Bio-Rad PDQuest 2-D Analysis Software - Manual (Page 43)

5.3.3 Step 3: Set Cut Options
The spot cutter has several cut and eject options. Multiple option can be selected, such as "cut
with turn and double eject while spinning". The Backed Gel option deselects all other options.
Before beginning a cut run using the Basic Excision Tool, you must select the cutter options for
that run.
Spin When Cutting; the cutting tip will spin as it cuts.
Spin When Ejecting; the cutting tip spins as it ejects the cut into a microplate well.
Cut Longer; the cutting tip holds in the "down" position longer when making a cut.
Double Eject; the ejection pin ejects twice while in the down position in a microtiter plate well.
No Spin when Lifting; the cutting tip will not spin when cut is complete.
Backed Gel Tip Motion Range; backed gel settings.
Gel Defaults; automatically selects the most useful options when cutting gels.
PVDF Defaults; automatically selects the most useful options when cutting PVDF membranes.
Free Gels
The most effective cutting method for free-standing gels is to "cut with turn". The optimum setting
for ejecting the gel spot is single eject. Keep water on the sample during cutting. A light layer of
water applied from a lab squirt bottle works well. Add liquid to the microtiter plate wells before
cutting.
Membrane Blots
For PVDF membrane cuts, select "Spin when cutting", "Double eject" and "Spin when ejecting" to
cut and deposit membrane spots. Keep water on the sample during cutting. A light layer of water
applied from a lab squirt bottle works well. Add liquid to the microtiter plate wells before cutting.
Backed Gels
The Backed Gels option is an optimized cut routine that cuts gels off a plastic backing. The tip
spins, lowers to cut through the gel, then moves from side to side to dislodge the gel from the
backing. The range of the cutting tip motion from side to side can be adjusted by the user. A
number from 0-5 is entered into the "motion range" box. Each unit represents 1.0 mm of lateral
motion of the cutting tip.
Older gels need more lateral motion to dislodge the gel piece. Therefore, the recommended
settings for plastic and glass backed gels are:
• New (less than 1 month old) gels: uses setting 2 or 3
• >1 month old gels use setting 4 or 5
The larger number will move the cutting tip farther in the side to side motion during the cut. The
result of a larger amount of movement will be slightly more gel debris in the area of the cut.
The cutting tip height must be set carefully for the plastic backed gel mode. Place the Cutting
mat in the platform, then click on the Cutting Tip Height adjustment icon. Place a piece of the
plastic backing from the gels you are using under the tip to adjust the cutting tip height. The tip
should lightly score the plastic sheet. If the tip is cutting too deeply, it will stick in the plastic backing,
prevent the tip from moving across the surface of the plastic backing and will not dislodge the gel
piece.
40