1. Select the Start Page tab in Proteome Discoverer.
  2. On the Start page, select New Study/Analysis.
  3. The New Study and Analysis dialog box opens.
  4. In the Study Name text field, enter a study name, for example, DIA example.
  5. (Optional) For Study Root Directory, change the folder for storing the study.
  6. NOTE

    The application stores all .msf and result files generated for any analyses used for these studies in this folder. Use a local hard drive with 30 GB of free space. Also, due to the amount of reading and writing to the study folder, use an SSD drive if available. USB drives are not recommended.

  7. For the Processing Workflow, browse and select PWF_Hybrid_DIA_CHIMERYS_MBR.
  8. For the Consensus Workflow, browse and select CWF_Comprehensive_Enhanced Annotation_DIA.
  9. Select OK.
  10. Refer to the Proteome Discoverer Help for information on the CHIMERYS node.
  11. Define the study factors.
  12. In the Study Factors area on the Study Definition pane, select the Add dropdown menu and select Numerical Factor.
  13. For the title of the factor, enter E coli (ng), and select Apply.
  14. In the New Factor dialog box, select Edit.
  15. Add the following items to the new study factor: 96 and 192.
  16. Select the Input Files tab, and then select Add Local Files.
  17. The Add Files dialog box opens.
  18. Locate the six RAW files that you downloaded and select Open.
  19. The files appear on the Input Files page.
  20. Select and drag the six files from the Input Files tab to the Files for Analysis section of the Analysis.
  21. Select the Samples tab.
  22. In the E coli (ng) column, make the following changes to the study factor:
  23. Change the A4 study factors to 96.
  24. Change the A5 study factors to 192.