Abstract: QuantWiz is a label-free ctuantitative software based on mass spectrometry, well used in ctuantitative pro- teomics. The increasing experimental data causes the enormous workload. Having hundreds of GFlops or even hFlops performance, GPU can speed up such compute-intensive quantitative proteomics applications. This article analyzed the software QuantWiz,to find the hotspot module of this software. Then we presented an accelerated program on GPU for this software called GPU-QuantWiz and implemented it under CUDA Framework. Statistical performance results show that the accelerated program can achieve good performance, with 9. 66 speedup. Moreover, our algorithm can be exten- ded on two or more GPUs,with a good scalability.

Key words: Label-free quantification, Proteome, QuantWiz, UPU, Parallel computing