After you add a sequence to the Sequence Manager, you can perform a peptide mapping analysis using the data-dependent MS2 data in BioPharma Finder software.

Prerequisites

  1. The BioPharma Finder software is open and connected to the Ardia Platform.
  2. You have added the appropriate protein sequence to the Sequence Manager.
  3. The *.raw file that includes the data-dependent MS2 data is saved to the Ardia Platform data repository.

Procedure

  1. On the BioPharma Finder software home page, double-click Peptide Mapping Analysis in the Experiment Types area.
  2. The Peptide Mapping Analysis page opens and contains five areas: Peptide Mapping Analysis Definition, Load Raw Data, Result Format for Multiple Raw Files, Protein Sequence, and Processing Method.
  3. In the Peptide Mapping Analysis Definition area, type the name of the experiment in the Experiment Name box.
  4. Experiment names can contain up to 50 characters, including alphanumeric characters, spaces, underscores, and periods.
  5. In the Load Raw Data area, select the Select Raw Data (“...”) button to locate and load the raw data files for the experiment from the Ardia Platform data repository.
  6. When 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.
  7. NOTE

    If the condition term equals to a part of the raw file name, then the condition is assigned to the corresponding raw file automatically.

  8. In the Condition box, enter the condition for each raw data file, separated by a space.
  9. In the Reference Condition box, select the reference condition from the dropdown list.
  10. Below the Load Raw Data parameters, the application lists the raw data file names and their associated conditions.
  11. To change the condition assigned to a raw data file, use the dropdown list in the Condition column to select a different condition.
  12. 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.
  13. You can process up to 10 raw data files in Multiconsensus mode.
  14. In the table in the Protein Sequence area, select the checkbox for a protein sequence to assign the sequence to the experiment.
  15. In the table in the Processing Method area, select the checkbox for the Basic Default Method to assign the processing method to the experiment.
  16. Select the Enable Automatic Parameter Values checkbox at the top of the Processing Method area to have the application automatically determine several component detection parameters and identification parameters.
  17. Select Edit Method to edit and save the processing method parameters.
  18. The processing method editing wizard opens, displaying the Component Detection page.
  19. Edit the following parameters in the processing method editing wizard:
  20. In the Identification subtab of the Parameters tab of the Component detection page, specify the Select Protease parameters.
  21. For more information about these parameters refer to the BioPharma Finder Software User Guide.
  22. In the Customize Results page, select the Enable Customize Results checkbox, enter an alias naming scheme into the Theoretical Digestion and Alias Naming table, and select Apply.
  23. On the Save Method page, enter a new name of your choice into the Method Name box and then select Finish on the command bar.
  24. If the experiment contains all required information and the input processing method parameters are valid, the application begins processing the experiment. If the experiment does not contain all required information or if the input processing method parameters are invalid, the application returns to the Peptide Mapping Analysis page.