Use real-time optimization (RTO) to reprocess results - BioPharma Finder Software - Use real-time optimization (RTO) to reprocess results - BioPharma Finder Software - BioPharma Finder Software

Prerequisites

1. For an intact mass analysis experiment, you have processed your experiment and are viewing the Process and Review page.

Procedure

1. On the Process and Review page, expand the Real-Time Optimization title bar to view the Component Detection and Identification subtabs.
2. The Component Detection pane expands and displays the parameters used for processing the current experiment.
2. On the Component Detection page of the Real-Time Optimization pane, select the Chromatogram & Source Spectra and Deconvolution Algorithm subtabs to update the corresponding parameters as needed.
3. See Edit the Component Detection page.

4. 

5. See the following topics for more information on changing the Chromatogram Parameters and Source Spectra Method parameters:
6. •Chromatogram Parameters area parameters
7. •Source Spectra Method area parameters
3. Under the Deconvolution Algorithm subtab, select the Basic subtab to update the basic parameters or the Advanced subtab to edit the advanced parameters.

4. 

4. Select the Identification tab and update the parameters as needed.
5. See Edit the Identification page.

6. 

7. See the following topics for more information on changing the Deconvolution Algorithm parameters:
8. •ReSpect deconvolution parameters
9. •Xtract deconvolution parameters
5. To edit the sequence(s) added to the experiment for target sequence matching, select Edit at the upper right area of the Sequences Added to Experiment table.
6. The Parameters > Identification page opens where you can add different sequences to the experiment or make other sequence-related changes as needed.
7. See Edit the Identification page.

8. NOTE

   Using RTO, you can add, remove, or edit full protein or oligonucleotide sequences. You cannot edit individual chains in a sequence.

   When editing a sequence using RTO, you can only change the modifications, glycosylation, or disulfide bonds information for a sequence.

6. When you are finished editing the sequence, select the Process and Review tab to return to the Process and Review page for processing.
7. If you add different sequences to the experiment, they appear in the Sequences Added to Experiment table
7. When you are finished editing the Real-Time Optimization parameters, select Process in the command bar of the Process and Review page.
8. The application reprocesses the experiment using the new processing method and deconvolution parameters.

9. NOTE

   Unlike the other workflows in the BioPharma Finder application, for intact mass analysis experiments, reprocessing an experiment using the RTO feature follows the same workflow as initially processing an experiment in Manual mode.

   Intact mass analysis RTO jobs are not submitted the run queue, but rather manually processed in real-time.

   See Process an experiment in Manual mode.

8. For intact mass analysis experiments, changes made to the processing method and any resultant changes to the experiment results are not automatically saved after performing RTO. To save the changes made to the processing method or to save the updated results, do the following:
1. Select Save Results As in the command to save the experiment results.
2. The Save Results As dialog box appears.

3. 

1. In the Save Results As dialog box, enter a name for the experiment in the Experiment Name box.
2. You can type a description for the experiment in the Description box underneath Experiment Name.

3. NOTE

   If you type the name of an existing experiment, the application will overwrite the previous experiment of the same name with the results of the current experiment.

1. Select OK.
2. To view your saved results, open the results from the Load Results page.
3. See Open results from the Load Results page.
1. (Optional) Select Save Method As in the command bar to save the processing method.
2. The Save Method As dialog box appears.

3. 

1. In the Save Method As dialog box, enter a name for the method in the Processing Method Name box.
2. You can type a description for the method in the Description box underneath Processing Method Name.

3. NOTE

   If you type the name of an existing processing method, the application will overwrite the previous method of the same name with the current method.

1. Select OK.
2. This command saves your processed results to a database that contains both the processing method parameter settings that you applied to the loaded raw data files and the results of the deconvolution.
3. The edited processing method 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.
9. If you are not satisfied with your experiment results, you can repeat the RTO process until you achieve the appropriate results.

10. NOTE

    When you are finished editing the experiment processing parameters using RTO, remember to save the results and processing method (optional).

    For intact mass analysis experiments, changes made to the processing method and any resultant changes to the experiment results are not automatically saved after performing RTO