GE Ettan IPGphor 3 User manual

GE Healthcare
Ettan IPGphor 3
Instrument User Manual
Ettan

Important user information
Allusersmustreadthisentiremanualtofullyunderstand
the safe use of Ettan IPGphor 3.
WARNING!
The following WARNING signs highlight instructions that
mustbefollowedtoavoidpersonalinjury.Itisimportant
not to continue until all stated conditions are met and
clearly understood.
WARNING! Lethal high voltage above 1 kV.
WARNING! Read the instructions to avoid
hazardous conditions.
CAUTION!
The Caution sign highlights instructions that
must be followed to avoid damage to the
productorotherequipment.Itisimportantnot
to continue until all stated conditions are met
and clearly understood.
Note The Note sign is used to indicate information
important for trouble-free and optimal use of
the product.
CE certification
This product meets the requirements of applicable CE-
directives. A copy of the corresponding Declaration of
Conformity is available on request.
The CE symbol and corresponding declaration of
conformity is valid for the instrument when it is:
– used as a stand-alone unit, or
– connected to other CE-marked GE Healthcare
instruments, or
– connected to other products recommended or
described in this manual, and
– used in the same state as it was delivered from GE
Healthcare except for alterations described in this
manual.

Ettan IPGphor 3 Instrument User Manual11-0034-58 Edition AB v
Contents
1 Ettan IPGphor 3 Isoelectric Focusing System function and
description
1.1 Unpacking ............................................................................................................9
1.2 System components .......................................................................................9
1.3 Specifications ...................................................................................................17
1.4 Associated documentation ........................................................................18
2 Instrument set up
2.1 Placing the instrument .................................................................................19
2.2 Power connection ..........................................................................................19
2.3 Serial port connector for a computer connection ..........................20
3 Operating instructions
3.1 Power up .............................................................................................................21
3.1.1 Ettan IPGphor 3 control panel......................................................................21
3.2 Using the Ettan IPGphor Cup Loading Manifold ..............................23
3.2.1 Rehydrating Immobiline DryStrip in the Rehydration Tray.............23
3.2.2 Positioning the manifold on the Ettan IPGphor 3.................................23
3.2.3 Positioning the IPG strips in the manifold................................................23
3.2.4 Sample cups.........................................................................................................24
3.2.5 Electrode paper wicks......................................................................................24
3.2.6 Positioning the electrodes..............................................................................24
3.2.7 Loading samples into the sample cups...................................................24
3.3 Using fixed-length Ettan IPGphor 3 strip holders ............................25
3.3.1 Preparing the strip holder(s)..........................................................................25
3.3.2 Optional: Sample rehydration under voltage........................................27
3.3.3 Optional: Applying electrode pads prior to IEF......................................28
3.3.4 Optional: Applying sample after rehydration........................................28
3.3.5 Positioning the strip holders..........................................................................29
3.3.6 Closing the safety lid.........................................................................................30
3.4 Running a pre-programmed protocol from the PC ........................32
3.4.1 Ettan IPGphor 3 Control Software...............................................................32
3.4.2 Starting the Ettan IPGphor 3 Control Software.....................................33
3.5 Creating, editing, and running protocol programs from the
Ettan IPGphor 3 control panel ..................................................................37
3.5.1 Protocol parameters.........................................................................................37
3.5.2 Editing protocol parameters..........................................................................38
3.5.3 Starting isoelectric focusing from the Ettan IPGphor 3 control
panel........................................................................................................................44
3.5.4 Pausing or stopping a protocol....................................................................48
3.5.5 Printing a log of instrument conditions....................................................48

Contents
vi Ettan IPGphor 3 Instrument User Manual 11-0034-58 Edition AB
4 Care and maintenance
4.1 Cleaning the Ettan IPGphor 3 ...................................................................49
4.2 Cleaning procedures .................................................................................... 50
4.2.1 Ceramic strip holders/manifold...................................................................50
4.2.2 Manifold Light......................................................................................................51
4.2.3 Electrodes...............................................................................................................51
4.3 Replacing fuses .............................................................................................. 52
5Troubleshooting
6 Customer service information
6.1 Technical service and repair ....................................................................57
6.2 Ordering information ...................................................................................57

Ettan IPGphor 3 Isoelectric Focusing System function and description 1
Ettan IPGphor 3 Instrument User Manual11-0034-58 Edition AB 7
1 Ettan IPGphor 3 Isoelectric Focusing System function
and description
TheEttan™IPGphor™ 3Isoelectric FocusingSystemperformsthefirstdimension
isoelectric focusing (IEF) step in 2-dimensional (2-D) electrophoresis. The system
comprises the Ettan IPGphor 3 unit, combined with separate strip holders or a
manifold. Two types of manifolds are available; the ceramic manifold and the
lightmanifold.TheIEF separationprotocolsareprogrammed,run and controlled
from the Ettan IPGphor 3control panel or from a PC running the Ettan IPGphor
Control Software.
The Ettan IPGphor 3 Isoelectric Focusing System includes the following features:
• an integrated high-voltage DC power supply delivering up to 10 kVolts
• temperature control by Peltier elements
• light exclusion during the run. Compatible withCyDye™ labeled proteins
and other light sensitive stains
• IEF runs are programmed from the Ettan IPGphor 3 controlpanel with up to
ten user-defined IEF protocols, each with up to 9 steps per protocol
• programmablefunctionsincluding:rehydrationtime, platformtemperature,
current limit, voltage limit foreach step, voltage gradient or step and step
duration
• Ettan IPGphor 3 Control Software. From a PC, protocols are created,
graphically displayed and stored onthe Ettan IPGphor3 unit. The software
records the run parameters over time and presents data as graphs and log
files. Data is saved or can be exported to Microsoft® Excel
• Ettan IPGphor 3 Control Software allows easy programming and
recommended protocols are generated by providing instrument
configuration, IPG strip length and pH gradient
• strip holders for rehydration and automated running
• Ettan IPGphor Cup Loading Manifold for easy running of up to 12 IPG strips.
Cup loading improves focusing results particularly when using basic IPG
strips
IMPORTANT! The Ettan IPGphor 3 system is intended for research use only
and should not be used in any clinical or in Vitro procedures for diagnostic
purposes.

1Ettan IPGphor 3 Isoelectric Focusing System function and description
8Ettan IPGphor 3 Instrument User Manual 11-0034-58 Edition AB
• for larger sample volumes the Ettan IPGphor Cup Loading Manifold
facilitates paper bridge loading and in gel rehydration loading
The Ettan IPGphor 3 Control Software hasan easy to use interface to the Ettan
IPGphor 3 instrument and providesenhanced protocol generation, presentation,
and storage.
Recommended standard protocols can be retrieved and used by the user simply
providing the instrument configuration, IPG strip length and pH gradient. Using
the advanced mode setting, earlier made custom protocols or entire new
protocolsaremade.Allprotocolsareedited and saved for later use. Theselected
protocol is loaded to Ettan IPGphor 3 Isoelectric Focusing Instrument.
During the run the control software monitors and records the running
parameters. All data is displayed as graphs and log file tables. When the run is
complete, graphandlog filesareprintedor/and saved. Ifdesired,thelogfilesare
exported to programs such as Microsoft Excel.
TheEttanIPGphor3ControlSoftwarecontrolsuptofourEttanIPGphor3 unitsat
one time, each running a different set of run parameters.
IPG strip manifolds are available in two models:
• One produced from a ceramic material providing greater temperature
uniformity
• One produced from a light polymeric material for less critical
experimentation
Both are designed for analytical analysisusing cup application and preparative
runs applying sample to the gel during the rehydration step or by paper bridge
loading. Using the Manifold Immobiline DryStrips are rehydrated in the
Rehydration Tray.
Fixed length strip holders are available. Once the IPG strip is placed inthe fixed-
length strip holder, no further handling is required. The holder is placed on the
Ettan IPGphor 3 electrode platformfor rehydration and can be immediately
followedbyisoelectricfocusing.Thesampleisintroduced during the rehydration
step. The Ettan IPGphor 3 accommodates up to 12 strip holders for any one
protocol.
IPG strips are available in five lengths 7,11, 13, 18, and 24 cm, and a number of
pH ranges, several linear and non-linear (listed in section 6.2 Ordering
information).

Ettan IPGphor 3 Isoelectric Focusing System function and description 1
Ettan IPGphor 3 Instrument User Manual11-0034-58 Edition AB 9
1.1 Unpacking
Carefully unpack all items delivered and make sure that all items are present by
comparing the contents with the packing list. If any part is missing, please
contact yourlocal GEHealthcare salesoffice.Inspectallcomponents.Ifanypart
appears damaged, please contact the courier immediately. Please keep all
packing material and use if damaged parts need to be returned for repair or
replacement.
1.2 System components
Fig 1-1. The Ettan IPGphor 3 instrument.
Positive (anode)
electrode area
Negative (cathode)
electrode area
Control panel
Safety lid

1Ettan IPGphor 3 Isoelectric Focusing System function and description
10 Ettan IPGphor 3 Instrument User Manual 11-0034-58 Edition AB
Fig 1-2. Light protective cover.
Fig 1-3. Location of mains power switch and serial port.
Light protective
cover
/
L
The mains power
switchislocatedonthe
rear panel.
Serial port (RS232) for
connection to a PC

Ettan IPGphor 3 Isoelectric Focusing System function and description 1
Ettan IPGphor 3 Instrument User Manual11-0034-58 Edition AB 11
Fig 1-4. Components of the Ettan IPGphor Cup Loading Manifold system. Only one of each
item shown.
A.
B.
C.
E
F
H.
I.
D.
G
J
A. Manifold, ceramic or light F. Pre-cut paper bridges
B. Pre-cut electrode wicks G. Sample cup insertion tool
C. Electrode assembly H. Cleaning solution
D. Sample cups I. Forceps
E. Cleaning brush J. Spirit level

1Ettan IPGphor 3 Isoelectric Focusing System function and description
12 Ettan IPGphor 3 Instrument User Manual 11-0034-58 Edition AB
Fig 1-5. Strip holders.
Note: All strips (and holders) used at any one time must be of the same length.
Fig 1-6. Lid adapter.
Five strip holder lengths are
available—7, 11, 13, 18, and 24 cm—
one for each IPG strip length.

Ettan IPGphor 3 Isoelectric Focusing System function and description 1
Ettan IPGphor 3 Instrument User Manual11-0034-58 Edition AB 13
Control panel The Ettan IPGphor 3 is controlled by a 7-key membrane keypad. Instrument
status is indicated on the LCD screen.
LCD screen The main screen is “Protocol #1, Name.” The default location of the cursor is
always under the protocol number “1.”
Select any protocol by pressing the up and down arrow keys to display the
number of the desired protocol. Once the selected protocol is started, the LCD
screen indicates the parameters of the step currently being carried out.
In “edit mode” the LCD displays the programmable parameters. Position the
cursor in the field to be edited using the right and left arrow keys and adjust the
value by pressing the up and down arrow keys.
COMMAND keys •TheEDIT key switches the display to "edit mode", in which protocol steps
can be programmed (see section 3.5). Pressing the EDIT key in edit mode
toggles between the identification screen withgeneral settings for all
steps andthe settings in thethreefirst protocol steps. Thekeyalso allows
the estimated run time remaining to be viewed while the unit is operating.
•Theleft arrow key moves the cursor to the left. Moving the cursor off the
screen to the left repositions the cursor at the left side of the next row. On
the bottom row the cursor is repositioned on the left side of the top row.
•Theright arrow key moves the cursor to the right. Moving the cursor off
thescreento the rightrepositionsthecursor at the leftofthenext row.On
the bottom row the cursor is repositioned on the left side of the top row.
•Theuparrowkeyincreasesthevalueoftheselectedfieldordigit,andthe
down arrow key decreases the value of the selected field or digit.
Exceptions when the cursor is positioned to the left under the Step
number S1-S9, down arrow change the display to the next group of three
protocol steps. Up arrow change to the previous group of three protocol
steps. During electrophoresis, the up/down arrow keys are used to toggle
between VhS, VhT, and Hrs.
•TheSTART key begins the selected protocol.
•TheSTOP keypauses the protocol. Pressing the STOP key a second time
cancels the protocol in progress.
HV ON indicator lamp The HV ON lamp indicates that the high voltage power supply is on and
isoelectric focusing is in progress. This lamp is not illuminated during the
rehydration phase of a protocol.
Serial port RS 232 Serial port for connection of a PC.

1Ettan IPGphor 3 Isoelectric Focusing System function and description
14 Ettan IPGphor 3 Instrument User Manual 11-0034-58 Edition AB
Platform The platform accommodates one manifold for the first dimension isoelectric
focusing (IEF) run.
Up to 12 fixed-length strip holders can be placed on the platform for rehydration
and IEF.
The embedded electrode areas provide the electrical connection between strip
holder or manifold electrodes and the integral power supply.
Platform temperature is controlled by Peltier thermoelectric modules.
Electrode areas Both electrode areas are gold-plated copper. Placing a manifold or a strip holder
so that it bridges both electrode areascompletes the electrical circuit (once the
safety lid is in position).
Safety lid The safety lid must be properly closed before power is applied.
Light protective cover When analyzing proteins labeled with light sensitive stains like CyDye®, a light
protective cover (Fig 1-2) is used. The cover is applied by magnetic force but is
easy to partially remove for checking the isoelectric focusing procedure,
especially the migration of bromo-phenol-blue at start.
Lid adapter for strip
holders When using the Ettan IPGphor 3 standard strip holders a lid adapter (Fig 1-6) must be used to apply the correct amount of pressure to the lids of the Ettan IPGphor 3
strip holders.
Ettan IPGphor 3
Control Software Ettan IPGphor 3 Control Software allows the user to control the Ettan IPGphor 3 Isoelectric Focusing Instrument. The software providesan enhanced functionality
in the areas of data presentation, data storage, and protocol handling. The PC is
connected to the Ettan IPGphor 3 over a serial cable or USB converter.
Ettan IPGphor 3 Control Software controls up to four Ettan IPGphor 3 units at one
time, each running a different set of run parameters.
Manifolds
Ettan IPGphor Cup
Loading Manifold
Ceramic
The manifold (Fig 1-4) is made of aluminum oxide ceramic for efficient heat
transfer and temperature control during IEF. The manifold accomodates up to 12
IPG strips from 7 cm to 24 cm long. Immobiline DryStrip is placed with the gel side
facing up.
Samples are applied in a cup. Cup loading has been found to improve protein
focusing patterns, particularly on basic IPG strips (pH 6-9 and 6-11). Larger
sample volumes can be applied by gel rehydration loading or anodic paper
bridge loading.
Protrusions along the channel inside the manifold align the rehydrated IPG strip,
keeping it straight and centered when placed inside the manifold. The manifold
has a coating to minimize protein adsorption. The unit may also be used for IPG
strip equilibration prior to second dimension electrophoresis.
The manifold is fragile and should be handled with care.

Ettan IPGphor 3 Isoelectric Focusing System function and description 1
Ettan IPGphor 3 Instrument User Manual11-0034-58 Edition AB 15
Ettan IPGphor Cup
Loading Manifold Light The manifold (Fig 1-4) is made of polymers polycarbonate and ABS (acrylonitrile- butadiene-styrene). The light manifold and the ceramic manifold have the same
design/measurementswith only the choice of materials the only difference. The
manifold accommodates up to 12 IPG strips from 7 cm to 24 cm long.
The unit may also be used for IPG strip equilibration prior to second dimension
electrophoresis.
Electrode Assembly These electrodes fit to both the ceramic and light manifold. The movable
electrodes (Fig 1-4) can be placed along the manifold to fit from 7 to 24 cm long
IPG strips.
Electrode pins make contact with the power supply electrode areas on the
platformof theEttanIPGphor3. The electrodeshavea platinum wirethat isstrung
across the bottom of the electrode teeth to provide electrical contact to the IPG
strips. The hold down teeth for paper bridge loading are found along the opposite
length of the electrode. Cams on the sides of the electrode secure the position.
Sample Cups Sample cups (Fig 1-4) can be placed along the length of the Ettan IPGphor
Manifold that is not blocked by a centering protrusion.
The sample cups are supplied in strips of 6 for easy handling and placement.
Each sample cup accommodates sample volumes of up to 150 µl.
IEF electrode paper
wicks The small, precut rectangular wicks (Fig 1-4) must be placed at both the anodal and cathodal ends of the rehydrated IPG strips just under the electrodes.
The wicks absorb excess water, salts, and proteins with pI values that lie outside
the pH range of the IPG strip.
Paper bridge loading
pads Paper Bridge loading pads (Fig 1-4) are used to load larger volumes of sample (375-500 µl). The bridges are 0.8 cm ×5.0 cm in size including the pointed ends.
One end of the pad is in contact with the IPG strip and is held in position by the
hold down teeth of the electrode assembly. The other end of the bridge loading
pad makes contact with a paper wick placed under the platinum wire of the
electrode assembly.
Immobiline DryStrip
Reswelling Tray When using the manifold the Immobiline DryStrip Reswelling Tray is required for proper strip rehydration. The longer Tray fits 7-24 cm strip lengths.
Strip holders The strip holders are made of aluminum oxide ceramic with electrodes of
platinum on titanium. The ceramic is very brittle so the holders are fragile and
must be handled with care.
The ceramic is treated with a special coating to minimize protein binding and
must be cleaned only with the Ettan IPGphor Cleaning Solution supplied to retain
that coating.
Strip holders are available for the following IPG strip lengths: 7, 11, 13, 18, and
24 cm.
Each fixed-length strip holder base holds a single IPG strip throughout
rehydration and isoelectric focusing. A matching length holder is available for
each size strip.

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16 Ettan IPGphor 3 Instrument User Manual 11-0034-58 Edition AB
Sample application
wells Each of the two wells accepts up to 15 µl of sample (7.5 µl on either side of the strip) in excess of the rehydration volume (i.e. 30 µl maximum for both wells).
Introduce the sample through the wells if it is not included in the rehydration
solution.
Cover The cover is made of acrylic and protects the IPG strip during rehydration. The
shape of the underside of the cover ensures electrical continuity during IEF by
pressing the strip against the electrode while allowing electrolysis gases to
escape.
Rehydration and separation progresscan be monitored visually through the clear
cover.

Ettan IPGphor 3 Isoelectric Focusing System function and description 1
Ettan IPGphor 3 Instrument User Manual11-0034-58 Edition AB 17
1.3 Specifications
Working surface
User interface
Operating environment
Electrode areas Gold-plated copper
Capacity Up to 12 fixed-length strip holders or one
manifold
Platform temperature 15–30 °C ±2 °C
Control panel 7-key membrane keypad.
Liquid crystal display (LCD) 4 lines, 24 characters per line
Programmable parameters Rehydration time, platform temperature,
maximum current limit per strip, voltage
limit in each step, voltage step or
gradient, and step duration.
Protocol capacity 10 protocols, with up to 9 steps each
Serial port RS232, 1200 or 9600 baud, 8 data bits 1
stop bit, no parity, no flow control.
9600 baud is mandatory for connection
with Ettan IPGphor 3 Control Software.
Temperature 15–32 °C
Relative humidity 0–70%*
* High relative humidity may result in condensation forming on the platform sur-
face. Runs conducted at a platform temperature of 20 °C and relative humidity
less than 70% will generally not cause condensation. Platform temperatures
greater than 20 °C allow for higher relative humidity without condensation. Envi-
ronments for which condensation occurs on the platform surfacemay vary. If
condensation occurs, the unit may require conditioned air to reduce tempera-
ture and relative humidity.

1Ettan IPGphor 3 Isoelectric Focusing System function and description
18 Ettan IPGphor 3 Instrument User Manual 11-0034-58 Edition AB
Power requirements
Electrophoresis
Physical parameters
Safety
1.4 Associated documentation
•TheEttan IPGphor 3 Software User Manual contains instructions for
controlling Ettan IPGphor 3 Isoelectric Focusing Unit from a PC.
•TheEttan IPGphor Cup Loading Manifold User Manual contains instructions
for first-dimension isoelectric focusing of proteins on IPG strips.
•TheEttan IPGphor 3 Safety Handbook contains safety information.
• Instructions attached to each package of Immobiline DryStrip.
Mains supply voltage 100-240 V AC ±10%
Frequency 50/60 Hz
Power consumption 230 VA
High voltage Up to 10 kV
Current Up to 1.5 mA
Dimensions (h ×w ×d) 160 ×278 ×471 mm
Weight 8.3 kg
Safety features Automatic voltage cutoff when safety lid
is opened
Safety certifications CE

Instrument set up 2
Ettan IPGphor 3 Instrument User Manual11-0034-58 Edition AB 19
2 Instrument set up
2.1 Placing the instrument
Positiontheinstrumentonaflatsurfacewiththespiritlevelinthecenter.Turnthe
leveling feet as necessary to make the instrument level and stable.
2.2 Power connection
Two power cords are supplied: one cord has a “North American” style (UL817)
3-prongedplugfor115V~poweroutlets,andtheotherhasa“Central European”
style (CEE7/VII) plug for 230 V~ power outlets.
1 Select the cord with the appropriate plug for the power outlet in your
laboratory. If neither of these cords are suitable for your power outlets,
obtain a detachable cord with an IEC/320/C13 (CEE22/V) outlet.
2 Plug the connectors into the power cord receptacle on the rear panel and
into a properly grounded power outlet.
WARNING! The vents at the front, back, and bottom of the instrument must
not be obstructed. Air must be free to circulate for the cooling apparatus to
function properly. Minimum free space behindthe rear panel should be
10 cm.
IMPORTANT! Select a place for Ettan IPGphor 3 where it is possible to access
the mains power switch on the rear panel of the instrument.

2Instrument set up
20 Ettan IPGphor 3 Instrument User Manual 11-0034-58 Edition AB
2.3 Serial port connector for a computer connection
TheRS232serialportforacomputerconnectionisattherearoftheunit.Thetype
ofcablerequired(shieldedstraightserialorshieldednullmodem)dependsonthe
type of device (DTE or DCE)that it is connected to:
• If the computer is configured to receive data on pin 2 and transmit on pin 3,
a regular straight serial cable is required.
• For any other configuration, a null modem cable is required.
Pin number assignmentsand device set up details follow:
To set the baud rate:
1PresstheUp and Down arrows together to access theBaud menu.
2UsetheUp or Down arrows to set the baud rate.
3UsetheRight arrow to exit to the main menu.
Ettan IPGphor 3 RS232 signal and pin number assignments:
Pin 2 Transmit
Pin 3 Receive
Pin 5 Ground
Other pins Not connected
The Ettan IPGphor 3 requires these settings in the device receiving data:
Baud rate 9600
Data bits 8
Stop bit 1
Start bit 1
Parity None
Flow control None
Serial Port Setup
Baud Rate: 9600
Set Up or Dn Exit>