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Open Access Open Badges Methodology article

Accelerating the scoring module of mass spectrometry-based peptide identification using GPUs

You Li1, Hao Chi23, Leihao Xia1 and Xiaowen Chu1*

Author Affiliations

1 Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong

2 Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China

3 Graduate University of Chinese Academy of Sciences, Beijing, China

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BMC Bioinformatics 2014, 15:121  doi:10.1186/1471-2105-15-121

Published: 28 April 2014



Tandem mass spectrometry-based database searching is currently the main method for protein identification in shotgun proteomics. The explosive growth of protein and peptide databases, which is a result of genome translations, enzymatic digestions, and post-translational modifications (PTMs), is making computational efficiency in database searching a serious challenge. Profile analysis shows that most search engines spend 50%-90% of their total time on the scoring module, and that the spectrum dot product (SDP) based scoring module is the most widely used. As a general purpose and high performance parallel hardware, graphics processing units (GPUs) are promising platforms for speeding up database searches in the protein identification process.


We designed and implemented a parallel SDP-based scoring module on GPUs that exploits the efficient use of GPU registers, constant memory and shared memory. Compared with the CPU-based version, we achieved a 30 to 60 times speedup using a single GPU. We also implemented our algorithm on a GPU cluster and achieved an approximately favorable speedup.


Our GPU-based SDP algorithm can significantly improve the speed of the scoring module in mass spectrometry-based protein identification. The algorithm can be easily implemented in many database search engines such as X!Tandem, SEQUEST, and pFind. A software tool implementing this algorithm is available at webcite