The study holds information necessary to run data analysis.


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

    The application stores all .msf and .pdResult files generated for any analyses used for these studies in this folder. Use a local hard drive with 1 GB of free space. Also, due to the amount of reading and writing to the study folder, use an SSD drive if available or a standard drive if not. Do not use a USB drive.

  8. Select the Processing workflow:
  9. ProcessingWF_LTQ_Orbitrap\PWF_OT_Precursor_Quan_and_LFQ_CID_SequestHT_Percolator.pdProcessingWF
  10. Select the Consensus workflow:
  11. ConsensusWF \ CWF_Comprehensive_Enhanced Annotation_LFQ_and_Precursor_Quan.pdConsensusWF
  12. Select OK.
  13. The Study Definition tab opens.
  14. To add a quantification method, do the following:
  15. Select the Study Definition tab.
  16. In the Quantification Methods pane, select the Add dropdown list, and then select SILAC 3plex (Arg6, Lys4 | Arg10, Lys8).
  17. The quantification method appears in the Quantification Methods pane.
  18. To add a data file to the study and associate the quantification method, do the following:
  19. Select the Input Files tab, and select Add Files.
  20. In Add Files, select the Chris_Ecoli_1_2_4.raw file, and then select Open.
  21. The file appears in the list of Input Files.
  22. In the Quan Method dropdown list, select SILAC 3plex.
  23. Add the raw file to the processing workflow by doing one of the following:
  24. Select the raw file and drag it into the Processing Step in the Analysis pane.
  25. Right-click the data file name, and select Set as Input File to >Step 1: Chris_Ecoli_1_2_4.msf.
  26. The raw file is now in the study.