Fig. 4: Internal and external FDR.
From: MaxDIA enables library-based and library-free data-independent acquisition proteomics
a, Number of identifications (blue: matches; green: peptides; red: protein groups) as a function of estimated FDR. The FDR is estimated once with the ‘internal’ target-decoy method implemented in MaxQuant (solid lines) and once with the ‘external’ method using mixing maize and human samples for generating the library and using only human sample in the DIA runs (dashed lines). b, Same as in a but using in silico predicted libraries generated using DeepMass:Prism15 c, Same as a but using the raw score instead of the machine learning–derived score. d, Same as b but using the raw score instead of the machine learning–derived score.
