Skip Navigation


Bioinformatics Advance Access originally published online on February 3, 2007
Bioinformatics 2007 23(6):724-731; doi:10.1093/bioinformatics/btl656
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
23/6/724    most recent
btl656v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (2)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Bogdan, I.
Right arrow Articles by Beynon, R. J
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Bogdan, I.
Right arrow Articles by Beynon, R. J
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Hardware acceleration of processing of mass spectrometric data for proteomics

Istvan Bogdan 1, Daniel Coca 1,*, Jenny Rivers 2 and Robert J Beynon 2

1Department of Automatic Control & Systems Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, UK, and 2Proteomics and Functional Genomics Group, Faculty of Veterinary Science, University of Liverpool, Crown Street, Liverpool L69 7ZJ, UK

*To whom correspondence should be addressed.


  Abstract

Motivation: High-resolution mass spectrometers generate large data files that are complex, noisy and require extensive processing to extract the optimal data from raw spectra. This processing is readily achieved in software and is often embedded in manufacturers’ instrument control and data processing environments. However, the speed of this data processing is such that it is usually performed off-line, post data acquisition. We have been exploring strategies that would allow real-time advanced processing of mass spectrometric data, making use of the reconfigurable computing paradigm, which exploits the flexibility and versatility of Field Programmable Gate Arrays (FPGAs). This approach has emerged as a powerful solution for speeding up time-critical algorithms. We describe here a reconfigurable computing solution for processing raw mass spectrometric data generated by MALDI-ToF instruments. The hardware-implemented algorithms for de-noising, baseline correction, peak identification and deisotoping, running on a Xilinx Virtex 2 FPGA at 180 MHz, generate a mass fingerprint over 100 times faster than an equivalent algorithm written in C, running on a Dual 3 GHz Xeon workstation.

Contact: D.Coca{at}sheffield.ac.uk

Associate Editor: Golan Yona

Received on September 25, 2006; revised on November 23, 2006; accepted on December 21, 2006

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.