HB, Gel Staining

user manual
DNA/Protein Labeling, Hybridization & Detection
Processor Plus
automated Western blot processing and gel staining
um
80-6446-89
Rev B/5-99
con
contents
1
Introduction to Processor Plus . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Optional printing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Protocol key . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Instrument Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Connecting the Processor Plus to a serial printer . . . . . . . . . 4
Navigating the Operating Software . . . . . . . . . . . . . . . . . . . . . . . . 5

Reviewing protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Reviewing the Setup parameters . . . . . . . . . . . . . . . . . . . . . . . . 7
Setting Up for Blot Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Configuring the blot processing tray and pump tubing . . . . . . 8
Vent line . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Leveling the tray . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Calibrating the pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
5
Operating Instructions for Blot Processing . . . . . . . . . . . . . . . . . 13

Prepare for blot processing . . . . . . . . . . . . . . . . . . . . . . . . 13
Starting at the beginning of the protocol . . . . . . . . . . . . . . . . . . 14
Starting at a particular step in the protocol . . . . . . . . . . . . . . . . 15
Interrupting a protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Cleaning protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
6
Editing Blot Processing Protocols . . . . . . . . . . . . . . . . . . . . . . . . 17

Editing a protocol name . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Editing step variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Port In . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Minutes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Multiplier . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Hold, Beep and Rock (HBR) . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Editing when the Processor Plus is not running a protocol . . . . . 19
Adding or inserting a step . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Deleting a step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Editing a protocol in progress . . . . . . . . . . . . . . . . . . . . . . . . . 20
Setup Parameters for Blot Processing . . . . . . . . . . . . . . . . . . . . . 22

Setup 1:
Setup 2:
Setup 3:
Setup 4:
Setup 5:
Setup 6:
Setup 7:
Manual pump operation . . . . . . . . . . . . . . . . . . . . . . . 22

Tray size . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Tray level . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Display protocol volume . . . . . . . . . . . . . . . . . . . . . . . 23
Print protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Print volume of protocol . . . . . . . . . . . . . . . . . . . . . . . 24
Pump calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Setting Up for Gel Staining . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Configuring the gel staining tray and pump tubing assembly 27
Leveling the tray . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Calibrating the pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Hoefer Processor Plus
Operating Instructions for Gel Staining . . . . . . . . . . . . . . . . . . . . 30

Prepare for gel staining . . . . . . . . . . . . . .
Starting at the beginning of the protocol . .
Starting at a particular step in the protocol
Interrupting a protocol . . . . . . . . . . . . . .
.
.
.
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. . . . . . . . . . . . . . . 30
. . . . . . . . . . . . . . . 30
. . . . . . . . . . . . . . . 31
. . . . . . . . . . . . . . . 31
Cleaning protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
10 Editing Gel Staining Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Editing a protocol name . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Editing step variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Port In . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Minutes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Port Out . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Hold, Beep and Rock . . . . . . . . . . . . . . . . . . . . . . . . . .
Editing when the Processor Plus is not running a protocol
Adding or inserting a step . . . . . . . . . . . . . . . . . . . . . . .
Deleting a step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Editing a protocol in progress . . . . . . . . . . . . . . . . . . . .
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11 Gel Staining Setup Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Setup 1:
Setup 2:
Setup 3:
Setup 4:
Setup 5:
Setup 6:
Manual pump operation . . . . . . . . . . . . . . . . . . . . . . . 38

Tray size . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Volume delivery . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Tray level . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Print protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Pump calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
12 Using the protocol key . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

13 Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
14 Care and Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Running the cleaning protocol . . . . . . . . . . . . . . . . . . . . . 47
Staining trays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Chemical Resistance . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Cleaning the splash guard . . . . . . . . . . . . . . . . . . . . . . . . 48
Replacing the tray gasket on the staining tray . . . . . . . . . . . 48
Pump Care and Maintenance . . . . . . . . . . . . . . . . . . . . . . 49
A
Pre-programmed Blot Processing Protocols . . . . . . . . . . . . . . . . 54
Pre-programmed Staining Protocols . . . . . . . . . . . . . . . . . . . . . . 58
Blot Process Protocol Worksheet . . . . . . . . . . . . . . . . . . . . . . . . 63
Gel Stain Protocol Worksheet . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Customer Service Information . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Ordering Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Safety Warnings and Precautions
Safety Warnings and Precautions

WARNING For Research Use Only. Not recommended or intended for diagnosis
of disease in humans or animals. Do not use internally or externally in humans or
animals.
WARNING Not recommended or intended for use with radioisotopes.
We recommend that this product is handled only by those persons who have been
trained in laboratory techniques and that it is used in accordance with the
principles of good laboratory practices, as all chemical should be considered as
potentially hazardous. When handling chemical reagents, wear suitable protective
clothing such as laboratory overalls, safety glasses and gloves. Avoid chemical
contact with skin or eyes. In case of contact with skin or eyes, wash the affected
area immediately with water.
If this equipment is used in a manner not specified by the manufacturer, the
protection provided may be impaired.
Plug the instrument into a properly grounded outlet. Always disconnect the
power cord before servicing.
Avoid spilling liquids on the body of the instrument.
Ensure that the vents at the side and bottom of the instrument are not blocked.
Use only the supplied reagent line assemblies. Detaching the rigid opaque tubing
or using different reagent lines invalidates the pump calibration.
Periodically check that no liquid is accumulating in the tray support.
Only accessories and parts approved or supplied by Amersham Biosciences
may be used for operating, maintaining, and servicing this product.
Introduction to Processor Plus
Introduction to Processor Plus
The Hoefer Processor Plus automates fluid delivery and timing steps for both
membrane processing and polyacrylamide gel staining.
The Processor Plus base unit consists of:
the electronic and mechanical parts, encased in a metal chassis. The

instrument control panelan LCD and keypadis on the front of the unit.
A peristaltic pump which works in conjunction with the 10-port valve to

transfer fluid from reagent bottles to the tray. Both the pump and the 10-port
valve are on the back of the unit.
Memory on the Processor Plus that can hold up to 24 protocols: 10 for

membranes and 14 for gels. Each protocol can hold up to 30 steps.
A tray and lid sit on top the base unit to hold either the gels or membranes during
staining or blot processing.
The blot processing tray option includes a tray support, two Mini trays, one
Standard tray and one blot processing lid that fits either tray.
The gel staining tray option includes a tray support and a choice of two tray
sizes125 ml and 250 mleach with its own lid and tray support.
Optional printing
You can connect the Processor Plus to a serial printer via a 9-pin cable and
adaptor (code no. 80-6427-70). See page 4 for instructions. When a serial printer
is connected to the Processor Plus while a protocol is running, a paper report of
each step in a protocol is generated, including:
the volume of reagents used in each step
the time, in minutes, for each step
a validation report form, with spaces for sample ID, date, and operator
When the Processor Plus is not in use, you can use the Setup menus to print all the
steps in a protocol or calculate the volume of each reagent needed.
Protocol key
The protocol key is a removable device that can store one protocol. You can use
the protocol key to record a protocol, then remove the protocol key and store it
in a safe place. Use the key to repeatedly run the stored protocol. The protocol
on the protocol key does not change unless you overwrite it.
For more information on using the protocol key, see page 41.
p1
Instrument Components
1
1
2
8
6
11
10
Fig 2-1 Processor Plus components and accessories

No.
p2
Component
Function
Rocker finger
Provides the rocking motion for agitating fluid.
Pivot ball assemblies

(2)
Fit into the sockets on the bottom of the tray

support.
LCD Screen
Displays protocol status and program steps.
Keypad
Provides keys to program protocols and control

the Processor Plus.
Protocol key slot
Accepts the protocol key
Reagent lines
Connects reagent bottles to 10-port valve.
10-port valve
Selects reagent line to connect to peristaltic

pump.
Peristaltic pump
Pumps fluids from the 10-port valve into the tray

and out of the tray to waste or bottle.
Pump tubing
Carries reagents through peristaltic pump.
10
Protocol key
Stores one protocol in removable memory.
11
Spirit level
Assists in leveling trays.
Tray support. Fits onto the pivot ball assemblies on top of the metal chassis to
hold the tray and its lid.
Blot processing trays (two sizes). The Mini tray has four chambers, each holds
a maximum of 50 ml for a 9 9.5 cm membrane. The Standard tray has two
chambers, each holds a maximum of 125 ml for a 16 16 cm membrane. Both
trays are disposable.
Blot processing tray lid. A manifold on top of the blot processing lid delivers
reagents to the surface of the membranes. Valves on the manifold control delivery
to chambers in the trays.
Staining trays (two sizes). Made of PTFE-coated stainless steel, the trays are
inert to most staining solutions. Two sizes are available: 19 29 and 29 35 cm.
Glass lid for gel staining (two sizes). Lids prevent spills and minimize exposure
to staining reagents while allowing observation of the staining process. Two sizes
are available: 19 29 and 29 35 cm.
Coated magnets (4). When placed on gel staining tray, magnets prevent gels
from sliding over one another and from coming in contact with the splash guard.
Placed on the corners of gels with plastic backing, they help keep gels submerged.
p3
Connecting the Processor Plus to a serial printer

An RS232C serial port with a 9-pin male D-sub connector is located on the
bottom of the Processor Plus (Fig 2-2). A 9-pin cable and an adaptor for the serial
printer connection is available in a serial printer cable kit (code no. 80-6427-70).
The signal and pin number assignments on the Processor Plus serial port are:
Pin 2
Transmit
Pin 3
Receive
Pin 5
Ground
Other pins
not connected
The serial printer must have the following settings:

Baud rate
1200
Data bits
Stop bit
Start bit
Parity
None
Flow control
None
To connect the Processor Plus to the serial printer:

1.
Attach the 25-pin male adaptor to the port on the serial printer.
2.
Connect one end of the 9-pin cable to the RS232C serial port on the
Processor Plus and the other end to the adaptor on the serial printer. See
Fig 2-2.
An example of a protocol printout
RS232C serial port
9-pin cable connector
Fig 2-2 Locating the RS232C serial port
p4
Navigating the Operating Software
The LCD on the Processor Plus displays the current status of the instrument.
When you turn on the power switch, located on the left side of the instrument, a
self-diagnostic cycle runs for approximately one minute. This cycle tests all
circuits and moving parts. During the self-diagnostic cycle, the pump starts and
stops, the instrument emits a beep, and the tray rocks.
If any component test fails, the self-diagnostic cycle stops and a message on the
screen indicates the source of the fault. Press START to skip to the next test.
Report component test failures to your nearest Amersham Biosciences
service representative.
Once the diagnostic cycle is successfully completed, the screen displays the name
of the last protocol run on the Processor Plus. Press STOP to return to the Main
menu.
The keypad (Fig 3-1) contains three types of keys: Program, Arrow and Protocol.
Table 3-1
Type
Keypad Keys
Key Names
Function
Program EDIT/SET, ADD, DEL

Arrow
!, ",
Protocol
START, STOP, PAUSE
Edit protocols and the variables in each step

of a protocol.
Move cursor and change values on the LCD
screen.
Control protocols and setups.
Program keys
Protocol keys
Arrow keys
Fig 3-1 The Keypad

The Main menu is the entry to all protocols and menus on the Processor Plus. Use
the keypad to navigate from the Main menu to either blot processing or gel
staining protocols (see Fig 3-3).
-> Process blot

Stain gel
Fig 3-2 The Main menu on the LCD
p5
Reviewing protocols
From the Main menu, choose to see either blot processing protocols or gel
staining protocols.
-> Process blot

Stain gel
Process blot
-> Stain gel
or
START
START
STOP
STOP
Blot Protocol 1
ECL Plus
Blot Processing Protocols
Press
Gel Protocol 1
DNA Silver
Press
Press
Blot Protocol 2
ECL
EDIT/SET
(Step 1 in Blot
Process
Gel Staining Protocols
Press
Gel Protocol 2
DNA Silver
STOP
STOP
EDIT/SET
(Step 1 in Gel
Stain Protocol)
Press
Press
Press
(Step 2 in Blot
Process
STOP
Press
STOP
(Step 2 in Gel
Stain Protocol)
Fig 3-3 Navigating through the protocols

1.
From the Main Menu, press or to switch between the set of Process blot
and Stain gel protocols.
The arrow on the LCD screen indicates which protocol set is selected.
2.
Press START to see the first protocol in the selected protocol set.
Press STOP to return to the Main menu.
3.
Press or to review all the protocols in the protocol set.
4.
Press EDIT/SET to see the first step in a selected protocol.
5.
Press or to review all the steps in the protocol.

Press STOP to return to the list of protocols.
p6
For more on using the blot processing protocols, go to page 8.
For more on using the gel staining protocols, go to page 26.
Reviewing the Setup parameters

The Processor Plus has two Setup menus, one for blot processing and one for gel
staining (see Fig 3-4). Use the parameters in the Setup menus to:
select a tray size
level the tray
set the volume of reagent pumped (for gel staining, only)
calibrate the pump
print a protocol
print or display the total volumes of reagents used in the protocol (blot
processing, only)
manually operate the pump
-> Process blot

Stain gel
1
or
START
START
STOP
Blot Processing Protocols
Blot Protocol 1
ECL Plus
Press and hold EDIT/SET
(Setup 1 in
Blot processing)
Process blot
-> Stain gel
STOP
Gel Protocol 1
DNA Silver
Press and hold EDIT/SET
3
STOP
STOP
(Setup 1 in
Gel staining)
Press
Press
Press
(Setup 2 in
Blot processing)
Gel Staining Protocols
Press
STOP
STOP
(Setup 2 in
Gel staining)
Fig 3-4 Navigating to the Setup menus

1.
From the Main Menu, press or to switch between the set of Process blot
and Stain gel protocols.
The arrow on the LCD screen indicates which protocol set is selected.
2.
Press START to see the first protocol in the selected protocol set.
Once you have selected the appropriate protocol set, you can go to the Setup
menu from any protocol.
Note You cannot use the Setup

menus when the Processor Plus is
running a protocol.
3.
Press and hold EDIT/SET until the Setup menu appears on the LCD.
4.
Press or to review the Setup parameters for the selected protocol set.
5.
Press STOP to return to the protocols.
p7
Setting Up for Blot Processing
The Hoefer Processor Plus allocates memory for ten blot processing protocols,
five of these are pre-programmed (Table 4-1). See page 17 for directions on
editing protocols.
The Processor Plus has two trays for blot processing (Table 4-2). One lid fits
either tray.
Table 4-1
Pre-programmed blot processing protocols
Protocol Name Applications

1 ECL Plus
ECL Plus Detection Kit
2 ECL
ECL Detection Kit
3 Standard
Immunodetection with 1 & 2 antibodies
4 Enhanced
Immunodetection with 1, 2 antibodies and avidin compounds
5 Clean
Rinses reagents out of tubings, valves and ports
Table 4-2
Tray
Mini
Standard
Tray Sizes for blot processing

Number of
membranes
Size of membranes
(cm)
Reagent Capacity
(ml /chamber)
9 9.5
16 16
1050
25125
14
1 to 2
Configuring the blot processing tray and pump tubing assembly

The lid assembly (Fig 4-1) on the membrane processing tray has:
an inlet manifold in the centre
a drain tube at the rear corner
four valves for controlling reagent delivery to chambers
Lid manifold
Tray drain tube
Inlet manifold tube
Fig 4-1 The membrane processing lid

The tubes from the lid assembly connect to the peristaltic pump. The tube from
the inlet manifold connects to the inner peristaltic pump. The drain tube in the
corner of the lid connects to the outer peristaltic pump. See Figure 4-2 on page 9.
p8
The Quick-Fit couplings on the peristaltic pump tubing have different

dimensions, keyed to the appropriate tubing connections on the trays. When the
appropriate male and female couplings are pressed together, you can hear a click
as they connect.
Inner peristaltic pump tube
Outer peristaltic
pump tube
Waste tube
Fig 4-2 Configuration of membrane processing tubes and tray
Waste tube. Place the end of the waste tube into the top of a large waste bottle or
suspend it over the edge of the sink. A vented waste bottle cap (38-430), provided
with blot processing trays, fits a narrow-mouth Nalgene bottle. If you use a
waste bottle that does not accept this cap, tape the end of the waste tube to the
top of the waste container. Do not let the end of the waste tube become
submerged in liquid.
Vent line
Important
For membrane processing, reagent line 0 (zero) is reserved for air venting. Do not
use reagent line 0 to deliver reagents.
The presence of detergent in some reagents creates bubbles. As a result, small
amounts of reagent may get into the vent line, but this does not affect membrane
processing quality. However, spray from these reagent drops escapes out the vent
line when the Processor Plus is operating. Suspend the end of the vent line over a
sink or large beaker to contain escaping spray.
After configuring the tubing and tray, level the tray and calibrate the pump.
Leveling the tray

For reliable and even movement of reagents across membrane surfaces, place the
Processor Plus on a level surface. Use Setup 3 and the spirit level to adjust the
default level position that the tray assumes when it is not rocking or tilting.
Important
When you switch from membrane processing trays to gel staining trays, you must
perform the leveling procedure for gel staining trays.
1.
Start the leveling procedure with only the tray support on top of the
Processor Plus base.
p9
2.
Place the spirit level on the flat, clear plate inside the tray support. The level
should sit in a line that is parallel to the direction in which the tray rocks
(Fig 4-3).
Level, in a line parallel to

the direction of rocking
Fig 4-3 Placing the level on the clear surface inside the tray support
3.
Go to Setup 3. (See page 7 for information on the Setup parameters.)
Setup 3: Adjust
tray level up/dn
4.
Press" to move the cursor to the second line, then press or to adjust the
tray level.)
Setup 3: Adjust
tray level up/dn
The angle of the tray changes in response to pressing or . The characters
on the LCD do not change.
5.
When the tray is level, place a blot processing tray on the Processor Plus and
put the lid on the tray.
6.
Press" to move the cursor to the first line. Press to advance to Setup 2 for
and select the tray size that matches the tray you are using.
For Blot processing, use either the Mini or the Standard tray. See page 23 for
a description of Setup 2.
7.
Press" to move the cursor to the first line. Press to advance to Setup 7 for
pump calibration.
p 10
Calibrating the pump

Use Setup 7 to calibrate reagent delivery. Repeat pump calibration at least once a
month and each time you change the tubing in the peristaltic pump. The pump
calibration procedure takes five minutes.
Note The calibration procedures for
Stain gel and Blot process protocols
are different. You must calibrate the
pump whenever you switch between
these protocol sets.
To calibrate the pump for membrane processing:

1.
Place the end of reagent tube 1 in a beaker of at least 400 ml water.
2.
Place the end of the drain tube in a 250-ml graduated cylinder or beaker.
3.
Select Setup 7 for membranes.
Setup 7: Calib
Press START
4.
Press START.
Tube 1 in water
Drn tube in cyl
The message on the screen confirms that you have configured the tubing for
calibration.
5.
Press START.
The Processor Plus delivers fluid to the tray and then out the drain tube.
When the pump stops, measure the amount of water in the graduated
cylinder.
Measured vol.1
= 200 ml
6.
Press " to move the cursor under the volume values and press or to
change the numbers. Enter the amount of water measured in step 5.
7.
Replace the end of reagent tube 1 in the beaker of water and the drain tube
in an empty graduated cylinder. Press START.
Tube 1 in water
Drn tube in cyl
calibration.
8.
Press START.
The pump again pumps water into the tray and out the drain tube. When the
pump stops, measure the amount of water in the graduated cylinder.
Measured vol.2
= 100 ml
p 11
9.
Enter the measured volume on the screen and press START.

When calibration is completed, the LCD returns to the protocols.
Whats happening. Processor Plus uses these two values volume 1 and volume
2 to establish a correlation between the number of times the pump turns and
the volume delivered. It then interpolates to determine the number of pump turns
necessary to delivery the required volume.
p 12
Operating Instructions for Blot Processing
To run a blot processing protocol, you must first prepare the tray and reagents.
After you place the tray on the tray support, you must:
Connect the tubing on the peristaltic pump to the tray lid
Level the tray (Setup 3)
Calibrate the pump (Setup 7)
Review the instructions for these procedures on pages 8 12.
Prepare for blot processing

1.
Prepare the membranes for processing. If dry, soak nitrocellulose first in

water and then in buffer. Soak PVDF membranes first in 100% methanol
and then buffer.
Important
Keep PVDF membranes immersed in buffer until you are ready to begin
processing.
2.
Place each membranes in an empty tray chamber.

Place the sides of the membranes that came in contact with the protein facing
up.
3.
Place the lid with the manifold on top of the disposable tray. Open the valves
on the inlet tube manifold to those tray chambers that contain membranes
(Fig 5-1). Close the valves to those tray chambers that do not contain
membranes.
Open
Closed
Fig 5-1 Adjusting valves on the top of the membrane processing tray lid
4.
Insert the reagent lines into the proper reagent bottles. See page 54 for
descriptions of pre-programmed blot processing protocols.
The conical centrifuge tubes supplied with the blot processing trays are ideal
for holding antibodies. Thread the reagent line through one of the pre-drilled
holes in the cap to hold the reagent line firmly while the pump is operating.
To assure complete removal of solutions, the tip of the reagent line should
extend down into the pointed end of the tube. Do not cover the second hole
in the cap, which serves as an air vent.
If you are using other containers for solutions, verify that the tip of the
reagent line is submerged in the solution. Tape the reagent line in place at the
p 13
rim of the open container to keep the line secure during pump operation. Do
not completely cover the opening, but allow some air to enter to assure
accurate delivery.
Note If the Processor Plus is not
connected to a serial printer, use
Setup 4 to review all volumes. See
page 23.
Note You can start the Processor

Plus at any step in a protocol. To
start after step one, see page 15.
If the Processor Plus is connected to a serial printer, use Setup 6 to verify that
the waste bottle will hold all the solutions used in the protocol. See page 24.
Starting at the beginning of the protocol

1.
From the Main Menu, select Process blot protocols.
2.
Press START to go to the first protocol in the set.
3.
Press or to review the protocols.
4.
Press START when the protocol you want appears on the screen.
If you have a serial printer connected to the Processor Plus, the printer begins
to print a validation form for the protocol you are about to run.
5.
Before the Processor Plus begins the protocol, enter the number of tray
chambers you are using on the top line of the screen. Press or to change
the value.
Verify that the tray description on the second line matches the tray you are
using. Press" to move the cursor to the second line on the screen. Press or
to change the tray size selected.
Note The maximum number of

chambers for the Mini tray is 4. The
maximum number of chambers for
the Standard tray is 2.
4 chambers
Tray: 4 Minis
6.
Press START.
Moving valve
to port 5
As the Processor Plus initiates the protocol, the 10-port valve moves to the
port position programmed in the selected first step.
Step 1, Pumping
in from port 5
The pump begins to deliver reagent into the level tray and the timer begins
counting. When pumping is complete, the tray begins to rock and the screen
reports the time remaining in the step and the duration of the entire protocol.
Step 1 10.0min
Total 1:50 hrs
Time remaining in step
Total time remaining
At the end of each step, the timer stops and the tray tilts back as the pump
empties the tray.
p 14
If you have connected a printer to the Processor Plus, at the end of each step
the printer records the step number, the length of the step in minutes, the
port used and the volume of reagent delivered.
Note The beep option is turned ON
in the last step of all preprogrammed
protocols.
When the protocol is completed, the Processor Plus emits a series of beeps
for 20 seconds if the beep option is ON in the last step. (See page 18.)
7.
Run the cleaning protocol, Protocol 5, to clean the reagent lines after
running a protocol. See page 16 for a description of the cleaning protocol.

Follow these steps to start a protocol at any step after step 1.
1.
Follow steps 13 of the procedure on page 14, Starting at the beginning of

the protocol.
2.
Note If you want to edit a step
when the instrument is not running,
you must press EDIT/SET when
finished to get out of the edit mode.
See page 17 for more on editing.
3.
Press EDIT/SET to see the first step in a selected protocol.

To review the steps in a protocol, press or with the cursor under the step
number.
4.
When you find the step at which you want to begin, press START.
Interrupting a protocol
You can temporarily stop or terminate a protocol in progress.
Press PAUSE to interrupt a protocol without cancelling it.
Press STOP to interrupt and terminate a protocol in progress.
Pause. You may temporarily stop a protocol to adjust reagent lines and tray
contents.
When you press PAUSE, the timer stops counting and the tray goes to the Level
position and stops rocking.
Tray Level
Press Start to continue
Note If you press PAUSE when the

pump is running, the interruption
does not begin until the pump is
finished.
While the Processor Plus is in PAUSE mode, the tray has three possible positions:
Level the tray stops rocking and maintains the level position.
Recover the tray tilts forward, in the direction opposite the drain line,
so that you can recover antibody solutions for re-use.
Rock the tray rocks slowly during the pause.
1.
Press or to change the tray position during a pause.
2.
To end the pause and continue the protocol press START.
STOP. When a protocol is terminated, the screen displays this message.

Stop cancel run
Start pump out
Press STOP to return to the protocol list.
p 15
Press START to start the pump and empty fluid in the tray.
You may also manually operate the pump to remove excess reagents from the
tray. See Setup 1: Manual pump operation on page 22.
Liquid in tray. If you press STOP to cancel the run and return to the protocol list,
liquid in the tray does not get pumped out. The next time you begin a protocol,
the Processor Plus displays a reminder.
Liquid in tray
Pause pump out
Press PAUSE to start the pump and empty fluid in the tray. When the tray is
empty, press START to continue.
Cleaning protocol
Note Run Protocol 5 before
switching from blot processing to gel
staining trays and protocols.
Use blot processing Blot Protocol 5, Clean, to completely rinse the reagent lines
and tray with distilled water or TBST (Tris-buffered saline, containing
Tween 20). The cleaning protocol requires approximately 10 minutes.
On the Mini tray, you may choose to rinse from one to four of the tray chambers.
On the Standard tray you may choose to rinse one or two chambers. By default,
the tray size corresponds to the last tray you used in a blot processing protocol.
To change the default tray size, use Setup 2 (see page 23).
1.
Place all the reagent lines, except line 0, into a container with at least
1.5 litres of distilled water or TBST.
2.
Place the waste tube from the outer peristaltic pump into the waste bottle.
3.
Open the valves on the tray lid to those chambers of the tray you wish to
clean. Close the other valves.
4.
Advance to Protocol 5 and press START.
Clean 4 wells
Tray: 4 Minis
5.
Select the number of wells, or tray chambers, you want to clean. If necessary,
move the cursor to the second line on the screen and press or to change
the tray size selected.
6.
p 16
Press START to continue the cleaning protocol.
Editing Blot Processing Protocols
There are three types of values you can edit on the Processor Plus: protocol
names, step variables, and setup parameters.
Editing a protocol name

A protocol name appears at the beginning of each of the series of 30 steps that
make up a protocol. It consists of a number on the first line of the screen and up
to 16 alpha-numeric characters on the second line.
The numbers on the first line advance from1 to 10 for the Blot process protocol
set. You can change the 16 characters in the second line of any protocol name.
1. Press or to review the protocols by number.
When you find the protocol name you want to modify, press ! or " to
move the cursor to the second line on the LCD screen.
2.
When the cursor is under a character or space you want to modify, press and
hold either or to scroll quickly through the available characters.
The available characters include: a blank space, 09, AZ.
3.
When finished modifying the protocol name, press ! or " to move the
cursor back to the top line.
Editing step variables

Step variables are parameters that may change in every step of a protocol. All
membrane processing protocols contain the following variables:
step number
step duration in minutes
port number for reagent input
a multiplier for the volume (in ml) of reagent delivered
end-of-step options: Hold (H), Beep (B) and Rock (R)
Step
duration
Step
number
H = Hold
B = Beep
R = Rock
S 1 60.0Min HBR
In5 10ml x2 ^
Port in
Caret (^)
indicates
option ON
Multiplier
Fig 6-1 Variables in each blot processing step
p 17
Table 6-1
Step variables and values used in blot processing
Variable
Available values
Steps
130
Port In*
19
Minutes
0.1900.0
Multiplier
15
Hold
on (^) or off
Beep
on (^) or off
Rock
on (^) or off
* Port 0 is reserved as an air vent in blot processing protocols
Port In
The port in determines the source of the reagent pumped in to the tray. For
example, if the Port In is 5, reagent is pumped into the tray from reagent line #5.
Minutes
Minutes are displayed on the LCD in integers and tenths of a minute. The timer
begins counting the minutes in each step at the same time that the pump begins
pumping reagent into the tray. Depending on the volume of reagent needed,
pumping may take up to 1 minute.
Multiplier
Note You cannot change the
minimum volume assigned to a tray.
To deliver less than the minimum
volume, fill the reagent bottle with
less than the minimum amount.
Use the multiplier to change the volume of reagent delivered to each tray chamber.
The minimum volume is the amount of reagent needed to reliably cover the
bottom of a tray chamber. For the Mini tray chambers, it is 10 ml; for the
Standard tray chambers, it is 25 ml. These minimum volumes are stored in the
Processor Plus memory and cannot be modified. You can increase the volume
delivered to a chamber by selecting a multiplier that is greater than 1.
In each protocol step, the Processor Plus determines the total volume to be
pumped by calculating the product of the minimum tray volume, the multiplier,
and the number of tray chambers being used.
Note The minimum volume is

adequate at room temperature.
When running the Processor Plus in
a cold room or overnight, you may
have to increase the multiplier to
ensure sufficient reagent.
For example, in Figure 6-1 on page 17 the multiplier in Step 1 is 2. If 3 chambers

were selected at the beginning of the protocol, the pump will deliver 60 ml (10 ml
2 3) of the reagent at port 5.
Hold, Beep and Rock (HBR)

Hold, Beep and RockH, B, and Rare options that can be turned off or on.
Table 6-2 on page 19 shows the effect of having different combinations of these
options on at the end of a step.
To turn an option off or on, move the cursor below the H, B, or R, then press
or . A caret (^) indicates the option is turned on.
Note You must set Hold to on if you want reagent to stay in the tray at the end of
the step. If only Beep and/or Rock are on, reagent is pumped out of the tray at the
end of the step.
p 18
Table 6-2
Possible H, B, R combination outcomes
H B R Outcome
^
Protocol pauses at end of step and reagent remains in level tray until
you press START to continue.
^ ^
Protocol pauses at end of step, reagent remains in level tray and beep
sounds every six seconds until you press START to continue. Without
attention, the beep stops after five minutes.
^ Protocol pauses at end of step, reagent remains in rocking tray until

^ ^ ^ Protocol pauses at end of step, beep sounds every six seconds,

reagent remains in rocking tray until you press START to continue.
Without attention, the beep stops after five minutes.
^
Beep sounds at end of step.

Edit when the Processor Plus is not running a protocol to save the changes in
memory.
1.
Select the protocol you want to edit.
2.
Press EDIT/SET to see the first step in the protocol.
3.
Press or to review each step in the protocol. You can edit the variables at
each step. Table 6-1 on page 18 shows the values available for each variable.
4.
Press ! or " to move the cursor from one variable to the next. To
switch H, B, or R, first move the cursor to the bottom, right corner of
the screen.
Press or to change the value of the selected variable. When a caret

(^) appears below H, B, or R, it indicates that option is ON.
Press EDIT/SET to complete the edit, save changes and return to the
beginning of the protocol.
Use Setup 5 to print a record of the revised protocol. See page 23.
Adding or inserting a step

You can add a step after any step in a protocol. The variables in the added step
contains the same values as the step that precedes it. Edit the variables in the new
step as needed.
1.
Follow steps 1 through 3 of the previous editing procedure to find the place
in the protocol to add a step.
2.
Press ADD to insert a new step after the step that is visible on the screen. The
new step has the next step number and the variable values found in the step
that precedes it. The step number of all subsequent steps increases by one.
p 19
Deleting a step
You can delete any step in a protocol. After you delete a step, the screen displays
the step that preceded the deleted step. The step number of all subsequent steps
decreases by one.
1.
Follow steps 1 through 3 of the procedure for editing (page 19) to find the
step you want to delete.
2.
Press DEL to delete the step that is visible on the screen.
Editing a protocol in progress

You can edit the protocol in progress while the Processor Plus is running. These
protocol changes are not permanent; the protocol in memory remains unchanged.
To save protocol changes, you must edit the protocol when it is not in progress.
You can make the following protocol edits when the Processor Plus is running:
Important
Note In the current step, you can

only change time. You must press
EDIT/SET to change variables in
subsequent steps.
Change the time only in the current step
Change the time, port number, multiplier, or switches in subsequent steps
Add or delete steps after the current step
You cannot interrupt pump operation. Do not press EDIT/SET while the pump is
running.
To change the time in the current step
Move the cursor to the time and press or to change the value.
To change a value in a subsequent step

1.
Press EDIT/SET to go into edit mode.

The LCD displays the next step in the protocol.
2.
Move the cursor under Step number, advance to the step you want to edit
and edit the values in that step.
3.
When you finish editing, press EDIT/SET to return to the step in progress.
To add one or more steps

Note You cannot add more steps
during the last step.
1.

2.
Move the cursor under Step number and advance to the step that precedes
the point where you want to add steps.
p 20
3.
Press ADD once for each step you want to add. Edit the new steps as needed.
4.
To delete one or more steps

1.

2.
Move the cursor under Step number and advance to the step you want to
delete.
3.
Press DEL once for each step you want to delete.
4.
Note If you delete the step that follows the step in progress, the software goes out
of edit mode and returns to the step in progress.
Power outages. If a power outage occurs after you have edited the protocol in
progress, the changes you made to the protocol are lost.
If a power outage occurs while you are editing a protocol in progress, the
instrument displays the Main menu when power returns. Restart the protocol at
the interrupted step. See page 15 for directions.
p 21
Setup Parameters for Blot Processing
Setup parameters are values that apply to an entire set of protocols. You cannot
use the setup parameters when a protocol is running.
The Processor Plus has seven Setup parameters for blot processing:
1.
Manual pump operation
2.
Tray size
3.
Tray level
4.
Display protocol volume
5.
Print protocol steps
6.
Print total volumes of reagents used in the protocol
7.
Pump calibration
To go to Setup menu for blot processing:
Note Be sure to begin from Process

blot to edit Setup parameters for
blot processing
In any process blot protocol, press and hold EDIT/SET until the screen
displays the Setup parameters.
Setup 1: Manual pump operation

Use to manually operate the pump when a protocol is not running. In Setup 1, the
pump by default operates as long as is necessary to deliver the same volume it
delivered in the last completed step.
1.
Go to Setup 1 for blot processing.
Setup 1: Port 3
pump out
2.
Press" to move the cursor under the port number, then press or to
select a port.
3.
Press" to move the cursor to the second line. Press or to switch between
in and out.
Note In blot processing Setup 1,

with the tray lid in place, pumping
out pumps some air from the tray lid
through the selected port.
Use in to pump fluid into the tray through a port
Use out to pump fluid out of the tray and into a reagent or waste bottle.
Press START to manually start the pump.

4.
When the pump stops, press" to move the cursor back under the Setup
number, then press or to review the other Setup parameters or press
STOP to return to protocols.
p 22
Setup 2: Tray size

Use to choose the tray size. Each protocol set has two pre-defined tray sizes.
Note The minimum volume is
adequate at room temperature.
When running the Processor Plus in
a cold room or overnight, you may
have to increase the multiplier to
ensure sufficient reagent.
A minimum volume in millilitres is assigned to each tray size, based on the

capacity of the tray (Table 7-1). You cannot edit tray sizes or the minimum
volume.
Table 7-1
Minimum Volume for Tray Sizes
Blot Process Tray
Minimum Volume
Mini
10 ml
Standard
25 ml
To use Setup 2:
1.
Select Setup 2 for Process blot.
Setup 2:
Tray: 4 Mini
2.
Press" to move the cursor to the second line. Then press or to select a
tray.
3.
Press" to move the cursor to the top line. Press or to go to another

setup parameter or press STOP to return to protocols.
Setup 3: Tray level

Use to adjust the level position of the tray, when it is not rocking or tilting. See
page 9 for instructions on leveling the blot processing trays.
Setup 4: Display protocol volume

Use to display the total reagent volume needed for each port for any blot
processing protocol.
Note Setup 4 only displays the volumes on the LCD. Use Setup 6 to print a report
of the total reagent volume needed at each port.
1.
Setup 4: Display
Vol of Prot. 2
2.
protocol.
3.
Press START.
4 chambers
Tray: 4 Minis
On the top line, enter the number of chambers. Press" to move the cursor to
the second line and select the appropriate tray size.
p 23
4.
Press START.
Port 1
total
volume = 40ml
The LCD displays the total volume of reagent needed at Port 1 for the
protocol, number of chambers and tray size specified.
5.
Continue to press START to see the volumes needed at each port.
Setup 5: Print protocol

Note See page 4 for directions on
connecting the Processor Plus to a
serial printer.
Use to print out the steps in a protocol when a protocol is not running.
1.
Setup 5: Print
Protocol # 10
2.
protocol.
3.
Press START.
Printing
Protocol # 10
The serial printer produces a record of all the step variables in the selected
protocol.
Setup 6: Print volume of protocol

serial printer.
Use Setup 6 to print a report of total reagent volume needed for each port and the
total of all volumes.
Note The value of the total volumes varies, depending on the tray size selected
and the number of chambers used.
1.
Setup 6: Print
Vol of Prot. 8
2.
protocol.
3.
Press START.
An example of a volume report printout
4 chambers
Tray: 4 Minis
On the top line, enter the number of chambers. Press" to move the cursor to
the second line and select the appropriate tray size.
p 24
4.
Press START.
Printing
Vol of Prot. 8
The serial printer generates a report of the total volumes needed at each port
for the selected protocol, based on the number of chambers used, the tray
size and the multiplier in each step.
Setup 7: Pump calibration

Use Setup 7 to calibrate volume delivery. Calibrate the pump at least once a
month and each time you change the tubing in the peristaltic pump.
Note The pump calibration for blot processing is not the same as pump
calibration for gel staining. You must calibrate the pump when you switch
between protocol sets.
See page 11 for pump calibration instructions.
p 25
Setting Up for Gel Staining
The Hoefer Processor Plus allocates memory for fourteen gel staining protocols;
nine of these protocols are pre-programmed (Table 8-1). Each protocol can
contain up to 30 steps. See page 33 for directions on editing these protocols.
The Processor Plus has two gel staining trays (Table 8-2) and each tray has its
own tray base and lid.
Table 8-1
Protocol Name
Applications
1 DNA silver
DNA Gels
1.0 mm unbacked gels

0.5 mm backed gels
2 Protein silver
SDS and Native
0.75 and 1.0 mm unbacked gels

0.5 mm backed gels
Immobiline DryPlates
3 Protein silver
SDS and Native
4 Protein silver
IEF
5 Protein Coomassie
SDS and Native

0.5 mm backed gels
6 Protein Coomassie
SDS and Native
7 Protein Coomassie
SDS and Native
8 Protein Coomassie
IEF
9 Clean
Rinses reagents out of tubings, valves and ports
Table 8-2
Tray
p 26
Pre-programmed gel staining protocols
Tray sizes for gel staining

Number of
gels
Gel Size
(cm)
Reagent Capacity
(ml/chamber)
19 29 cm
1
1
2
4
14 16
11 26
11 13
78
125 200
29 35 cm
1
2
2
2
6
20 26
14 16
11 13
11 26
78
250 400
Important
Thoroughly rinse the staining tray with deionized water after each use. Clean and
dry instrument surfaces after each use. To avoid scratching the PTFE coating, do
not use metallic instruments on this surface.
Important
Do not introduce any hot volatile reagents into this instrument.
Configuring the gel staining tray and pump tubing assembly

For gel staining, only one tube connects the gel staining tray to the inner
peristaltic pump (Fig 8-1). The tray lid has no tubing inlets. Gel staining
protocols do not use the outer peristaltic pump tube.
When the appropriate male and female Quick-Fit couplings are pressed together,
you can hear a click as they connect.
Tray drain tube
Inner peristaltic
pump tube
Outer peristaltic
pump tube
Fig 8-1 Gel staining tube and tray configuration
Leveling the tray

For reliable and even movement of reagents across gels, place the Processor Plus
on a level surface. Use Setup 2 to select the tray size that matches the tray you are
using. Use Setup 4 and the spirit level to adjust the default level position that the
tray assumes when it is not rocking or tilting.
Important
Each tray has its own level position. Each time you change trays, use the spirit
level to verify that the tray is level.
1.
Place a gel staining tray on the Processor Plus and put the lid on the tray.
2.
Go to Setup 2 and select the tray size that matches the tray you are using.
For gel staining, use either 19 29 cm or 29 35 cm. (See page 39 for a
description of Setup 2.)
3.
Place the level on the tray lid. The level should sit in a line that is parallel to
the direction in which the tray rocks (Figure 8-2 on page 28).
p 27
Level
Front of tray
Direction of tray rocking

Fig 8-2 Placing the level on the surface of the tray lid, viewed from above
4.
From Setup 4 for Stain gel, press" to move the cursor to the second line,
then press or to adjust the tray level up or down.
Setup 4: Adjust
tray level up/dn
The angle of the tray changes in response to pressing or . The characters
on the LCD do not change.
5.
When the tray is level, press" to move the cursor to the first line. Press to
advance to Setup 6, pump calibration.
Calibrating the pump

Use Setup 6 to calibrate reagent delivery. Repeat pump calibration at least once a
month and each time you change the tubing in the peristaltic pump.
Note The calibration procedures for
Stain gel and Blot process protocols
are different. You must calibrate the
pump whenever you switch between
the two protocol sets.
To calibrate the pump for gel staining:

1.
Place the end of reagent tube 1 in a beaker of at least 400 ml water.
2.
Place the end of tube 0 in a 250-ml graduated cylinder or beaker.
3.
Select Setup 6 for membranes.
Setup 6: Calib
Press START
4.
Press START.
Tube 1 in water
Tube 0 in cyl
calibration.
5.
p 28
Press START.
The Processor Plus delivers fluid to the tray and then out tube 0. When the
pump stops, measure the amount of water in the graduated cylinder.
Measured vol.1
= 200 ml
6.
Press " to move the cursor under the volume values and press or to
change the numbers. Enter the amount of water measured in step 5.
7.
Replace the end of reagent tube 1 in the beaker of water and tube 0 in an
empty graduated cylinder or beaker. Press START.
Tube 1 in water
Tube 0 in cyl
calibration.
8.
Press START.
The pump again pumps water into the tray and out tube 0. When the pump
stops, measure the amount of water in the graduated cylinder.
Measured vol.2
= 100 ml
9.
Enter the measured volume on the screen and press START.
Calibration
complete
When calibration is completed, the LCD returns to the protocols.
Whats happening. Processor Plus uses these two values volume 1 and volume
2 to establish a correlation between the number of times the pump turns and
the volume delivered. It then interpolates to determine the number of pump turns
necessary to delivery the required volume.
p 29
Operating Instructions for Gel Staining
To run a protocol, you must first prepare the tray and reagents.
The first time you prepare the tray, you must:
Note Each time you change tray

sizes, select the tray size in Setup 2
and level the tray in Setup 4.
Configure the tubing on the peristaltic pump
Level the tray (Setup 4)
Calibrate the pump (Setup 6)
Review the instructions for these procedures on pages 27 29.
Prepare for gel staining

Note Calibrate the pump whenever
you change tubing in the peristaltic
pump, or at least once a month.
1.
Carefully place the gels in the empty tray.

Place plastic-backed gels with the backing side down. If using gels without
backing, you may trim off any low-percentage stacking layer before staining.
2.
Place the magnets on the tray as needed to prevent gels from overlapping or
piling up around the drain.
Use the magnets to create separate processing areas for multiple gels. The
magnets can also be placed on the corners of plastic-backed gels to keep
them submerged.
3.
Place the plain glass lid on the tray. Note the moulded indentations at both
sides allow easy lid placement and removal.
4.
Put the ends of the reagent lines into the appropriate reagent bottles.
Refer to the Automated Gel Stainer Protocol Guide for descriptions of each
gel staining protocol. See also Pre-programmed Staining Protocols on
page 58.
Starting at the beginning of the protocol

Note You can start the Processor
Plus at any step in a protocol. To
start after step one, see page 31.
1.
From the Main Menu, select Stain gel protocols.
2.
Press START to go to the first protocol in the selected protocol set.
3.
Press or to review the protocols in the selected protocol set.
4.
Press START when the protocol you want appears on the screen.
If you have a serial printer connected to the Processor Plus, the printer begins
to print a validation form for the protocol you are about to run.
5.
On the top line, verify the volume of reagent to be pumped for each step.
Press or under a number to change its value.
Volume: 175 ml
Tray: 19 x 29 cm
6.
Press" to move the cursor to the second line and verify the tray selection.
Press or to select the appropriate tray description, then press START.
p 30
Moving valve
to port 1
As the Processor Plus initiates the protocol, the 10-port valve moves to the
port position programmed in the selected first step. The pump begins to
deliver reagent into the tray, the tray rocks and the timer begins counting.
Step 1, Pumping
in from port 1
When pumping is complete, the screen reports the time remaining in the step
and the duration of the entire protocol.
Note The tray rocks during every

step.
Step 1 9.3 min

Total 0:10 hrs
Time left in step

Total time left in protocol
At the end of each step, the timer stops and the tray tilts back as the pump
empties the tray.
If you have connected a printer to the Processor Plus, at the end of each step
the printer records the step number, the length of the step in minutes and the
ports used.
When the protocol is completed, the Processor Plus emits a series of beeps
for 20 seconds if the beep option is ON in the last step. (See page 34.)
Important
Clean the staining tray thoroughly after each use. See page 47 for cleaning
instructions. See page 32 for a description of Protocol 9, the cleaning protocol.

Follow these steps to start a protocol at any step after step 1.
Note If you edit a step when the

instrument is not running, you must
press EDIT/SET when finished to
end edit mode. See page 33 for
more on editing.
1.
Follow steps 13 of the previous procedure on page 30.
2.
Press EDIT/SET to see the first step in the protocol.
3.
To review the steps in a protocol, press or with the cursor under the step
number.
4.
When you see the step at which you want to begin, press START.
Interrupting a protocol
You can temporarily stop or terminate a protocol in progress.
Press PAUSE to interrupt a protocol without cancelling it.
Press STOP to interrupt and terminate a protocol in progress.
Pause. You may temporarily stop a protocol to adjust reagent lines and tray
contents. See page 20 for directions on editing a protocol in progress.
p 31
Note If you press PAUSE when the

pump is running, the interruption
does not begin until the pump is
finished
When you press PAUSE, the timer stops counting and the tray goes to the Level
position and stops rocking.
Tray Level
Press Start to continue
While the Processor Plus is in PAUSE mode, the tray has three possible positions:
Level the tray stops rocking and maintains the level position defined in
Setup 4.
Recover the tray tilts forward so that you can recover solutions.
Rock the tray rocks slowly during the pause.
1.
Press or to change the tray position during a pause.
2.
To continue the protocol after a pause, press START.
STOP. When the protocol is terminated, the screen displays this message.
Stop cancel run
Start pump out
Press STOP to return to the protocol list.
Press START to start the pump and empty the tray.
You may also manually operate the pump to remove excess reagents from the
tray. See page 38.
Cleaning protocol
Note Run Protocol 9 before
switching from gel staining to blot
processing trays and protocols.
Use gel staining Gel Protocol 9, Clean, to completely rinse the tubing and tray
with distilled water. The cleaning protocol requires approximately 10 minutes.
1.
Place the reagent line labelled 0 into a container with at least 1.5 litres of
distilled or deionized water. If you are using the 29 35 tray, the container
should hold 3 litres of distilled or deionized water.
2.
Place all the other reagent lines into a waste bottle that can hold at least
4 litres.
3.
Advance to Protocol 9 and press START.
Volume: 175 ml
Tray: 19 x 29 cm
4.
p 32
Adjust the volume and tray size, if necessary, and press START.
Editing Gel Staining Protocols
10
Important
Design gel staining protocols so that the same reagent lines always deliver the
same reagents. This consistency minimizes contamination of the reagent lines and
decreases the potential for mixing incompatible reagents.
There are three types of values you can edit on the Processor Plus: protocol
names, step variables, and setup parameters.
Editing a protocol name

A protocol name appears at the beginning of each of the series of steps that make
up a protocol. It consists of a number on the first line of the screen and up to
16 alpha-numeric characters on the second line. The numbers on the first line
advance from 1 through 14 for gel staining protocols. You can change any of the
16 characters in the second line of the protocol name.
1.
From the Main Menu, select the Stain gel protocols and press START.
2.
Press or to review the protocols by number.

When you see the protocol name you want to modify, press ! or " to move
the cursor to the second line on the LCD screen.
3.
When the cursor is under a character or space you want to modify, press and
hold either or to scroll quickly through the available characters.
The available characters include: a blank space, 09, AZ.
4.
Press ! or " to move the cursor back to the first line.
Editing step variables

Step variables are values that may change in every step of each protocol (Fig 101). The LCD screen displays each step in a protocol. Steps in all gel staining
protocols contain the following variables:
step number
port number for reagent input
step duration in minutes
end-of-step options: hold (H), beep (B) and rock (R)
port number for reagent output

Step
duration
Step
number
H, B, R
options
S 1 60.0 min HBR

In5 out 7 ^
Port in
Caret (^)
indicates option ON
Port out
Fig 10-1 Variables in each gel staining step
p 33
Table 10-1
Step variables and values used in gel staining protocols
Variable
Available values
Steps
130
Port In
09
Minutes
0.1900.0
Port out
09
Hold
on (^) or off
Beep
on (^) or off
Rock
on (^) or off
Port In
The port in defines the reagent line through which reagent enters the tray. For
example, if the Port In is 5, reagent is pumped into the tray from reagent line #5.
Minutes
Minutes are displayed on the LCD in integers and tenths of a minute. The timer
begins counting the minutes in each step at the same time that the pump begins
pumping reagent into the tray. Depending on the volume of reagent needed,
pumping may take up to 1 minute.
Port Out
Port out defines the reagent line used to carry fluid out of the tray. You can collect
all waste in one bottle or divide it according to composition. For example, the
pre-programmed protocol for silver staining divides waste into three bottles:
waste that contains silver into one waste bottle, via Port Out 9
waste that contains formaldehyde or glutardialdehyde into the second waste

bottle, via Port Out 8
waste that contains waste water, ethanol, acetic acid, EDTA and glycerol into
a third waste bottle, via Port Out 7.
Hold, Beep and Rock

Hold, beep, and rock are options that can be turned off or on. Table 10-2 on
page 35 shows the effect of having different combinations of these options on in a
step.
To turn an option off or on, move the cursor below the H, B, or R, then press
or . A caret (^) indicates the option is on.
Note You must switch Hold to on if you want reagents to stay in the tray at the
end of the step. If only Beep and/or Rock are on, reagent is pumped out of the
tray at the end of the step.
p 34
Table 10-2 Possible HBR combination outcomes

H B R Outcome
^
Protocol pauses at end of step and reagent remains in level tray until
^ ^
Protocol pauses at end of step, reagent remains in level tray and beep
sounds every six seconds until you press START to continue.
^ Protocol pauses at end of step, reagent remains in rocking tray until

^ ^ ^ Protocol pauses at end of step, beep sounds every six seconds,

reagent remains in rocking tray until you press START to continue.
^
Beep sounds at end of step.

Edit when the Processor Plus is not running a protocol to save the changes in
memory.
1.
From the Main menu, select Stain gel protocols. Press START to go to the
first protocol.
2.
Press or to review the protocols in the protocol set.
3.
Press EDIT/SET to see the first step in a protocol.

If necessary, press ! or " to move the cursor under the step number.
4.
Press or to advance the step number through a protocol. You can edit
the variables at each step. Table 10-1 on page 34 shows the values available
for each variable.
5.
Press ! or " to move the cursor from one variable to the next. To
change the status of H, B, or R, move the cursor to the bottom, right
corner of the screen.
Press or to change the value of the selected variable. When a caret

(^) appears below H, B, or R, it indicates that option is ON.
Press EDIT/SET to complete the edit, save the changes and return to the
protocols.
Use Setup 5 to print a record of the revised protocol. See page 40.
p 35
Adding or inserting a step

You can add a step after any step in a protocol. The variables in the added step
contains the same values as the step that precedes it. Edit the variables in the new
step as needed.
1.
Follow steps 1 through 3 of the previous editing procedure, (page 35) to find
the place in the protocol where you want to add a step.
2.
Press ADD to insert a new step after the step on the screen. The new step has
the next step number but contains the variable values found in the step that
precedes it. The step number of all subsequent steps increases by one.
Note The Processor Plus contains empty protocols that contain only one step.
Add steps to these protocols to enter your own custom protocols.
Deleting a step
You can delete any step in a protocol. After you delete a step, the screen displays
the step that preceded the deleted step. The step number of all subsequent steps
decreases by one.
1.
Follow steps 1 through 3 of the editing procedure (page 35) to find the step
you want to delete.
2.
Press DEL to delete the step on the screen.
Editing a protocol in progress

You can edit the protocol in progress while the Processor Plus is running. These
protocol changes are not permanent; when the protocol ends it reverts to its
original definition. To save protocol changes, you must edit the protocol when a it
is not in progress.
You can make the following protocol edits when the Processor Plus is running:
Important
Note In the current step, you can

only change time. You must press
EDIT/SET to change variables in
subsequent steps.
Change the time only in the current step
Change the time, port in, port out, or end-of-step options in subsequent steps
Add or delete steps after the current step
You cannot interrupt pump operation. Do not press EDIT/SET while the pump is
running.
To change the time in the current step
Move the cursor to the time and press or to change the value.
To change a value in a subsequent step

1.

2.
Move the cursor under Step number, advance to the step you want to edit
and edit the values in that step.
3.
p 36
To add one or more steps

1.

2.
Move the cursor under Step number and advance to the step that precedes
the point where you want to add steps.
Note During the last step, you

cannot add more steps.
3.
Press ADD once for each step you want to add. Edit the new steps as needed.
4.
To delete one or more steps

1.

2.
Move the cursor under Step number and advance to the step you want to
delete.
3.
Press DEL once for each step you want to delete.
4.
Note If you delete the step that follows the step in progress, the software goes out
of edit mode and returns to the step in progress.
Power outages. If a power outage occurs after you have edited the protocol in
progress, the changes you made to the protocol are lost.
If a power outage occurs when you are in edit mode and a protocol is in progress,
the instrument does not return to the protocol when power returns. Instead it
displays the Main menu. To continue the interrupted protocol, restart at the
interrupted step. See page 31 for directions.
p 37
Gel Staining Setup Parameters
11
Setup parameters are values that apply to an entire set of protocols. You cannot
use the setup parameters when a protocol is running.
The Processor Plus has six Setup parameters for gel processing:
1.
Manual pump operation
2.
Tray size
3.
Volume delivered
4.
Tray level
5.
Print protocol
6.
Pump calibration
To go to the Setup mode for gel staining:
Note Be sure to begin in Stain gel

to see the Setup parameters for gel
staining.
1.
In the Main Menu, select Stain gel.
2.
Once you are in the gel staining protocol set, press and hold EDIT/SET until
the screen displays the Setup parameters.
Setup 1: Manual pump operation

Use Setup 1 to manually operate the pump when a protocol is not running. In
Setup 1, the pump by default operates as long as is necessary to deliver the same
volume it delivered in the last step completed.
Setup 1: Port 3
pump out
1.
From Setup 1 for Stain gel, press ! or " to move the cursor under the port
number, then press or to select a port.
2.
Press ! or " to move the cursor to the second line, under in or out. Press
or to switch between in and out.
Use in to pump fluid into the tray through a port
Use out to pump fluid out of the tray, into a reagent or waste container
Press START to manually start the pump.

3.
When the pump stops, press" to move the cursor back under the Setup
number, then press or to review the other Setup parameters, or press
STOP to return to protocols.
p 38
Setup 2: Tray size

Use to review the available tray sizes. Gel stain has two pre-defined tray sizes.
Note You can also modify the tray
size and volume at the beginning of
a protocol.
You cannot edit tray sizes, but you can edit the volume associated with the tray in
Setup 3. Use the Setup 2, tray size, in conjunction with Setup 3, Volume Delivery.
Each tray size in Setup 2 determines the range of available values in Setup 3. See
Table 11-1.
Table 11-1
Relation of tray sizes to values in Setup 3
Setup 2 Tray
Setup 3 Range
(ml)
Recommended
Volume (ml)
19 29 cm
125200
125
29 35 cm
250400
250
Setup 2: Tray
19 x 29 cm
1.
From Setup 2 for Stain gel, press " to move the cursor to the second line.
Then press or to review the tray options.
2.
3.
Select a tray size.

Press " to move the cursor to the top line and then press to advance to
Setup 3: Volume Delivery.
Setup 3: Volume delivery

Use to define the of reagent (ml) delivered to the tray in each step of the gel
staining protocols.
Setup 3 Volume
pumped = 175 ml
1.
From Setup 3 for Stain gel, press" to move the cursor to the second line,
under the number you want to modify. Then press and hold or to
change the number.
2.
When finished, press" to move the cursor to the first line. Press or to
advance to another Setup parameter or press STOP to return to protocols.
Setup 4: Tray level

Use to adjust the level position of the tray, when it is not rocking or tilting. See
page 27 for directions on using Setup 4.
p 39
Setup 5: Print protocol

serial printer.
Use to print out the steps in a protocol either before or after running a protocol.
1.
Select Setup 5 for Gel stain.
Setup 5: Print
Protocol # 14
2.
protocol.
3.
Press START.
Printing
Protocol # 14
Setup 6: Pump calibration

Use to calibrate reagent delivery. Repeat calibration at least once a month and
each time you change the tubing in the peristaltic pump.
Important
The calibration procedures for Stain gel and Process blot protocols are different.
You must calibrate the pump for each set of protocols.
To calibrate the pump for gel staining, see page 28.
p 40
Using the protocol key
12
Note The Processor Plus cannot
read the protocol key when it is in
the Edit mode or in one of the Setup
menus.
When you insert the protocol key into the protocol key slot, the instrument reads
the key and writes it in the last protocol in the protocol set. Any protocol that is
already in memory in this last position will be overwritten by the protocol on the
protocol key.
Reading protocol
key...Please wait
If the protocol on the protocol key is a gel staining protocol, it is written into
Gel Protocol 14. You can copy a gel staining protocol from the key into any
of the 14 gel staining protocols on the Processor Plus.
If the protocol on the protocol key is a blot processing protocol, it is written

into Blot Protocol 10. You can copy a blot processing protocol from the key
into any of the 10 blot processing protocols on the Processor Plus.
Protocol
14
MyNew Stain
You can also copy any protocol from the Processor Plus onto the protocol key.
Note You cannot copy a gel staining protocol on the key into memory on the
Processor Plus that is reserved for a blot processing protocol, or vice versa.
Editing with the protocol key in the slot. If you leave the protocol key in the
slot while you edit the last protocol in the protocol setProtocol 10 in blot
processing or Protocol 14 in gel staining the Processor Plus automatically
overwrites the protocol on the key when you press either STOP or EDIT/SET to
exit the edit mode.
Important
To prevent accidentally overwriting the protocol on the protocol key, remove the
protocol key before you begin editing protocols.
To copy a protocol from the key to the Processor Plus

Note If you copy a protocol from the key into a protocol on the Processor Plus
that already contains defined steps, you overwrite those steps and replace them
with the protocol on the key.
1.
With the key in the protocol key slot, use the arrow keys to advance to a
protocol number on the Processor Plus.
2.
Press DEL.
Reading protocol
key...Please wait
The Processor Plus writes a copy of the protocol on the key into the selected
protocol number. Remove the protocol key to prevent accidentally
overwriting the protocol on the key.
p 41
To copy from the Processor Plus to the protocol key

The protocol key can hold only one protocol at a time. When you copy a protocol
onto the key, you overwrite the protocol already on the key.
1.
With the key in the protocol key slot, use the arrow keys to advance to the
protocol number on the Processor Plus that you want to copy onto the key.
2.
Press ADD.
Writing protocol
key...Please wait
The Processor Plus emits one long beep as it copies the protocol onto the key.
To edit a protocol on the protocol key

To edit the protocol on the protocol key, copy an edited protocol from the
Processor Plus on to the protocol key.
p 42
Tr o u b l e s h o o t i n g
13
Troubleshooting
Pumping irregularities. If you observe a pumping irregularity while a protocol is

in progress, record the port currently indicated on the LCD. Then press STOP to
terminate the protocol. Remove the gels or membranes from the tray. Remove the
reagent line from the reagent bottle and insert it into a bottle of deionized water.
Pump water in and out several times to dislodge any precipitates or obstructions.
If unable to clear the reagent line, replace it with a new line of the same length
and diameter.
Power Outage. If a power outage of 10 minutes or less occurs during a protocol,

the Processor Plus resumes the interrupted step when power returns. See page 21
and page 37 for additional information about power outage consequences.
Instrument-based problems
Symptom
Possible cause
Recommended action
Diagnostics cycle indicates

component failure.
Component failure.
Press START to continue to next

test. Call your local Amersham
Biosciences office for further
information.
Pumped volume higher than

expected volume.
Tray size being used does not

match tray size in Setup 2.
Check the tray size selected in Setup

2.
Incorrect reagent line

assemblies.
Use only reagent lines supplied with

the Processor Plus. Do not shorten
the tubing. Do not attach pipettes in
place of rigid, opaque tubing.
Pump out of calibration.
Calibrate the pump.
Tray size being used does not

match tray size in Setup 2.

2.
Incorrect reagent line

assemblies.
Use only the reagent lines supplied

with the Processor Plus.
Reagent line has come out of

reagent bottle or the liquid
level is below the end of the
opaque rigid tubing.
Make sure rigid tubings are fully

immersed in the reagent bottle and
there is sufficient reagent in the
bottle.
Reagent tubing damaged or

cracked.
Replace reagent tubing.
Obstructions or constriction in
reagent line or 10-port valve.
Run the cleaning protocol or replace

the reagent line.
Pump head tubing worn.
Replace the tubing and recalibrate

the pump.
Reagent line connection loose

or improperly attached.
Adjust fitting of reagent line and

connection.
Pumped volume lower than

expected volume.
Leaks in reagent line at

staining tray drain port or
pump head tubing inlet or
outlet.
Leaks in reagent lines at 10- Positioning controls out of

port valve.
adjustment.
Turn off mains power switch and

then turn on again to test the
positioning controls.
p 43
Troubleshooting
Instrument-based problems, continued

Symptom
Possible cause
Recommended action
Pump does not empty the

tray completely.
Obstruction in splash guard.
Clean the splash guard (staining

tray).
Tray not level.
Adjust the tray level.
Obstructions or constriction in
reagent lines.
Run the cleaning protocol to clear

obstructions or change the reagent
lines.
Solution is splashing against Tray or unit not level.

the lid.
Liquid accumulating under

pump.
Make sure unit sitting on level

surface. Adjust the tray level.
Tray used does not match tray

selected in Setup 2.

2.
Pump tubing worn.
Replace the pump tubing.
Insufficient reagent volume in

Setup 3.
Increase the volume delivered in Gel

stain Setup 3.
Gel Staining problems

Gel sticks to the staining
tray.
Check the troubleshooting section of

the Protocol Guide for modifications
that may help prevent gel sticking.
Uneven staining.
Reagent buildup on tray and

reagent lines.
Rinse the staining tray with distilled

water after each use.
Gels sticking to tray surface.

the Protocol Guide for modifications
that may help prevent gel sticking.
Gels crowded or overlapping in Make sure each gel has adequate

tray.
processing area. Rearrange the
magnets to allow more movement.
Contaminants in reagent lines. Always run the cleaning protocol
before switching to a different
protocol to minimize mixing of
reagents.
Insufficient reagent volume in
Setup 3.
Increase the delivered volume to

ensure that the gel is fully
submerged. It may help to turn the
gels over during the staining process
to increase exposure to reagents.
the Protocol Guide for more
information.
High background or poor

sensitivity
p 44

the Protocol Guide for more
information.
Tr o u b l e s h o o t i n g
Blot Processing problems

Symptom
Possible cause
Weak or no signal. Inefficient transfer.
Recommended action
Confirm protein transfer by staining
residual gel.
Check nitrocelullose or PVDF membranes
for sample with Ponceau S reversible stain.
With nylon, use Rainbow Molecular Weight
Markers instead of Ponceau S.
Confirm that the electrical conditions and
transfer buffers used match the
recommendations of the manufacturer of
the transfer unit.
Transfer of higher mass proteins can be
improved by extending the transfer time or
by using a lower percentage separating gel.
Check for uniform, bubble-free contact
between the gel and membrane during
transfer.
Poor binding of proteins to

membrane.
Do not used aged membranes, which may

not wet properly or may not bind proteins.
Add methanol in Towbin buffer to improve
the protein binding to membranes.
Add 0.1% SDS to improve transfer from
the gel. (SDS may impair binding
efficiency to nitrocellulose membranes.)
Gel transferred the wrong

direction.
Use Rainbow Molecular Weight Markers to

confirm transfer or stain membrane with
Ponceau S prior to processing. Do not use
Ponceau S with nylon.
Insufficient protein loaded on

the gel.
Load more protein.
Antibody concentration too low.
If commercially prepared, follow

manufacturers suggested dilutions, titre up
and down from the starting point.
Concentration and titre of antibodies are
both important.
Some antigens may be affected

by the treatments required in
electrophoresis.
Test binding efficiency with slot blot or

other blotting method. Denaturation during
SDS electrophoresis may affect antibody
binding.
Detection reagents degraded

or not properly stored.
Prepare fresh reagents.
Membrane degraded.
Keep nitrocellulose in a closed bag away

from heat, light and moisture. It will
degrade if not stored properly. Check
membrane wetting. Nitrocellulose should
quickly absorb water. PVDF should be wet
in methanol prior to equilibration in
transfer buffer.
p 45
Troubleshooting
Blot Processing problems, continued

Symptom
Possible cause
Weak or no signal. Antibodies/reagents not

delivered.
Recommended action
Check that the correct reagent line is in the
vessel and that the opaque reagent tubing
reaches to the bottom of the container.
Check protocol to ensure steps or ports
have not been modified.
Check that valves above the tray are in the
open positions.
Excessive washing.
Reduce number or duration of wash steps.

Reduce concentration of detergents, such
as Tween 20, if used.
Excessive signal.
Too much protein loaded on the Load less protein.

gel.
Antibody concentrations too
high.
Try lower concentrations of antibody.
Inadequate washing.
Increase the number of washes or extend

the wash times.
Non-specific
binding.
Impure antibodies or other

proteins reacting with similar
binding sites as antigen.
Try lower concentrations of antibody or

further purify antibody.
Uneven, splotchy
background.
Membrane not fully or properly

rehydrated.
Pre-wet membranes prior to incubation.

Wet nitrocellulose membranes in water,
then equilibrate with wash buffer. Wet
PVDF first in methanol, then equilibrate
with wash buffer.
Fingerprints, marks or damage Wear gloves and use forceps when handling
to the membrane can cause non- membranes. Membranes are very fragile.
specific binding artifacts.
Avoid tearing, folding or creasing
membranes to minimize processing
artifacts.
Areas of the blot were not fully
coated with blocking agent or
the membrane partially dried
during incubation.
Ensure proper volumes used for each tray

position. Ensure reagent lines are secured
into reagent vessels and that the opaque
reagent tubing reaches to the bottom of the
container.
Membrane has moved into the

drain ramps.
Make sure the processed membrane is at

least 1.5 cm2, on the Mini Trays, or
2.5 cm2, on the Standard Trays, to deter
flow into drain ramp.
High background. Inadequate blocking.
p 46
Blocking agent contaminated or too dilute.
Inadequate washing between

antibody steps.
Extend the time, volume or number of

washes.
Choice of membrane.
Avoid using nylon membranes.
Contaminated buffers.
Prepare fresh buffers.
Cross-reactivity with blocking

reagents.
Try a different blocking agent, such as

0.1% Tween-20, 3% BSA,
5% non-fat dry milk, casein or fish gelatin.
Care and Maintenance
14
Always turn the mains power switch off and unplug the power cord before doing
any maintenance.
Important
Do not autoclave any component of the Processor Plus.

After each use, clean the unit with a mild detergent and water, rinse thoroughly
with distilled water and allow to air dry. Never use abrasive cleansers or solvents.
Do not expose the unit to solutions or vapours of aromatic or halogenated
hydrocarbons, ketones, esters, alcohols (over 30%), or concentrated acids (over
25%).
Running the cleaning protocol

Run the pre-programmed cleaning protocols:
after every protocol
before switching to a protocol that uses different reagents
before switching from gel staining protocols to blot processing protocols, or

vice versa
before changing the peristaltic pump tubing
whenever the instrument has not been in use for several days
The cleaning protocol requires approximately 10 minutes to completely rinse the

reagent lines.
See page 16 for directions on using the blot processing Clean protocol. See
page 32 for directions on using the gel staining Clean protocol.
Staining trays
Note Residual silver stain can accumulate on the staining trays, giving them a
black appearance. This black residue is inert. It does not interfere with routine
staining or cause black spots on gels.
Important
To prevent the accumulation of residual silver stain, thoroughly clean the staining
tray after each use.
1.
First wipe residual staining solution from the tray with a lint-free tissue.
2.
Detach the drain line from the drain port and lift the staining tray out of the
tray support.
3.
Clean the staining tray with detergent and a non-abrasive cloth. Rinse
thoroughly with distilled water.
Avoid scratching the PTFE coating on the tray. Do not use metallic
instruments on the tray surface.
p 47
Chemical Resistance
The parts of the instrument that come into contact with liquid reagents are
resistant to chemicals typically used in Coomassie and silver staining and Western
blot processing. Before introducing any other chemicals into the system, first test
the exposed parts. Never use ketones, hot or strong acids, or hydrocarbon
solvents. Refer to Table 14-1 for more information on the chemical susceptibility
of components.
Table 14-1 Chemical susceptibility of Processor Plus components

Instrument Component
Material
Susceptible to
10-port valve, exterior
PVDF
ketones, esters and hot acids
10-port valve gasket,

internal
Fluoro rubber
hot strong acids, esters, ketones

and bleach
Tubing
10-port valve to tray
Reagent lines
Tygon
PVC
Pump head tubing
C-flex
esters, ketones and hydrocarbons

hot acids, ketones and
hydrocarbons
hydrocarbons, ethers, ketones,
phenol, oils
Processing tray
Styrene
hydrocarbons, strong acids and

bases, absolute methanol
Staining tray
PTFE-coated
stainless steel
long exposure to highly

concentrated acids and bases
Cleaning the splash guard

If gel fragments or particulate matter clogs the splash guard or drain, first
disconnect the drain line from the bottom of the staining tray, then lift the tray
out of the tray support. Rinse the drain tube from the bottom and run water
through the splash guard from the top to remove any lodged material.
Replacing the tray gasket on the staining tray

The gasket around the staining tray supports the glass lid and creates a seal to
contain reagents inside the tray (Fig 14-1). If the gasket is damaged, pull it away
from the tray edge. Fit a new gasket around the tray edge, pressing the groove in
the gasket over the tray edge completely around the tray.
Gasket
Fig 14-1 Placement of gasket on staining tray
p 48
Pump Care and Maintenance

Calibrating delivery volume
For Blot processing, see page 11. For Gel staining, see page 28.
Changing reagent lines

The valve at the back of the instrument houses ten valve ports. Ten reagent line
assemblies connect to these valve ports. Replace reagent lines as they become
soiled or worn.
.
10-port valve
Ten reagent line

assemblies
Fig 14-2 10-port valve and reagent line assemblies

Each of the ten reagent line assemblies consists of two types of tubing that fit
together.
Important
Any modifications to the reagent line assembly will affect pump performance and
calibration. Use only reagent lines supplied by Amersham Biosciences
(code no. 80-6342-58). Do not detach the opaque, rigid tube from the end of the
reagent line.
1.
When removing the flexible end of the reagent line from the valve port, tug
the line gently just where it slips over the valve port and pull it straight out.
To avoid breaking valve ports on the 10-port valve, do not work the line
from side to side.
2.
To install the new reagent lines, press the flexible end of the new line onto
the valve port.
p 49
Changing the peristaltic pump tubing

Change the peristaltic pump tubing when the white tubing inside the pump leaks
or becomes worn.
The peristaltic pump on the rear of the instrument consists of two pump heads.
The two pump heads are held together and in place by four wingnuts on the ends
of four threaded studs.
Two pieces of tubing wrap around the pump heads. The four ends of the tubing
that come out of the pump are shown in Fig 14-3.
Fig 14-3 The four pieces of tubing coming out of the peristaltic pump
Your selection of either the blot processing trays or the gel staining trays
determines how these four pieces of tubing are connected. Table 14-2 details the
connections for each tray configuration.
Table 14-2
Tubing #
Pump tubing connections

Blot Process
Gel Staining
To 10-port valve
To 10-port valve
To lid input manifold
To staining tray drain
To waste bottle
Not in use
To tray drain tube
Not in use
Keep a supply of paper towels handy to absorb any water that may run out of the
tubing during disassembly.
1.
To minimize contact with reagents, run the cleaning protocol to rinse the
reagent lines with distilled water before replacing the pump head tubing.
See page 16 for a description of the Clean protocol for blot processing; see
page 32 for a description of the Clean protocol for gel staining.
p 50
2.
Disconnect the pump tubing from either the blot processing tray lid (# 2 and
#4 in Fig 14-3) or the gel staining tray (#2).
3.
Disconnect the short translucent tubing (#1 in Fig 14-3) from the 10-port
valve.
4.
Unscrew the four wingnuts that hold the two heads of the peristaltic pump
against the rear panel.
5.
Pull the outer pump head off the four threaded rods.
6.
Pull the top half of the outer pump head off. Peel the pump head tubing
away from the pump shaft and discard it. This is the tubing that ends with
# 3 and #4 in Fig 14-3.
7.
Place the new pump head tubing around the pump shaft (Fig 14-4).
As shown in Fig 14-4, hold the pump head with the tang end facing up. The
tubing end with the QuickFit connector (#4) should protrude only 8 cm
(3 in.) from the body of the pump.
Important
Be sure to use the replacement tubing with the appropriate diameter.
Tang facing up
3
4
Fig 14-4 Replacement tubing wrapped around the shaft of the outer pump
8.
Press the pump head shell over the tubing, making sure not to pinch the
tubing at any point.
9.
Turn the pump head over, so that the tang points away from you. Press a
piece of dampener tape over the centre slot on the rear of the pump head. See
Figure 14-5 on page 52.
Dampener tape is clear polyester film with adhesive backing. A strip with 10
rectangular pieces of dampener tape, 13 14 mm each, are included in
replacement tubing sets. As the name implies, dampener tape muffles the
sound of the pump in operation.
p 51
Placement of
dampener tape
Fig 14-5 Press dampener tape over centre slot on rear of pump head
Set this outer pump head aside while you replace the tubing on the inner
pump head.
10. Pull the inner pump head off the four threaded rods. Pull the top half of the
inner pump head off, remove and discard the pump head tubing.
11. Wrap the replacement tubing around the shaft of the inner pump.
A tie wrap attaches a short segment of translucent tubing, 0.32 cm I.D.
(1/8 in), to one end of the tubing assembly for the inner pump (#1 in Fig 146). Keep this tie wrap close to the inner pump head housing.
Tang
Fig 14-6 The assembled inner pump, with tubing in place, tang facing up
12. Press the pump head shell over the tubing, making sure not to pinch the
tubing at any point (Fig 14-6).
13. Turn the pump head over, so that the tang points away from you. Press a
piece of dampener tape over the centre slot on the rear of the inner pump
head, as shown in Figure 14-5 on page 52.
14. Align the holes in the inner pump head housing with the four threaded rods
that protrude from the rear of the unit. Slip the inner pump head over these
rods.
p 52
Attach the short piece of translucent tubing (#1 in Fig 14-7) to the port on
the outside of the 10-port valve. Do not allow kinks to form in this tubing.
Tang
Fig 14-7 The inner pump head in place on the rear of the unit
15. Use your fingers to turn the tang on the end of the pump head shaft (Fig 147) until it aligns with the tang on the end of the motor drive shaft. When the
two tangs are in alignment, the inner pump head sits flush against the unit,
with no gaps between the pump housing and the unit.
Note The pump head tang does not move easily. You will encounter some
resistance when turning the tang.
16. Now slip the outer pump head on, over the four threaded rods. Turn the tang
on the end of the outer pump head until it aligns with the tang on the inner
pump head. The tang does not move easily.
17. When the outer pump head is in place, replace the four wingnuts on the ends
of the threaded rods and tighten them hand tight.
18. Connect the pump tubing to the tray/lid assembly. See Table 14-2 on page 50
for a description of the connections.
Important
Always re-calibrate the pump after changing the pump head tubing.
For blot processing, see page 11 for a description of the pump calibration.
For gel staining, see page 28 for a description of the pump calibration.
p 53
Pre-programmed Blot Processing Protocols
Appendix A
Protocols
Pre-programmed Blot Processing
In the pre-programmed blot processing protocols, port numbers correspond to

the following reagents:
Port Reagent
Description
Block
A buffer, containing protein or detergent, that

blocks unbound sites on membranes and
prevents antibodies from sticking to unbound
regions. Non-fat dry milk, casein, Tween 20 or
BSA are often used.
Wash buffer
Tris-buffered saline containing Tween 20 (TBST)

or
Phosphate-buffered saline containing Tween 20
(PBST)
Primary (1) ab
Secondary (2) ab
Enhancement reagent
Air vent
Table A-1
Avidin or stepavidin conjugate or complex.

Enhances signal by adding more binding sites
for detection components.
Summary of Pre-programmed Blot Processing Protocols
Protocol
Name
Application
Steps
Approx. Time
(min.)
1. ECL Plus
ECL Plus Detection Kit
24
340
2. ECL
ECL Detection Kit
18
350
3. Standard
Immunodetection with 1 & 2 ab
4. Enhanced
Immunodetection with 1 & 2 ab and

avidin products
5. Clean
Clean reagent lines
210
13
285
10
Protocol 1. ECL Plus, for use with the ECL Plus Western Blotting Detection
system.
Table A-2
Step
p 54
Protocol 1, ECL Plus

Reagent
In-Port
Multiplier
Time (min.)
Block
60
Wash
Wash
1 Antibody
60
Wash
Wash
Wash
15
Wash
Wash
10
Wash
Step
Reagent
In-Port
Multiplier
Time (min.)
11
Biotinylated 2 antibody
60
12
Wash
13
Wash
14
Wash
15
15
Wash
16
Wash
17
Wash
18
Strepavidin HRP
60
19
Wash
20
Wash
21
Wash
15
22
Wash
23
Wash
24
Wash
Protocol 2. ECL, for use with the ECL Western Blotting Detection system. If
biotinylated 2 antibody is used in Step 9, then strepavidin HRP is used in Step
15.
Table A-3
Step
Protocol 2, ECL
Reagent
In-Port
Multiplier
Time (min.)
Block
60
Wash
15
Wash
Wash
1 Antibody
60
Wash
15
Wash
Wash
Biotinylated 2 ab or
2 ab HRP conjugate
60
10
Wash
15
11
Wash
12
Wash
13
Enhancement (optional)
60
14
Wash
15
15
Wash
16
Wash
17
Wash
18
Wash
p 55
Protocol 3. Standard, for Immunodetection with primary and secondary

antibodies
Table A-4
Step
Protocol 3, Standard
Reagent
In-Port
Multiplier
Time (min.)
Block
60
1 antibody
60
Wash
Wash
Wash
2 antibody conjugate
60
Wash
Wash
Wash
Protocol 4. Enhanced, for Immunodetection with primary and secondary

antibodies and avidin products
Table A-5
Step
p 56
Protocol 4, Enhanced
Reagent
In-Port
Multiplier
Time (min.)
Block
60
1 antibody
60
Wash
Wash
Wash
Biotinylated 2 antibody
60
Wash
Wash
Wash
10
A conjugate of:
Strep HRP or AP
Avidin HRP or AP
60
11
Wash
12
Wash
13
Wash
Protocol 5. Cleaning reagent line assemblies

Table A-6
Step
Protocol 5, Clean
Reagent
In-Port
Multiplier
Time (min.)
Distilled water or TBST
p 57
Pre-programmed Staining Protocols
Appendix B
Table B-1
Summary of Pre-programmed Gel Staining Protocols
Protocol
Name
Application
Steps
Approx. Time
(min.)
1. DNA Silver
DNA Gels
1.0-mm unbacked gels
0.5-mm backed gels
100
2. Protein Silver
SDS and Native

0.75- and 1.0-mm unbacked gels
0.5-mm backed gels
Immobiline DryPlate gels
14
160
3. Protein Silver
SDS and Native

14
180
4. Protein Silver
IEF
0.5- and 1-mm backed gels
18
300
5. Protein Coomassie SDS and Native

0.5-mm backed gels
320

250

460
8. Protein Coomassie IEF

0.5- and 1-mm backed gels
350
Protocol #1. DNA silver staining, for staining 1-mm thick, unbacked DNA gels
or 0.5-mm thick, DNA gels on plastic backing (ExcelGel or CleanGel). For use
with PlusOne DNA Silver Staining Kit.
Table B-2
Step #
p 58
Protocol 1, DNA silver staining
Solution
IN-port
OUT-port
Time (min.)
Fixing solution
30
Silver solution
30
Water
Developing solution
Stopping/preserving solution
30 (+ hold)
Protocol #2. Protein silver staining, for unbacked 0.75 and 1.0 mm thick SDS
and native polyacrylamide gels, or 0.5 mm thick SDS and native polyacrylamide
gels on plastic backing (ExcelGel or CleanGel). Can also be used to stain
Immobiline DryPlate gels. For use with PlusOne Silver Staining Kit, Protein.
Table B-3
Step #
Protocol 2, Protein silver staining

Solution
IN-port
OUT-port
Time (min.)
Fixing solution
30
Sensitizing solution
30
Water
Water
Water
Silver solution
20
Water
Water
Developing solution
10
Stop solution
10
11
Water
12
Water
13
Water
14
Preserving solution
30 (+ hold)
Protocol #3. Protein silver staining, for unbacked 1.5 mm thick SDS and native
polyacrylamide gels. For use with PlusOne Silver Staining Kit, Protein.
Table B-4
Step #

Solution
IN-port
OUT-port
Time (min.)
Fixing solution
30
30
Water
10
Water
10
Water
10
Silver solution
30
Water
Water
Developing solution
10
Stop solution
10
11
Water
12
Water
13
Water
14
Preserving solution
30 (+ hold)
p 59
Protocol #4. Protein silver staining: A silver staining protocol for carrier
ampholyte-containing IEF gels on plastic backing. For use with PlusOne Silver
Staining Kit, Protein.
Table B-5
Step #

Solution
IN-port
OUT-port
Time (min.)
Fixing solution #1
45
Fixing solution #2
30
5% Methanol
15
5% Methanol
15
30
5% Methanol
30
5% Methanol
30
Water
Water
10
Silver solution
20
11
Water
12
Water
13
Developing solution
14
Stop solution
10
15
Water
16
Water
17
Water
18
Preserving solution
30 (+ hold)
Protocol #5. Protein Coomassie staining, for 1.0 mm thick unbacked gels, or
0.5 mm thick SDS-polyacrylamide gels on plastic backing (ExcelGel or CleanGel).
For use with Coomassie tablets, PhastGel Blue.
Table B-6
Step #
p 60
Protocol 5, Protein Coomassie staining

Solution
IN-port
OUT-port
Time (min.)
Fixing solution
20
Destain solution
0.02% Coomassie Blue
60
Destain solution
10
Destain solution
30
Destain solution
80
Destain solution
80
Preserving solution
30 (+ hold)
Protocol #6. Protein Coomassie staining, for 0.75 mm thick unbacked SDSpolyacrylamide gels. For use with Coomassie tablets, PhastGel Blue.
Table B-7
Step #

Solution
IN-port
OUT-port
Time (min.)
Fixing solution
15
Destain solution
1.5
45
Destain solution
7.5
Destain solution
22.5
Destain solution
60
Destain solution
60
Preserving solution
30 (+ hold)
Protocol #7. Protein Coomassie staining, for 1.5 mm thick unbacked SDSpolyacrylamide gels. For use with Coomassie tablets, PhastGel Blue.
Table B-8
Step #

Solution
IN-port
OUT-port
Time (min.)
Fixing solution
30
Destain solution
90
Destain solution
15
Destain solution
45
Destain solution
120
Destain solution
120
Preserving solution
30 (+ hold)
p 61
Protocol #8. Protein Coomassie staining, for 0.5- or 1.0-mm thick carrier
ampholyte-containing IEF gels on plastic backing (Ampholine PAGplate or
CleanGel IEF). For use with Coomassie tablets, PhastGel Blue.
Table B-9
Step # Solution
IN-port OUT-port
Time (min.)
Fixing solution #1
20
Fixing solution #2
30
Destain solution
0.02% Coomassie Blue, 0.1% CuSO4
60
Destain solution
10
Destain solution
30
Destain solution
80
Destain solution
80
Preserving solution
30 (+ hold)
Protocol #9. Clean

Table B-10 Protocol 9, Clean
Step # Solution
p 62
IN-port OUT-port
Time (min.)
Distilled water
0.5
Distilled water
0.5
Distilled water
0.5
Distilled water
0.5
Distilled water
0.5
Distilled water
0.5
Distilled water
0.5
Distilled water
0.5
Distilled water
0.5
Blot Process Protocol Worksheet
Appendix C
Protocol #________
Blot Process Protocol Worksheet
Processor tray
Mini
Standard
Membrane type________________________________
Date__________
Number of Membranes______
Experiment_____________________________________________________________
____________________________________________________________________
Step # Solution
IN-port Multiplier Time (min.)
1
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
p 63
Gel Stain Protocol Worksheet
Appendix D
Gel Stain Protocol Worksheet
Protocol #___
Stain Silver
Coomassie
Gel
DNA
Protein
Tray
19 29 cm 29 35 cm
Step # Solution
1
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
p 64
Date______
Number of Gels___
Thickness______
Volume______ml
IN-port OUT-port Time (min.)
Specifications
Appendix E
Specifications
Blot Processing Trays

Mini
Standard
Styrene
10 50 ml per chamber
25 125 ml per chamber
Gel Staining Trays
PTFE (polytetrafluoroethylene)-coated stainless

steel
125 200 ml
250 400 ml
19 29 cm
29 35 cm
Reagent ports
Programmable parameters
Blot processing
Gel Staining
10
Input port, Volume multiplier, Time, Rock, Hold,
Beep
Input port, Output port, Time, Rock, Hold, Beep
Protocols
10 for Blot Processing

14 for Gel Staining
Protocol key
Removable, holds 1 protocol
Keypad
10-key membrane switch
Display
Liquid crystal display (LCD), two lines, 16

characters per line
Alarm
Programmable, audible beep
Operating temperature
440 C
Relative humidity
Less than 80% for 431 C,

decreasing linearly to 50% for 3140 C
Line voltage
115 V or 230 V
Frequency
60 Hz or 50 Hz
Maximum power
60 W
Dimensions (h w d)
22.5 40 51 cm (with Mini or Standard tray)

21 30 47 cm (with 19 29 cm tray)
21 35 47 cm (with 29 35 cm tray)
Weight, maximum
12.0 kg (with 29 35 cm tray)
Safety certifications
*CE, UL, CSA
*This declaration of conformity is only valid for the instrument when it is:
used in laboratory locations, and
used as delivered from Amersham Biosciences , except for alterations

described in the User Manual.
p 65
Customer Service Information

Technical Service and Repair
Amersham Biosciences offers complete technical support for all our
products. If you have any questions about how to use this product, or would like
to arrange to repair it, please call or fax your local Amersham Biosciences
representative.
Important repacking instructions

1.
Request a copy of the Amersham Biosciences Health and Safety

Declaration Form before returning the item. No items can be accepted for
servicing or return unless this form is properly completed.
2.
The rocker finger must be in the down position before repacking the unit,
but it must never be moved manually. To reposition it, turn the power off and
then on. During the diagnostic cycle, the rocker finger moves along its range
of motion. Turn the power off when the finger is in the down position, then
pack the instrument.
p 66
Ordering Information
Qty
Code No.
Processor Plus, Blot Processing System

Hoefer Processor Plus, base unit
Includes pump and reagent lines, protocol key
80-6444-04
Blot Processing Tray Pack

Includes tray support, disposable Mini and Standard
trays, lid with tubing, four reagent bottles and a rack,
waste bottle cap (38-430), spirit level, lid stand,
Membrane Processing Technical Manual
80-6444-23
Replacement Parts for Blot Processing

Blot Processing tray, disposable Mini (3/pkg)
1 pkg 80-6444-42
Blot Processing tray, disposable Standard (3/pkg)
1 pkg 80-6444-61
Blot Processing Tubing Set, complete

Includes lid manifold with valves, pump tubing,
dampeners, couplings, and reagent lines
1 kit 80-6448-22
Reagent line Set
10
80-6342-58
Pump tubing Set
1 set 80-6448-03
Reagent bottles, 4/pkg
1 pkg 80-6448-79
ECL and ECL Plus Reagents

ECL Western blotting reagents
For 1000 cm2 membrane
1 kit
1 kit
1 kit
RPN2109
RPN2209
RPN2106
ECL Western blotting analysis system
RPN2108
ECL Plus Western blotting detection reagents

RPN2132
Hybond-C pure
20 20 cm, sheets
20 cm 3 m, roll
30 cm 3 m, roll
10
1
1
RPN2020W
RPN203W
RPN303W
Hybond-P
20 20 cm, sheets
30 cm 3 m, roll
10
1
RPN2020F
RPN303F
Hybond ECL
6 8 cm, sheets
20 20 cm, sheets
30 cm 3 m, roll
50
10
1
RPN68D
RPN2020D
RPN303D
Hybond-C extra
20 20 cm, sheets
20 50 cm, sheets
20 cm 3 m, roll
30 cm 3 m, roll
10
5
1
1
RPN2020E
RPN3050E
RPN203E
RPN303E
Protein Membranes
p 67
Qty
Code No.
Processor Plus, Gel Staining System

Hoefer Processor Plus, base unit
Includes pump and reagent lines, protocol key
80-6444-04
Gel Staining Tray Pack (19 x 29 cm tray)

Includes tray support, PTFE-coated staining tray, lid,
magnets, gasket, level and Gel Staining Protocol Guide
80-6444-80
Gel Staining Tray Pack (29 x 35 cm tray)

Includes tray support, PTFE-coated staining tray, lid,
magnets, gasket, level and Gel Staining Protocol Guide
80-6445-18
80-6444-99
Glass lid, 19 x 29 cm
80-6341-82
Tray gasket, for 19 x 29 cm tray
80-6341-44
Tray support, for 19 x 29 cm tray
80-6344-29
80-6445-37
Glass Lid, 29 x 35 cm
80-6341-63
Tray gasket, for 29 x 35 cm tray
80-6341-25
Tray support, for 29 x 35 cm tray
80-6345-05
Splash Guard for delivery port
80-6342-01
Magnets
80-6342-20
Replacement Parts for Gel Staining

Staining Tray, PTFE-coated, 19 x 29 cm
Staining Tray, PTFE-coated, 29 x 35 cm
Gel Staining Tubing Set, complete

Includes tubing for tray and pump, QuickFit couplings,
reagent lines and dampeners
Reagent line Set
Pump Tubing Set
1 set 80-6445-56
10
80-6342-58
1 set 80-6448-03
Staining Kits
PlusOne DNA Silver Staining Kit
17-6000-30
PlusOne Silver Staining Kit, Protein
17-1150-01
Coomassie tablets, PhastGel Blue
40
17-0518-01
Protocol key
80-6342-77
Power cord, 115V
80-6106-03
Power cord, 230V
80-6230-10
Serial printer cable + adaptor
80-6427-70
Spirit Level
80-6087-60
Protocol Guide: Automated Silver and Coomassie

Staining of Polyacrylamide Gels
80-6343-34
Technical Manual: Membrane Processing
80-6447-27
Quick Reference Card
80-6447-08
Processor Plus User Manual
80-6446-89
Additional Replacement Parts and Accessories
p 68
index
H
Hold 18, 34
NNumerics
10-port valve 2
keypad 2, 5
adding a step 19, 20, 36, 37

arrow keys 5
autoclave, avoiding 47
LCD 2
level tray position 15, 32
magnets 3
Main menu 5
manual pump operation
blot processing 22
gel staining 38
multiplier, for minimum volume 18, 34
Beep 15, 18, 31, 34

blot processing 825
clean protocol 16
leveling tray 9, 23
manual pump operation 22
preparation 13
print protocol 15
protocols 5457
pump calibration 11
reagent volume 18, 23
setup parameters 2225
step variables 17
tray sizes 3, 23
worksheet 63
C
clean protocol
blot processing 16
gel staining 32
cleaning exterior and trays 47
D
deleting a step 20, 21, 36, 37
E
EDIT/SET key 5, 7
editing
a protocol in progress 20, 36
protocol name 17, 33
step variables 17, 33
end-of-step options 17, 33
G
gel staining 2640
clean protocol 32
leveling tray 27, 39
manual pump operation 38
preparation 30
print protocol 31, 40
protocols 5862
pump calibration 28
reagent volume 34, 39
setup parameters 3840
step variables 33
tray sizes 3, 26, 39
worksheet 64
O
operating software navigation 57
P
PAUSE mode 15, 32
peristaltic pump 2
tubing 2, 50
pivot ball assembly 2
Port In 18, 34
Port Out 34
power outage 21, 37, 43
preparing
gels 30
membranes 13
printing 1, 4
protocol
blot processing 15
gel staining 31
Processor Plus
components 2
specifications 65
Protocol 5
Clean, blot processing 16
Protocol 9
Clean, gel staining 32
Protocol key 1, 2
slot 2
use 41
p 69
protocols
adding a step 19
blot processing 5457
cleaning 16, 32
deleting a step 20
displaying volume 23
editing 19
gel staining 5862
interrupting 15, 31
printing
blot processing 24
gel staining 40
printing volume 24
start operation 14, 15, 30, 31
termination 15, 32
pump calibration
blot processing 11
gel staining 28
pump head tubing
changing 50
PVDF
chemical susceptibility 48
Q
Quick-Fit couplings 9, 27
R
reagent lines 2
reagent tubing assembly 49
changing 49
cleaning 16, 32
Recover, tray position 15, 32
Rock 18, 34
rocker finger 2
S
self-diagnostic cycle 5
Setup 1
blot processing 22
gel staining 38
Setup 2
blot processing 23
gel staining 39
Setup 3
blot processing 23
gel staining 39
Setup 4
blot processing 23
gel staining 27
Setup 5
blot processing 24
gel staining 40
Setup 6
blot processing 24
gel staining 28
Setup 7
blot processing 11
Setup menus 7
p 70
Setup parameters
blot processing 2225
gel staining 3840
silver stain residue 47
software navigation 57
specifications 65
spirit level 2
splash guard 3
cleaning 48
step variables
blot processing 17
gel staining 33
Table
blot processing 18
gel staining 34
stopping a protocol 15, 32
T
tray gasket replacement 48
tray level
blot processing 23
gel staining 39
tray sizes
and volume 23, 26, 39
blot processing 23
gel staining 26, 39
troubleshooting 4345
V
valves, on blot processing lid 13
volume delivery
blot processing 23
gel staining 30, 39
W
worksheet
blot processing 63
gel staining 64
Amersham Biosciences
UK Limited Amersham Place Little Chalfont Bucks HP7 9NA England

AB SE-751 84 Uppsala Sweden
Inc 800 Centennial Avenue PO Box 1327 Piscataway NJ 08855 USA
Europe GmbH Postfach 5480 9 D-79021 Freiburg
ECL, ExcelGel, CleanGel, Hoefer, Hybond, PlusOne, and Rainbow are trademarks of Amersham Biosciences Limited or its subsidiaries.
Amersham and Amersham Biosciences is a trademark of Amersham plc
Coomassie is a trademark of ICI plc
Nalgene is a trademark of Nalge Nunc International
Tween is a trademark of ICI Americas, Inc.
All goods and services are sold subject to the terms and conditions of sale of the company within the Amersham Biosciences group which
supplies them. A copy of these terms and conditions is available on request.
Amersham Biosciences 1999All rights reserved.
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user manual

DNA/Protein Labeling, Hybridization & Detection

Introduction to Processor Plus . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Navigating the Operating Software . . . . . . . . . . . . . . . . . . . . . . . . 5

Setting Up for Blot Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Leveling the tray . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Operating Instructions for Blot Processing . . . . . . . . . . . . . . . . . 13

Editing Blot Processing Protocols . . . . . . . . . . . . . . . . . . . . . . . . 17

Setup Parameters for Blot Processing . . . . . . . . . . . . . . . . . . . . . 22

Manual pump operation . . . . . . . . . . . . . . . . . . . . . . . 22

Setting Up for Gel Staining . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Hoefer Processor Plus

Operating Instructions for Gel Staining . . . . . . . . . . . . . . . . . . . . 30

11 Gel Staining Setup Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Manual pump operation . . . . . . . . . . . . . . . . . . . . . . . 38

12 Using the protocol key . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

Pre-programmed Blot Processing Protocols . . . . . . . . . . . . . . . . 54

Pre-programmed Staining Protocols . . . . . . . . . . . . . . . . . . . . . . 58

Blot Process Protocol Worksheet . . . . . . . . . . . . . . . . . . . . . . . . 63

Gel Stain Protocol Worksheet . . . . . . . . . . . . . . . . . . . . . . . . . . 64

Hoefer Processor Plus

Safety Warnings and Precautions

Safety Warnings and Precautions

Hoefer Processor Plus

Introduction to Processor Plus

Introduction to Processor Plus

the electronic and mechanical parts, encased in a metal chassis. The

A peristaltic pump which works in conjunction with the 10-port valve to

Memory on the Processor Plus that can hold up to 24 protocols: 10 for

the volume of reagents used in each step

the time, in minutes, for each step

Hoefer Processor Plus

Fig 2-1 Processor Plus components and accessories

Hoefer Processor Plus

Provides the rocking motion for agitating fluid.

Pivot ball assemblies

Fit into the sockets on the bottom of the tray

Displays protocol status and program steps.

Provides keys to program protocols and control

Protocol key slot

Accepts the protocol key

Connects reagent bottles to 10-port valve.

Selects reagent line to connect to peristaltic

Pumps fluids from the 10-port valve into the tray

Carries reagents through peristaltic pump.

Stores one protocol in removable memory.

Assists in leveling trays.

Hoefer Processor Plus

Connecting the Processor Plus to a serial printer

The serial printer must have the following settings:

To connect the Processor Plus to the serial printer:

An example of a protocol printout

RS232C serial port

9-pin cable connector

Fig 2-2 Locating the RS232C serial port

Hoefer Processor Plus

Navigating the Operating Software

Navigating the Operating Software

Program EDIT/SET, ADD, DEL

START, STOP, PAUSE

Edit protocols and the variables in each step

Fig 3-1 The Keypad

-> Process blot

Hoefer Processor Plus