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A tool allowing accurate quantification from NMR spectra including outlier detection. The tool comes as executable file for Windows and as Matlab code.

MetaboQuant is a tool developed by Matthias S. Klein that allows reliable quantification from nuclear magnetic resonance (NMR) spectrum peak integrals by using individual calibration factors for each peak. Additionally, several outlier detection methods have been implemented to exclude overlapped and corrupted peaks from quantification. Detailed information about MetaboQuant can be found in the manual that is included in the file MetaboQuant.zip (to be found in the Download section).

System Requirements

MetaboQuant may be run as stand-alone application using the following operating
• Windows (Windows 2000 or newer)

On other operating systems such as Linux or Mac OS, you may run MetaboQuant from
within Matlab (The Mathworks, Natick, MA, USA). For this you need:
• Matlab version (R14) Service Pack 3 or newer

Installation Instructions

To install MetaboQuant, download the following files from the Download section:
• MCRInstallerR2007b.exe
• MetaboQuant.zip. 

Run the file MCRInstallerR2007b.exe to install the required Matlab run-time
routines. Extract the file MetaboQuant.zip to a new folder. To run MetaboQuant,
double-click on the file MetaboQuant.exe. Starting MetaboQuant may take some
minutes, as the Matlab run-time environment takes some time to be loaded.

Running MetaboQuant from Within Matlab

Download the following file from the Download section:
• MetaboQuant.zip

Extract the file to a new folder.
Start Matlab and change the working directory to the MetaboQuant installation
folder, e.g. using the command cd. To run MetaboQuant, type MetaboQuant in the Matlab command line.

Getting Help

For all fields of the main window, a help text is available that will pop up when you hold the mouse cursor over the field.

Additionally, you may want to read the user manual included in the program download fil. The manual is also to be found separately in the Download section.


The current version of MetaboQuant can be downloaded here: 


You will need to install the Matlab R2007b runtime environment to be able to use MetaboQuant:


The manual can be downloaded here (is also part of the MetaboQuant .zip file):


A urinary spike-in data set of eight 1D 1H and 1H-13C HSQC spectra was prepared for testing MetaboQuant quantification performance. It can be downloaded here in Bruker format. The .zip file also contains the parameters for repeating our measurements on a 600 MHz Avance III spectrometer. Also, peak integrals and MetaboQuant input and output files are included in the .zip file.




Older versions of MetaboQuant can be found below, although these versions may contain bugs. It is strongly recommend to only use the current version found above. Please note that until version 1.2, MetaboQuant was named QUANTIFY.





A urinary spike-in data set of eight HSQC spectra was prepared for testing quantification performance. It can be downloaded here in Bruker format. The .zip file also contains a parameter set for repeating our measurements on a 600 MHz Avance III spectrometer.


The input and output files (peak integral and concentration values) of the above spike-in data set can be found in the following .zip file:


  1. Department of Medicine
  2. Institute of Functional Genomics