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 LFQ 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 Import from File, select the browse button, and then select the LFQ Example.txt file.
  8. For Processing Workflow, browse and then select ProcessingWF_Hybrid \ PWF_Hybrid_MPS_SequestHT_INFERYS_Rescoring_Percolator_2stage.pdProcessingWF.
  9. For the Consensus Workflow, browse and then select ConsensusWF\CWF_Comprehensive_Enhanced Annotation_LFQ_and_Precursor_Quan.pdConsensusWF.
  10. Select OK.
  11. Refer to the Proteome Discoverer User Guide for more information about defining study factors in an Excel or text file.
  12. Refer to the Help for information on the INFERYS Rescoring Node.
  13. NOTE

    If you have an active CHIMERYS subscription, you could use the processing workflow PWF_Hybrid_LFQ_CHIMERYS.pdProcessingWF instead. This workflow will produce a significant increase in the number of identified and quantified proteins and peptides for this dataset. We will include additional notes for this exercise about how to set CHIMERYS parameters and interpret results.