Thesis final - after defense-7 - Jacobs University

Chapter 1
protein towards purification of the main protein contaminants in a host cell proteome. The use
of the cell proteome in relation with the chromatographic method will produce more authentic
and realistic data and can be stored in databases. These databases can be used to generate the
purification models for easy in silico downstream processing of proteins (19). Several
conclusions have been made in that work although the approach was not complete in its
essence. The mass spectrometry and computational methods were missing in that report and
the data reported was not enough to design a model. In this work, a complete picture has been
presented ranging from chromatographic fractionation of the yeast cell proteome to the
characterization of proteins at molecular level. The proteins properties have been used to
correlate proteins at the molecular level to their separation behavior during HIC.
1.8. Goal of the work
Complementing all the above discoveries made by several authors, the current work further
progressed to a more comprehensive understanding of the hydrophobic adsorbents and their
effects on the separation behavior of a cell proteome during HIC. The adsorbents are usually
composed of ligands and base supports. The comparison of the adsorbents (different ligands)
hydrophobicity has been reported before with model proteins. However, the adsorbents
hydrophobicity has been never studied comparatively with a proteome wide approach. The
reason could be the experimentally demanding and laborious approach which no one ventured
to adopt for their studies. Therefore, this study was planned for the comparative analysis of
the hydrophobic adsorbents as a function of yeast cell proteome and in relation to protein
properties.
Under the frame of the current research work, the following objectives were targeted.
• To explore the influence of different hydrophobic ligands in HIC as a function of
complex cell proteome.
21