last modified 2011.07.13

Multiple/Selected reaction monitoring is an increasingly used technique for hypothesis driven protein research. Two major computational steps are involved when performing an MRM experiment:

mQuest/mProphet automates the second step, the analysis of MRM data and provides probabilistic scoring of targeted peptide identifications and comprehensive quantification. mQuest/mProphet relies on the use of decoy transitions in the measurements which act like negative controls.

This software is licensed under the Apache License Version 2.0. This software and associated documentation is provided "as is" and there is no warranty for this software.

This software is written in Perl and the R statistical programming language. mInteract coordinates the modules and will perform a data analysis with one command.
Following input is necessary:

A detailed description how to convert the raw data of Thermo and AB-Sciex instruments to mzXML can be found in the manual (download section).
For the probabilistic part of the software some decoy transitions have to be measured in the experiment. Please, see the manual in the download section for more details.

The main output of the software is a spreadsheet containing all informtion such as transition meta data, confidence of identification, a transition interferrence score and quantification information.
The raw data and data analysis can also be browsed with a web browser.

The software allows to browse the raw data and analysis with a web browser. Because svg vector graphics is used to graphically display the analysis, Chrome or Opera is required as a web browser. The transitions are displayed including the meta data, scoring of the peak groups and the quality assignment.

Please see this link for an example data set derived from a human plasma sample. Click on an .shtml file to see the analysis of one LC-MS run.

mGen
generates decoy transitions for a list of target transitions. The data derived from the decoy transitions is used by mProphet to derive a statistical error model.

mMap
links together the raw data (mzXML) with the MRM meta data (spreadsheet of transitions).

mQuest
scores the MRM data according to different experimental workflows and also makes the quantification.

mProphet
performs the statistical analysis and generates an error statistics that allows to filter the data according to an objective quality criterion (FDR).

mInteract
coordinates mMap, mQuest and mProphet and allows a one command analysis.

Software installation

Virtual machine

We provide a virtual machine with the software already installed. The software is configured to run locally (e.g. on a windows laptop). Prerequisites are a x64 CPU that supports virtualization (most modern CPUs).

1. install VMware on your computer
2. download the virtual machine
3. unzip the virtual machine on your computer
4. choose "Open a Virtual Machine" in the VMware Player Menu and browse to the unzipped folder
5. choose "copied it" while importing the virtual machine
6. run the virtual machine (the user name is 'mprophet', the password is 'mprophet')

You might have to turn on virtualization in your BIOS to get the virtual machine to run. See the VMware help for how to do this.

choose "example data analysis" on the desktop and click an .shtml file to browse through an example data set.

Visualization is enabled in Apache for the folder /usr/local/apps/biognosys/mquest/www. You can link any folder in there to enable visualization. This was already done for /home/mprophet/mProphet/mProphet_data_analysis.

To connect the virtual machine to the host file system and analyze experimental data on the virtual machine choose:
Virtual Machine -> Virtual Machine Settings -> Options -> Shared Folders
The folder will then be mounted in /mnt

Ubuntu Linux package

1. open a terminal
2. append the following line to /etc/apt/sources.list:
   sudo gedit /etc/apt/sources.list
   line:
   deb http://systemsx03.ethz.ch/SybitDebRepo/binary/ubuntu10.04/DEBS/ /
   sudo will give you super user rights which is needed to edit the system file sources.list
3. Generate the text file packager.key with the content from the link
   gedit packager.key 
4. for security reasons it's obligatory to install a public key:
   sudo apt-key add packager.key
   
5. update the repositories with the command:
   sudo apt-get update
6. install either of the two package versions using the command:
   
   • sudo apt-get install mquestweb: recommended, Apache2 allows browsing through results
     
   • sudo apt-get install mquest: no Apache2 installation and hence no browsing through results
   for the web installation make sure to enter the correct domain name during installation (e.g. mquest.uni.edu or 131.63.230.61). If no host is entered when prompted, the visualization in the browser will be accessible locally via http://localhost.

Howto analyze data

After successful installation of the package with apt-get on an Ubuntu Linux, the software is installed per default in the path:
/usr/local/apps/biognosys/mquest/bin/
In the following we describe howto analyze a data set derived from human plasma and reference peptides spiked into the sample. The data in the form of mrml.xml files can be downloaded below. Please see the manual for a description howto convert your mass spectometric data to mrml.xml.

Manual and downloads

• detailed description of the software, how to convert raw data to mzXML, the transition list file format and more in the manual
• decoy transition generator mGen as a standalone program
  
• example input and output file of mGen
• skyline transition export report format mProphet.skyr to use as input for mGen
• mQuest/mProphet software for manual installation including mGen, mMap, mQuest and mProphet 
  dependencies have to be manually installed
• mrml files of an experiment derived from human plasma

Support on zendesk

Please use http://biognosys.zendesk.com/home for feedback and support.

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