1. Select Edit to the right of the Consensus Step within the Analysis section.
  2. Select the Fragment Ions Quantifier node.
  3. For peptides to use, select Unique.
  4. For the Normalization Mode parameter, select Specific Protein Amount.
  5. For the Proteins for Normalization parameter, select the Homo sapiens FASTA database.
  6. Select the Protein Annotation node.
  7. For the Protein Database parameter, select the Homo sapiens database and the E. coli FASTA database from the dropdown list.
  8. Under the Peptide and Protein Filter node, ensure Keep lower Confident PSMs is set to True.
  9. This will display the medium confidence PSMs used for MS2 Quan.