Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for Seamless End-to-End Metaproteomics Data Analysis

Tim Van Den Bossche; Pieter Verschaffelt; Kay Schallert; Harald Barsnes; Peter Dawyndt; Dirk Benndorf; Bernhard Y Renard; Bart Mesuere; Lennart Martens; Thilo Muth

doi:10.1021/acs.jproteome.0c00136

Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for Seamless End-to-End Metaproteomics Data Analysis

J Proteome Res. 2020 Aug 7;19(8):3562-3566. doi: 10.1021/acs.jproteome.0c00136. Epub 2020 Jun 11.

Authors

Tim Van Den Bossche^{1

2}, Pieter Verschaffelt^{1

3}, Kay Schallert^{4

5}, Harald Barsnes^{6

7}, Peter Dawyndt³, Dirk Benndorf^{4

5

8}, Bernhard Y Renard^{9

10}, Bart Mesuere^{1

2

3}, Lennart Martens^{1

2}, Thilo Muth^{9

11}

Affiliations

¹ VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.
² Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, St. Pietersnieuwstraat 33, 9000 Ghent, Belgium.
³ Department of Applied Mathematics, Computer Science, and Statistics, Ghent University, Krijgslaan 281-S9, 9000 Ghent, Belgium.
⁴ Bioprocess Engineering, Faculty for Process and Systems Engineering, Otto von Guericke University, Universitaetsplatz 2, 39106 Magdeburg, Germany.
⁵ Microbiology, Department of Applied Biosciences and Process Technology, Anhalt University of Applied Sciences, Bernburger Straße 55, 06366 Köthen, Germany.
⁶ Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Postboks 7804, NO-5020 Bergen, Norway.
⁷ Computational Biology Unit (CBU), Department of Informatics, University of Bergen, Postboks 7804, N-5020 Bergen, Norway.
⁸ Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße, 39106 Magdeburg, Germany.
⁹ Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany.
¹⁰ Hasso-Plattner-Institute, Faculty of Digital Engineering, University of Potsdam, Prof.-Dr.-Helmert-Straße 2 - 3, 14482 Potsdam, Germany.
¹¹ eScience Division (S.3), Federal Institute for Materials Research and Testing, Unter den Eichen 87, 12205 Berlin, Germany.

PMID: 32431147
DOI: 10.1021/acs.jproteome.0c00136

Abstract

Although metaproteomics, the study of the collective proteome of microbial communities, has become increasingly powerful and popular over the past few years, the field has lagged behind on the availability of user-friendly, end-to-end pipelines for data analysis. We therefore describe the connection from two commonly used metaproteomics data processing tools in the field, MetaProteomeAnalyzer and PeptideShaker, to Unipept for downstream analysis. Through these connections, direct end-to-end pipelines are built from database searching to taxonomic and functional annotation.

Keywords: metaproteomics; pipelines; software.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Data Analysis*
Microbiota*
Proteome
Proteomics
Software

Substances

Proteome