MapReduce implementation of a hybrid spectral library-database search method for large-scale peptide identification.

ABSTRACT:

Summary

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.

Availability

The sour

SUBMITTER: Kalyanaraman A 

PROVIDER: S-EPMC3198583 | biostudies-literature | 2011 Nov

REPOSITORIES: biostudies-literature