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J Proteomics. 2018 Jan 16;171:11-22. doi: 10.1016/j.jprot.2017.05.022. Epub 2017 May 24.

High-throughput metaproteomics data analysis with Unipept: A tutorial.

Author information

1
Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium. Electronic address: bart.mesuere@ugent.be.
2
Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.
3
Laboratory for Protein Biochemistry and Biomolecular Engineering, Ghent University, Ghent, Belgium.
4
VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium.

Abstract

In recent years, shotgun metaproteomics has established itself as an important tool to study the composition of complex ecosystems and microbial communities. Two key steps in metaproteomics data analysis are the inference of proteins from the identified peptides, and the determination of the taxonomic origin and function of these proteins. This tutorial therefore introduces the Unipept command line interface (http://unipept.ugent.be/clidocs) as a platform-independent tool for such metaproteomics data analyses. First, a detailed overview is given of the available Unipept commands and their functions. Next, the power of the Unipept command line interface is illustrated using two case studies that analyze a single tryptic peptide, and a set of peptides retrieved from a shotgun metaproteomics experiment, respectively. Finally, the analysis results obtained using these command line tools are compared with the interactive taxonomic analysis that is available on the Unipept website.

KEYWORDS:

Biodiversity; Data analysis; Metaproteomics; Tutorial

PMID:
28552653
DOI:
10.1016/j.jprot.2017.05.022
[Indexed for MEDLINE]

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