Table II Number of identified proteins if raw files are processed in three disjointed sets

Set 1 includes A549, HEK293, GAMG, and HeLa. Set 2 includes HepG2, Jurkat, K562, and MCF7. Set 3 includes RKO, LNCap, and U2OS. Union refers to the union of the proteins identified in the individual sets. True is the number of forward hits, decoy the number of decoy hits, and FDR is the corresponding false discovery rate.

Set 1Set 2Set 3Union
True9,9229,6909,05412,211
Decoy10310593226
FDR1.03%1.07%1.02%1.82%