Thesis final - after defense-7 - Jacobs University

Chapter 3
hydrophobicity of the ligands was investigated in this work with the yeast cell proteome.
However, the comparison of ligands has not fully differentiated with the proteome wide
approach (Figure 19). The reason could be the involvement of several protein properties
affecting the retention behavior in HIC. Several protein properties have been demonstrated for
their correlation with protein retention and their ability to differentiate among the
hydrophobic ligands. The protein properties such as average surface hydrophobicity, average
hydrophobicity, average flexibility and average polarity have shown a correlation with the
chromatographic separation of the proteins. However, these properties may have less ability
to differentiate among the ligands (Table 8).
Table 8: Protein properties and their ability to differentiate among ligands and correlation with
chromatographic behavior during HIC
Protein properties
Differentiation Correlation
Average hydrophobicity × +
Average polarity × -
Average flexibility × +
Average bulkiness × ×
Average surface hydrophobicity Trend +
+; indicates positive correlation, - ; indicates negative correlation; ×; indicates no correlation
The results revealed that ligands cannot be fully differentiated based on protein properties and
can only be estimated based on retention time of the model proteins. The reason could be that
several proteins are supposed to be eluted at specific retention time during chromatographic
separation of a cell proteome as a function of ligand chemistry. Another observation was that
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