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patterns across gels, thereby negating the problem of inter-gel variation. By
this technique, it is possible to plot the relative abundance of each protein on
different gels against the normalized internal standard. This allows accurate
quantitation of samples, with an associated increase in statistical significance.
Both the DeCyder software (GE-Healthcare) and Delta2D (Decodon GmbH)
can be used to automatically apply statistical tests. These tests compare the
average ratio and variation within each group to the average ratio and variation
in the other group to see if any changes between the groups are significant.
All proteomic data can be assembled into an adaptational network consisting
of a large number of stress and starvation stimulons and regulons. An essential
feature of this network is the interplay between the various regulation groups,
because the individual stress and starvation stimulons are tightly connected. The
visualization of such a complex protein expression pattern requires specialized
software tools, such as the “color coding” tool of Delta2D. Using this tool, one
can display proteins induced by more than one stimulus by a specific color code,
thus providing convenient intuitive visualization of complex regulation patterns
(
see
Fig. 6
and Color Plate 4, following p. 46). By applying this technique,
one can display already known and probably new overlapping regions within
the regulatory network.
pH 7
pH 4
≥ 2x repression
fermentation
62
149
120
anaerobic respiration
≥ 2x induction
fermentation
57
88
59
anaerobic respiration
Fig. 6. Multicolor imaging of protein expression patterns of
Staphylococcus aureus
COL under anaerobic conditions in the presence and absence of nitrate. Delta2D
software is used to visualize complex protein expression patterns on the 2D image in
the standard pH range 4-7. The color code is represented on the right side. (
See
Color
Plate 4, following p. 46.)
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