When you submit an Intact Mass Analysis experiment in Manual mode on the Intact Mass Analysis page, the application opens the Process and Review page in Manual mode. On the Process and Review page, you can adjust the parameters in the Real Time Optimization, Chromatogram, and Source Spectrum panes to manually set up your Intact Mass Analysis experiment.

IMPORTANT

The Auto Peak Detection deconvolution method is not supported for Intact Mass Analysis experiments processed in Manual mode.

You must select a processing method using the Average Over Selected Retention Time or Sliding Windows deconvolution method to process an Intact Mass Analysis in Manual mode.

IMPORTANT

The Batch Processing results format is not supported for Intact Mass Analysis experiments processed in Manual mode.

You must select the Multiconsensus results format to process an Intact Mass Analysis in Manual mode.

Figure Process and Review page for a Manual mode Intact Mass Analysis experiment
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No.DescriptionNo.Description

1

Process and Review tab

5

Deconvoluted Spectrum pane (blank before processing)

2

Real Time Optimization pane

6

Source Spectrum pane

3

RTO subpage navigation bar

7

Results table (blank before processing)

4

Chromatogram pane

8

Process button

Prerequisites

  1. On the Intact Mass Analysis page, you have entered an experiment name, loaded the raw data files and entered the conditions (if applicable), and selected a sequence (optional).

Procedure

  1. On the Intact Mass Analysis page, select the Manual Process button at the bottom of the Processing Method area.
  2. The Process and Review page opens in Manual mode, displaying the following panes:
  3. The Real Time Optimization pane, which displays the Component Detection and Identification subpages with editable processing method parameters.
  4. The Chromatogram pane, which displays the chromatogram plot from each raw data file that you loaded.
  5. The Deconvoluted Spectrum pane, which is empty.
  6. The Source Spectrum pane, which is either empty or displays the selected source spectra.
  7. In the Real Time Optimization pane, specify the appropriate Component Detection and Identification parameters for the experiment.
  8. If you select the Average Over Selected Retention time source spectra (deconvolution) method, you must select the source spectra before manually processing the experiment.
  9. When you are finished manually setting up your Intact Mass Analysis experiment, select the Process button on the command bar.

Procedure

  1. When you are finished manually setting up your Intact Mass Analysis experiment, select the Process button on the command bar.

  2. TIP

    For Sliding Windows experiments, a status icon, , appears on the command bar to indicate the progress of the processing job for each raw data file in the experiment. During the deconvolution process, the sliding windows appear and move across the chromatogram in real time.

    To cancel a Sliding Windows experiment without saving the results, select the status icon. To enable the Process button after canceling, change one or more parameter settings on the Process and Review page.

  3. NOTE

    If the application determines that the processing method parameters specified for a Sliding Windows experiment are suboptimal, a warning message appears.

    If this warning box appears, take one of the following steps:

    • Use the recommended parameter settings suggested in the warning box by selecting Run Recommended.
    • Use the original parameter settings by selecting Run User Specified.
    • Select Cancel and update the parameter settings.

    This choice guarantees that the processing job will run to completion.

    This choice cannot guarantee that the processing job will run to completion.

  4. When the application completes processing, review the experiment results on the Process and Review page.
  5. If you are not satisfied with your processing method parameter settings and/or experiment results, repeat the process until you achieve the appropriate results.
  6. To save the processing method parameters, do the following:
  7. Select Save Method As in the command bar to save the processing method.
  8. In the Save Method As dialog box, enter a name for the method in the Processing Method Name box and (optional) a description for the method in the Description box.
  9. Select OK.
  10. The processing method created in Manual mode is added to the list of processing methods available on the Intact Mass Analysis page. You can now use this processing method in Automatic mode for future Intact Mass Analysis experiments.
  11. To save the experiment results, do the following:
  12. Select Save Results As in the command to save the experiment results.
  13. In the Save Results As dialog box, enter a name for the experiment in the Experiment Name box adn (optional) a description for the experiment in the Description box.
  14. Select OK.
  15. The experiment results generated in Manual mode are saved to the BioPharma Finder experiment database. You can open your results from the Load Results page.