Supplementary Figure 2 : Influence of protein length on the peptide-query-level and protein-level q-value estimation.

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

Supplementary Figure 2

a) Protein length distribution of all proteins in the combined human assay library (CAL), all proteins inferred at 1% peptide-query-level FDR in the global context of all 229 DIA runs of the SWATH-MS interlaboratory comparison study, and all proteins inferred at 1% global protein FDR respectively. b) Histogram of protein length distribution for the differently filtered protein subsets of the CAL. The distributions show that there is no bias for protein length when selecting the best peak group as proxy for protein-level q-value estimation.