NOTE

Specifying conditions is required for Peptide Mapping Analysis and Oligonucleotide Analysis experiments.

This step is optional for Intact Mass Analysis and Top Down Analysis experiments.

TIP

For hydrogen deuterium exchange (HDX) experiments within the Peptide Mapping Analysis workflow, follow the condition assignment guidelines outlined in Workflow: Hydrogen deuterium exchange (HDX) experiments the Peptide Mapping Analysis User Guide.

Prerequisites

  1. You are setting up an experiment on the appropriate workflow page.
  2. You have loaded one or more raw data files to your experiment.

Procedure

  1. In the Load Raw Data area, in the Condition box, type the experiment condition for each raw data file, separated by a space.
  2. 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.

  3. 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.

  4. 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.
  5. In the Reference Condition box, select the reference condition for the experiment from the dropdown menu.

  6. NOTE

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

  7. 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.
  8. 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.

  9. NOTE

    For Intact Mass Analysis and Top Down Analysis experiments, you can process up to 10 raw data files using the Multiconsensus results format.

    For Peptide Mapping Analysis and Oligonucleotide Analysis experiments, there is no restriction on the number of raw data files.

  10. Loaded raw data files and conditions for an HDX Peptide Mapping Analysis experiment
    Figure Loaded raw data files and conditions for an HDX Peptide Mapping Analysis experiment