Dataset Information

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 source code along with user documentation are available on http://compbio.eecs.wsu.edu/MR-MSPolygraph.

Contact

ananth@eecs.wsu.edu; william.cannon@pnnl.gov.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Kalyanaraman A

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

REPOSITORIES: biostudies-literature

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Publications

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

Kalyanaraman Ananth A Cannon William R WR Latt Benjamin B Baxter Douglas J DJ

Bioinformatics (Oxford, England) 20110916 21

<h4>Summary</h4>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 reduc ...[more]

PMID: 21926122

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Project description:We describe the creation of a mass spectral library composed of all identifiable spectra derived from the tryptic digest of the NISTmAb IgG1?. The library is a unique reference spectral collection developed from over six million peptide-spectrum matches acquired by liquid chromatography-mass spectrometry (LC-MS) over a wide range of collision energy. Conventional one-dimensional (1D) LC-MS was used for various digestion conditions and 20- and 24-fraction two-dimensional (2D) LC-MS studies permitted in-depth analyses of single digests. Computer methods were developed for automated analysis of LC-MS isotopic clusters to determine the attributes for all ions detected in the 1D and 2D studies. The library contains a selection of over 12,600 high-quality tandem spectra of more than 3,300 peptide ions identified and validated by accurate mass, differential elution pattern, and expected peptide classes in peptide map experiments. These include a variety of biologically modified peptide spectra involving glycosylated, oxidized, deamidated, glycated, and N/C-terminal modified peptides, as well as artifacts. A complete glycation profile was obtained for the NISTmAb with spectra for 58% and 100% of all possible glycation sites in the heavy and light chains, respectively. The site-specific quantification of methionine oxidation in the protein is described. The utility of this reference library is demonstrated by the analysis of a commercial monoclonal antibody (adalimumab, Humira®), where 691 peptide ion spectra are identifiable in the constant regions, accounting for 60% coverage for both heavy and light chains. The NIST reference library platform may be used as a tool for facile identification of the primary sequence and post-translational modifications, as well as the recognition of LC-MS method-induced artifacts for human and recombinant IgG antibodies. Its development also provides a general method for creating comprehensive peptide libraries of individual proteins.

Dataset Information

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

Summary

Availability

Contact

Supplementary information

Publications

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

Similar Datasets

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