Create a new Peptide Mapping Analysis experiment on the Peptide Mapping Analysis page. On this page, enter the experiment name, load the raw data files, select a protein sequence, and select a processing method.

TIP

For information on running a hydrogen deuterium exchange (HDX) Peptide Mapping Analysis experiment, see Hydrogen deuterium exchange (HDX) experiments

Figure Peptide Mapping Analysis page
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No.DescriptionNo.Description

1

Enter experiment name

5

Select processing method

2

Load raw data files and assign conditions

6

Open the processing method editing wizard

3

Specify results format

7

Submit experiment for processing

4

Select protein sequence

Prerequisites

  1. (Optional) You have added a protein sequence to the Sequence Manager.

Procedure

  1. On the BioPharma Finder Home page, in the Experiment Types pane, select the Peptide Mapping Analysis workflow link.
  2. The Peptide Mapping Analysis page opens.
  3. In the Peptide Mapping Analysis Definition area, type the name of the experiment in the Experiment Name box.

  4. TIP

    Experiment names can contain up to 50 characters, including alphanumeric, space, underscore (“_”), and period (“.”) characters.

  5. IMPORTANT

    You can overwrite a completed 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.

  6. In the Load Raw Data area, select the Select Raw Data (“...”) button.
  7. The Add Analysis File(s) dialog box opens.

  8. NOTE

    The default file location for raw data files is C:\Xcalibur\data.

  9. In the Add Analysis File(s) dialog box, locate and select the raw data files (.raw) you want to add to the experiment.

  10. TIP

    To add a set of raw data files to the experiment (for example, replicates of the same sample or samples with various experiment conditions), select contiguous files using the SHIFT key or noncontiguous files using the CTRL key.

  11. Select Open.
  12. The application adds the imported raw data files to the table in the Load Raw Data area.
  13. The order of the files in this table defines the order that they appear in the Results tables on the Process and Review page.
  14. In the Load Raw Data area, in the Condition box, type the experiment condition for each raw data file, separated by a space.
  15. If an entered condition matches a portion of a raw data file name, the application automatically assigns that condition to one or more matching raw data files.

  16. TIP

    If your experiment data includes a blank, type the word "blank" as a condition to identify the blank raw data file for background subtraction.

  17. To change the condition assigned to a raw data file, use the drop-down menu in the Condition column next to the corresponding raw file name to select a different condition.
  18. In the Reference Condition box, select the reference condition for the experiment from the drop-down menu.

  19. NOTE

    The default reference condition is the first entered condition in the Condition box.

  20. The application uses the indicated reference condition to calculate various analytical ratios during processing. These ratios are reported in the Results table(s) on the Process and Review page.
  21. If you load multiple raw data files for an experiment, in the Result Format for Multiple Raw Files area, select either the Batch Processing or Multiconsensus option.

  22. TIP

    For more information on these results formats, see Result formats: Batch Processing and Multiconsensus.

  23. (Optional) In the Sequence area, select the checkbox in the table row for the sequence you want to assign to the experiment.
  24. The application applies the selected sequence to the experiment during processing.

  25. IMPORTANT

    Selecting a sequence is optional for non-targeted Peptide Mapping Analysis experiments, but required for targeted and hydrogen-deuterium exchange (HDX) experiments.

    If you do not select a sequence for your experiment, the application still performs component detection, but entries in the Results tables have no identification information.

  26. TIP

    If you initially process an experiment without applying a sequence, you can identify components later by importing or creating a sequence and then using real-time optimization (RTO) to apply the sequence to your results.

  27. In the Processing Method area, select the checkbox for the processing method you want to use or customize for your experiment.
  28. (Optional) Select the Enable Automatic Parameter Values checkbox if you want the application to automatically determine several parameters for the experiment, such as the absolute signal threshold and retention time shift, using the raw data files.
  29. Then, do either of the following:
  30. Select Start Processing to submit your experiment for processing.
  31. Select Edit Method to open the processing method editing wizard and edit the experiment parameters before processing.
  32. Once you submit the experiment for processing, the Queue page opens, displaying the jobs in the run queue table.