1. On the BioPharma Finder home page, select the Peptide Mapping Analysis, Oligonucleotide Analysis, Intact Mass Analysis, or Top Down Analysis workflow link in the Experiment Types pane or below the splash graphic.
  2. The corresponding workflow page opens.
  3. In the Load Raw Data pane, select the Select Raw Data (“...”) button to locate and load the raw data files for the experiment.
  4. The default file location for raw data files is C:\Xcalibur\data.
  5. You can specify the default folder from which to load your raw data files so that the Browse dialog box automatically opens to this folder location.
  6. TIP

    To add a set of raw data files (for example replicates of the same sample or samples with various conditions) together with a given method, select either contiguous file names using the SHIFT key or noncontiguous file names using the CTRL key.

  7. Select one or more raw data files for processing.
  8. Select Open.
  9. The application displays the selected raw data files in the table in the Load Raw Data area.
  10. The order of the files in this table defines the order that they appear in the Results tables when you view the processed results.
  11. If you load multiple raw data files, assign a condition for each raw data file and select the reference condition for the experiment, as follows:
  12. In the Condition box, type the condition for each raw data file, separated by a space.
  13. Below the Load Raw Data parameters, the application lists the raw data file names and their associated conditions.
  14. If an entered condition matches a portion of a raw data file name, the application automatically assigns that condition to the matching raw data file. It is possible that the application assigns one condition to multiple matching raw data files. To change the condition assigned to a raw data file, use the drop-down menu in the Condition column to select a different condition.
  15. For peptide mapping analysis or oligonucleotide analysis experiments, the application requires that you assign conditions to each file. The Start Processing button is not enabled until you specify the conditions.
  16. Furthermore, for hydrogen deuterium exchange (HDX) experiments within the peptide mapping analysis workflow, you must follow the condition assignments outlined in Workflow: Hydrogen deuterium exchange (HDX) experiments the Peptide Mapping Analysis User Guide.
  17. For intact mass analysis or top down analysis, assigning conditions to each file is optional.
  18. If your experiment uses a blank file, type the word "blank" as a condition to identify a blank group for background subtraction.
  19. In the Reference Condition box, select the reference condition from the drop-down menu.
  20. The default reference condition is the first entered condition in the Condition box.
  21. Upon processing, the application calculates the ratio between the average component areas for the different conditions and the area for reference condition and then displays these ratios in the Results table on the Process and Review page.
  22. Loaded raw data files and conditions for an HDX peptide mapping analysis
    Loaded raw data files and conditions for an HDX peptide mapping analysis