The Reporter Ions Quantifier node and the Precursor Ions Quantifier node classify which peptide groups are used for protein quantification.
Use the following parameters to control the classification of peptide groups:
- The Consider Protein Groups for Peptide Uniqueness parameter determines which peptide groups are unique. If you set it to True, the Reporter Ions Quantifier node and the Precursor Ions Quantifier node consider a peptide unique if it is included in only one protein group. If you set it to False, the node considers a peptide unique if it is included in only one protein.
- The Peptides to Use parameter determines which peptides to use.
- Unique: Uses only unique peptide groups.
- Unique + Razor: Uses both unique peptide groups and peptide groups containing razor peptides for the best associated master protein. Razor peptides are shared among multiple protein groups or proteins. When you set the Consider Protein Groups for Peptide Uniqueness parameter to True, the node uses peptide groups that are not unique for all proteins belonging to the protein group of the best master protein. The best master protein is the protein with the largest value in the # Protein Unique Peptides column on the Proteins page and with the smallest value in the Coverage column (the longest protein).
- All: Uses all peptide groups, whether they are unique or not.
When it classifies peptide groups, the Reporter Ions Quantifier node and the Precursor Ions Quantifier node create the following columns in the result file:
- Quan Info column on the Peptide Groups page, which displays No Quan Values for peptide groups that have no abundance value. It displays Not Unique or Unique for all other peptide groups.
- # Razor Peptides column on the Proteins page, which displays the number of razor peptides for proteins when you use razor peptides for quantification.