Use the Study and Analysis dialog box for the most efficient method of choosing the data files, workflows, and quantification methods for the study. The dialog box does not cover all areas of a study (for example, study factors), but the more fields that you can complete, the more configuration the application handles.

You must complete the study name field, which cannot be modified later. If you are not sure of the correct entry for other fields, leave them blank.

NOTE

To use a custom quantification method, you must create it before adding it to a study. See Create a quantification method.

Label-free quantification does not require you to associate a quantification method with the raw data file or files.

Procedure

  1. Do one of the following:
  2. On the Start Page, select New Study/Analysis.
  3. Select File > New Study/Analysis.
  4. Select the Create New Study/Analysis .
  5. The New Study and Analysis dialog box opens.
  7. In the New Study and Analysis dialog box, do the following:
  8. In the Study Name box, enter the study name.

  9. NOTE

    The study name is required; you cannot modify it later.

    If you do not name the study, the application generates a default study name, for example, New Study 1, New Study 2, and so on.

  10. For Study Root Directory, select the Browse for study folder button (...), and locate where you want to store the study folder.

  11. NOTE

    Studies store the output of the processing workflows.

  12. TIP

    Use a directory on the local hard drive. Storage of the studies and results on a network drive often leads to workflow failures.

  13. For Import from File, select the Browse for study definition file button (...), and select a study definition file.
  14. If there is an Excel or tab-delimited text file that defines the study factors and maps them to quantification factors, select the file here.
  15. For more information about how to create such a file, see Creating a custom study definition file. A study definition file or study mapping file is used to import the study factors, the quantification method, and the associated quan channels when creating the new study.
  16. For Processing Workflow, select the Browse for a processing workflow template button (...), and select the workflow template.
  17. For Consensus Workflow, select the Browse for a consensus workflow template button (...), and select the workflow template.
  18. Select OK.
  19. The study_name page opens. This example shows the Analysis panel closed.
  20. In the folder that you specified as the study root directory, the application creates the folder study_name, which contains the file study_name.pdStudy. (The application appends a .pdStudy extension to the study file name.)
  22. To add or change any of the information, see Add or change basic study information.