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| Content Provider | IEEE Xplore Digital Library |
|---|---|
| Author | Jian Zhang McQuillan, I. FangXiang Wu |
| Copyright Year | 2011 |
| Description | Author affiliation: Department of Mechanical Engineering and Division of Biomedical Engineering, University of Saskatchewan, Canada (FangXiang Wu) || Department of Computer Science, University of Saskatchewan, Canada (Jian Zhang; McQuillan, I.) |
| Abstract | Tandem mass spectrometry is a powerful experimental tool used in molecular biology to determine the composition of protein mixtures. In a tandem mass experiment, peptide ion selection algorithms generally select only the most abundant peptide ions for further fragmentation. Because of this, the low-abundance proteins in a sample rarely get identified. A Real-Time Peptide-Spectrum Matching algorithm (RT-PSM) [1] was introduced to achieve real-time peptide identification for solving this abundance related biases. Profiling results show that the Peptide-Spectrum similarity scoring is one of the most time-consuming module of RT-PSM. In this study, we develop a parallel algorithm for Peptide-Spectrum scoring using NVIDIA CUDA technology [2]. As RT-PSM employs a scoring function based on shared peak counts, our algorithm can also be applied to other software that uses similar scoring schemes. Moreover, we introduce an algorithm to reduce the number of comparisons in calculating shared peak counts. In addition, as the CUDA architecture is unique, we introduce optimizations for the CUDA architecture to achieve better performance. A simulation shows a 190-fold speedup on the scoring module and a 26-fold speedup on the entire process. The developed algorithm can be employed to develop real-time control methods for tandem mass spectrometry. |
| Starting Page | 208 |
| Ending Page | 213 |
| File Size | 364266 |
| Page Count | 6 |
| File Format | |
| ISBN | 9781612848518 |
| e-ISBN | 9781612848525 |
| DOI | 10.1109/ICCABS.2011.5729882 |
| Language | English |
| Publisher | Institute of Electrical and Electronics Engineers, Inc. (IEEE) |
| Publisher Date | 2011-02-03 |
| Publisher Place | USA |
| Access Restriction | Subscribed |
| Rights Holder | Institute of Electrical and Electronics Engineers, Inc. (IEEE) |
| Subject Keyword | Proteins CUDA Databases Peptides Parallelizing Computer architecture Ions Amino acids MS/MS Spectra GPU Graphics processing unit |
| Content Type | Text |
| Resource Type | Article |
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