Supplementary Figure 2: MAYU-estimated FDRs with respect to iProphet probability thresholds.
From: Building high-quality assay libraries for targeted analysis of SWATH MS data
The software MAYU estimates the FDRs on PSM (mFDR), peptide (pepFDR), and protein (protFDR) level with respect to the applied iProphet probability threshold. The data is based on the case study described in the protocol, which consists of three whole cell lysates of yeast. As comparison the protein FDR of a very large data set of 331 runs of different human cells and tissues is shown (Pan Human Library as described by Rosenberger and colleagues23).
