title: Hardware-accelerated protein identification for mass spectrometry.
abstract: An ongoing issue in mass spectrometry is the time it takes to search DNA sequences with MS/MS peptide fragments (see, e.g., Choudary et al., Proteomics 2001; 1: 651-667.) Search times are far longer than spectra acquisition time, and parallelization of search software on clusters requires doubling the size of a conventional computing cluster to cut the search time in half. Field programmable gate arrays (FPGAs) are used to create hardware-accelerated algorithms that reduce operating costs and improve search speed compared to large clusters. We present a novel hardware design that takes full spectra and computes 6-frame translation word searches on DNA databases at a rate of approximately 3 billion base pairs per second, with queries of up to 10 amino acids in length and arbitrary wildcard positions. Hardware post-processing identifies in silico tryptic peptides and scores them using a variety of techniques including mass frequency expected values. With faster FPGAs protein identifications from the human genome can be achieved in less than a second, and this makes it an ideal solution for a number of proteome-scale applications.
authors.affiliation: Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, Ontario, M5S 3G4 Canada.
authors.forename: Anish T
authors.initials: AT
authors.lastname: Alex
authors.forename: Michel
authors.initials: M
authors.lastname: Dumontier
authors.forename: Jonathan S
authors.initials: JS
authors.lastname: Rose
authors.forename: Christopher W V
authors.initials: CW
authors.lastname: Hogue
mesh_terms: D004867:Equipment Design; D019544:Equipment Failure Analysis; D020869:Gene Expression Profiling / Q000295:instrumentation* / Q000379:methods; D016247:Information Storage and Retrieval / Q000379:methods; D013058:Mass Spectrometry / Q000295:instrumentation* / Q000379:methods; D009862:Online Systems; D011506:Proteins / Q000032:analysis* / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment / Q000295:instrumentation* / Q000379:methods; D017422:Sequence Analysis, DNA / Q000295:instrumentation* / Q000379:methods; D020539:Sequence Analysis, Protein / Q000295:instrumentation* / Q000379:methods
chemical_list: D011506:Proteins