Acceleration of Tandem Mass Spectrometry Analysis Software CoCoozo using Multi-core CPUs and Graphics Processing Units

摘要

Tandem mass spectrometry, a method involving multiple steps of mass spectral selection, is widely used in various biological fields. In recent years, steady improvements have been made with respect to speed, and the number of protein databases available for analysis has rapidly increased. Consequently, computational analysis has become the bottleneck in tandem mass spectrometry. To overcome this problem, we attempted to improve the tandem mass spectrometry analysis software CoCoozo. To accelerate the program, we improved the algorithm and also incorporated utilization of multi-core CPU and GPGPU. As a result of algorithm improvements, when all mass spectral data files had precursor data, we achieved 8.9-fold speedups compared with the original software. In addition, in the case of no precursor data, by using a 12-core CPU and a GPU card we achieved 18.1-fold speedups compared with the original software.