Use the Top Down Analysis page to create a new top down analysis experiment. On this page, you can enter the experiment name, load the raw data files, select a protein sequence, and select a processing method for your experiment.


  1. To open the Top Down Analysis page, from the BioPharma Finder home page, double-click Top Down Analysis in the Experiment Types area.
  2. The Top Down Analysis page opens and contains five areas: Top Down Analysis Definition, Load Raw Data, Result Format for Multiple Raw Files, Protein Sequence, and Processing Method.
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    Top Down Analysis page
  4. In the Top Down Analysis Definition area, type the name of the experiment in the Experiment Name box.
  5. Experiment names can contain up to 50 characters, including alphanumeric, space, underscore (“_”), and period (“.”) characters.
  6. 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.
  7. See Process an experiment on the Queue page.
  8. In the Load Raw Data area, select the Select Raw Data (“...”) button to locate and load the raw data files for the experiment.
  9. See Select raw data files.
  10. 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.
  11. Below the Load Raw Data parameters, the application lists the raw data file names and their associated conditions.
  12. To change the condition assigned to a raw data file, use the drop-down menu in the Condition column to select a different condition.
  13. 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.
  14. See Batch and multiconsensus result formats.
  15. You can process up to 10 raw data files in Multiconsensus mode.
  16. If your experiment contains a single raw data file, the Result Format for Multiple Raw Files area is inactive.
  17. In the table in the Protein Sequence area, select the checkbox for one or more protein sequences to assign the sequence to the experiment.
  18. See Select one or more sequences.
  19. NOTE

    For top down analysis experiments, only sequences assigned the category “Top Down” appear in the table. If your protein sequence does not appear in the table, you can change its assigned category to “Top Down” using the Protein Sequence Editor.

  20. In the table in the Processing Method area, select the checkbox for a processing method to assign the processing method to the experiment.
  21. The application provides the Top Down Default Method for top down analysis experiments.
  22. Select Start Processing to proceed.
  23. The processing method editing wizard opens and prompts you to edit the component identification and identification parameters in the method and save them to a new file to create a custom method for your experiment.
  24. See Working with a top down processing method.
  25. To process an experiment, the application requires the following input on the Top Down Analysis page:
  26. •Experiment name
  27. •One or more raw data files
  28. •Conditions for each raw data file (if there are multiple files)
  29. •Protein sequence(s)
  30. •Processing method
  31. If the experiment contains all required information and the input processing method parameters are valid, the application begins processing the experiment.
  32. If the experiment does not contain all required information or if the input processing method parameters are invalid, the application returns to the Top Down Analysis page.