Bio-Rad EXQuest Spot Cutter - Manual (Page 19)

PDQuest User Guide
1-6
Matching and Editing
After you have detected the spots in a gel or set of gels, you are ready to create a
matchset. A matchset is composed of the Raw 2-D, Filtered and Gaussian images of
the gel(s) in an experiment.
In a matchset, the protein spots from the different gels are matched to each other and
are included in a synthetic image called a matchset standard. The standard includes all
the information about the spots in the matchset.
As you match the spots in a matchset, you will correct the results of automatic spot
detection by comparing the Gaussian spots with the original spots in the Filtered
image.
Data Analysis
PDQuest provides a variety of analytical tools to help you determine which spots are
statistically and scientifically meaningful.
You can normalize the spot quantities in different gels for more accurate comparison.
You can define replicate groups of duplicate gels. You can create groups of spots that
are quantitatively, qualitatively, and statistically significant using analysis sets. You
can compare the similarity of gels using scatter plots, and review the quantitation of
individual spots using the Spot Review Tool.
Many of these tools are interactive with the matchset, so you can study the actual
spots in the images as you review their quantities and other data.
You can create high-level matchsets to compare the results of different experiments.
And the powerful annotation tool allows you to annotate your spots, link to Internet
protein databases or other files, and create HTML pages of spot data.
Spot Cutting and Mass Spec Analysis
PDQuest is part of Bio-Rad’s ProteomeWorks protein analysis package, and controls
Bio-Rad’s ProteomeWorks Spot Cutter. You can cut spots from gels or membranes,
digest them, and perform advanced protein analysis using MicroMass’s mass
spectrometry instruments and software. Data from MicroMass can then be imported
back into PDQuest to be included in spot annotations.