MetaProteomeAnalyzer (MPA) software for analyzing and visualizing MS-based metaproteomics data.
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README.md

MetaProteomeAnalyzer (MPA)


MetaProteomeAnalyzer Publications:


News

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.

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.

MPA Portable version 1.6.0 has been released with the following new features:

  • Added new import function for mzIdentML files: this feature supports the re-analysis of result identification data stored in mzIdentML format.
  • Added new Import menu which contains the import function for "MPA Experiment" (see Release version 1.5.0).
  • Added the feature to import MPA experiment files without requiring the corresponding MGF files.
  • Added the indexing of peptide sequences for FASTA databases: this feature allows to retrieve all protein identifications contained in the reference proteomes (and more than the default hits suggested by the search engines).

MPA Portable version 1.5.0 has been released with the following updates:

  • Added "Import MPA Experiment" feature: saved experiment files (*.mpa) can now be loaded into into a project
  • Updated "Export MPA Experiment" feature: experiment files (*.mpa) are stored together with the original MS/MS spectra
  • Added "Update UniProt Entries" feature (see MetaProteomeAnalyzerCLI for details)
  • Various bugfixes and GUI improvements

Downloads

[Download software] MPA Portable version 1.8.0 - Windows and Linux 32-bit/64-bit - released on November 17, 2017

[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


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).


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).


Command Line Usage

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


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.


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

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.


Conda Package

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

conda install mpa-portable -c bioconda 

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)