Getting Started


Metaproteomics is the study of microbiology using LC-MS/MS based metaproteome analysis for the functional characterization of different microbial species directly in their environment. The prospects for metaproteomics research are the development of medical applications for non-invasive diagnostics using fecal samples, the monitoring and improvement of biotechnical processes and new insights into the environmental impact of microorganisms.

Heyer R, Schallert K, Zoun R, Becher B, Saake G, Benndorf D. Challenges and perspectives of metaproteomic data analysis. J Biotechnol 261, 24-36 (2017).

The MetaProteomeAnalyzer software (MPA) is an intuitive open-source tool for metaproteomics data analysis and interpretation, which includes multiple search engines and the feature to decrease data redundancy by grouping protein hits to so-called metaproteins. The MPA provides a complete pipeline from peak lists generated by the mass spectrometer software to statistical analysis of results produced by protein database search. Since the MPA was developed for metaproteomics, many features focus on taxonomic and functional analysis of the discovered proteins. The protein groups called metaproteins constitute a core functionality of the MPA to properly abstract biologically relevant information from raw results. The MPA is not applicable to specialized proteomics questions like post-translational modifications (PTM) or quantification via isotope labelling.

The workflow of the Remote Desktop version of the MetaProteomeAnalyzer
The results view of the MPA software
Some features of the MPA, A: Taxonomy table view lists protein results by taxonomy allowing dynamic selection/deselection, B: Pie chart for spectrum count for UniProtKB Keyword ontologies, C: Chord diagram available on the server version, D: KEGG Colored Pathway metabolic map generated by the MPA

Start using the MetaProteomeAnalyzer

MPA Remote Server

The development of the MPA software is ongoing and many useful features have been added since the original version was published. Furthermore, the de.NBI partner project MetaProtServ was started in 2017, which aims to make the MPA easily available to researchers. To this end, the MPA is now provided as a central remote server solution by the de.NBI network that can be freely accessed and used by researchers worldwide, resembling a major step towards completely cloud based data analysis solutions.

Get access to the remote server version by sending us an email:

Learn how to use the MPA

We provide instructions on how to use the MPA in the form of video tutorials and as a manual. Both tutorials follow the standard “workflow”, meaning you will learn about all aspects neccessary to perform your metaproteomics data analysis.


The MetaProteomeAnalyzer was developed between 2011-2014 and the first release of the software was published in 2015. Several research groups already used the first MPA version to conduct their metaproteomics data analysis and published their results. A list of publications can be found here.

Local Installation

It is also possible to install the MPA locally using our download package. Please follow our installation tutorial in order to properly install third party software and correcly configure the MPA to run.

Further development

The MetaProteomeAnalyzer is provided to the research community by the German Network for bioinformatics infrastructure (de.NBI). The remote server solution represents the transformation from a local version, requiring complex maintenance by specialists and dedicated computer hardware towards an easy-to-use cloud version utilizing de.NBI cloud hardware and central maintenance. The software is constantly developed further to adapt to changing requirements of researches. Full user support is also offered thanks to de.NBI.