Supplementary Figure 1 : Estimation of q-values at the peptide-query level, the peptide level and the protein level.

From: Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses

Supplementary Figure 1

The peptide-query-level (left), peptide-level (middle) and protein-level (right) discriminant score density plots (a) and p-value histograms (b) for one DIA run of the SWATH-MS interlaboratory study that was analyzed with the combined human assay library (CAL) are shown. a) The distributions indicate a large (false target)/(total target) ratio (π0 0.6) on the peptide-query level. The q-value estimation was adapted for peptide and protein level by using the best scoring peak group per peptide or protein across all samples for both targets and decoys. The (false target)/(total target) ratio decreases slightly on peptide level and more on protein level (π0  0.5), compared to the peptide-query level. b) On the peptide-query level and the peptide level, the estimation of π0  is anticonservative, indicated by a lower density of p-values after the p-value threshold of λ=0.4. On the protein level, the estimation of π0 is more accurate with a consistent density of p-values.