Biology Reference
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a few pairs of spots representing the same proteins in different gels —
a landmarking step. These landmarks are then used to warp the gel
images and correct possible distortions, and consequently improve the
matching quality. However, this additional step has the inconvenience
of being time-consuming and labor-intensive for end-users. Figure 2
is an example of a differential analysis between two groups of gels. Each
group has three replicate gels. Control gels belong to one group
(left column), while gels from drug-treated samples are in a second
group (right column). Notably, the insert in the bottom right of this
figure shows that two neighboring spots present in the control sample
are absent from the drug-treated sample. Either these proteins are
not expressed in the drug-treated samples or they have undergone
posttranslational modifications, causing them to migrate to another
position on the 2-D gel.
In the early 1980s, the first packages of proteomics imaging software
became available, and some of them have survived the computational
evolution of the last two decades. Among these are PDQuest™ (com-
mercialized by BioRad)
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and Melanie
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developed by the PIG at the SIB
and commercialized by GeneBio S.A. Currently, several other dedicated
software packages are also commercialized, such as DeCyder (from GE
Healthcare) and Progenesis (from Nonlinear Dynamics).
Most current packages include two-dimensional difference gel elec-
trophoresis (2-D DIGE)
a
analysis. In this fluorescent technique for pro-
tein labeling,
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each sample is labeled with a fluorescent dye (Cy2, Cy3,
or Cy5) prior to electrophoresis and then the samples are coseparated on
the same 2-D gel. Scanning the gel at a specific wavelength for each dye
reveals the different proteomes. These images are then overlaid using the
above-mentioned software and the differences in abundance of specific
protein spots can be detected. One advantage of this technique is that
variation in spot location due to gel-specific experimental factors is the
same for each sample within a single DIGE gel; consequently, the rela-
tive amount of a protein in a gel in one sample compared to another is
unaffected. From the bioinformatics point of view, only the spot detec-
tion function requires some adaptation when the software processes
a
Also called multiplex experiments.
