Use real-time optimization (RTO) to reprocess results - BioPharma Finder Software - Peptide Mapping Analysis User Guide - View Peptide Mapping Analysis results - Use real-time optimization (RTO) to reprocess results - BioPharma Finder Software - BioPharma Finder Software

Prerequisites

1. For a Peptide Mapping Analysis experiment, you have processed your experiment and are viewing the results on the Process and Review page.

Procedure

1. On the Process and Review page, expand the Real-Time Optimization title bar to view the Sequence, Component Detection, Identification, Host Cell Protein, and Customize Results subtabs.
2. The Sequence pane expands and displays the Protein Sequence Map area (left side), which displays the protein sequence, and the Sequence area (right side), which displays sequence information including the assigned protease, static/variable modifications, and glycosylation for the currently open analysis.
2. To edit the Sequence, Component Detection, Identification, Host Cell Protein, and/or Customize Result subpages, select the corresponding subtab to open the subpage and edit the parameters.
3. On the Sequence subpage, you can edit the input protein sequence and modifications for a non-targeted or targeted Peptide Mapping Analysis.
4. For a non-targeted Peptide Mapping Analysis experiment:
1. To edit the Sequence parameters, select Edit to open the Protein Sequence Editor and change the parameters as needed.
2. To save your changes, select Save As New and type a new name for the edited protein sequence in the New Sequence Name box.

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5. For a targeted Peptide Mapping Analysis experiment:
1. To edit the Sequence parameters for a targeted Peptide Mapping Analysis, select Edit to open the Workbook Editor and change the parameters as needed.
2. See Edit a workbook.
2. Select Update to apply your changes to the targeted components.
3. To save your changes, select Save.
4. You can choose to save the edited workbook under a new workbook name or overwrite the existing workbook. The application uses this workbook as the protein sequence when you reprocess the targeted Peptide Mapping Analysis.
5. The application automatically converts the peptide workbook into a protein sequence and names each chain as "X: Sequence X" where X is a number correlated to the Relative Quantitative Group Number assigned to the peptide component in the workbook. The application also consolidates any duplicate sequences to avoid multiple entries for the same peptide.

6. 

6. On the Component Detection subpage, select a task from the Select Task to be Performed drop-down menu and edit Basic/Advanced parameters related to the detection of components in your analysis.
7. For more information on these parameters, see Edit the Component Detection page.
7. On the Identification subpage, edit Peptide Identification, Advanced Search, Disulfide Search, and Protease parameters by selecting the individual subtabs.
8. For more information on these parameters, see Edit the Identification page.

9. NOTE

   On the Advanced Search subpage, the Glycosylation parameter is read-only and automatically populated with the N, O Glycan selection made in the Sequence Editor.

   To edit this value, you must change it on the Sequence subpage of the Real-Time Optimization pane.

10. NOTE

    The protease options "Nonspecific", “No enzyme”, or any protease with cleavage sites at both the N- and C-terminals are not supported for theoretical digestion at this time.

    Thus, if you enable the Customize Results subpage of the Real-Time Optimization pane to view theoretical digestion results, do not use these protease options.

8. On the Host Cell Protein subpage, select the Enable HCP checkbox to prompt the application to utilize biotherapeutic databases to detect, quantify, and trace Host Cell Protein contaminants in your sample.
9. Once enabled, you can edit Basic, Advanced, and Protease parameters as well as Modifications by selecting the individual subtabs.
10. For more information on these parameters, see Edit the Host Cell Protein (HCP) page.
9. On the Customize Results subpage, select the Enable Customize Results checkbox to activate the Theoretical Digestion and Alias Naming feature.
10. Once enabled, you can apply a custom naming scheme to your peptide components and customize theoretical digestion parameters.
11. After entering the appropriate parameters, select Apply.
12. For more information of these parameters, see Edit the Customize Results page.

13. NOTE

    The Enable Customize Results checkbox can only be selected if an appropriate protease was previously selected on the Identification subpage of the Real-Time Optimization pane.

    The protease options "Nonspecific", “No enzyme”, or any protease with cleavage sites at both the N- and C-terminals are not supported for theoretical digestion at this time.

    Thus, if you enable the Customize Results subpage of the Real-Time Optimization pane to view theoretical digestion results, do not use these protease options.

10. When you are finished editing the Real-Time Optimization parameters, select Process in the command bar of the Process and Review page.
11. In the Reprocess Experiment dialog box, enter the experiment and method names.
12. You can choose to save the experiment under a new name or overwrite the existing experiment. You cannot overwrite an experiment that is currently submitted to the run queue or is actively processing or canceling.
13. You can choose to save the method under a new name or overwrite the existing method (unless the method is a default processing method, which you cannot overwrite).
14. For both the experiment name and method name , use only alphanumeric, space, underscore, and/or period characters.
15. If the application finds invalid parameter entries, an error dialog box appears indicating the parameters that must be changed. To continue, enter the required parameter values within the appropriate ranges and select Process again to proceed.

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12. Select Reprocess.
13. The application clears the previous results on the Process and Review page and submits a new processing job including your changes to the run queue.
14. The RTO job moves to the top of the run queue, behind the currently running job. If no job is currently running, the application reprocesses the RTO immediately.
15. While the new job is processing, you remain on the Process and Review page.
16. When reprocessing is completed, the Process and Review page automatically displays the new results.
17. For more information on the features and navigation of the Process and View page, see Process and Review page.

18. NOTE

    You cannot edit hydrogen deuterium exchange (HDX) parameters using the RTO feature.

    To reprocess an HDX experiment, create a new HDX experiment, change the processing method parameters as needed, and submit the experiment for processing.

19. NOTE

    If you open another results file while the application is reprocessing your experiment, the application will not automatically update the display with the results of the reprocessed experiment.

    In this case, you can open your reprocessed experiment in the run queue by selecting the experiment name and then selecting Open Results or by double-clicking the experiment name.