Table IV AUCs and mean absolute percentage errors. Table showing the AUC of the ROCs and the mean absolute percentage error (MAPE) of the respective method on the peptide and protein level. The MAPE was calculated between the median of achieved and expected protein/peptide fold changes, on log2 transformed ratios. The values can be interpreted as deviation between the achieved and expected ratio in percent
PeptideProtein
AUCMAPEAUCMAPE
DDA0.6165.20%0.8857.77%
DirectDIA0.9216.16%0.8721.67%
MM IS 60.8518.45%0.9723.15%
GS IS 150.9213.99%0.9522.84%
GS IS 300.8817.08%0.8725.92%
MM F Prot 200.7316.10%0.8221.41%
MM F Pep 160.6815.39%0.8027.21%
IS and F all 780.6315.12%0.9327.52%
Pulsar GS IS 150.7613.78%0.8817.69%
Pulsar MM F Prot 200.6312.91%0.9419.53%