10 μg 293T was spiked with different amounts ( 0.2, 0.3, 0.4, 0.5 μg) of E.coli. Performed the ablation analysis to evaluate the DNN model in DeepRTAlign. Compared DeepRTAlign with Quandenser. Compared DeepRTAlign with MaxQuant’s MBR and FragPipe’s MBR. Generalizability evaluation on simulated datasets.