Software platforms for quantitative proteomics

In recent years, it has become obvious that mRNA expression does not always correlate with protein expression. It seems that a full understanding of the complexity of life can only be obtained by examining abundances of proteins under varying conditions. Accurate measurements of these expression values is crucial. This field of research also requires new computational efforts since the data, often from mass spectrometry experiments, is very complex. We present two academic software platforms that offer means to reduce, analyse and compare protein expression data gained from liquid chromatography coupled with mass spectrometry. We outline their methodology and compare them to our own project, OpenMS, which is currently developed in our research group at the Free University Berlin in collaboration with the Kohlbacher group at Tuebingen University.