Method development for MS-based protein analyses in proteomics

The typical workflow for efficient protein analysis in proteomics using mass spectrometry (ESI or MALDI) comprises:

I) hydrolysis of the protein sample with specific endoproteinase
II) separation of the peptides by liquid chromatography (LC
III) ionization of the peptides in the mass spectrometer
IV) determination of the m/z values (precursor mass) of ionized peptides (MS spectrum)
V) selection and fragmentation of peptides within the mass spectrometer;
     vi) recording of the fragment spectra (MSMS spectra)
VI) database search of the m/z values of the fragment spectra together with the exact precursor mass using search engines
VII) protein identification
VII) determination of the false positive rate.

Our main focus in this area is the general improvement of sample preparation, LC separation and database search.