title: MapReduce implementation of a hybrid spectral library-database search method for large-scale peptide identification.
abstract: CONCLUSIONS
  A MapReduce-based implementation called MR-MSPolygraph for parallelizing peptide identification from mass spectrometry data is presented. The underlying serial method, MSPolygraph, uses a novel hybrid approach to match an experimental spectrum against a combination of a protein sequence database and a spectral library. Our MapReduce implementation can run on any Hadoop cluster environment. Experimental results demonstrate that, relative to the serial version, MR-MSPolygraph reduces the time to solution from weeks to hours, for processing tens of thousands of experimental spectra. Speedup and other related performance studies are also reported on a 400-core Hadoop cluster using spectral datasets from environmental microbial communities as inputs.
  
  
  BACKGROUND
  The source code along with user documentation are available on http://compbio.eecs.wsu.edu/MR-MSPolygraph.
  
  
  BACKGROUND
  ananth@eecs.wsu.edu; william.cannon@pnnl.gov.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA 99164-2752, USA. ananth@eecs.wsu.edu
authors.forename: Ananth
authors.initials: A
authors.lastname: Kalyanaraman
authors.forename: William R
authors.initials: WR
authors.lastname: Cannon
authors.forename: Benjamin
authors.initials: B
authors.lastname: Latt
authors.forename: Douglas J
authors.initials: DJ
authors.lastname: Baxter
mesh_terms: D030562:Databases, Protein; D013058:Mass Spectrometry / Q000379:methods*; D010455:Peptides / Q000737:chemistry*; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D010455:Peptides