MSQuant is open source software for quantitative proteomics/mass spectrometry and processes spectra and LC runs to find quantitative information about proteins and peptides. Learn much more in through the MSQuant menu item.  MSQuant is released at SourceForge

Latest papers!: 

Regulation of Epidermal Growth Factor Receptor Trafficking by Lysine Deacetylase HDAC6
Sci Signal. 2009-12-22

MSQuant, an Open Source Platform for Mass Spectrometry-Based Quantitative Proteomics
J Proteome Res. 2009-11-18

Identification of SUMO target proteins by quantitative proteomics
Methods Mol Biol. 2009-10-31

Matrix protein 2 of influenza A virus blocks autophagosome fusion with lysosomes
Cell Host Microbe. 2009-10-22

Receptor tyrosine kinase signaling: a view from quantitative proteomics
Mol Biosyst. 2009-10

The Center for Experimental Bioinformatics (CEBI) was established in 1998 through a grant by the Danish National Research Foundation.  The Center was originally made up of four separate research groups but has undergone restructuring and now consists of the research group  under the direction of Prof. Mann. While Prof. Mann is remaining as Center leader for CEBI he has now taken up a position as director at the Max Planck Institute of Biochemistry in Martinsried.

The group is a continuation of the Peptide & Protein Group at EMBL Heidelberg where Prof. Mann was group leader from 1992 to 1998 and six of its initial members were recruited from EMBL. The goal of the group is to apply modern methods of mass spectrometry and "Proteomics" to the functional analysis of genes. The group currently has 24 members divided about equally between analytical specialties and biological specialties. We have a full range of techniques and equipment both in molecular biology/cell biology and in mass spectrometry/proteomics.

Current projects are in signal transduction, structures in the nucleus (in collaboration with Prof. Angus Lamond), secreted proteins and quantitative proteomics.

Analytical topics include development of large scale methods for protein identification, methods for generic isolation of multi-protein complexes, searching of mass spectrometric data in sequence databases including genomic databases, use of mass spectrometry for the large scale analysis of protein function (functional proteomics).