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


RESULTS
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.


CONCLUSIONS
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 http://www.comp.hkbu.edu.hk/~youli/ProteinByGPU.html.
You
Y
Li
Hao
H
Chi
Leihao
L
Xia
Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong. chxw@comp.hkbu.edu.hk.
Xiaowen
X
Chu
D000465:Algorithms; D030562:Databases, Protein; D010455:Peptides / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods; D057386:Search Engine; D020539:Sequence Analysis, Protein; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*
D010455:Peptides; D011506:Proteins