Hardware Accelerated Novel Protein Identification

  • Anish Alex
  • Jonathan Rose
  • Ruth Isserlin-Weinberger
  • Christopher Hogue
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3203)


The proteins in living organisms perform almost every significant function that governs life. A protein’s functionality depends upon its physical structure, which depends on its constituent sequence of amino acids as specified by its gene of origin. Advances in mass spectrometry have helped to determine unknown protein sequences but the process is very slow. We review a method of de-novo (novel) protein sequencing that requires a fast search of the genome. In this paper, we present the design of a hardware system that performs this search in a very fast, cost-effective manner. This hardware solution is more than 30 times faster than a similar search in software on a single modern PC, and up to 40 times more cost effective than a computer cluster capable of the same performance. The hardware is FPGA-based to reduce the cost and allow modification of the algorithm, both key requirements of practical protein analysis tools.


Search Engine Protein Identification Tryptic Peptide Custom Hardware Mass List 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Choudary, Joyti, S., Blackstock, Walter, P., Creasy, M., Cottrell, D., John, S.: Interrogating the human genome using uninterpreted mass spectrometry data. Proteomics 1, 651–667 (2001)CrossRefGoogle Scholar
  2. 2.
    Lesk, A.M.: Introduction to Bioinformatics, pp. 6–7. Oxford Press, NY (2002)Google Scholar
  3. 3.
    McLuckey, S.A., Wells, J.M.: Mass Analysis at the Advent of the 21st Century. Chem. Rev. 101(2), 571–606 (2001)CrossRefGoogle Scholar
  4. 4.
  5. 5.
    Pappin, D.J.C., Hojrup, P., Bleasby, A.J.: Rapid identification of proteins by peptide mass fingerprinting. Curr. Biol. 3(6), 327–332 (1993)CrossRefGoogle Scholar
  6. 6.
    Sourdis, I., Pnevmatikatos, D.N.: Fast, Large-Scale String Match for a 10Gbps FPGA-Based Network Intrusion Detection System. In: FPL 2003, pp. 880–889 (2003)Google Scholar
  7. 7.
    Alex, A.: Hardware Accelerated Protein Identification., Master’s Thesis, University of Toronto (2003),
  8. 8.
    Decypher ®, TimeLogic Corporation,
  9. 9.
    Lewis, D., Betz, V., Jefferson, D., Lee, A., Lane, C., Leventis, P., Marquardt, S., McClintock, C., Pedersen, B., Powell, G., Reddy, S., Wysocki, C., Cliff, R., Rose, J.: The Stratix Routing and Logic Architecture. In: FPGA 2003, pp. 15–20 (February 2003)Google Scholar
  10. 10.
    Transmogrifier 3A, University of Toronto,

Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Anish Alex
    • 1
  • Jonathan Rose
    • 1
  • Ruth Isserlin-Weinberger
    • 2
  • Christopher Hogue
    • 2
  1. 1.Department of Electrical and Computer EngineeringUniversity of TorontoTorontoCanada
  2. 2.Department of Biochemistry, Wim RoelandtsUniversity of TorontoTorontoCanada

Personalised recommendations