Process an experiment in Manual mode - BioPharma Finder Software - Process an experiment in Manual mode - BioPharma Finder Software - BioPharma Finder Software

Prerequisites

1. For an intact mass analysis experiment, you entered an experiment name, loaded the raw data files and entered the conditions (optional), and selected a protein or oligonucleotide sequence (optional) on the Intact Mass Analysis page.

Procedure

2. On the Intact Mass Analysis page, select the Manual Process button at the bottom of the Processing Method section.
1. On the Intact Mass Analysis page, select the Manual Process button at the bottom of the Processing Method section.

2. NOTE

   The Batch Processing results format and the automatic peak detection deconvolution method are not supported in Manual mode.

   You must select the Multiconsensus results format and either the average over selected retention time or sliding windows deconvolution method to run an intact mass analysis in Manual mode.

3. The Process and Review page opens in Manual mode, displaying the following panes:
4. •The Real Time Optimization pane, which displays the Component Detection and Identification subpages with editable processing method parameters.
5. •The Chromatogram pane, which displays the chromatogram plot from each raw data file that you loaded.
6. •The Deconvoluted Spectrum pane, which is empty.
7. •The Source Spectrum pane, which is either empty or displays the selected source spectra.

2. In the Real Time Optimization pane, specify the appropriate parameters for the processing method.
3. See the following topics for information on these parameters:
4. •Edit the Component Detection page
5. •Edit the Identification page
6. •Use real-time optimization (RTO) to reprocess results
3. If you select the Average Over Selected Retention time source spectra (deconvolution) method, you must select the source spectra before manually processing the experiment. To select the source spectra, do one of the following in the Chromatogram pane:
1. Select a single retention time (RT) or scan in the chromatogram.
2. Select a RT range or a range of scans in the chromatogram.
4. When you are finished manually setting up your intact mass analysis experiment, select Process in the command bar.
5. When processing an experiment using the sliding windows deconvolution method, a status icon, , appears in the command bar on the Process and Review page to indicate the real-time percentage of completion (in green) for each raw data file loaded in the experiment. The sliding windows appear and move across each chromatogram in real time.
6. To cancel a sliding windows deconvolution, select the status icon. When you cancel, the application does not save the results. For other types of experiments, during processing, the cursor becomes a progress circle. You cannot stop the processing for these experiments.
7. To enable the Process button after canceling, change one or more parameter settings on the Process and Review page.
8. If the application determines that the processing method parameters specified for your sliding windows experiment are sub-optimal, a warning message appears.
9. When you process a sliding windows deconvolution, a warning box similar to the one shown in the following figure might appear if the selected parameters are suboptimal for obtaining results. For multiconsensus experiments, the application assesses the suitability of the specified processing method parameters for the data in the first loaded raw data file.

10. 

5. If this warning box appears, take one of the following steps:
1. Use the recommended parameter settings suggested in the warning box by selecting Run Recommended.
2. This choice guarantees that the processing job will run to completion.
1. Use your original parameter settings by selecting Run User Specified.
2. This choice cannot guarantee that the processing job will run to completion.
1. Select Cancel and enter other parameter settings.
6. When the application is finished processing the experiment, review the results on the Process and Review page.
7. See Viewing the Process and Review page for intact mass analysis.
7. If you are satisfied with your processing method parameter settings and/or experiment results:
1. 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 processing method you 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.
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.
8. If you are not satisfied with your processing method parameter settings and/or experiment results, repeat the process for manually processing your intact mass analysis experiment until you achieve the appropriate results.