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

You Li*, Xiaowen CHU

*Corresponding author for this work

Research output: Chapter in book/report/conference proceedingConference contributionpeer-review

3 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 languageEnglish
Title of host publicationProceedings 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
Pages1315-1320
Number of pages6
DOIs
Publication statusPublished - 2012
Event14th 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 201227 Jun 2012

Publication series

NameProceedings 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

Conference14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 - 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012
Country/TerritoryUnited Kingdom
CityLiverpool
Period25/06/1227/06/12

Scopus Subject Areas

  • Software

User-Defined Keywords

  • GPU computing
  • protein identification
  • spectral dot product

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