PMID- 20013371
OWN - NLM
STAT- MEDLINE
DCOM- 20100223
LR  - 20211020
IS  - 1940-6029 (Electronic)
IS  - 1064-3745 (Linking)
VI  - 604
DP  - 2010
TI  - A high-performance reconfigurable computing solution for Peptide mass 
      fingerprinting.
PG  - 163-85
LID - 10.1007/978-1-60761-444-9_12 [doi]
AB  - High-throughput, MS-based proteomics studies are generating very large volumes of 
      biologically relevant data. Given the central role of proteomics in emerging 
      fields such as system/synthetic biology and biomarker discovery, the amount of 
      proteomic data is expected to grow at unprecedented rates over the next decades. 
      At the moment, there is pressing need for high-performance computational 
      solutions to accelerate the analysis and interpretation of this data.Performance 
      gains achieved by grid computing in this area are not spectacular, especially 
      given the significant power consumption, maintenance costs and floor space 
      required by large server farms.This paper introduces an alternative, 
      cost-effective high-performance bioinformatics solution for peptide mass 
      fingerprinting based on Field Programmable Gate Array (FPGA) devices. At the 
      heart of this approach stands the concept of mapping algorithms on custom digital 
      hardware that can be programmed to run on FPGA. Specifically in this case, the 
      entire computational flow associated with peptide mass fingerprinting, namely raw 
      mass spectra processing and database searching, has been mapped on custom 
      hardware processors that are programmed to run on a multi-FPGA system coupled 
      with a conventional PC server. The system achieves an almost 2,000-fold speed-up 
      when compared with a conventional implementation of the algorithms in software 
      running on a 3.06 GHz Xeon PC server.
FAU - Coca, Daniel
AU  - Coca D
AD  - Department of Automatic Control & Systems Engineering, University of Sheffield, 
      Sheffield, UK. d.coca@sheffield.ac.uk
FAU - Bogdan, Istvan
AU  - Bogdan I
FAU - Beynon, Robert J
AU  - Beynon RJ
LA  - eng
GR  - BB/F004745/1/BB_/Biotechnology and Biological Sciences Research Council/United 
      Kingdom
PT  - Journal Article
PL  - United States
TA  - Methods Mol Biol
JT  - Methods in molecular biology (Clifton, N.J.)
JID - 9214969
SB  - IM
MH  - Algorithms
MH  - *Computers
MH  - *Computing Methodologies
MH  - Databases, Protein
MH  - Equipment Design
MH  - Mass Spectrometry/*methods
MH  - Peptide Mapping/economics/*methods
MH  - Proteomics/economics/*methods
EDAT- 2009/12/17 06:00
MHDA- 2010/02/24 06:00
CRDT- 2009/12/17 06:00
PHST- 2009/12/17 06:00 [entrez]
PHST- 2009/12/17 06:00 [pubmed]
PHST- 2010/02/24 06:00 [medline]
AID - 10.1007/978-1-60761-444-9_12 [doi]
PST - ppublish
SO  - Methods Mol Biol. 2010;604:163-85. doi: 10.1007/978-1-60761-444-9_12.