The application calculates the quantification values for the protein as the sum of the intensity or S/N values for all PSMs belonging to the proteins that are marked as being usable. Whether the application considers a PSM usable is determined by the parameters of the Reporter Ions Quantifier node and the Precursor Ions Quantifier node, including those labeled Peptides to Use and Consider Protein Groups for Peptide Uniqueness. The Use Only Unique Peptides parameter includes the quantification peptides that do not occur in other proteins. The Proteins Groups for Peptide Uniqueness parameter defines peptide uniqueness on the basis of protein groups rather than individual proteins.
When it determines peptide uniqueness for classification in the PSM Ambiguity column on the PSMs page, the application only considers the PSMs that it considered when creating the protein groups, if you select the Use Only Unique Peptides parameter. For example, it does not use for quantification a PSM of low confidence that it did not use to create the protein groups.
The following flowchart shows how the application classifies PSMs for protein quantification. It displays this classification in the Quan Info column of the results report.