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

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 f...

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Detalles Bibliográficos
Autores principales: Riffle, Michael, May, Damon H., Timmins-Schiffman, Emma, Mikan, Molly P., Jaschob, Daniel, Noble, William Stafford, Nunn, Brook L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5874761/
https://www.ncbi.nlm.nih.gov/pubmed/29280960
http://dx.doi.org/10.3390/proteomes6010002
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author Riffle, Michael
May, Damon H.
Timmins-Schiffman, Emma
Mikan, Molly P.
Jaschob, Daniel
Noble, William Stafford
Nunn, Brook L.
author_facet Riffle, Michael
May, Damon H.
Timmins-Schiffman, Emma
Mikan, Molly P.
Jaschob, Daniel
Noble, William Stafford
Nunn, Brook L.
author_sort Riffle, Michael
collection PubMed
description 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/.
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spelling pubmed-58747612018-04-02 MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data Riffle, Michael May, Damon H. Timmins-Schiffman, Emma Mikan, Molly P. Jaschob, Daniel Noble, William Stafford Nunn, Brook L. Proteomes Article 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/. MDPI 2017-12-27 /pmc/articles/PMC5874761/ /pubmed/29280960 http://dx.doi.org/10.3390/proteomes6010002 Text en © 2017 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Riffle, Michael
May, Damon H.
Timmins-Schiffman, Emma
Mikan, Molly P.
Jaschob, Daniel
Noble, William Stafford
Nunn, Brook L.
MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data
title MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data
title_full MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data
title_fullStr MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data
title_full_unstemmed MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data
title_short MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data
title_sort metagomics: a web-based tool for peptide-centric functional and taxonomic analysis of metaproteomics data
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5874761/
https://www.ncbi.nlm.nih.gov/pubmed/29280960
http://dx.doi.org/10.3390/proteomes6010002
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