MetaProteomeAnalyzer (MPA)

• News
• Downloads
• Introduction
• MPA Portable
• Command Line Usage
• MzIdentML Import
• Features
• System Requirements
• Conda Package
• MPA GUI Startup

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MetaProteomeAnalyzer Publications:

• Muth et al.: Anal Chem. 2018 90(1):685-689.
• Muth et al.: J Proteome Res. 2015 14(3):1557-65.
• If you use MetaProteomeAnalyzer as part of a publication, please include the reference(s). Thank you!

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News

*MPA Portable version 2.0.0 (December 2019) has been released with the following features:

• The graphical user interface now supports a direct connection to the Unipept web interface (https://unipept.ugent.be/): identified peptides are directly mapped to the Unipept service (using the MPA Export menu --> Export peptides to Unipept).
• UniProt JAPI was updated to the version 1.0.28

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MPA Portable version 1.9.0 (June 2019) has been released with the following updates:

• MPA now has full Maven support
• UniProt JAPI was updated to the latest version 1.0.26 (fixing errors occurring during the retrieval of UniProt meta-information)
• Minor bugfixes were performed

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MPA Portable version 1.8.0 (November 2017) has been released with the following features/bugfixes:

• MS-GF+ parameter for fragmentation method (CID, ETD, HCD) can be chosen on the command line.
• UniProt JAPI was updated to the latest version 1.0.16 (fixing errors occurring during the retrieval of UniProt meta-information)
• Batch scripts are now available in the main folder of the software.
• Various bugfixes and improvements within the code.

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MPA Portable version 1.7.0 (August 2017) has been released with the following new features:

• Added taxon-based two-step searching feature (in addition to the protein-based strategy).
• MapDB was updated to the latest version (ver. 3.0.5) to accelerate the peptide indexing.
• Peptide indexing is now available as optional feature on the command line.
• Disabled emPAI and NSAF quantification features in the GUI to accelerate the results retrieval.

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Downloads

[Download software] MPA Portable version 2.0 - Windows and Linux 32-bit/64-bit - released on December 18, 2019

[Download example data set] Microbial community sample data set (from Ebendorf biogas plant)

[Download example FASTA database] Methanomicrobiales protein sequence database (UniProtKB FASTA format)

[Download MPA tutorial] Guided MPA portable tutorial including graphical and command line interface usage

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Introduction

MetaProteomeAnalyzer (MPA) is a scientific software for analyzing and visualizing metaproteomics (and also proteomics) data. The tool presents a MS/MS spectrum data processing application for protein identification in combination with an user-friendly interactive graphical interface. The metaproteomics data analysis software is developed in the Java programming language and provides various features for an user-defined querying of the results. In addition, MPA can also be executed on the command line (see below).

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MPA Portable

MPA Portable is a light-weight and stand-alone software for the identification of proteins and in-depth analysis of metaproteomics (and also proteomics) data. The MPA software currently supports the database search engines Comet, MS-GF+ and X!Tandem taking MGF spectrum files as input data. User-provided FASTA databases (preferably downloaded from UniProtKB) are formatted automatically.

Please note: MPA Portable can be run directly on your desktop PC or laptop and no separate installation is needed: just double-click the provided JAR file or use the provided batch file (see below on this page). Otherwise, you can use the command line interface (MetaProteomeAnalyzerCLI).

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Command Line Usage

MPA can also be used via the command line, see MetaProteomeAnalyzerCLI for details.

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MzIdentML Import

It is also possible to import results in mzIdentML format which have been generated in other database search tools, see MzIdentML-Import for details.

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Features

The MPA metaproteomics software comes with the following key features:

• Intuitive graphical user interface
• Project management for MS/MS experiments
• Shotgun protomics data analysis tool
• Integrates the search algorithms Comet, MS-GF+ and X!Tandem
• Import and re-analysis of results stored in mzIdentML data format: cross compatibility with various proteomics tools.
• Detailed analysis of taxa, ontologies, pathways and enzymes
• Grouping of redundant protein hits to so-called "meta-proteins" (protein groups)
• Label-free quantification methods
• Command line interface (for high-throughput processing tasks)
• Interactive overview for each result set
• Platform-independet portable application

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System Requirements

• Operating system: (Tested on Windows XP, Windows Vista, Windows 7/8/10 and various Linux systems)
• Memory: The more memory, the better! (preferably 4 GB at least, but highly recommended are 8 or 16 GB of RAM)

Please download the latest version of mpa-portable-X.Y.Z.zip (where X, Y and Z represent the current version of the software).

Before starting the MPA Portable version, please make sure that you have Java 1.8 installed. To check the currently installed java version, open a console/bash window and type:

java –version

If you haven't installed Java 1.8, please go directly to Java.com to download the latest Java version.

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Conda Package

MPA Portable can installed directly as Miniconda package from the bioconda channel:

conda install mpa-portable -c bioconda 

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MPA GUI Startup

After downloading the zip file, simply unzip the file and use the provided script from the built folder, i.e. mpa-portable.bat for Windows or mpa-portable.sh for Linux (granting the access rights accordingly!).

You can also double-click on the JAR file, however this will give you no options to change the memory settings (see below).

Another possiblity is to use the command line directly:

java -jar mpa-portable-X.Y.Z.jar -XmxXXXXm 

Note: -XmxXXXXm stands for maximum assigned memory (in megabytes of RAM)