysis.

The editable parameters on this page vary depending on the loaded raw data file or files and the selected deconvolution algorithm (Xtract or ReSpect).


Top down analysis currently supports both the Xtract and ReSpect deconvolution algorithms for full-scan MS data processing.

For MS2 data, only Xtract is supported.


  1. For a top down analysis experiment, you entered an experiment name, loaded the raw data files and entered the conditions (if applicable), and selected a protein sequence on the Top Down Analysis page.


  1. To open the Component Detection page, select a processing method in the Processing Method area on the Top Down Analysis page by selecting the checkbox.
  2. Select Start Processing to use the processing method editing wizard.
  3. The processing method editing wizard opens on the Parameters page and displays the first subpage, Component Detection. The Parameters page contains three subpages (Component Detection, Identification, and Save Experiment) that can be accessed by selecting the appropriate subtab.
  4. On the left side of the page, there are two panes containing editable parameters: Peaks (containing a Peak Selection section for each added peak) and Peak # − Deconvolution Parameters (with Intact Fragmentation and Intact Deconvolution tabs).
  5. image/svg+xml Xtract parameters Select thisbox to view theadvancedparamaters Navigationbar Peak selectionarea Peak #Deconvolutionparametersarea
    Component Detection page parameters (left side of page)
  6. On the right side of the page, the chromatogram, intact fragmentation source spectrum, and intact deconvolution source spectrum for each raw data file in the experiment are displayed for the selected peak number.
  7. image/svg+xml Selected peak Tabs for uptoten loadedraw data files Peak# -Intact DeconvolutionSourceSpectrumpane Peak# - Intact SourceSpectrumFragmentationpane Chromatogrampane
    Component Detection page chromatogram and source spectra (right side of page)
  8. For more information on the chromatogram and source spectra plots, see Plots on the Component Detection page.
  9. For more information on the commands available in the plots, see Component Detection page commands.
  10. The Peak Selection area contains all of the parameters specific to each peak you specify for the analysis, including the retention time (RT) range, scan filter, activation type, protein sequence, and fragmentation mass tolerance. To select a peak, enter the appropriate RT Range in the Peak Selection area. Alternatively, select a single scan (single RT time point) or a range of averaged scans (RT range) directly on the chromatogram.
  11. For more information on selecting a peak or range of peaks, see Plots on the Component Detection page.
  12. Specify the appropriate parameter values for each individual peak, adding or deleting peaks as necessary.
  13. For an experiment with multiple loaded raw data files, select the Multiple File Parameters button (...) to select the scan filters and activation type for each file.
  14. image/svg+xml
    Multiple File Parameters dialog box
  15. (Optional) To set the parameters for deconvolving full-scan MS data, select the Intact Deconvolution checkbox. Selecting this checkbox activates the Intact Deconvolution page in the Peak # − Deconvolution Parameters area underneath the Peak Selection area.
  16. image/svg+xml Click here to deletethe active peak. Click here to add a peak. Select a peak, in this case, peak 3.
    Selecting, adding, or deleting peaks in the Peaks pane
  17. In the Chromatogram pane, a shaded box indicates the currently selected peak (or range). Only the parameters for the active peak are editable.
  18. When you select Add Peak, the parameter settings of the new peak are the same as the parameter settings from the first peak by default. The new peak becomes the active peak where you can update the parameters as needed.
  19. You can add up to 10 peaks. At least one parameter value must be different for each peak.
  20. When you select Delete Peak, the application deletes the selected peak and all of its corresponding parameters.
  21. See Peak Selection parameters.
  22. The parameter values you set apply to the currently selected peak and all of the raw data files loaded for the experiment.
  23. The Peak # − Deconvolution Parameters section displays the parameters specific to each peak on either the Intact Fragmentation page (for MS2 data) or the Intact Deconvolution page (for full-scan MS data). Do one of the following:
  24. Select the Intact Fragmentation tab to specify the appropriate parameter values for processing MS2 data.
  25. Select the Intact Deconvolution tab to specify the values for processing full-scan MS data.
  26. See Spectral deconvolution for top down analysis for more information on selecting a deconvolution method.
  27. You must select the Intact Deconvolution checkbox in the Peak Selection area to activate the Intact Deconvolution page.
  28. You can edit advanced options by selecting the Show Advanced Parameters checkbox. These advanced parameters are hidden by default and typically do not need to be modified.
  29. Select a particular deconvolution algorithm, ReSpect (Isotopically Unresolved) or Xtract (Isotopically Resolved), and enter the appropriate parameter values.
  30. See the following topics:
  31. ReSpect deconvolution parameters
  32. Xtract deconvolution parameters
  33. NOTE

    Top down analysis currently supports both the Xtract and ReSpect deconvolution algorithms for full-scan MS data processing.

    For MS2 data, only Xtract is supported.

    See "Deconvolution algorithms" in the Intact Mass Analysis User Guide.

  34. NOTE

    Attempting to apply an algorithm the wrong type of spectral data can lead to unreliable results.

    In most cases, the Xtract algorithm fails to identify any components if you apply it to isotopically unresolved spectra as the components do not have isotopic profiles.

    If you apply the Respect algorithm to isotopically resolved spectra, it might attempt to identify each isotopic peak as a separate component, rather than an isotopic composition of a single component.

  35. When you are finished editing the parameters on the Component Detection page, select Next on the command bar to advance to the Identification page.