Agena BIOSCIENCE MassARRAY Nanodispenser RS1000 User manual

For Research Use Only. Not for Use in Diagnostic Procedures.
MassARRAY®
Nanodispenser RS1000
USER GUIDE v2.1

MassARRAY Nanodispenser RS1000 v2.1 User Guide
USG-CUS-059 Rev05
11/9/18
Copyright 2014-18. All rights reserved. No part of this publication may be reproduced, distributed, or
transmitted in any form or by any means, electronic, mechanical, photocopying, recording, or
otherwise, or stored in a database or retrieval system, for any reason other than a licensee's internal
use, without the prior written permission of Agena Bioscience. Printed in the United States of
America.
TRADEMARKS
MassARRAY, iPLEX, SpectroCHIP Array, and Agena Bioscience are registered trademarks of Agena
Bioscience, Inc. MassCLEAVE and UltraSEEK are trademarks of Agena Biosicence. All other
trademarks or service marks set forth herein are the property of their respective owners.
PATENTS
Agena Bioscience’s patented nucleic acid analysis by mass spectrometry methods and products
are protected under United States patent rights including but not limited to; 6,440,705; 6,558,623;
6,730,517; 6,979,425; 6,994,969; 7,019,288; 7,025,933; 7,332,275; 7,390,672; 7,501,251; 7,888,127;
7,917,301; 8,003,317; 8,315,805; 8,349,566; 9,249,456; 9,310,378; 9,394,565; 9,669,376; and
9,896,724, and patents pending including but not limited to US20130017960, and foreign
counterparts including but not limited to EP1173622B1, EP1727911B1, EP1546385B1, EP1332000B1,
EP1613723B1, EP1660680B1, and EP2107129B1.
[0818]
Revision History
Revision Number Date Changes Made
R05 11/9/18 • Updated patent list.
• Added full-skirted plates as an option in Table 1.8.
• Added wet resin desalting instructions for
UltraSEEK panels (page 21).
R04 4/11/18 • Added instructions for desalting analyte
(instructions are no longer in panel user guides).
• Updated Table 2.3 Recommended Dispense
Settings. Includes changes to dispense speed,
calibrant dispense speed, and addition of target
volume and upper/lower limit recommended
values (target volume for UltraSEEK is now 25 nL,
for iPLEX Pro Sample ID Panel is now 12 nL).
• Updated maintenance chapter: cleaning supply
and waste tanks monthly is only necessary for
users running fewer than 10 SpectroCHIP Arrays
per month.
• Changed recommended 96-well plate type to
only non-skirted.
• Added double-dispensing as a troubleshooting
method for UltraSEEK panels.
• Updated Asia Pacific office address.

USG-CUS-059 Rev05MassARRAY® Nanodispenser RS1000 v2.1 User Guide
For Research Use Only. Not for use in diagnostic procedures.
Contents
Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . 3
Overview . . . . . . . . . . . . . . . . . . . . . . . 3
Instrument Description . . . . . . . . . . . . . . . . . . . 4
Required and Recommended Equipment and Consumables . . . . . . 13
Safety. . . . . . . . . . . . . . . . . . . . . . . . . 14
Contacting Agena Bioscience . . . . . . . . . . . . . . . . 17
Chapter 2 Dispensing to SpectroCHIP Arrays . . . . . . . . . . . . . . . 19
Dispensing Overview . . . . . . . . . . . . . . . . . . . 19
Desalting the Analyte . . . . . . . . . . . . . . . . . . . 21
Instrument start up and shut down . . . . . . . . . . . . . . . 22
Pre-run checks. . . . . . . . . . . . . . . . . . . . . . 28
Setting up the dispensing run. . . . . . . . . . . . . . . . . 30
Microtiter plate checks . . . . . . . . . . . . . . . . . . . 39
Setting up the instrument deck . . . . . . . . . . . . . . . . 43
Starting the dispensing run . . . . . . . . . . . . . . . . . 46
Dispensing run activities . . . . . . . . . . . . . . . . . . 49
Clearing the instrument deck . . . . . . . . . . . . . . . . . 54
Accessing dispense volume data from previous runs . . . . . . . . . 56
Chapter 3 Methods and Mappings . . . . . . . . . . . . . . . . . . . . 57
About method files . . . . . . . . . . . . . . . . . . . . 57
About mapping files . . . . . . . . . . . . . . . . . . . . 58
Creating a custom method file . . . . . . . . . . . . . . . . 63
Deleting a method file . . . . . . . . . . . . . . . . . . . 73
Creating a custom mapping file . . . . . . . . . . . . . . . . 74
Deleting a mapping file . . . . . . . . . . . . . . . . . . . 86
Chapter 4 Maintenance Procedures . . . . . . . . . . . . . . . . . . . 89
Tank valve positions . . . . . . . . . . . . . . . . . . . . 89
Maintenance overview . . . . . . . . . . . . . . . . . . . 90
Pin soak . . . . . . . . . . . . . . . . . . . . . . . . 90
Daily maintenance . . . . . . . . . . . . . . . . . . . . 91
Monthly maintenance . . . . . . . . . . . . . . . . . . . 104
Quarterly maintenance . . . . . . . . . . . . . . . . . . . 111
Repairs . . . . . . . . . . . . . . . . . . . . . . . . 116

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For Research Use Only. Not for use in diagnostic procedures.
Appendix A Changing the Pin Format. . . . . . . . . . . . . . . . . . . 117
Adapting an instrument to 6-pin or 1-pin format . . . . . . . . . . 118
Appendix B Manually Adjusting Dispense Speed . . . . . . . . . . . . . . 131
Appendix C External Tanks . . . . . . . . . . . . . . . . . . . . . . . 135
External tanks vs. internal tanks . . . . . . . . . . . . . . . 135
Setting up an external supply tank . . . . . . . . . . . . . . 136
Setting up an external waste tank . . . . . . . . . . . . . . . 138
Manually priming the water supply system . . . . . . . . . . . . 139
Checking the external supply and waste tanks . . . . . . . . . . 141
Cleaning and flushing the wash system (for external tanks only) . . . . 143
Appendix D Troubleshooting . . . . . . . . . . . . . . . . . . . . . . 151
Appendix E Licensing . . . . . . . . . . . . . . . . . . . . . . . . . 153
Appendix F Warranty. . . . . . . . . . . . . . . . . . . . . . . . . . 157

USG-CUS-059 Rev05MassARRAY® Nanodispenser RS1000 v2.1 User Guide
For Research Use Only. Not for use in diagnostic procedures.
Chapter 1
Introduction
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Instrument Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Required and Recommended Equipment and Consumables . . . . . . . . . . . . . . . . . . . . . . 13
Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Contacting Agena Bioscience . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
1.1 Overview
The MassARRAY® Nanodispenser RS1000 is used to transfer analytes from microtiter
plates to SpectroCHIP® Arrays, which are subsequently analyzed on the MassARRAY
Analyzer. The Nanodispenser RS1000 supports all Agena Bioscience® genetic analysis
applications.
This user guide provides instructions for using the Nanodispenser RS1000 version 2.1.
For instructions for using the Nanodispenser RS1000 version 1.2, please refer to the
MassARRAY Nanodispenser RS1000 v1.2 User Guide, available from AgenaCx.com.
Contact Agena Bioscience Customer Support (page 17) if you are unsure which software
version you have.
Table 1.1 provides an overview of the dispensing workflow. This user guide explains how
to operate and maintain the Nanodispenser RS1000. It does not provide instructions for
Figure 1.1 MassARRAY Nanodispenser RS1000

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other workflow steps such as biochemical sample processing or processing SpectroCHIP
Arrays on a MassARRAY Analyzer.
For instructions on the procedures not covered in this user guide, please refer to the
MassARRAY user guide for your MassARRAY application or analyzer, available from
AgenaCx.com.
Table 1.1 Overview of Dispensing Workflow
1.2 Instrument Description
MassARRAY
Nanodispenser RS1000
instrument versions
The MassARRAY Nanodispenser RS1000 is a self-contained, enclosed instrument that
uses computer-controlled robotics to dispense nanoliter volumes of fluid from microtiter
plates onto SpectroCHIP Arrays. There are three versions of the instrument (Table 1.2).
Table 1.2 Differences Between Nanodispenser RS1000 Versions
Step See
Page
1. Desalt the analyte. 21
2. Perform the daily maintenance procedures and pre-run checks. 28
3. Set up the dispensing run in the software. 30
4. Perform the microtiter plate checks. 39
5. Set up the instrument deck. 43
6. Start the dispensing run. 46
7. Clear the instrument deck when the run is finished. 54
Description of Changes Deck Plate Left Side Panel Front Panel
Initial configuration
Relocated the waste
drain valve from the front
cover to the side panel
and removed the tank
level indicators.
Added a fitting for
vacuum waste to the
side panel and a switch
for the vacuum drain on
the front panel.

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The Nanodispenser RS1000 has a factory-installed pin array format that can be adapted
to a different dispensing format using an optional adapter kit (Table 1.3).
Table 1.3 Pin Arrays
Overview of instrument
components
Figure 1.2 through Figure 1.7 show the main components of the Nanodispenser RS1000.
Deck plate modified to
accept plate flatteners
instead of microtiter
plate (MTP) clips and
spacer blocks to enable
384-96 compatibility.
Description of Changes Deck Plate Left Side Panel Front Panel
Instrument Pin
Format Available Adapter Kit Type of Dispensing
24-pin Set 1 Pin Adapter Kit
(part no. 11329)
Note: This adapter kit
is not compatible with
the 38496 system
pin heads.
Automatic dispensing from a 384-well microtiter plate
to a 384 SpectroCHIP Array.
Manual dispensing from a single well of a 384-well
microtiter plate to a single pad on a 384 SpectroCHIP
Array (using the 1 Pin Adapter Kit).
6-pin Set 1 Pin Adapter Kit
(part no. 10255)
Note: This adapter kit
is not compatible with
certain 6-pin heads.
Automatic dispensing from a 96-well microtiter plate
to a 96 SpectroCHIP Array.
Manual dispensing from a single well of a 384-well
microtiter plate to a single pad on a 384 SpectroCHIP
Array (using the 1 Pin Adapter Kit).
24-pin Set
(38496
compatible)
1 and 6 Pin Adapter Kit
(included with
instrument)
(part no. 10254)
Note: This adapter kit
is not compatible with
older 24-pin heads.
Automatic dispensing from a 384-well microtiter plate
to a 384 SpectroCHIP Array.
Automatic dispensing from a 96-well microtiter plate
to a 96 SpectroCHIP Array (using the 6 Pin Adapter
Kit).
Manual dispensing from a single well of a 384-well
microtiter plate to a single pad on a 384 SpectroCHIP
Array (using the 1 Pin Adapter Kit).

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Figure 1.2 Instrument Front
Stop Button
Immediately stops
motion
Touchscreen
Controls the
instrument
Figure 1.3 Instrument Back: Power Switch and Ports
For more information about these ports, see External ports, page 12.
Power Switch
I/O Port: Future expansion
USB 2.0 Ports (2): Data transfer,
keyboard, or mouse
VGA Port: External display
Ethernet Port: Sample tracking, data
transfer

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Figure 1.4 Instrument Left Side With 3 Ports
Figure 1.5 Instrument Left Side With 2 Ports
Waste Port
Waste tank drains
through this port.
Supply Port
Supply tank is filled through this port;
can also be used to connect external
supply tank.
Warning: The water from the waste
ports may contain ethanol and
residual DNA sample. It must be
disposed of properly according to
local regulations.
Vac Waste Port
Vacuum tank
drains through
this port.
Caution: Connect the supply port
to a Type 1, >18.2 MΩ water source
only.
Supply Port
Supply tank is filled through this port; can also
be used to connect external supply tank.
Vac Waste Port
Vacuum tank drains
through this port. Caution: Connect the supply port to
a Type 1, >18.2 MΩ water source
only.

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NOTE
On a 6-pin instrument, a 6-pin vacuum cover is installed on the dry station. Do not remove the
vacuum cover. See Figure A.4, page 119 for an illustration of the vacuum cover.
Figure 1.6 Overhead View of instrument
Pin Array Assembly
Contains the pin array
used to load and
dispense liquid; allows
up-and-down
movement.
X-Axis Transport
Allows side-to-side
movement of pin array
assembly.
Y-Axis Transport
Allows front to back
movement of pin array
assembly.
Figure 1.7 Overhead View of Instrument Deck
Ultrasonic Wash
Supply Bottle
Supplies solution to
the ultrasonic wash.
Ultrasonic Wash
Cleans pin array
using ultrasound
through fluid.
Rinse Station:
Flushes pin array
with Type 1, >18.2
MΩ water
Dry Station
Dries the pin array
using vacuum.
SCOUT Plate
Holds the SpectroCHIP Arrays
Microtiter Plate Holders
Calibrant
Reservoir
Holds calibrant

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Main door and front
access panel CAUTION
!
Opening the main door disengages the safety interlock and aborts the dispensing run in progress.
See page 15 for more details on the enclosure safety interlocks.
Opening or closing the main door
To open the main door, lift the door fully open using the handle (Figure 1.8). Once the
door is approximately half-way open, the gas springs will assist lifting the door. The door
remains in the open position until you close it. The safety interlock message is displayed
while the door is open (Figure 1.9).
To close the main door, grasp and hold the handle as you close the door. Tap the HOME
button in the Safety Interlock message after the door is closed.
WARNING
!
WARNING! Do not place hands in the main door pathway when closing it. When lowering the
main door, do not let go of the handle until the door is completely closed. The gas springs support
the door as it is lowered, but stop providing support when the door is almost closed. If you do not
hold onto the door handle, the door may slam closed.
Figure 1.8 Nanodispenser RS1000 front side
Handle

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Opening or closing the front access panel
The front access panel enables access to the valves that control filling the supply tanks
and emptying the waste tanks.
CAUTION
!
Opening the front access panel disengages the safety interlock and aborts a dispensing run in
progress.
To open the front access panel:
1. Open the main door. (See page 9 for more details).
NOTE
The main door must be opened to allow the front access panel to open fully. The front access
panel flips up. If the main door is closed, its handle prevents the front access panel from fully
opening.
2. Grasp the front access panel at the bottom and lift upward until it locks in the open
position (Figure 1.10).
Figure 1.9 Safety Interlock Disengaged Message

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To close the front access panel:
1. Grasp the sides of the front access panel.
There are two brackets, one under each side of the panel that hold it open.
Simultaneously lift up on the access panel lightly and press the brackets up to
disengage them from the locked position.
2. Lower the access panel closed.
CAUTION
!
Be careful not to pinch fingers underneath the panel as you close it against the body of the
instrument. Do not place hands in the main door pathway when closing it.
3. Press the access panel toward the body of the instrument until it snaps shut.
CAUTION
!
Do not push on the access panel when closing; release brackets and close carefully.
Figure 1.10 Opening the Front Access Panel
Front access panel

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External ports The Nanodispenser RS1000 can be connected to an external:
• Keyboard with a USB connector
• Pointing device (for example, mouse or trackball with a USB connector)
• Monitor with a VGA connector
Figure 1.3, page 6 shows the port locations.
The keyboard and pointing device can be used to control the instrument instead of the
touch screen. A monitor connected to the VGA port acts as a “clone” display which
shows an image identical to that on the instrument touch screen.
The Ethernet port should be used to connect the instrument to a network solely for
transmitting sample-tracking and processing data, and for remote servicing by
Agena Bioscience Customer Support. The Ethernet port should not be used for
general networking. The I/O port is not currently used. It is reserved for future expansion.
Instrument
specifications
Table 1.4 Nanodispenser RS1000 Dimensions and Weight
Table 1.5 Nanodispenser RS1000 Power Supply and Consumption Characteristics
Table 1.6 Acceptable Operating Environmental Conditions
Table 1.7 Physical Clearance Requirements
Item Specification
Width 28.4 inches (72.0 cm)
Height 25.9 inches (65.8 cm)
Depth 27.5 inches (69.8 cm)
Weight 155 pounds (70.3 kg)
Item Description
Site power 100-240 VAC 50-60 Hz, 15A, properly grounded
Fuse T4AL 250V, 5x20 mm
Voltage detection Instrument automatically detects and selects proper
voltage within above range
Power consumption 3.2A maximum
Item Description
Temperature 61-75 °F (16-24 °C)
Humidity 30-75% relative humidity
Area Next to
Instrument Description
Above 16 inches (40.6 cm) to allow the main door to open fully.
Left 12 inches (30.5 cm) to allow access to supply and waste ports.
Right 12 inches (30.5 cm) to allow access to the power switch and cable on the
back of the instrument.
Rear 6 inches (15.2 cm) to allow access to power switch and space for power
cable and ventilation.

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1.3 Required and Recommended Equipment and Consumables
Table 1.8 Required Consumables
See MassARRAY System: Recommended Lab Equipment and Set-up, available on the
AgenaCx.com (Product Support > Applications & Systems > MassARRAY System), for
more detail information on recommended lab set up and equipment and consumables
needed for running panels on the MassARRAY System.
Item Specifications
384 or 96 SpectroCHIP Arrays Included with Agena Bioscience
SpectroCHIP Array and Clean
Resin Kits
Clean Resin Included with Agena Bioscience
SpectroCHIP Array and Clean
Resin Kits
Calibrant Included with Agena Bioscience
Reagent Kits
Tweezers Included with Agena Bioscience
MassARRAY Analyzer 4
Accessory Kit
Plate centrifuge Min. RCF: 3200 x g, min. speed:
4000 rpm
Plate/tube rotator 360º rotation, with standard
rotisserie
Resin dimple plate and scraper Supplied with Agena Bioscience
MassARRAY System
Ethanol Absolute (200 proof)
NaOH 0.1 M
HPLC-grade water Residue after evaporation ≤2ppm
Sterile, nuclease- & DEPC-free.
>18.2 MΩ
Type 1 water >18.2 MΩ, NCCLS, CAP, or ATSM
Single-channel pipette 10 µL – 100 µL
12-channel multi-pipette 20 µL - 200 µL
Compressed air Clean dry air
Towels Clean, lint-free (paper or cloth)
Tissues Lint-free (e.g., chem wipes)
Tween 20 (optional; may be needed for
troubleshooting)
Nonionic detergent solution, 10%
w/v
For 96-format experiments:
96-well non-skirted microtiter plates (MTPs)
OR
96-well full-skirted, low-profile MTPs
Working volume: 0.2 mL
Max fill volume: < 0.3 mL
Max fill volume: 0.2 mL
96-well fully-skirted MTP plate base (only required if
using a non-skirted plate)
Agena Bioscience p/n 179108
(included with Nanodispenser
RS1000)
For 384-format experiments:
384-well full-skirted microtiter plates Working volume: 25 µL
Max volume: 40 µL

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1.4 Safety
This section explains basic safety precautions for safe operation of the MassARRAY
Nanodispenser RS1000. Read this section carefully before operating the instrument.
Follow all safety guidelines, cautions, and warnings indicated on the instrument and in
this manual.
Pay close attention to the cautions and warnings presented in this manual.
CAUTION
!
A caution describes a situation that could introduce sample errors or contamination, or result in
data loss.
WARNING
!
WARNING! A warning describes a situation that could cause personal injury, damage to the
instrument, or pose environmental concerns.
WARNING
!
WARNING! Use the Nanodispenser RS1000 as specified by Agena Bioscience in this manual and
other supporting documents. Any other use may impair the protections provided by the
instrument.
Stop button The instrument has a Stop button located on the front panel (Figure 1.11). Push the Stop
button in case of an emergency such as imminent personal injury or damage to the
instrument. Pushing this button immediately stops all instrument motion.
CAUTION
!
If a dispensing run is in progress when the Stop button is pressed, the run is aborted.
To resume from a quick stop, push the Stop button again so that it is flush with the panel
surface. See page 16 for more information about resuming after a quick stop.

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Enclosure safety
interlocks
The instrument has a safety interlock system that prevents it from operating if the:
• Stop button is pressed
• Main door is open
• Front access panel is open
If any of the above occurs, all motion is immediately stopped.
CAUTION
!
If a dispensing run is in progress when the safety interlock system is triggered, the run is aborted.
Even if a run is paused, pressing the Stop button, opening the main door, or opening the front
access panel will abort the run.
WARNING
!
WARNING! Do not attempt to override or circumvent the safety interlocks to operate the
instrument with the main door or front access panel open.
The safety interlock is considered “engaged” when all of the instrument doors are closed
and the Stop button is not pressed. It is “disengaged” if a door is opened or the Stop
button is pressed. When the safety interlock is triggered, the screen displays the
message shown in Figure 1.12.
Figure 1.11 Enclosure Safety Interlocks
Main door interlock
Front panel interlock
Stop button

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To resume operating the instrument:
1. Press the Stop button again so it returns to its original position (flush with the instrument
surface).
2. Close the main door.
3. Close the front access panel.
4. Touch HOME in the safety interlock message.
The pin array assembly moves to the home position and the instrument is ready for
use.
NOTE
If a run is aborted, in most cases you can redo the run using the same microtiter plate of analyte.
There should be enough analyte remaining in the wells for another transfer. However, you should
use a new SpectroCHIP Array.
Personal protection You must wear laboratory gloves, a laboratory coat, and safety glasses when handling
microtiter plates and reagents.
Handling fluids Avoid spills onto the instrument when handling fluids.
Proper grounding The instrument must be connected to a properly grounded power source.
WARNING
!
WARNING! Connecting the instrument to a non-grounded power source creates a shock hazard
and can damage the instrument or cause personal injury.
WARNING
!
WARNING! Interrupting or disconnecting the ground conductor creates a shock hazard and can
damage the instrument or cause personal injury.
Figure 1.12 Safety Interlock Message

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Instrument location The instrument must be placed on a work surface capable of supporting its weight. The
work surface must not subject the instrument to vibration. See page 12 for instrument
specifications.
There must be adequate clearances around the instrument as described in Physical
Clearance Requirements, page 12.
Lifting the instrument
WARNING
!
WARNING! The instrument weighs 155 pounds (70.3 kg). Do not attempt to lift the instrument by
yourself. At least two people are required to lift the instrument. Disconnect the instrument from its
power supply before attempting to move it.
The instrument should be lifted only from the sides, along the bottom edges between the
stabilizing feet (Figure 1.13).
1.5 Contacting Agena Bioscience
Please contact your local Agena Bioscience office for customer support.
CORPORATE HEADQUARTERS & NORTH AMERICA
Agena Bioscience, Inc.
4755 Eastgate Mall
San Diego, CA 92121
USA
Phone: [phone]
Order Desk: 1-858-202-9301
Order Desk Fax: [phone]
Order Desk Email: [e-mail]
Help Desk: 1-877-4-GENOME or ([phone]
E-mail: [email protected]
Figure 1.13 Safe Lifting Points on the Nanodispenser RS1000

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EUROPE
Agena Bioscience GmbH
Mendelssohnstrasse 15D
D-22761, Hamburg
Germany
Phone: [phone]
Fax: [phone]
Order Desk: [e-mail]
Email: [e-mail]
ASIA PACIFIC
Agena Bioscience, Inc.
Ground Floor, 27 Jeays Street
Bowen Hills, QLD 4006
Australia
Phone: [phone]
Fax: [phone]
Email: [email protected]
CHINA
Agena Bioscience (Shanghai) Co., Ltd.
Room 1609-1613, Building A
Fenglin International Center
No. 380 Fenglin Road
Xuhui District
Shanghai 200032
PR China
Phone: [phone]
Fax: [phone]
Email: [email protected]
[0418]