Speeding up scoring module of mass spectrometry based protein identification by GPU

You Li; Xiaowen CHU

doi:10.1109/HPCC.2012.194

Speeding up scoring module of mass spectrometry based protein identification by GPU

You Li^*, Xiaowen CHU

^*Corresponding author for this work

Department of Computer Science

Research output: Chapter in book/report/conference proceeding › Conference proceeding › peer-review

5 Citations (Scopus)

Abstract

Database searching is a main method for protein identification in shotgun proteomics, and many research efforts are dedicated to improving its effectiveness. However, the efficiency of database searching is facing a serious challenge, due to the ever fast growth of protein and peptide databases resulted from genome translations, enzymatic digestions, and post-translational modifications (PTMs). On the other hand, as a general-purpose and high performance parallel hardware, Graphics Processing Units (GPUs) develop continuously and provide another promising platform for parallelizing database searching based protein identification. It becomes very important to study how to speed up database search engines by GPUs for protein identification. In this paper, we mainly utilize GPUs to accelerate the scoring module, which is the most time-consuming component. Specifically, we study two popular scoring method: spectral dot product based method, which is used by X!Tandem, and kernel spectral dot product, which is used by pFind.

Original language	English
Title of host publication	Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012
Pages	1315-1320
Number of pages	6
DOIs	https://doi.org/10.1109/HPCC.2012.194
Publication status	Published - 2012
Event	14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012 - Liverpool, United Kingdom Duration: 25 Jun 2012 → 27 Jun 2012 https://ieeexplore.ieee.org/xpl/conhome/6331801/proceeding

Publication series

Name	Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012

Conference

Conference	14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012
Country/Territory	United Kingdom
City	Liverpool
Period	25/06/12 → 27/06/12
Internet address	https://ieeexplore.ieee.org/xpl/conhome/6331801/proceeding

Scopus Subject Areas

Software

User-Defined Keywords

GPU computing
protein identification
spectral dot product

Access to Document

10.1109/HPCC.2012.194

Cite this

Li, Y., & CHU, X. (2012). Speeding up scoring module of mass spectrometry based protein identification by GPU. In Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012 (pp. 1315-1320). Article 6332330 (Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012). https://doi.org/10.1109/HPCC.2012.194

Li, You ; CHU, Xiaowen. / Speeding up scoring module of mass spectrometry based protein identification by GPU. Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012. 2012. pp. 1315-1320 (Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012).

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abstract = "Database searching is a main method for protein identification in shotgun proteomics, and many research efforts are dedicated to improving its effectiveness. However, the efficiency of database searching is facing a serious challenge, due to the ever fast growth of protein and peptide databases resulted from genome translations, enzymatic digestions, and post-translational modifications (PTMs). On the other hand, as a general-purpose and high performance parallel hardware, Graphics Processing Units (GPUs) develop continuously and provide another promising platform for parallelizing database searching based protein identification. It becomes very important to study how to speed up database search engines by GPUs for protein identification. In this paper, we mainly utilize GPUs to accelerate the scoring module, which is the most time-consuming component. Specifically, we study two popular scoring method: spectral dot product based method, which is used by X!Tandem, and kernel spectral dot product, which is used by pFind.",

keywords = "GPU computing, protein identification, spectral dot product",

author = "You Li and Xiaowen CHU",

note = "Copyright: Copyright 2012 Elsevier B.V., All rights reserved.; 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012 ; Conference date: 25-06-2012 Through 27-06-2012",

year = "2012",

doi = "10.1109/HPCC.2012.194",

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series = "Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012",

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Li, Y & CHU, X 2012, Speeding up scoring module of mass spectrometry based protein identification by GPU. in Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012., 6332330, Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012, pp. 1315-1320, 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012, Liverpool, United Kingdom, 25/06/12. https://doi.org/10.1109/HPCC.2012.194

Speeding up scoring module of mass spectrometry based protein identification by GPU. / Li, You; CHU, Xiaowen.
Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012. 2012. p. 1315-1320 6332330 (Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012).

Research output: Chapter in book/report/conference proceeding › Conference proceeding › peer-review

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AU - CHU, Xiaowen

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AB - Database searching is a main method for protein identification in shotgun proteomics, and many research efforts are dedicated to improving its effectiveness. However, the efficiency of database searching is facing a serious challenge, due to the ever fast growth of protein and peptide databases resulted from genome translations, enzymatic digestions, and post-translational modifications (PTMs). On the other hand, as a general-purpose and high performance parallel hardware, Graphics Processing Units (GPUs) develop continuously and provide another promising platform for parallelizing database searching based protein identification. It becomes very important to study how to speed up database search engines by GPUs for protein identification. In this paper, we mainly utilize GPUs to accelerate the scoring module, which is the most time-consuming component. Specifically, we study two popular scoring method: spectral dot product based method, which is used by X!Tandem, and kernel spectral dot product, which is used by pFind.

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Li Y, CHU X. Speeding up scoring module of mass spectrometry based protein identification by GPU. In Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012. 2012. p. 1315-1320. 6332330. (Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012). doi: 10.1109/HPCC.2012.194

Speeding up scoring module of mass spectrometry based protein identification by GPU

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