Bio-Rad PDQuest 2-D Analysis Software - Manual (Page 44)

The plastic backing on the gel must maintain contact with the cutting mat. Before placing a
plastic backed gel on the cutting mat, dry the cutting mat and blot dry the gel backing that will
contact the cutting mat.
Note: a small amount of gel debris during cutting is normal in the backed gel mode. This is the
result of the side to side motion required to dislodge the gel from the backing. In testing during
development we have found that this small amount of gel debris does not contribute to
contaminated mass spectrometry results. Ask for the ProteomeWorks Plus application note on
this subject.
Glass backed gels
Glass backed gels use the same settings as plastic backed gels. For newer gels, use the soft-
ware setting of 2 or 3, for older gels use 4 or 5.
Note: only the 1.0 mm cutting tip is recommended for cutting plastic or glass backed gels.
It is very important to set the cutting tip height to the glass plate being used. Most glass plates are
thick enough that the cutting mat should be removed. The glass plate is placed directly into the
empty gel holding area of the platform. If thinner glass plates are being used and the gel is sitting
too low in the well for the maximum range of the cutting tip, add plastic sheets or the cutting mat
to raise the glass-backed gel to a height that is within the range of the cutting tip height adjustment.
Once the height of the glass is approximately correct, adjust the cutting tip height so that the tip
just contacts the glass surface. Use Section 2.12 for directions on adjusting the cutting tip height.
5.3.4 Step 4 - Set Wash Options
This feature allows the selection of up to four optional wash well stations for the cutting tip. The
wash stations are selected by clicking a check in the box next to the station. The orientation of
the tubes is as it is listed on the software screen. Once the cutting tip has deposited a cut into a
microtiter plate well, it will then move to the selected wash well(s). The cutting tip lowers into the
cleaning solution of the wash tube(s), spins and ejects to clean the tip, and proceeds to the next
cut.
Well number and cut position
Immediately below the image display area the well number and cut position spot annotation can
be activated. Each selected spot on the display can be annotated with the microtiter plate well
number and or the x, y coordinates of the cut position.
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