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Proteomes 2018, 6(1), 2; doi:10.3390/proteomes6010002

MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data

1
Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
2
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
3
Department of Ocean, Earth, and Atmospheric Sciences, Old Dominion University, Norfolk, VA 23529, USA
*
Authors to whom correspondence should be addressed.
Received: 21 November 2017 / Revised: 19 December 2017 / Accepted: 21 December 2017 / Published: 27 December 2017
(This article belongs to the Special Issue Metaproteomics)
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Abstract

Metaproteomics is the characterization of all proteins being expressed by a community of organisms in a complex biological sample at a single point in time. Applications of metaproteomics range from the comparative analysis of environmental samples (such as ocean water and soil) to microbiome data from multicellular organisms (such as the human gut). Metaproteomics research is often focused on the quantitative functional makeup of the metaproteome and which organisms are making those proteins. That is: What are the functions of the currently expressed proteins? How much of the metaproteome is associated with those functions? And, which microorganisms are expressing the proteins that perform those functions? However, traditional protein-centric functional analysis is greatly complicated by the large size, redundancy, and lack of biological annotations for the protein sequences in the database used to search the data. To help address these issues, we have developed an algorithm and web application (dubbed “MetaGOmics”) that automates the quantitative functional (using Gene Ontology) and taxonomic analysis of metaproteomics data and subsequent visualization of the results. MetaGOmics is designed to overcome the shortcomings of traditional proteomics analysis when used with metaproteomics data. It is easy to use, requires minimal input, and fully automates most steps of the analysis—including comparing the functional makeup between samples. MetaGOmics is freely available at https://www.yeastrc.org/metagomics/. View Full-Text
Keywords: metaproteomics; proteomics; bioinformatics; software; data visualization; mass spectrometry; gene ontology metaproteomics; proteomics; bioinformatics; software; data visualization; mass spectrometry; gene ontology
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Riffle, M.; May, D.H.; Timmins-Schiffman, E.; Mikan, M.P.; Jaschob, D.; Noble, W.S.; Nunn, B.L. MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data. Proteomes 2018, 6, 2.

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