Abstract: We introduced the design and the testing results of protein quantification software. The analytical results indicate that the testing size reaches 2048 cores, when P-QuantWiz runs on the clusters of DAWNING 6000，and the speed-up ratio still increases when we use 256 cores. Compared with the results of P-QuantWiz which is ran on one CPU, the speed-up ratio of PGQuantWiz on one single GPU is 8.1. Compared with the results which is ran on one GPU, the speed-up ratio of PGQuantWiz on 16 GPU is 14.18, and the parallel efficiency is 89%.

Key words: MPI, CUDA, Protein ctuantification