About Us


MSQuant has been developed at the Center for Experimental Bioinformatics (CEBI) at University of Southern Denmark. CEBI was established in 1998 through a grant by the Danish National Research Foundation. The goal of the group is to apply modern methods of mass spectrometry and "Proteomics" to the functional analysis of genes.

Contact information

General queries: go to the CEBI group members page.

Limited support for MSQuant is offered through this E-mail address.

The story so far

MSQuant has been developed over many years. It started in 2001 as a way to automate what was otherwise a purely manual process of quantitating each MS spectrum from a Sciex QSTAR massspectrometer.

In the middle of 2003 the program was made open source and a project page for MSQuant was created at SourceForge. This page is no longer actively used - most activty is through this page.

The scope has been extended and the program has become more general - e.g. it is now handling 3 different mass spectrometers and an arbitrary number of SILAC dishes. In one application it was used to quantify 5 way SILAC labelling

Main software developer:

Peter Mortensen

Technical writers and users driving new features:

Jacob Bunkenborg

Kristoffer Rigbolt


Jens Andersen

External software developers:

Joost Gouw

Past software developers, technical writers and users driving new features:

Matthias Mann

Jesper Olsen

Leonard Foster

Shao-En Ong