Bio-Rad EXQuest Spot Cutter - Manual (Page 57)

Figure 6-23. Step 2 – Select Gels: Select from List
Auto-select
a. Choose Auto-select to let PDQuest automatically select the best gel(s) to cut based on spot
quantity and quality. Spot quantity usually varies between gels in an analysis set. In general, you
want to cut from gels where the spot quantity is higher (to get more sample).
Figure 6-24. Step 2 – Select Gels: Auto-select
b. Set the Tolerance. The tolerance value is used to determine the spot quantity range that is
acceptable when choosing the gel from which a particular spot will be cut. If the quantity of a
spot in only one gel falls within the tolerance, that gel will be auto-selected for the spot cut.
However, if the quantity of a spot in two or more gels falls within the tolerance range, then the
auto-select mechanism will consider which gels will best minimize the time and effort required to
switch gels on the spot cutter platform. For example, if you have five gels in an analysis set with
the tolerance ratio set to 1 (the lowest setting), auto-selection specifies different cuts in all five
gels, requiring you to change gels in the spot cutter five times. However, by increasing the
tolerance ratio slightly, auto-select finds that three gels contain spots whose quantities fall within
the specified tolerance, and it adjusts the cuts so that only those three gels are selected. This
will save you considerable time and effort switching gels in the spot cutter. As you adjust the
tolerance, monitor the number of gels selected by the tolerance setting.
c. Check the Include quality box to consider spot quality when auto-selecting spots. When this
checkbox is selected, a well-resolved spot of sufficient quantity will be favored over a less
well-resolved spot of higher quantity (within the specified tolerance ratio). After checking the
Include quality box, look to see if it has changed the number of gels selected from which cuts
will be made.
ANALYSIS SET EXCISION TOOL
6-15