Start a new intact mass analysis experiment: Automatic mode - BioPharma Finder Software - Start a new intact mass analysis experiment: Automatic mode - BioPharma Finder Software - BioPharma Finder Software

Procedure

1. To open the Intact Analysis page, from the BioPharma Finder home page, double-click Intact Mass Analysis in the Experiment Types area.
2. The Intact Mass Analysis page opens and contains five areas: Intact Mass Analysis Definition, Load Raw Data, Result Format for Multiple Raw Files, Sequence, and Processing Method.

3. 

2. In the Intact Mass Analysis Definition area, type the name of the experiment in the Experiment Name box.
3. Experiment names can contain up to 50 characters, including alphanumeric, space, underscore (“_”), and period (“.”) characters.
4. You can overwrite an existing experiment by entering the same experiment name. You cannot overwrite an experiment that is currently submitted to the run queue or is actively processing or canceling in the run queue.
5. See Process an experiment on the Queue page (Automatic mode).
3. In the Load Raw Data area, select the Select Raw Data button (“...”) to locate and load the raw data files for the experiment.
4. See Load raw data files.
4. If you load multiple raw data files for an experiment, you must enter a condition for each raw data file and select the reference condition for the experiment. In the Condition box, type the condition for each raw data file, separated by a space. In the Reference Condition box, select the reference condition from the drop-down menu.
5. Below the Load Raw Data parameters, the application lists the raw data file names and their associated conditions.
6. To change the condition assigned to a raw data file, use the drop-down menu in the Condition column to select a different condition.
5. If you load multiple raw data files for an experiment, in the Result Format for Multiple Raw Files area, select either Batch Processing or Multiconsensus.
6. See Batch and multiconsensus result formats.
7. You can process up to 10 raw data files in Multiconsensus mode.
8. If your experiment contains a single raw data file, the Result Format for Multiple Raw Files area is inactive.
6. In the table in the Sequence area, select the checkbox for one or more protein or oligonucleotide sequences to assign the sequence to the experiment.
7. See Select one or more sequences.
8. To run a target sequence matching experiment, you must select a sequence.
9. For all other processing methods, this selection is optional.

10. NOTE

    For intact mass analysis experiments, only protein sequences assigned to the “Intact Protein” category and oligonucleotide sequences assigned to the “Intact Deconvolution” category appear in the table.

    If your sequence does not appear in the table, you can change its assigned category to “Intact Protein” or "Intact Deconvolution" using the appropriate Sequence Editor.

7. In the table in the Processing Method area, select the checkbox for the processing method that you want to assign to your experiment.
8. The application provides several default processing methods for intact mass analysis experiments.
9. See Default processing methods for intact mass analysis.

10. NOTICE

    For IonTrap data, you must use a processing method with the ReSpect deconvolution algorithm. The application cannot process IonTrap data with the Xtract deconvolution algorithm.

    IonTrap data acquired in centroid mode is not supported by either the ReSpect algorithm or the Xtract algorithm.

8. For experiments using a processing method with the sliding windows source spectra method, you can select the Enable Automatic Sliding Windows Parameter Values checkbox above the table in the Processing Method area to automatically optimize the following parameters:
9. In the Sliding Windows Definition area:
10. •Target Avg Spectrum Width
11. •Target Avg Spectrum Offset: Scan Offset and % Offset
12. In the Sliding Windows Merging Parameters area:
13. •Merge Tolerance
14. •Merge Scheme (Legacy Merge Scheme or Improved Merge Scheme)
15. •Max RT Gap
16. •Min. Number of Detected Intervals
17. Instead of the default values set for the processing method, the application reads the scan data from the raw data file (for an experiment using only one file) or from the first file (for an experiment using multiple files) to optimize these parameters. For more information on these automatically optimized parameters, see Source Spectra Method area parameters.

18. NOTE

    The application does not optimize these parameter values in a custom processing method. You must use a default processing method to enable automatic sliding window parameter values.

9. Select Edit Method to review the processing method parameters, edit the deconvolution algorithm, and save the method before processing.
10. See Create or edit a processing method.
11. When you are finished editing the processing method, the processing method editing wizard returns you to the Intact Mass Analysis page.
10. Select Add to Queue.
11. To start processing a new job, the application requires the experiment name, the raw data file or files, the result format selection when you load multiple raw data files, and a processing method.
12. When all requirements are met for processing, the application saves all entered information for the new job and then opens the Queue page.
13. See Process an experiment on the Queue page (Automatic mode).