Thermo Scientific MATRIX PLATEMATE 2x3 User manual

Part No. 801-10010

1 Introduction
The Thermo Scientific Matrix PlateMate™ 2x3 Liquid Transfer Device is a
member of the Thermo Scientific Matrix PlateMate line with (8)
interchangeable air and positive displacement pipetting systems. A small
footprint and unprecedented operator safety mechanisms make it the instrument
of choice for a wide range of liquid-handling applications. This platform offers all
the tools and flexibility for assay development and low to medium throughput.
The device can easily be implemented as a core pipetting system in any
integrated robotic environment.
The Thermo Scientific Matrix PlateMate 2x3 combines a stepper-motor
controlled stage (X and Y motion) with a vertically adjustable pipetting head,
enabling reliable tip access into all standard lab ware (96 – 1536). It also has the
added capability to perform serial dilutions in both portrait or landscape layouts
(96 and 384 well plates).
With user-friendly software running under MS-Windows (ControlMate PlateMate
2xY ver. 1.1.2 or newer), operators in chemical, biological, physical and in-vitro
medical laboratories can quickly and easily customize specific laboratory
protocols.
1.1 System Features
The Thermo Scientific Matrix PlateMate 2x3 base unit provides a universal
platform upon which a flexible automated workstation is built. This platform
supports a deck offering simultaneous vessel placement for up to six vessels in
any user-definable position, deep or shallow well plates,any of the standard
interchangeable pipetting heads, and a host of other system accessories.
User Manual 1

Chapter 1 Introduction
Figure 1: Thermo Scientific Matrix PlateMate 2x3 System
A base unit includes these following standard features:
xA variable-position (portrait or landscape) microplate deck for easy plate or
reservoir placement onto the device.
xHigh-resolution linear plate movement allows accurate (r0.05mm) microplate
positioning of 96, 384, 864, and 1536 well plates.
xTwo power-interrupt safety sensors guard access to the pipetting area:
Sliding door that stops vertical pipettor movement if it is opened during an
operation
Front light curtain that stops vertical pipettor movement if it detects motion
(e.g., an operator’s hand) entering the pipetting area during an operation.
xStepper motors provide operator safety and prevent instrument damage.
xTwo peristaltic pumps with integrated liquid level detection enable onboard
reagent or wash fluid replenishment.
xOne vacuum pump provides waste fluid removal from the tip wash station,
which reduces cycle time and sample carryover.
x(8) Interchangeable pipetting heads are a powerful feature that provides
optimal performance and flexibility for either 96 or 384 channel pipetting
applications. Pipetting heads can be easily replaced as needed depending on
the plate format or volume range requirements.
xOne switched 24 volt DC supply outlets for additional externally controlled
devices.
2Thermo Scientific PlateMate™ 2x3

1.2 About this Manual
Efficient pipette tip replacement
Matrix D.A.R.Ts¥(Disposable Automated Research Tips) are compatible with the
Thermo Scientific Matrix PlateMate 2x3 pipetting heads. Tips held in the
disposable magazine are placed on the device and seal directly against a
silicone pad. This forms a definitive seal without the use of conventional tip
fittings or 0-rings. In addition to providing a cleaner seal that presents less
opportunity for contamination, this method provides the added benefit of ensuring
uniform tip height across all 96/384 pipette tips, which facilitates consistent drop
delivery onto fiat-bottom microplate surfaces. Filter tip options are available for
disposable tips.
Serial dilution feature
To further expand the versatility of the Thermo Scientific Matrix PlateMate 2x3,
Matrix has designed the system to support 8-, 12-, 16-, or 24- channel serial
dilution applications. This is accomplished by using a dedicated 8-, 12-, 16-, or
24-channel tip magazine. The instrument's discrete x/y advancement design
allows for incremental plate movement needed to accomplish row-by-row or
column by column dilutions directly on the Thermo Scientific Matrix PlateMate
2x3.
Volumetric calibration
Thermo Scientific Matrix PlateMate 2x3 systems are factory calibrated using
distilled water at room temperature (20°C). In cases where liquids of varying
specific gravity are to be pipetted, the instrument can be recalibrated accordingly.
This feature ensures accurate liquid delivery no matter what fluids are being
dispensed. Calibration for specific liquids can be performed quickly in the lab.
Many calibration settings can be stored in memory and applied when needed.
Volume calibration is a feature found on all Thermo Scientific Matrix liquid
handling systems.
1.2 About this Manual
To use your new Thermo Scientific Matrix PlateMate 2x3 properly and safely,
read this Operation Manual. Due to changing technologies and product
enhancements, this manual may be changed without notice. However, if you
want to receive product updates on the Thermo Scientific Matrix PlateMate
2x3, please contact your local sales representative.
We have made every effort to ensure that this document is accurate and
comprehensive. However, if you discover an error or omission, please contact
your local distributor or Thermo Fisher Scientific, Hudson, New Hampshire,
immediately, at the address on the cover of this manual.
Thermo Fisher Scientific will not be responsible for any damage or claims of loss
suffered as a result of use of this equipment in any application or in any manner
other than that for which it was originally and expressly designed.
Any transfer of all or any part of this manual to a third party without permission is
prohibited.
User Manual 3

Chapter 1 Introduction
1.3 Manual Conventions
References to other sections in the
manual are shown in italic text.
See Chapter 3, ControlMate Software,
for software installation and operation.
Software buttons and menu
selections are shown in bold text.
Select “Pipettor and tips”. Click “Start”.
Notes provide additional information
and are shown in shaded boxes Note: Passwords are case sensitive.
Important notes provide essential
information and are shown in shaded
boxes
IMPORTANT: Use All with blowout if a
piston reset is required.
Cautions alert you to conditions that
can cause equipment damage and
are shown in shaded boxes.
CAUTION! Do not restrict movement
of the microplate carriage.
Warnings alert you to conditions
that can cause personal injury and
are shown in shaded boxes next to
the warning icon.
WARNING! Do not use a
power cord that is frayed or cut.
�
4Thermo Scientific PlateMate™ 2x3

2 System Overview
2.1 General Description
The Thermo Scientific Matrix PlateMate 2x3 Automated Microplate Pipetting
System is a flexible, multichannel, automated, pipetting workstation, capable of
performing various routine liquid manipulations. In either the 96-channel or 384
channel mode, operations such as reagent addition, serial dilution, microplate
replication and sample dilution can be easily accommodated.
Using air displacement technology and Matrix's filtered or non-filtered disposable
automation research tips (D.A.R.Ts), the Thermo Scientific Matrix PlateMate
2x3 provides fast, flexible and precise automated liquid delivery while ensuring
zero carryover, thereby greatly reducing the risk of contamination. The Thermo
Scientific Matrix PlateMate 2x3 is also compatible with a selection of positive
displacement (syringe-based) pipetting heads in 96 and 384 well format for liquid
handling tasks that involve viscous solutions or low volume pipetting.
2.2 Instrumentation
2.2.1 System Configuration
This section summarizes the standard components in the base system.
The Thermo Scientific Matrix PlateMate 2x3 Base Units:
Two base unit models are available. Both models share the following list of
standard features:
xflexible six-position deck
xhigh-resolution linear microplate movement
xtwo peristaltic pumps (stepper-motor controlled)
with integrated non-contact liquid level detection
xone vacuum pump
xone 24VDC input/output switches
xuniversal operating voltage (100 – 240VAC)
xbar-code reading capability (using the barcode reader accessory)
xStepper motors for plate positioning (supports 96, 384, 864,
and 1536 well plates; also supports deep or shallow wells)
xKeyboard unit for manual control
xControlMate Windows-based PC interface software for sequence-based
program creation and editing, plus OLE option for robotic integration
User Manual 5

Chapter 2 System Overview
The Standard Base Unit
The standard base unit is designed with
operator safety as a first priority. This
model features an integrated light curtain
safety shield as standard. An operator’s
hand activates an interrupt system that
temporarily pauses all movement ensuring
unparalleled operator safety. Once the
obstruction is removed the device is
allowed to resume processing.
Figure 2-1: Thermo Scientific Matrix PlateMate 2x3Standard Base Unit
(Cat. No. 801-10001)
The Robotic-Friendly
Base Unit
The robotic-friendly base unit has been
designed for the purpose of robotic
integration and access. This base unit
configuration is not equipped with a light
curtain interrupt system and has been
modified for easy front or side access by
a robotic arm.
Figure 2-2: Thermo Scientific Matrix PlateMate 2x3 Robotic-Friendly Base Unit
(Cat. No. 801-10005)
6Thermo Scientific Matrix PlateMate™ 2x3

2.2 Instrumentation
2.2.2
2.2.3 System Components
10. Peristaltic
Pum
p
s
1. Pipettor
Hood
8. Light Curtain
Safety Shield
9. Liquid Level
Sensors
2. Safety
Shields
1 2
3 4
5 6
6. Power Switch
7. Microplate Stage
3. I/O Connector
5. Vacuum Pump
(
inside base unit
)
4. Stepper Motors
(inside base unit)
Figure 2-3: Thermo Scientific Matrix PlateMate 2x3 Components
Main System Components
Base Unit: Contains two stepper motors that provide X and Y motion of the
6-position microplate stage. The motors are software-controlled through the PC
or manual keyboard. This component also contains all of the electronic controls.
The Base Unit includes the following components:
(Refer to Figure 2-3)
1. Pipettor Hood: Houses pipettor head and tips magazine. Front panel can be
raised to allow access to the internal components.
2. Safety Shields: Plastic covers on both sides of the instrument provide safety
to the operator and reduce possible contamination of the work area.
3. I/O Connector: One connector on either side of the deck allow for additional
externally operated devices. Power to the connector is software-controlled.
4. Stepper motors: Stepper motors move the 6-position microplate deck
vertically and horizontally.
5. Vacuum pump: Removes waste fluid from the tip wash station.
6. Power switch: Rocker switch turns Thermo Scientific Matrix PlateMate
2x3 on or off.
User Manual 7

Chapter 2 System Overview
7. 6-Position Microplate deck: Microplate deck contains six microplate
positions. Platform is SilverStone®(PTFE®) coated for easy cleaning.
Supports 96, 384, 864, and 1536 well plates; also supports deep or shallow
wells). Supports a variety of standard SBS conforming labware (microwell
plates and reservoirs):
Stage 1: microplate, deep well block, tube rack, or reagent reservoir
Stage 2: microplate, deep well block, tube rack, reagent reservoir, or tip
wash station (Stage 2 only)
Stage 3: microplate, deep well block, tube rack, manually filled reservoir,
vacuum manifold, or sepraseal piercing manifold
Stage 4: microplate, deep well block, tube rack, manually filled reservoir, or
sepraseal piercing manifold
Stage 5: microplate, deep well block, tube rack, manually filled reservoir, or
sepraseal piercing manifold
Stage 6: microplate, deep well block, tube rack, manually filled reservoir, or
sepraseal piercing manifold
8. Light curtain safety shield: Safety sensors cover the front entry to the
instrument. If an operator attempts to access the pipetting area during an
operation, the instrument automatically stops to prevent possible injury.
9. Liquid-level sensors: Two non-contact, liquid-level sensors monitor liquid
levels in the reagent reservoir during reagent filling.
10. Peristaltic pumps: Two pumps, mounted on the side of the base unit,
supply fluid to the reagent reservoir or tip wash station on the microplate
deck. Quick-release handles allow for quick and easy tube replacement.
11. Keypad: Manual keypad provides direct control
of the microplate deck for basic microplate
positioning or troubleshooting.
12. ControlMate Software (not shown): Windows-based PC interface software
for sequence-based program creation and editing, plus OLE option for robotic
integration.
Other System Components:
Pipettor Head: Air and positive displacement
interchangeable pipetting heads that can be easily inserted
into or removed from the base unit. Air displacement
pipetting heads contain a silicone gasket that forms an
airtight seal with tips in the tips magazine. Pipettor heads
are available with 96 and 384 channels.
8Thermo Scientific Matrix PlateMate™ 2x3

2.2 Instrumentation
Tips Magazine: Aluminum or plastic frame that holds 96
or 384 pipette tips. Disposable tips magazines (D.A.R.Ts)
can be used with the Thermo Scientific Matrix
PlateMate 2x3. Tips magazines with PTFE-coated,
stainless steel tips and partial row tips are also available.
Tips transfer tool (not shown):Transfers D.A.R.T.s tips from a container to the
tips magazine.
Tip wash station: Used for washing disposable or
PTFE-coated stainless steel pipet tips, both interior and
exterior walls. It is mounted on a microplate stage and
connects to the buffer and waste lines; liquid-level sensor
prevents overflow. Tip wash stations are available in 96
and 384 format tall and standard height versions.
Reagent reservoir: Reagent vessel for dispensing
limited volume of reagent. Automatic fill reservoir is
mounted on a microplate stage. A separate buffer line
connects to the peristaltic pump and buffer bottle. The
reservoir provides a continuous supply of reagent; liquid-
level sensor prevents overflow.
Barcode reader: Optional component that is mounted to the
side of the pipettor hood and reads the barcode label on the
side of a microplate when it is moved in position for pipetting.
The barcode reader supports the following barcode types:
iCode39
iITF
iIndustrial 2 of 5
iCodabar
iEAN/UPC (A.E)
iCDOE 128
iCOOP 2 of 5
iRead Error
iCODE93
Vacuum Manifold: An optional accessory that can be used on
stage position 3 to perform filtration procedures on the Thermo
Scientific Matrix PlateMate 2x3 deck. The manifold accessory kit
includes (5) plate lifters to accommodate for the height restrictions
when using short 96 or 384 format D.A.R.T.s. The manifold is
compatible with 96 and 384 filtration labware.
User Manual 9

Chapter 2 System Overview
Sepraseal Piercing Manifold: An optional deck accessory that
allows for the simultaneous piercing of 96 seprasealed storage
tubes. The piercing manifold is compatible with 1.4mL, 0.7mL, and
0.5mL Tubes. Separate piercing head is required for sepraseal
piercing applications.
10 Thermo Scientific Matrix PlateMate™ 2x3

2.2 Instrumentation
2.2.4 Pre-installation Requirements
The Thermo Scientific Matrix PlateMate 2x3, with its compact size and small
footprint requires little bench space. However, additional bench space is needed
for reagents, buffers, waste container, and computer system.
29.5”
(749 mm) 25”
(635mm)
23”
(584 mm)
Figure 2-4: Selecting the Proper Location
Consider the following requirements when selecting a place for your system:
xFlat surface capable of holding 110 lbs (50 kg) plus weight of computer
xVentilation space: 23 in. (584 mm) height + 29.5in (749 mm) depth + 25 in
(635 mm) width (space around instrument)
xBench space on left side for computer and monitor (6.5 ft. serial cable is
provided)
xBench space on right side for reagent supplies (approx. 1 ft.; 3 ft. tubing
provided)
xGrounded wall outlet supporting 110/220 VAC (standard outlet for instrument,
plus outlets for PC system)
xPC system for ControlMate software
User Manual 11

Chapter 2 System Overview
2.3 Software Interface (ControlMate)
2.3.1 Overview
ControlMate is a Windows-based PC application that provides a graphical
programming interface for creating and executing device and module control
programs. The commands can be logically structured, according to the control
requirements. The application provides a standard method by which control
programs are created; the configuration defines the device module in use.
Note: See Chapter 3, ControlMate Software, for installation and
operating instructions.
2.3.2 Creating a Program
Pipetting programs are created in ControlMate by clicking the icons
in the Toolbox. Each icon represents either a software command or
pipetting command.
When you click an icon, the command it
represents is added to the sequence of
commands, called the Command Tree.
While the command is
highlighted, you can enter
the Command settings that
are specific to that command
After you create a program, you can validate it in ControlMate before running it
on the Thermo Scientific Matrix PlateMate 2x3.
12 Thermo Scientific Matrix PlateMate™ 2x3

2.3 Software Interface (ControlMate)
2.3.3 Running a Program
Before running a program, you can check for setup instructions or last-minute
notes in the Notepad. This feature is ideal for documenting any assumptions that
are made during the creation of a pipetting program. It serves as a reference for
the user when the program is implemented.
When you are ready, you can run the pipetting sequence.
At any time during the pipetting sequence, you can click “Stop” to interrupt the
program.
User Manual 13

Chapter 2 System Overview
2.3.4 Changing Thermo Scientific MatrixPlateMate 2x3
Components
ControlMate software also provides step-by-step instructions to change Thermo
Scientific PlateMate 2x3 components, such as pipetting tips or pipetting heads.
2.3.5 Calibrating Liquids
For liquids that require an accuracy adjustment during volume dispensing, you
can determine the calibration factor that adjusts to the specific gravity of the
liquid. The Volumetric Calculation option in ControlMate adjusts the movement
of the piston motor to improve pipetting accuracy for specified liquids.
14 Thermo Scientific Matrix PlateMate™ 2x3

2.3 Software Interface (ControlMate)
2.3.6 Controlling Reservoir Pumps
The reservoir pumps can be used to fill reservoir vessels and can also provide
finite control over the speed at which the liquid flows in either direction (fill or
empty). Typically there are two pumps and their respective outlets available;
these are positioned on either side of the pipetting head.
The pumps can be controlled by either filling until a reservoir liquid level sensor is
activated or by filling for a fixed length of time. Using a sensor rather than a fixed
duration to control pump motor activation will reduce the operating time of a
process if the reservoir is to be used many times during a run.
The Overfill timeout option serves as a backup to the pump sensor. The pump
shuts off after the specified time (default is 60 seconds) in case the non-contact
sensor fails.
The “Empty” option reverses the direction of the pump and returns any liquid in
the tubing to its container. The “Duration” (in seconds) depends on the length of
the tubing.
User Manual 15

Chapter 2 System Overview
2.3.7 Connecting to External Devices
One connector exists in the rear center of the deck by which additional externally
operated devices can be attached. This command will control the activation of
the DC supply to the connectors. This supply can be switched on or off and also
constant or momentarily.
16 Thermo Scientific Matrix PlateMate™ 2x3

2.4 Overview of Operation
2.4 Overview of Operation
2.4.1 Laboratory Application
Some of the possible laboratory applications for the Thermo Scientific Matrix
PlateMate 2x3 are outlined below:
xPreparation for enzyme immunoassays (EIA):
iEnzyme immunoassays in the ultra-micro-liter volume range
iRotavirus antigen, antibodies against toxoplasma gondii, antibodies against
adenoviruses
iDouble antibody sandwich assay for determining AFP, TSH, HGH, IgE, Lipid A
antibodies, DNA antibodies, potato viruses, antibodies against bovine leucosis
viruses
xPreparation for agglutination reactions with subsequent quantitative
photometric analyses:
iBlood group determinations in the ABO and Rh systems
iCoombs-reactive antibodies
iLatex agglutination tests
xApplication in cell cultivation:
iHybridoma screening for working with cell cultures
iCell seeds, cell cloning
iChanging the nutrient medium of cell cultures
xDosing the scintillation solution in microplate LSC
xDosing and transfer steps in PCR
xSimple reagent (liquid) addition
xSerial dilution across 8/12 or 16/24 columns for sensitivity analysis
xPlate to plate replication
xAutomating IC-50 assays
User Manual 17

Chapter 2 System Overview
2.4.2 General Operation
The following outline summarizes the tasks you would perform for a pipetting
operation. Not all of the tasks may be needed, depending on the instrument
setup and the pipetting program you use.
1. Start ControlMate
2. Start Thermo Scientific Matrix PlateMate 2x3
3. Set up Thermo Scientific Matrix PlateMate 2x3
Change pipettor head
Change tips
Attach Reagent Reservoir
Attach Tip Wash Station
4. Run pipetting program
5. Shut down Thermo Scientific Matrix PlateMate 2x3
Each task is described in more detail in Section 4, System Operation.
2.4.3 Device Precision
The Thermo Scientific Matrix PlateMate 2x3 was tested for precision at
volumes ranging from 0.5 µl to 5.0 µl. The results are summarized below. To
review the raw data, go to Appendix C, Precision Data.
Table 2-1: Device Precision
Volume Plate average Plate SD Plate C.V.
0.5µl into a dry 384 well plate 1303.5 95.54 7.3%
1.0µl into a dry 384 well plate 1996.5 105.06 5.26%
2.5µl into a wet 384 well plate 4877.8 208.78 4.28%
5.0µl into a wet 384 well plate 10073 253.67 2.52%
18 Thermo Scientific Matrix PlateMate™ 2x3

2.5 Specifications
2.5 Specifications
2.5.1 System Specifications
Instrument Dimensions
Base unit weight 190 pounds (85.5 kilograms)
Dimensions Height 23 inches (584 millimeters)
Depth: 29.5 inches (749 millimeters)
Width: 25 inches (635 millimeters)
Liquid Capacity
Pipetting Volume 96-Channel Head 384-Channel Head
Tip 1: 0.5 µl – 30.0 µl Tip 3: 0.5 µl – 30.0 µl
Tip 2: 5.0 µl – 300.0 µl Tip 4: 1.0 µl – 100 µl
Plate Access 96, 384, 864, 1536
shallow wells
384 & 1536
shallow wells
96 deep well 384 deep well
Reagent Reservoirs 96 channel 100 mL 384 channel 50 mL
(with automatic fluid replenishment and level detection)
Tip Wash Station 96 channel (tall and
standard height)
384 channel (tall and
standard height)
System Control
Keypad control Liquid crystal touch-panel. Dialog-type input for
programming mode operations.
PC control PC: 64 MB RAM, 400 MHz processor,
Windows platform, with a serial port.
Software: ControlMate Software, version 1.06 or later
I/O Switch Input/Output Switch for External Devices
User Manual 19