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
