Table III False positive rate. Number of FP and resulting FP rate after correlation and low-fold change filtering on protein and peptide level
Protein levelPeptide level
FP (filtered)FP rateFP (filtered)FP rate
DDA520.00%12442.61%
DirectDIA1328.89%11835.22%
MM IS 6825.00%11940.61%
GS IS 15514.29%12334.36%
GS IS 30616.22%12532.81%
MM F Prot 201429.79%16743.04%
MM F Pep 161230.77%12943.58%
IS and F all 781428.57%22642.56%
Pulsar GS IS 151226.67%18840.26%
Pulsar MM F Prot 201430.43%21443.50%