DS2™ Automated ELISA System

Operator’s Manual

For Use with Matrix™ version 1.14 and above

IMPORTANT
Please read carefully before using the DS2
Revision History
Manual Version Revision Date:
Revision D June 2008

This publication is for the operators of the DYNEX DS2 Automated Microplate
Processing System using DS Matrix software.
Due to continuing software development, dialog boxes displayed in this manual
may differ from those actually seen in the software screens. Every effort has
been made to ensure the information in this manual is accurate, updated and
consistent with the product it describes. DYNEX reserves the right to make
technical improvements to the DS2 and documentation without prior notice as
part of a continuous program of product development.
The information in this manual is of a proprietary nature. No part of this
publication may be reproduced, stored in a retrieval system, translated,
transcribed, or transmitted in any form or by any means without prior written
permission of DYNEX.
DYNEX does not assume liability for the use of this manual. If the DS2 is not
used according to the description in this manual DYNEX does not assume
responsibility for any consequent effects.

This manual supersedes all previous editions and is published by DYNEX

Technologies, Inc.
Questions or comments regarding the content of this manual can be directed to
the address below or to your supplier.
DYNEX Technologies, Inc.
14340 Sullyfield Circle
Chantilly, VA 20151 USA

Part No. 91000200

 Table of Contents

Table of Contents

Table of Contents ........................................................................................................ i

About This Manual......................................................................................................iii
Chapter 1 – Overview................................................................................................. 5
INTRODUCTION .....................................................................................................................5
DS2 SPECIFICATIONS ...........................................................................................................6
DESCRIPTION OF HARDWARE COMPONENTS ........................................................................9
SOFTWARE DESCRIPTION ...................................................................................................18
SOFTWARE FUNCTIONS ......................................................................................................18
Chapter 2 – Safety.................................................................................................... 21
WARNING LABELS ..............................................................................................................21
SAFETY PRECAUTIONS .......................................................................................................22
Chapter 3 – Installation ............................................................................................ 24
UNPACKING ........................................................................................................................24
CONNECTING THE COMPUTER SYSTEM ..............................................................................27
CONNECTING THE DS2 POWER CORD ................................................................................30
INSTALLATION OF DS MATRIX™ SOFTWARE.....................................................................31
STARTING THE SYSTEM ......................................................................................................32
INITIALIZATION ..................................................................................................................33
Chapter 4 – Setting System Parameters.................................................................. 34
DATABASE MAINTENANCE .................................................................................................35
SYSTEM CONFIGURATION...................................................................................................39
ABSORBANCE FILTER .........................................................................................................52
IMPORT/EXPORT .................................................................................................................53
RESET AUTO RECOVERY ....................................................................................................55
EVENT LOG ........................................................................................................................57
FLUID LEVEL TRACKING ....................................................................................................65
Chapter 5 – Programming a New Assay.................................................................. 71
DEFINING ASSAY PARAMETERS .........................................................................................71
PROGRAMMING ASSAY OPERATIONS .................................................................................81
Chapter 6 – The Worklist........................................................................................ 125
CREATING A WORKLIST ...................................................................................................125
Chapter 7 – Starting the Run.................................................................................. 140
GENERAL CONSIDERATIONS .............................................................................................140
PREPARING THE SYSTEM ..................................................................................................141
STARTING THE RUN ..........................................................................................................142
Chapter 8 – Routine Service and Maintenance ..................................................... 152
ROUTINE MAINTENANCE PROCEDURES ............................................................................152
CLEANING AND DECONTAMINATION ................................................................................153
REPLACING THE ABSORBANCE MODULE BULB ................................................................155
REPLACING AN ABSORBANCE MODULE FILTER ...............................................................158
REPLACING THE TUBING ..................................................................................................160
CLEANING THE WASH HEAD ASSEMBLY ..........................................................................167
REQUESTING SERVICE ......................................................................................................167

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Table of Contents

LIMITED WARRANTY........................................................................................................168
DYNEX TECHNOLOGIES CONTACT INFORMATION ..........................................................169
Appendix A – Arm Calibration Tool........................................................................ 170
Appendix B – Labware Specifications.................................................................... 180
Appendix C – Curve Fit Equations......................................................................... 182
LINEAR REGRESSION ........................................................................................................182
POLYGON FIT ...................................................................................................................184
QUADRATIC, CUBIC AND QUARTIC REGRESSION ..............................................................184
CUBIC SPLINE CURVE FITTING .........................................................................................186
AKIMA FIT ........................................................................................................................186
EXTRAPOLATION OF NON-LINEAR CURVES ......................................................................187
SIGMOID FIT .....................................................................................................................188
LOG – LOGIT CURVE FIT ..................................................................................................189
USING LOGARITHMIC AXES FITTING ................................................................................189
Appendix D – Equation Functions.......................................................................... 191

2 DS2® System Operator’s Manual

 About This Manual

About This Manual

The following instructions for using the DS2 Automated ELISA System
(DS2) are included in this manual:
• Installing the DS2
• Configuring the DS2 hardware for specific application requirements
• Creating or modifying assays using the DS2
• Running assays by using worklists
• Performing required preventive maintenance
• Servicing the DS2

DS2® System Operator’s Manual 3

About This Manual

This page is intentionally left blank

4 DS2® System Operator’s Manual

Chapter 1 – Overview

Chapter 1 – Overview

Introduction
The DS2 Automated ELISA System is a computer-controlled microplate
processing system that fully automates the following steps of microplate
ELISA assays:
• Sample distribution
• Reagent addition
• Incubation
• Plate washing
• Signal Detection

The DS2 is intended for use in clinical, research, and industrial laboratories.

Figure 1: The DS2 Automated ELISA System (Cover Open)

DS2® System Operator’s Manual 5

Chapter 1 – Overview

DS2 Specifications
DS2 Instrument Dimensions
Width <540 mm (21.3 inches)
Depth <680 mm (26.8)
Height <660 mm (26.0)
Weight <48 kg (106.0)

Power Supply
Voltage 100-240 V auto-switching
Frequency 50/60 Hz
Power Consumption <300 VA

Reader Specifications

Dynamic Range −0.100 to 3.000 OD

Spectral Range 405 nm to 690 nm

Precision <1% CV (for <2.00 OD); <2% CV (for 2 to 3.0 OD)

Linearity ± 1% (for <2.00 OD); ± 1.5% (for 2 to 3.0 OD)

Accuracy ± 0.005 OD or 2.5% (whichever is greatest)

Read Time <30 sec (single wavelength)

Washer Specifications

Manifold Configuration 8-Way

Dispense Volume Range 50 to 1000 µL

Wash Buffers 2 x 2L

Input connector for external Clean fluid bottle must be provided (any size)
clean fluid bottle provided

Waste Container 1 x 1.5L

Residual Wash Volume <3 µL with super sweep

6 DS2® System Operator’s Manual

Chapter 1 – Overview

Incubator Specifications

Temperature Range Ambient plus 4°C up to 40°C

Temperature Accuracy ± 1°C at 370 C

Shaking 15 Hz periodic or continuous

Instrument Capacity

Number of Plates 2

Number of Assays/Run 12

Number of Sample Tubes 100 (5 racks of 20)

Number of Reagents 10 x 15 mL tubes and

8 x 25 mL tubes

Number of 24 x 2 mL tubes
Standards/Controls

Number of Sample Tips 216

Number of Dilution Deep 96

Wells

Sample Tube Dimensions 10 to 16 mm external diameter

40 to 100 mm height

Number of Reagent Tips 20

DS2® System Operator’s Manual 7

Chapter 1 – Overview

Sample Pipetting Specifications

Sample Tip Size 300 µL

Single-shot Sample 10 to 250 µL

Pipetting Volume

Time to Dispense <20 minutes

96 x 50 µL

Single-shot Dispense <3% CV

Precision at 50 µL

Single Shot Dispense ± 2%

Accuracy at 50 µL

Reagent Pipetting Specifications

Reagent Tip Size 1300 µL

Reagent Pipetting Volume 20 to 1000 µL

Reagent Pipetting Precision <3% CV

Reagent Pipetting Accuracy ± 2%

8 DS2® System Operator’s Manual

Chapter 1 – Overview

Description of Hardware Components

System Cover

The system cover encloses the workspace, the arm and the pipette module.
The cover should be closed during operation to prevent accidents.

CAUTION: The system cover prevents accidental interaction

with the arm.

To open the cover, lift the cover handle until the cover is in the upright
position. To close the cover, pull down on the cover handle until the cover is
fully closed. The system cover will rest on the side panels when it is
completely closed.

CAUTION: Pinching hazard. Be sure that your hands and

fingers are clear of the cover when closing.

Cover
Handle

System Cover

Cover Resting
Point

Indicator Light

Power Switch

Figure 2: External Components of the DS2 System

DS2® System Operator’s Manual 9

Chapter 1 – Overview

Workspace Components

• X-Drive, Y-Drive and the Z-Drive

• Reader Assembly (which contains the Incubation Chamber, Reading
Optics (under the Sample Tip Trays) and the Pipetting/Washing area
(under the Sliding Cover))
• Barcode Scanner
• Wash Head

Incubation
Chamber

Reading
Optics

Pipetting/
Washing Area

Wash Head

Barcode Incubator
Scanner Door Lever

Sliding Cover

Figure 3: Workspace Components of the DS2 System

10 DS2® System Operator’s Manual

Chapter 1 – Overview

Microplate Incubation Chamber

The incubation chamber can hold up to two microplates during a run. During
an incubation step, the reader sliding cover and incubator door are closed to
ensure proper temperature equilibration.

Barcode Scanner

The barcode scanner reads barcode labels on the sample tubes as well as
the positioning barcode labels located on the sample tube racks.
The barcode scanner is an IEC60825-1+A2:2001 Class 1 Laser Product that
complies with 21 CFR1040.10 and 1040.11 except for deviations pursuant
to Laser Notice 50 dated 7-26-01.
CAUTION: The barcode scanner has a maximum radiated
power output of 1.0 milliwatt. Do not stare into the beam of
the barcode scanner without appropriate protective
equipment (e.g. protective glasses). Obey the warning label
(shown below) that is on the front of the barcode scanner.

Pipette Module

The Pipette Module travels in the x-, y-, and z- directions to pipette samples,
controls and standards, dispense reagents, and to perform dilutions. The
Pipette Module is also used to slide the cover to the Incubation Chamber
open and close, as well as to pick up and eject the plate Wash Head
Assembly.
The pipette module has the following sub-components and functions:

Component Function(s)

Pipetting Pipettes samples, standards and controls (using

(liquid level disposable sample pipette tips) and reagents (using
detection) disposable reagent pipette tips).
Liquid level detection is performed by sensing
pressure changes.
Tip Detection Verifies that a tip has been picked up or ejected.

Wash Head Verifies that wash head assembly has been picked up
Detection or ejected.

DS2® System Operator’s Manual 11

Chapter 1 – Overview

The pipetting system of the DS2 Automated ELISA System includes ESP™
(Electronic Signature Pipetting) software. ESP™ software automatically
detects gross pipetting inaccuracies caused by blockages or bubbles.
Wash Head Assembly

The DS2 uses a modular Wash Head Assembly stored in the front left
corner of the workspace. The wash head assembly is picked up by the
pipetting arm to perform wash operations. The Wash Head Assembly is
designed to wash 8 well strips of a full or partial 8 x 12 microplate.

Pipetting Arm

Wash Head
Assembly

Figure 4: Pipetting Arm Picking Up the Wash Head Assembly

12 DS2® System Operator’s Manual

Chapter 1 – Overview

Wash Head

The Wash Head portion of the Wash Head Assembly contains two sets of
pins. The shorter pins (the dispense pins) dispense fluid and the longer pins
(the aspirate pins) aspirate fluid. The aspirate pins and the dispense pins
are closely spaced so that fluid can be aspirated from and dispensed into
wells of a microplate at the same time.
During operation, the wash head assembly is automatically lowered to insert
the pins into the microplate wells or raised to remove the pins from the
wells. Lowering the wash head assembly allows the aspiration of the well
contents, or performing a wash cycle at the well bottom. Raising the wash
head assembly allows the movement of the wash head to another column
for filling or washing.

Aspirate Pin

Dispense Pin

Aspirate Line

Dispense
Line
Figure 5: Wash Head with Wash Pins

DS2® System Operator’s Manual 13

Chapter 1 – Overview

Wash Buffer Containers

Different wash buffers may be placed in the two wash buffer containers (A
and B) located at the front left of the instrument.
The maximum capacity of the wash buffer containers is two liters. The wash
buffer container must have a minimum of 500mL of fluid for a wash
operation to take place.

Quick
Disconnect
Fitting

Float Switch
Connector

Wash Buffer
Container A

Figure 6: Wash Buffer Container A

14 DS2® System Operator’s Manual

Chapter 1 – Overview

Wash Head Cleaning Fluid Container (Container C)

Distilled or deionized water may be used to clean the wash head after plate
washing is complete. The user must program this step into the assay using
the Assay Editor. A user supplied bottle (Container C) is attached to the rear
of the DS2 using the supplied tubing. The supplied tubing is attached to the
Quick Disconnect valve located at the right rear of the DS2.

Wash Head
Cleaning Fluid
Container C
Quick
Disconnect

Container C Connection
Tubing

Figure 7: Wash Head Cleaning Fluid Container C

DS2® System Operator’s Manual 15

 Chapter 1 – Overview

Waste Containers

Fluid that is used during wash operations is collected in the Liquid Waste
Container. Used sample and reagent pipette tips are ejected into the Tip
Waste Container. Both waste containers are located at the front of the
instrument.

Float Switch
Connection
(level sensor)

Tip Waste
Container

Quick Disconnect
Fittings

Liquid Waste
Waste Cap Container

Figure 8: Waste Containers

The Liquid Waste Container holds up to two liters of waste. A waste fluid
level sensor alerts the operator when the Liquid Waste Container is full and
should be emptied.

16 DS2® System Operator’s Manual

Chapter 1 – Overview

Absorbance Module

The Absorbance Module measures the optical density (OD) of the

microplate wells. OD is also known as absorbance. The wavelength(s) at
which the optical density is measured is specified when programming the
assay.

Single and Dual Wavelength Modes

The DS2 Reader is able to take readings in two different wavelength modes:
• Single - using one analytical test wavelength
• Dual - using one reference wavelength and one analytical test
wavelength
The single wavelength mode is sufficient for most applications.
Blanking

The Reader allows subtraction of a reference value from well ODs. Air is
automatically used as a reference, but the absorbance of a reagent solution
can also be subtracted from the test result. Blank wells may be single wells
or an average of multiple wells.

DS2® System Operator’s Manual 17

Chapter 1 – Overview

Software Description
DS Matrix software is used to control the DS2 Automated ELISA System.
The software automates the sample distribution, incubation, reagent
addition, and washing and detection steps of assays as defined by the user.
The DS Matrix software also provides the user interface for configuration of
the DS2 and management of consumables.
The Matrix software includes assay definition options that allow the user to
customize assay parameters, assay steps, OD reading settings, result
calculations, quality control checks, and report formats.
Additional information about the software can be found in the DS2 Online
Help, which is accessible from the Help menu.

Software Functions
DS2 Configuration

The following DS2 System parameters can be configured from the Tools
menu: database maintenance, pipetting options, OD read limits, system
configuration, Levey Jennings assay parameters, absorbance filters, and
user notifications.

Consumables Definitions

The DS Matrix software stores parameters for all consumables and fluids
used on the DS2 in a database. A consumable or fluid must be defined in
the database before it can be selected for use in an assay.
The parameters for fluids and consumables that are stored in the database
are summarized below:

Consumable Parameters

Bottles Dimensions, capacity, and shape of reagent and

standard/control bottles, sample tubes, reagent tubes,
microtiter plates, and deep well strips

Plates Type, dimensions, well characteristics

Neat Fluids Fluid name and type, pipetting profile, load settings
(location, bottle type).
(Sample and
Reagent Fluids)
Wash Fluids Fluid name and load position

Tips Length, capacity, and maximum fill volume

18 DS2® System Operator’s Manual

Chapter 1 – Overview

Assay Programming

The Assay Editor screen allows the user to program the sequence of
pipetting, incubation, dispensing, washing, and reading operations
performed on samples. Data reduction and reporting are also programmed
using the Assay Editor screen.
Worklist Creation

The worklist defines the sample ID which corresponding to each sample

tube and the assay(s) to be run on each sample tube. A worklist can include
information for up to four microplates. More than one assay can be
performed on a plate if the assays have the same incubation, washing,
reading, and shaking specifications.

Note: An assay must be created before it can be assigned to a

 worklist.

Worklist Execution

Once a worklist is created, at the beginning of the run, the operator is

prompted to load any microplates and consumables that are required.
Data Analysis

The Optical Density results for each sample ID in the worklist are analyzed
according to the criteria specified in the assay.
Results Reporting

The run report may be viewed when the assay is complete.

DS2® System Operator’s Manual 19

Chapter 1 – Overview

20 DS2® System Operator’s Manual

Chapter 2 – Safety

Chapter 2 – Safety

Warning Labels
The DS2 Automated ELISA System or its components may contain labels
that warn the user of a hazard or an electrical connection. The description
of the labels is described below. Potential personal injury to the operator or
damage the DS2 can result if the labels are not followed.

Label Description

Alternating current is present

Caution symbol. Refer to the

Routine Maintenance chapter

Caution, motion hazard

Caution, pinching or mechanical hazard

Caution, hot surface

Laser radiation – Do not stare into beam

Protective conductor terminal

Earth (ground) terminal

Caution, risk of electric shock

Caution, biohazard

DS2® System Operator’s Manual 21

Chapter 2 – Safety

Safety Precautions
The following information aids in the safe and efficient use of the DS2.
In addition to the warning labels and other cautions previously described in
this manual, consider the following:
1. Appropriate precautions must be taken when working with
biohazards. Technicians must be trained in the safe handling
and clean up of potential blood borne pathogens. Universal
precautions, appropriate hygiene, and decontamination of
surfaces are recommended. Consult the reagent kit
manufacturer for precautions on handling potentially hazardous
substances.
2. Appropriate personal safety precautions must be made when
opening and closing the DS2 cover. A gas spring holds the
tension to keep the cover open. The DS2 cover should be able
to be opened 8 inches (approximately 203mm) without falling. If
the cover drops instantly above this height then the gas spring
should be replaced. The cover may creep down slowly from this
point due to the nature of gas springs and this is acceptable.
Gas springs will inevitably lose pressure depending on
frequency of use, so it is important for the user to take note if
the cover begins to give way over time and notify the service
provider of this circumstance.
3. When the cover is up and the run has started, do not encroach
upon the work area unless prompted by the software for user
input of materials or manual intervention.
4. Attend to error messages when the system prompts and stops.
These messages indicate a need for user action.
5. Sample tubes must be pushed down in the sample racks to
prevent the pipette module from being obstructed.
6. Place the sample racks securely onto the DS2. Push the rack
firmly towards the back of the DS2 the rack clicks in place.
7. Periodically inspect the sample rack springs to ensure proper
tube alignment. Replace the springs as necessary.
8. Barcode quality is critical to successful sample tube barcode
scanning. Scanning is in accordance with ASTM E1466-92
defining barcode quality, position, and orientation of barcode
labels. The use of non-standard barcodes or barcodes with
poor print quality may be problematic. Barcode labels should
be applied using a vertical orientation. The barcode label
should be oriented so that it faces out of the opening in the
sample rack.

22 DS2® System Operator’s Manual

Chapter 2 – Safety

9. Periodic back up of assay and data files is recommended.

Copy the files to a disk for storage or archive the data on a
secure server
10. Changes made to assay files may impact the suitability and
plotting of data using the Levey-Jennings control-charting
feature.

DS2® System Operator’s Manual 23

Chapter 3 – Installation

Chapter 3 – Installation

Unpacking
Packing List for DS2 Installation

(DYNEX Part Number 62000)

P/N Description Qty

13500010 DS2 Automated Instrument 1
50600167 USB Cable 1
N/A Power Cord (dependent upon order request 1
configuration)
352101800 Cleaning Wire, 0.018 “ (Dispense) 2
352104000 Cleaning Wire, 0.040 “ (Aspirate) 2
62800-113 CD Containing Matrix Software Setup 1
(numbers after the hyphen may change
depending on the current version)
62810-101 Arm Calibration Tool CD (numbers after the 1
hyphen may change depending on the
current version)
91000200 DS2 Operator’s Manual (this document) 1
92000040 CD Containing DS2 Operator’s Manual 1
N/A Instrument Configuration Report (Check List) 1
13500560 Wash Buffer Container 2
13500430 Liquid Waste Container 1
13500770 Tip Waste Container 1
24900065 Reagent Rack 2
13500501 Sample Rack 5
13500100 8-Way Wash Head Assembly 1
24900081 Purge Tray, Wash Head 1
22500810 Transit Bracket 1
DS2FIX017 Calibration Tool 1
DS2FIX029 Calibration Collar 1
65910 Sample Tips (Four Racks of 108) 1
65921 or Reagent Tips (One Rack of 108) 1
65920 (Partial) Part numbers have equivalent function and
either may be used and packed at the
discretion of Dynex Technologies.
(Standard for Part No. 65921: Four Racks)

24 DS2® System Operator’s Manual

 Chapter 3 – Installation

62910 (Partial) Deep Well Strips (Sample Pack: 12 Strips) 1

(Standard for Part No. 62910: 250 Strips)

62920 Reagent Tubes, 25 mL (Pack of 10) 1

62930 Reagent Tubes, 15 mL (Pack of 10) 1
65940 Control Vials (Pack of 33) 1
394000100 Purge Tray, Wash Calibration 5
42000810 Hex Key, 2mm 1
816400700 Tubing, 3mm x 5mm 1 (Meter)
43000491 Elbow Fitting 1
DSFIX044 DS2 Calibration Plate 1
42000070 Hex Key, 2.5mm 1
42000830 Hex Key, 4mm 1
9055720009 Warranty Card 1
N/A Declaration of Conformity 1
N/A Customer Installation Report 1

DS2® System Operator’s Manual 25

Chapter 3 – Installation

 IMPORTANT: These installation procedures are intended for

trained personnel

Unpacking the Components

1. Obtain a wheeled cart or lift capable of holding the weight of the DS2.
With large flat blade screwdriver remove the crate clips holding the
top to the sides and then remove the top. Remove the clips holding
the sides to the base and to each other. Remove the sides. Lift the
DS2 off the base.
CAUTION: The contents of the crate are heavy. Two people are required
to lift the DS2 safely. The DS2 should be lifted from the bottom of the
instrument. Do not use the cover handle or the plastic molded sides to lift
the DS2.

2. Place the DS2 near the bench or table where it will be located.
3. Examine the packaging to verify that all of the materials listed in the
packing list have been removed. Store the packaging material for
future use.
4. Inspect the DS2 and its components for damage. If damage is
observed, contact your shipper or service representative.

26 DS2® System Operator’s Manual

 Chapter 3 – Installation

Positioning the Instrument

1. Determine where the DS2 will be located. The bench space
requirement for the DS2 Automated ELISA System is
approximately:
54 cm (21.3 inches) wide
75 cm (29.5 inches) deep
110 cm (43.3 inches) high, with the cover open
2. The DS2 must be positioned on a level surface that does not
support other devices that produce vibration (centrifuges,
shaker bath, etc.).
3. If a Wash Head Cleaning Fluid Container C is not being used,
there must be at least 10 cm (3.9 inches) of space at the rear of
the DS2 to allow for sufficient ventilation. If a Wash Head
Cleaning Fluid Container C will be attached, there must be at
least 25 cm (9.75 inches) clearance at the rear of the DS2.

Connecting the Computer System

Computer Minimum Specifications

The computer system that is used for operation of the DS2 Automated
ELISA System must meet the following minimum specifications:
1. Intel Core/Core2/Pentium 4/Celeron family or compatible
processor recommended
2. 2 GHz or higher processor clock speed recommended; 1.8 GHz
minimum required
3. 10 GB hard drive with at least 100 MB of free space
4. Microsoft® Windows® XP Professional operating system with
Service Pack 2 or later
5. Microsoft® Windows® compatible display adapter (card or built
into motherboard) with 32-bit color (Highest setting) at 1024x768
or more resolution
6. 1 gigabytes (GB) of random-access memory (RAM)
recommended, 512 megabytes (MB) minimum required
7. One unused USB port is required for connecting the computer to
the DS2 Automated ELISA System
8. Mouse or other pointing device supported by Windows®
9. Microsoft® Windows® compatible CD-ROM or DVD Drive

DS2® System Operator’s Manual 27

Chapter 3 – Installation

10. Microsoft® Windows® compatible printer and sound card.

11. Network/LAN connection, 10/100 network interface (optional)

Connecting the Computer System

1. Place the computer, keyboard, monitor, and printer next to the
DS2.
2. Plug the USB communication cable into an unused USB port on
the computer.
Note: Refer to the instructions accompanying the
 computer for the location of the ports and for
information on connecting components.

3. Plug the other end of the USB communication cable into the USB
port on the right rear side of the instrument.
4. Connect the keyboard, monitor, and printer cables to the
computer.
5. Connect the power cords to the computer, monitor, and printer.

28 DS2® System Operator’s Manual

 Chapter 3 – Installation

USB Port Cooling

Fan

Cooling
Fan

Power Cord
Connector

Figure 9: View of the Rear of the DS2 Automated ELISA System

DS2® System Operator’s Manual 29

Chapter 3 – Installation

Connecting the DS2 Power Cord

The power cord connection to the DS2 is located in the rear of the system.

Note: Depending upon local electrical codes and electrical service

 quality, an optional uninterruptible power supply (UPS) may be
required in your laboratory. The use of a UPS is optional but
strongly recommended. A UPS can be purchased from an
electronic supply house.

CAUTION: The DS2 System must be connected to properly

grounded electrical outlets. Obtain assistance from a qualified
electrician to verify that your electrical outlets are properly
grounded.

Before connecting the power cable, be sure that the

components have been connected to each other as outlined
in the previous section.

Connecting the Power Cord

1. Plug the power cord into the connector at the rear of the
instrument (See Figure 9).
2. Connect the other end of the power cord to the laboratory
electrical supply outlet.

30 DS2® System Operator’s Manual

 Chapter 3 – Installation

Installation of DS Matrix™ Software

Installation Instructions
1. Insert the installation CD into the CD ROM. The InstallShield®
Wizard for Matrix starts automatically.
Note: If the InstallShield Wizard does not start
automatically, select Start and then Run from the
Windows task bar.

In the Run dialog box, browse to the CD ROM drive,

select setup.exe, click Open, and then click OK.

2. Click Next and follow the wizard instructions.

3. InstallShield Wizard Complete is displayed when the
installation is done. Click Finish and remove the installation CD
from the CD ROM.
4. Access Matrix software from the Windows program group: Dynex
Technologies > DS-Matrix > DS-Matrix.

Note: A printer driver must be installed for run

 reports to be viewed using the Matrix software.

Creating a Shortcut on the Desktop

A shortcut should automatically be created during installation, but in the

event it is not follow the instructions below:
To place a Matrix shortcut icon on your computer desktop:
1. Open Microsoft Windows Explorer.
2. Locate the Matrix program:
C:\Program Files\Dynex Technologies\DS-Matrix.
3. Click MatrixApp (.exe) to highlight it.
4. Select File > Create Shortcut from the Windows menu toolbar.
5. Resize the window so the desktop and window are both visible.
6. Drag the shortcut to matrixapp.exe to the desktop.
7. Close Microsoft Windows Explorer.

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Chapter 3 – Installation

Starting the System

CAUTION: Before starting the system, be sure that all racks
are properly seated and that the lids are removed from all
tubes, plates, and sample tip racks.

CAUTION: Power is on to the system whenever the blue

indicator DS2 is illuminated.

Starting the DS2 System

1. Power on the DS2 System.
2. If not powered on, power ON the computer, monitor, and
printer.
3. Double-click the DS- Matrix shortcut icon. Run modes are
displayed for selection.

Figure 10: Matrix DS2 Run Mode Dialog Box

4. Select Normal Mode to operate the DS2 System. Select

Simulation Mode to operate the software without connecting
to the DS2.
5. The DS2 performs a series of self tests before the instrument
is available for running an assay (see the Initialization section
of this manual).

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 Chapter 3 – Installation

Initialization
The DS2 will perform a series of initializations before it is ready to start a
run, including picking up and dropping the wash head assembly, opening
and closing the incubator door, and moving the microplate carrier to and
from the incubation and reader chambers.

CAUTION: Do not interrupt the DS2 while it is performing

initialization.

Following these steps, the main DS Matrix screen is displayed.

Timeline
Toolbar Incubator
Temperature

Figure 11: Main Runtime Screen

The Timeline Toolbar contains icons for starting and stopping the run,
changing the display, and setting run options. Certain functions may not be
available depending upon the run status.

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Chapter 4 – Setting System Parameters

Chapter 4 – Setting System Parameters

The DS2 Matrix software contains a set of system parameters that are set
globally for all assays. These parameters can be found in the Tools Menu,
and are listed below:

• Database Maintenance

• System Configuration

• User Notification

• Absorbance Filter

• Import/Export

• Reset Auto Recovery

• View Event Log

• Levey Jennings Criteria

• ESP Calibration

• Fluid Level Tracking

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Database Maintenance
The DS Matrix software database includes a description of all consumables
(plates, racks, and tips) and fluids (reagent controls, standards, wash
buffers, stop solutions, substrates, etc.) used on the DS2. A consumable or
fluid must be defined in the database in order for it to be available for
selection from a drop-down list when creating or editing an assay.

Editing Parameters for Consumables

 Note: Factory provided settings are read-only and

cannot be modified. Settings can be duplicated by
copying a consumable or fluid and saving the settings
under a different name.

 IMPORTANT:
It is the burden of the user to perform appropriate
validation of any consumable parameters to ensure proper
assay performance. Factory defined consumable settings
will not necessarily work with all consumables.

1. Select Tools > Database Maintenance from the menu bar.

2. Select the appropriate consumable category using the drop-down
menu:
BottleType, PlateType, NeatFluid
WasherFluid, TipType, RackType

Edit
Consumables

Figure 12: Database Maintenance Screen

3. To update an existing definition, highlight the desired
consumable and click the edit button (see Figure 12). Factory
defined consumables are read-only and cannot be edited.

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Chapter 4 – Setting System Parameters

4. Definitions may be changed on the next screen by editing the

values in the text boxes.
5. Click Save to save the new parameters.

DELETE
COPY EXIT HELP
Delete Add Edit Copy Exit Help

Figure 13: Database Maintenance Screen – button definitions

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Adding a Consumable

1. Click on the ADD button, enter the consumable name and click OK.
a. Consumables from the same assay should have a similar
beginning to the name so that they are grouped together in
the drop down list. This will make fluids easier to locate when
writing assays. For example:
1. Lyme Substrate
2. Lyme Positive Control
3. Lyme Cutoff Calibrator
b. If fluids are used universally across many assays they may
be given a generic name, such as the name of the kit
manufacturer. For example:
1. Dynex Wash Buffer
2. Dynex Stop Solution
3. Dynex Substrate Solution
c. Once the consumable name is entered, the data entry
window opens (see Figure 14 for an example). Enter the
required parameters..

2. Click SAVE. The new consumable will be added to the database for
selection from the drop down list.

Figure 14: Neat Fluid Addition Screen

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Chapter 4 – Setting System Parameters

3. To EDIT a consumable, highlight the desired consumable and click

the EDIT button. Change the desired parameters, and save the
changes.

4. To COPY a consumable, click the COPY button. Copied

consumables must be saved under a different name.

5. When finished with the consumables database, click the EXIT

button.

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System Configuration
System configuration parameters are universal for every assay that is run on
the DS2. Therefore, changing any of the parameters on the System
Configuration screen will update the parameters used for every assay.

Container Mixing Pipetting

Types Parameters Profile Options

Figure 15: System Configuration Fluids Screen

Defining System Configuration Fluids Parameters

1. Select Tools > System Configuration from the main Matrix
screen. The window opens to the Fluids tab.
2. The Deep Well Strip type and Sample Tube type that will be
used on the system are set to the default types and cannot be
changed by the user unless instructed to do so by Dynex
personnel.
3. Mix Volume (μL) is the amount of fluid that will be aspirated and
dispensed into a deep well strip to mix the sample during dilution
steps. If using a smaller dilution volume, the mix volume should
be changed accordingly to avoid bubbles.
4. Acceptable Error for fluid volume levels (μL) ensures that the
fluid level detection is within the % error limits as fluids are
consumed.

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Chapter 4 – Setting System Parameters

5. By enabling the clot detection check box, the system will alert the
user if a clot (which prevents aspiration) is detected. Clot
detection will not alert the user if subtle fluid aspiration changes
occur.
6. Enable the Save All ESP (Electronic Signature Pipetting)
parameters option to create an ESP calibration profile for each
fluid in the system. This option allows users with engineering
capabilities to monitor fluid aspirations and dispenses for
uniformity. Statistics generated by this feature can only be
viewed in engineering mode.
7. The ESP score is also used in engineering mode. The ESP
score defines the passing calibration score for all fluids when
monitoring the ESP calibration data. Ramp times, pipetting
speeds and pressures are all taken into account when calculating
the ESP score.

Specifying Pipetting Options

7. The aspirate and dispense profiles specify the rate at which the
samples are aspirated or dispensed from the pipette tip.
Separate pipetting profiles ranging from 1 to 5 can be selected
for any fluid except wash buffer (only sample aspirate and
dispense speeds are specified on the system configuration tab).
The higher number, the faster the rate of the aspiration or
dispense, therefore caution must be taken in setting these
profiles. At a higher velocity bubbles or aerosols may occur
which can affect the accuracy and precision of an assay.

Note: For any pipetting device, fluid properties such as

 viscosity and surface tension can influence the aspirate
and dispense accuracy. DYNEX Technologies calibrates
and verifies all pipettes using an aqueous calibration fluid
which, when used with a special calibration apparatus,
provides traceability to a NIST standard and gravimetric
method.
It is the burden of the user to perform the validation
studies necessary to assure proper assay performance.

8. Serial vs. Parallel Pipetting: If the same sample is used on

multiple plates or within multiple assays on the same plate, the
user can choose to pipette the samples serially or in parallel.
Serial pipetting pipettes all samples and controls in the
specified well order, starting will well A1 and pipetting down
columns to well H12 (unless the pipetting order dictates
differently (see the pipetting operation section of the assay
editor section). The “Parallel Pipette, across assays only” option
will pipette a sample into all assigned wells on plate 1 before

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pipetting the next sample. Once plate 1 has been completely

pipetted, the samples will be pipetted in the same manner on
Plate 2. The “Parallel Pipette, across plates and assays” option
will pipette a sample into all assigned wells on Plate 1 and Plate
2 prior pipetting the next sample.
Matrix selects serial pipetting by default.

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Chapter 4 – Setting System Parameters

Defining System Configuration Operations Parameters

Figure 16: System Configuration Operations Tab

1. Enable the Duration Learn by checking the check box.
a. When the Duration Learn is enabled (check box is
checked), the DS2 will collect timing information on
individual runs in order to improve timing estimates when
scheduling assay steps.
b. Duration Learn should not be used during assay
development and validation. Duration Learn should only
be used once assays are in their final configuration.
2. Enable Squeeze Template by checking the check box.
Squeeze Template allows the user to define control or calibrator
wells at the end of the assay template and have those controls or
calibrators pipetted following the last specimen well, instead of
being pipetted into the wells exactly as depicted in the template.
For an example, please refer to the assay template pictured in
Figure 17.

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Figure 17: Microplate Pipetting Template with Controls

Assume that 3 samples will be run on this assay in the worklist
defined by the user. If Squeeze Template is enabled, the NC2 and
PC2 wells would be pipetted into the first available wells (A2 and
B2). If Squeeze Template is not enabled, the NC2 and PC2 wells
will be pipetted in G12 and H12. All other wells in column 12 will
remain empty, as will wells in columns 2-11.
3. Enable the Enable Boolean Function Assays option by
checking the check box. This option enables spreadsheet
functionality necessary to perform data reduction for certain
unique assays. This is a custom functionality option designed for
use with specific assays. Contact Dynex Technologies Technical
Support for more information on this functionality.
4. Enable the Debug Log by checking the check box.
a. The Debug Log is used to determine the root cause of a
system crash. Dynex recommends that this feature be
enabled (check box is checked) so better technical
assistance can be provided.

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Defining System Configuration Data Read Limits

OD Limits

Numerical
Conversion

Figure 18: Over / Under OD Conversion

1. Set the OD OVER/UNDER Range for plate data results. The

OVER/UNDER Range indicates the highest allowable OD to be
reported. The reader is accurate between 0 to 3 OD (2.5 OD if
reading for a quantitative assay). If a value is over the specified
Over Range or below 0, there will be no result for the sample
reported and “****” will appear as the OD result for the sample.
2. When the OVER/UNDER Conversion option is enabled (the
check box is checked), any values over or under the specified
detection limit will be changed to reflect the values specified in
the Over Value and Under Value text boxes. Therefore, an OD
result will appear on the report and a result can be calculated for
the sample. The values in the Over Value and Under Value text
boxes are user configurable.

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Defining System Configuration Laboratory Information

Enter Laboratory
Information

Figure 19: Laboratory Information Entry

1. Enter the Laboratory information into the designated information

fields. This information may be automatically inserted into assay
reports if the user has configured the report to contain laboratory
information.

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Defining System Barcodes

Figure 20: Barcode Options Tab

The DS2 Barcode Scanner is able to read 6 symbologies (See Figure 20).

1. Enable the check box Use Check Digit if the last numerical digit is
used to verify that the rest of the barcode is correct. If enabled, the
Check Digit will not appear as part of the sample ID. If disabled the
last number in the bar code will be part of the sample ID.

2. Enable the check box Use Leading Zero if the first numeric digit in
the bar code is a 0.

3. The Codabar barcode symbology drop-down menu becomes

available if Use Check Digit is enabled. The options listed in the
menu are Modulo 10, Modulo 16, and Modulo 7, which are
calculations used to produce the Check Digit number.

4. The IATA barcode symbology drop-down menu becomes available if

the Use Check Digit is enabled. The options listed in the menu are
Coupon+Form+Serial, Form+Serial, and All Data, which are formulas
used to produce the Check Digit number.

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Defining System Configuration, Self Test Report Options

Figure 21: System Configuration: Self Test Report Options Tab

1. When the LIS Link software is installed the LIS Service

Information will automatically fill in. The Enable LIS Support
checkbox will also be active.

2. Click the Enable LIS Support checkbox to activate the LIS option
within Matrix.

a. If the Automatically save self test report check box is

enabled, the user may select the format for which the
report should be saved (either Excel® or pdf) and the
location the file should be saved. The default location to
store the file is the self-test report folder in the DS Matrix
directory (recommended to keep default location)

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Defining System Configuration, Database Backup Options

Figure 22: System Configuration, Database Backup Options Tab

1. Set the Backup Frequency.

a. Select the desired database backup frequency from the drop

down list.

b. The default location for database backup files is: C:\Program

Files\Dynex Technologies\DS-Matrix\DatabaseBackup.
Dynex recommends that the default file location should not
be changed.

c. The user may specify the date and time when the specified
backup frequency should begin.

d. The Matrix software will display when the last back-up took
place and when the next back-up will take place

2. The user may also choose to Restore a database from the

Database Backup Options tab.

a. Click on the button to browse to the desired backup

database.

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b. Click Restore to update the current database display with the

selected database information. Any information in the current
working database will be over-written and any changes made
since the most recent back-up was performed will be lost.

3. The user should empty the database backup folder, with the
exception of one or two early clean databases and some of the
more recent databases, on a monthly basis to save space.

Defining System Configuration, LIS Options

Figure 23: System Configuration, LIS Options Tab

1. The LIS options tab becomes available when the system is

connected to an LIS system via LISLink™ software. If
LISLink software is not in use, the selections on this tab will
remain grayed out.

2. The LIS Service Information will automatically fill in when

connectivity is achieved.

3. Enable the Reprocessing and Export Options as desired.

DS Matrix User Notification

DS Matrix software can be configured to display an error, sound an alarm,
or send E-mail to a specified E-mail address when system error conditions
occur.

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Chapter 4 – Setting System Parameters

 Note: An E-mail server and internet connection are

required.

Configuring the DS Matrix User Notification

1. Click on Tools > User Notification from the main Matrix menu toolbar.
The following screen will be displayed:

Sender
E-mail
Address

Figure 24: User Notification Options Dialog Box

2. Click on the Setup tab. In the To textbox, type in the E-mail address for
the recipient of the user notification E-mail sent from the DS2 Matrix
software.
3. In the From textbox, type in the E-mail address of the sender (for
example the e-mail address of the lab manager).
4. In the SMTP Server textbox, type in the SMTP server for the sender’s E-
mail address.
5. Click on the Save button to save these parameters, or click the Send
Test E-Mail button to test the settings.
6. Click on the Manual tab to send E-mails manually. The screen below will
be displayed:

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E-mail
Addresses

E-mail
Message
Body

Figure 25: E-mail Setup Screen for User Notification

7. Fill in the recipient’s email address and the sender’s E-mail address,
along with the E-mail text.
8. Click the Send E-Mail button to send the e-mail.

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Absorbance Filter
Four standard absorbance filters are included with the DS2. The
wavelengths of these filters are 405, 450, 490, and 620. The user may
order a custom filter set specific to their assay(s) by purchasing them from
the supplier. Up to 6 filters may be installed in the DS2 filter wheel.

Note: It is important that the filter wavelength matches

 the position of the filter that is installed, or the assay
results will be affected.

Editing Absorbance Filter Definitions

1. Click on Tools > Absorbance Filter from the main Matrix menu
toolbar.
2. Edit the wavelength values for Filters 1-6. The 405 nm filter
MUST be in position 1 for the DS2 to perform a successful
self-test.

Note: The 405nm filter must be in Position 1 of the filter

 wheel for the DS2 to perform a successful self-test.

3. If no filter is installed at any position, list the wavelength value as

“0” for this position.
4. Click OK when finished. Filter
Wavelength
Value

Figure 26: Absorbance Filter Designation

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Import/Export
Assay and OD data files may be imported or exported for use in other DS2
instruments or in other software applications.

Exporting an Assay File

1. Click on the Export radio button.
2. Enable the Assay checkbox. Highlight the desired assay..
3. The Assay File Filter will sort the assay names displayed by name,
category, or Last Edited Date.

4. Click on and browse to the desired file location. Enter a file

name. An *.xml extension will be assigned to the file when it is saved.
5. Click Export.

Note: Assay files cannot be opened in document or

 spreadsheet applications. DS Matrix assays can only
be imported back into DS Matrix.

Sort Assay Files

Click to
Browse

Click to Export File

Figure 27: Import/Export Dialog Screen (export options)

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Importing an Assay File

1. Click on the Import selection button.

2. Select the filename to be imported by clicking on the button

and navigated to the current file location.
3. Select the desired assay file (*.xml files only).
4. Click the Import button.
Note: Only files that have been generated using DS Matrix
 software programs can be imported into DS Matrix software.

Import Selection

Browse for File

Import

Figure 28: Import/Export Screen (import options)

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Exporting a Data File

1. Click on the Export radio button.
2. Choose to export the data as either an XDB (Matrix) format or as

a CSV comma delimited spreadsheet type file. Click on the

button, find the desired file location, and name the export file,
and click Save. DS Matrix will assign the file extension.
If choosing to export as an XDB file, the data file can only be
opened in DS Matrix.
3. Choose plate data by highlighting the desired plate identifier in
the list.
4. Click Export.
5. If the data is imported into a spreadsheet, the well location data
will be in the first column and the OD data will be in the second
column.

Importing a Data File

1. Click on the Import radio button.

2. Click on the button and find the desired files.

Note: Plate Data files must have the *.XDB extension. Assay files
 must have the *.XML extension

3. Click the Import button.

Note: Plate Data files can only be imported that were created
 using DS Matrix and saved as *XDB files. Data cannot be
imported into DS Matrix from other software applications such as
spreadsheet (*.CSV) files.

4. When plate data is imported into a database, the associated

assay information will also be imported into the database.

Reset Auto Recovery

Auto Recovery is a mechanism that allows the DS2 Matrix software to
automatically recover from errors during a run without user intervention.
When an error occurs, Matrix will display a list of potential corrective actions,

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Chapter 4 – Setting System Parameters

and the user is prompted to select the most appropriate action in order to
correct the problem (see Figure 29).

Error
Recovery
Options

Figure 29: Error Recovery Screen

On the same screen (underneath the drop down list options), the user can
check the Auto Recovery checkbox to instruct Matrix to carry out the same
action the next time the exact same error is encountered. Matrix can then
carry out some corrective actions without any user interaction.

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Figure 30: Reset Auto Recovery Screen

The Reset Auto Recovery (see Figure 30) function erases the settings for
the user-selected corrective action for a particular error. The next time the
error occurs Matrix will prompt the user to select a corrective action instead
of carrying out corrective actions without user intervention. To remove a
specified auto recovery action from Matrix, check the checkbox associated
with the undesired recovery action and then click Delete. Auto recovery will
no longer be performed the next time the error is encountered.

Note: Use the Reset Auto Recovery function with great caution.

Event Log
The Event Log lists every function the DS2 performs during an assay. To
view the event log, click Tools > View Event Log, and the Event Log
displaying events which occurred since the current software session began
will be displayed. A new Event Log is created each time the software is
started.
1. To view logs from previous software sessions performed on a prior
date, click the View History button.
2. Choose a date on the calendar, highlight the desired Event Log and
click open. Each operation performed is recorded in the event log.

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Figure 31: Example Event Log

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Levey-Jennings Criteria
Levy-Jennings charts monitor the performance of an assay over time. Levy-
Jennings charts include plots of the individual results versus assay data to
analyze the dispersion of results about the cumulative mean value.
Typically, a specific well or sample type is used, such as a control or other
sample type, for which an expected value is available.
Levey-Jennings charts on the DS2 can be displayed by Matrix software for
specified wells on an assay plate using raw OD values or calculated results
(concentrations or ratios). Westgard rules may also be applied.

Specifying Levey-Jennings Criteria

1. Select Tools > Levey Jennings from the Matrix main menu
toolbar.
2. The following options screen will be displayed.

Time Assay
Range

Figure 32: Levey-Jennings Criteria Parameters Screen

3. Select the Assay for which the Levey-Jennings analysis is to be

carried out by highlighting the desired assay in the drop down
list.
4. Select the Time Range over which the assay will be analyzed.
Selecting All displays data for every run of that assay stored in
the plate database. Otherwise select a time frame of one week,
one month or one year to analyze data generated within that time
period. The user may also choose a starting date from which all
data generated from that point in time will be analyzed. Lastly, a
number of the most recent data sets (1,2,3,4…) can be selected.

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5. Click Apply.

Well Calculation
Selection Method
Plates

Figure 33: Levey-Jennings Plate and Well Selection

6. Select the Plates to be analyzed. Uncheck the check box for a

plate if the data for the specified plate should not be analyzed.
Check the check box for the wells containing the control (or other
sample type) to be used in the Levy-Jennings plot. Click the
Average Replicates box if desired.
7. The number of plates chosen will equal the number of points on
the graph.
8. If Raw OD data is used to generate the graph, select the Plate
Data radio button. To use calculated data following a Curve Fit,
Threshold, or Ratio Operation, select the Data Reduction radio
button.
9. If pass/fail criteria are to be used, select the appropriate Quality
Control cutoffs.
10. Click Run to display the plotted results in the lower portion of the
window.

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Figure 34: Levey-Jennings Results

11. Click on the Report button to bring up a printable version of the

results, including the graph with header information of assay
name, quality control test results, etc.
12. To save the data, click on the Save button.
13. To retrieve saved data and regraph, click on the Load button.
Data must be saved prior to trying to load it, or a message will
appear that no results are available.
14. Click the OK button to close the Levey Jennings window.

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ESP Calibration
Electronic Signature Pipetting (ESP™) is a sophisticated technique used by
the DS2 for detection of gross pipetting errors often caused by the presence
of particulate matter, clots, foam, or bubbles in the sample.
Correct use of ESP requires calibration of acceptable sample transfers for a
given fluid with a given pipetting profile and volume. This data is collected
and stored in a database and is used by Matrix as a reference for good data
to compare against subsequent dispenses. Insufficient sample transfer can
therefore be detected and reported to the operator during a run.

Performing ESP Calibration

1. Click on Tools > ESP Calibration from the main Matrix screen.
2. The following screen will be displayed (See Figure 35).
3. Type in the Fluid Name (ex: water), Volume, and Aspirate and
Dispense profiles. The aspirate and dispense profiles should
match the programmed aspirate and dispense profile values for
the fluid in the fluids database, The volume must match the
volume programmed to be pipetted during an assay.
4. Specify the number of transfers to calculate the calibration
values. .
5. Select the source of the fluid being calibrated.
6. Select the destination of the fluid being calibrated.
7. Click Run
8. Follow the instructions in the load wizard to prepare the system.
Click Done. The DS2 will then perform the fluid transfer and
display the results (See Figure 36).

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Number of
Fluid Name Volume Transfers

Run Button

Figure 35: ESP Calibration Main Screen

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Chapter 4 – Setting System Parameters

Figure 36: ESP Calibration – Results

9. Click accept to accept the calibration results and click reject if

the results are not acceptable for that particular transfer. The
profile should appear relatively smooth without unexpected sharp
peaks or dips.
10. Repeat steps 7 and 9 for all transfers (see the value in number
of transfers). The load wizard will only appear once.
11. The data displayed can be changed by changing the selections
in the View area. The user may select all to view data for all
transfers, or the user may select the specific transfer number.
Checking the checkbox for min will display the data compared to
the minimum value for the data set. Checking the check box for
max will display the data compared to the maximum value for the
data set. Checking the checkbox for mean will display the data
compared to the mean of the data set. The user may choose to
have all three checkboxes selected at the same time as this may
assist in determining if the transfer is within acceptable ranges.
12. If the calibration results are acceptable, click Save.
13. If the calibration results are not acceptable, click Done. Select
Yes in response to the prompt to leave the ESP calibration
window without saving data.

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Fluid Level Tracking

Note: Do not use Fluid Level tracking with default Dynex supplied
 bottles and vials. Fluid Level tracking is only required when using
user supplied bottles and vials.

Fluid level tracking requires gravimetric calibration for each liquid in a

specified bottle or tube.. During the calibration routine, the operator adds a
set volume of liquid to the bottle or tube to be calibrated
(ex:1000 µL to a test tube).
During the fluid level tracking procedure, the DS2 aspirates a set volume of
liquid from the bottle or tube (ex: 100 µL) and dispenses the liquid into a
waste container. The operator is then prompted to reweigh the bottle or
tube. This aspirate and weigh cycle is repeated several times, and the
resulting weights are entered on the calibration screen.

Performing Fluid Level Tracking Calibration

1. To start the fluid level tracking calibration, click on Tools >
Fluid Level Tracking. The DS2 will provide detailed
instructions on the completion of the calibration routine in the
Message Center text box in the instruction screens (See
Figure 37)
2. Additional screens with instructions on collecting weight data
before and after the DS2 aspirates liquid from the bottle will
be displayed. Follow the instructions on the screens to
complete the calibration.

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Message
Center
(operator
prompts)

Select Bottle
Type

Click Accept

Bottle
Description

Figure 37: Fluid Tracking Calibration Start Screen

Fluid Level Tracking Calibration Steps

1. Select the bottle or tube type.

• Note: the user defined bottle or tube must be entered in the

Bottle Type database in order for the bottle or tube to be
selectable from the drop down list.
2. Click Accept.

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Operator Instructions

Figure 38: Fluid Tracking Calibration Data Entry Screen

3. Tare the empty bottle or tube to use for fluid tracking.

NOTE: An analytical balance that can weigh to the nearest

 0.001 g is needed to complete the calibration routine.

4. Click Accept

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Enter Bottle Weight

Figure 39: Fluid Tracking First Fluid Weight Entry

5. Follow the instructions in the Message Center and enter the

first bottle weight. Press Accept.
6. Follow the Load wizard prompts to prepare the system for the
fluid tracking calibration procedure.
7. Click Done when the load wizard is complete.
8. Click Accept to confirm that the items specified in the message
center have been loaded on the instrument.
9. Close the system cover and click Accept to begin the
calibration procedure.
10. The DS2 will pick up a tip, aspirate fluid from the source bottle,
dispense the fluid into the waste bottle, prompt the user to
weigh the bottle for the second time, and to enter the second
weight.

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11. The range of weights to be entered is displayed. A different

amount of water will be used for different bottle types.
12. A total of ten calibration points are used. Decreasing bottle
weights will be entered as fluid is aspirated out of the source
bottle.
13. At any time during the fluid level tracking procedure, click
Cancel to cancel the calibration program, or Restart to reset
the program.

Number
Calibration Point

Enter Next
Decreasing
Weight

Figure 40: Fluid Tracking Calibration Point 5 Weight Entry

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 Chapter 5 – Programming a New Assay

Chapter 5 – Programming a New Assay

Defining Assay Parameters

The first step in programming a new assay is to define the assay parameters. Select File >
Assay Editor from the main Matrix menu. All assays must include the three default icons
shown in the Assay Screen (Assay Title Page, Microplate Pipetting Template, and Report
Format Set-up) plus at least one operation, such as a read or dispense operation. All
assays open to the Assay Title Page.
Assay operation icons must be dragged from the Operations toolbar into the Programming
Toolbar in their proper sequence.
Microplate Operations
Assay Title Pipetting Toolbar
Page Template

Programming
Toolbar
Report
Format
SetUp

Figure 41: Assay Title Page Screen

NOTE: At least one assay must be created before a

 worklist can be defined and run.

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Creating An Assay
The Assay Title Page
1. Select File > Assay Editor from the menu bar

Figure 42: Assay Title Page

2. The assay opens with the Assay Title Page displayed. Enter the assay Title and
Author in the text boxes. The assay title may be different from the filename the
assay is saved under. If a password is entered, subsequent attempts to open the
assay will require the user to enter the password in order to view or edit the
assay parameters.
3. Lot Information for kits may be specified, including the kit name (Name), lot
number (number) and expiration date. Kit lot information can be recorded when
the assay is created or information can be requested at run time when the
consumables are loaded.

• If the user checks the check box for Request kit lot data at runtime, it is
not necessary to enter kit information on the Assay Title Page, however
the user will be required to enter lot and expiration information for all
consumables and fluids each time the assay is run. The user can choose
not to enter lot information when prompted, however the user will be
prompted to enter lot information for every fluid.

• If kit lot data is required to match at runtime, check the check box for
Require runtime kit lot to match and enter data for the kit lot in the Lot

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Data table. Upon running the assay the user will be to confirm matching
kit lot and consumable data at runtime. If lot numbers and expiration
dates have been entered previously for consumables, the user will be
asked to confirm that these lot numbers have not changed and that the lot
number stored in the system is a match for the lot number of consumable
being used. If a lot number has not been entered for a particular
consumable, the user may opt to enter the lot information or to click
Cancel and no lot information will be entered.

4. Click Validate when finished.

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The Microplate Pipetting Template

The Microplate Pipetting Template allows users to determine the plate position of well types
such as Standards, Controls, and Test Samples. Wells will always be used for the well type
with every run of the assay.

Defining Wells (See Figure 43)

1. Click on the Microplate Pipetting Template icon in the Programming toolbar.
2. Click on the Clear All button to clear the plate so wells can be defined.
3. Click on the radio button for the desired Well Type definition (NC, negative
control; PC, positive control; CO, cut-off control, etc.). To change a well type
definition, refer to the section of this manual concerning Well Type Definitions.

• Note: If a curve fit is used in the data reduction, the default Standard well
type must be used to define the assay standards on the template.
4. Select the number of Replicates desired by clicking the up and down arrows.
5. Determine if the replicates are to be oriented By Row or By Column by selecting
the appropriate radio button in the Replicates area. When replicates are added
by row, one replicate will be placed (for example) in column 1 (A1) and one
replicate will be placed in column 2 (A2). Replicates which are added by column
will be added to the template serially (A1, B1).
6. The user can click on each well individually, or the user can click and drag the
cursor over the desired wells to define them as the selected well type.
7. Repeat steps 3 through 6 until the entire plate has the desired well definitions for
standards, controls, empty, samples, etc.
8. To clear an individual well, click the Empty radio button, and then click on the
desired well location in the template. Click on the Clear All button to reset all well
types.
9. Choose the microplate type which will be used for the assay from the
Microplates drop-down list. Only microplate types which are defined in the
plates database will appear in the drop-down list.
10. Click Validate when finished.

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Microplate Replicates
Pipetting Number
Template Well Type
Options

Empty
Single Well

Toggle
Blank
Changing a Well
Type Definition

Clear All
Well Types
Button

Microplate
Choices

Figure 43: Microplate Pipetting Template with Wells Defined

Well Type Definitions

By default, all 96 well positions in the microplate template are tests

(T1,T2, etc.). When Well Types have been assigned, the well becomes color coded for the
well-type defined by the user, and will be labeled with a symbol for the well type followed by
a sample number. Wells that are dispensed as replicates will have the same sample number
(e.g. T1).
Labels for Control wells can be changed and custom color-coded by clicking on the
“Change Label” radio button, with the exception of Standard (S) and Control (C), which are
default wells.
Any well on the template can be made a Blank well by clicking the Toggle Blank radio
button, then clicking on the desired well (s) on the template that will be used as blanks. If
more than one well is selected to be a toggled blank, the ODs will be averaged from the
specified wells and the average subtracted from all other wells on the plate.

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Well Type Labels

Label Definition
S Standard
C Control
T Test Sample
NC Negative Control
PC Positive Control
CO Cut-off Control
PR Positive Reference
SC Serum Control
AC Antigen Control
N Negative

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Report Format Set-up

1. Click on the Report Format Set-up icon.
2. Click on the Report Layout tab.
3. By default all the information in the left column will be included in the final report.
To remove unwanted information from the report printout, highlight an item in the
right column and then click on the Remove button. The order in which
information is displayed on the report can be changed by clicking the Move Up
and Move Down . Clicking Add will add the highlighted item in the left column to
the bottom of the right column. Clicking Insert will insert the highlighted item in
the left column above the highlighted item in the right column. Add All will add all
items in the left column to the right column in the order it appears in the left
column. Information that already exists in the right column will be duplicated.
Clear will remove all items from the right column.
4. Click Validate when finished.

Information that will

be included on the
Report

Function
Buttons

Figure 44: Report Layout Definition Screen

Report Format
1. Click on the Report Formats tab.

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2. Select Format Type by selecting the appropriate radio button (raw data, ratio,
threshold, curve fit, or spreadsheet). Data will be reported according to one or
more of these options as programmed in the assay. The user must define a
format type for each of the different operation types that will appear in the assay
report.
3. Check the Create Matrix check box for results to be displayed in an 8 x 12 array
format.
4. Check the Create Table check box for data to be displayed in a tabular format.
Use the check boxes in the Table Options area to indicate which data to include
in the table. In the Results Order area of Table Options, select the order of
results. Items can be added to the list via the following method:

a. Highlight the desired well type, then click on the button to add the
parameter to the list.

b. Highlight the desired well type from the list, and then click on the button
to remove it from the list.
c. Click on the Add All button to move all well types into the list.

d. Click on the Remove All button to remove all well types from the list.
e. Click the up or down arrow next to the right column to move highlighted well
types up or down in the list.
f. Click Validate when finished.
5. In the Numeric Options area, check the check box to Average the replicates if
needed. Enter the desired number of decimal places the numeric data should be
rounded to. In the Mean area:
a. Select the radio button for Arithmetic mean to perform calculations using
addition (+), subtraction (-), multiplication (*), and division (/). The arithmetic
mean of replicate determinations will be reported.
b. Select the radio button for geometric mean to perform calculations using the
antilog of the mean of the logarithms of replicates. Reporting the geometric
mean is useful when there is imprecision built into the result data.

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Source of
data being
reported

Matrix or
Table
Option

Figure 45: Report Format Definition Screen

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Header Footer
1. Click on the Header Footer tab.
2. Select the desired Header and Footer options to be put at the top and /or
bottom of each report page by checking the check boxes associated with each
piece of information.
3. Click Validate when finished.

Footer
Options

Header
Options

Figure 46: Header / Footer Options Screen

Output to File
1. Click on the Output to File tab.
2. If the data report is to be used with software such as external spreadsheets,
check the Enabled check box.
3. Information can be divided for export using a tab, comma, space or semi-colon
separator by choosing the radio button associated with the desired option in the
Separator area.
4. Select the data to be exported by checking the check box associated with the
desired data in the Select Data to Export area.

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5. Assign a file name and path where the output files will be exported by clicking

on the button in the Output File Name area. The selected data will
automatically export as a CSV (text type) file every time the assay is run.
6. Click Validate when finished.

 Note: A printer driver must be installed for reports to be

viewed using the Matrix software.

Programming Assay Operations

The following Operations can be programmed into an assay:

1. Dilution of controls, standards, and test samples
2. Dispensing of reagents
3. Pipetting standards, controls, and test samples based on the microplate pipetting
template
4. Well-fill verification (to verify pipetting volumes)
5. Plate incubation (from ambient to 500 C)
6. Plate shaking
7. Plate washing
8. Plate reading at a specified wavelength
9. Quality Control assay verification
10. Ratio, Threshold, Curve Fit, Spreadsheet, and Boolean (custom) data reduction

Adding, Deleting, and Changing the Order of Operations in an Assay

1. To add operations to an assay, click on the desired operation icon and drag and
drop the operation icon to the desired location in the programming toolbar.
2. Define the parameters of the operation by clicking on the icon in the
programming toolbar and setting the parameter values in the operation
programming screen.
3. Delete operations from the assay by clicking on the operation icon in the
programming toolbar and dragging and dropping the icon into the trash can icon
in the upper right corner of the Assay Editor window. Click OK to confirm the
action. Click Cancel if the assay should remain unchanged.
4. The order of operations may be changed by dragging and dropping an icon
before or after another icon in the programming toolbar.
5. As the assay is created, text describing the actions taking place in each assay
operation appears on the right side of the screen. Text describing the operation

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icon which is currently highlighted will have blue font. Text describing all other
operations will have black font.

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Programming Assay Operations

Drag & Drop icons from the Operation Operation Toolbar
Toolbar to the Programming Toolbar Delete Icon

Programming Toolbar

Text
Detailing
Assay
Creation

Figure 47: Assay Programming Screen

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Dispense Operation
Defining Dispense Parameters

The dispense operation is used to pipette reagents (reagent blanks, conjugate,

substrate, etc.) to the microplate. Fluids defined as standards, controls and specimens
cannot be transferred to the plate using a dispense operation.
Select All/
Clear All

Dispense Icon

Select
Reagent
Select
Wells

Enter
Volume

Figure 48: Programming Dispense Operation

1. Select the wells the selected reagent will be dispensed to by clicking and
dragging the cursor over center of the wells, by clicking on each well
individually, or by clicking the Select All button.
2. Selected wells will have a yellow √ mark .
3. Use the Fluid drop-down list to select the reagent to be dispensed.

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• If a new fluid must to be added to the Fluids Database, click on the Fluids

button. Click on the button to add a new fluid to the database. (See
Figure 49)

Fluids
Button

Figure 49: Add Fluids Dialog Box

4. Enter the Volume of the reagent fluid to be dispensed.

5. Click Validate.

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Pipetting Operation
About Diluting Samples

The DS2 Automated ELISA System can dilute samples, controls and standards. Dilutions
can be performed in a single stage in standard microplates or in two stages using deep-well
strips. The DS2 adds diluent to a plate or deep well before the sample is added. Clicking
once on a well or well type in the microplate pipetting template allows dilution in the deep-
well strips. The selected wells are outlined red. Clicking a second time on the template
allows dilution in the plate. The outlines around the selected wells will change from red to
green.

The dilution ratios allowed for various microplate types are described below:

Dilution Mode Allowed Dilution Ratios

Microplate Ratios of sample to diluent range from 12.5:1 to

Dilution 1:29 (e.g. 10 μL sample combined with
290 μL of diluent to yield a 1:29 dilution).
Deep-well Strip Ratios of sample to diluent range from 12.5:1 to
Dilution 1:199 (e.g. 10 μL sample combined with 1990
μL of diluent to yield a 1:199 dilution).
Two Stage Deep- Ratios of sample to diluent range from 156:1 to
well Strip Dilution 1:39,601 (e.g. 10 μL sample combined with
1990 μL of diluent in a deep-well, from which 10
μL is combined with
1990 μL of diluent in a second deep-well to
yield a 1:39,601 dilution).

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Setting Dilution Parameters

1. Drag the pipetting operation icon into the programming toolbar.

Pipetting Operation Icon

Drag and Drop

Figure 50: Programming the Pipetting Operation

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2. Click the well locations on the template which will contain a diluted sample, control or
standard.
a. If clicked once, a red circle will appear around the well, indicating that
dilution will take place in a deep well.
b. If clicked twice, then a green circle will appear around the well, indicating
that dilution will take place directly in the well on the plate.

Figure 51: Dilution in Deep-Wells

3. Click on the Definition tab.

4. Choose the “neat” fluid to be used from the drop-down menu.

• Note: When a Test Well type is selected, the neat fluid will automatically
be designated as “sample” and cannot be changed by the user.
5. Choose the Diluent to be used from the drop-down menu.
6.. Select the dilution ratio or absolute volume.

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Definition Tab

Figure 52: Programming Pipette / Dilution Operation

7. Enter the desired dilution formula for each well:

Figure 53: Programming the Pipette Operation (Example of defining a specified

volume)

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Dilution Formula Explanation

1 to …. A ratio of one part concentrate to a specified number of
parts diluent, for a total of parts C + D.

EX: 1 to 10 parts is made up of 1 part concentrate plus 10

parts diluent for a total of 11 parts.

1 in ……. A factor of one part concentrate in a total number of

specified parts. EX: 1 in 10 equals 1 part concentrate and
9 parts diluent for a total of 10 parts.

Volume specified The exact amount of volume of diluent will be pipetted into
deep-well strip or plate. Enter a neat fluid volume and a
diluent volume. If using a deep well for dilution, specify
the target volume. The target volume is the volume of
diluted specimen to be transferred to the microplate
following the dilution step.

8. To perform a two stage dilution in the deep well strip, check the “Two Stage Dilution”
checkbox. Enter in the dilution formula information on the initial dilution tab, then
select the secondary dilution tab and enter in the dilution formula information for
the secondary dilution tab.
9. When performing the assay, if the user should be able to change the dilution
volumes at runtime, enable the option to Allow sample dilutions to be changed at
runtime
10. When diluting specimens in the deep wells, the user may elect to have the
specimens stay in the deep wells a specified length of time prior to being transferred
to the plate by entering the desired time into the Let deep wells stand before
pipetting field. Deep wells may incubate for up to 60 minutes prior to transfer.
Alternatively, the user may elect to pipette diluted specimens immediately after
dilution is completed by checking the pipette immediately after dilution check box.
If neither option is selected, the software will perform all required dilutions prior to
transferring diluted material to the plate.
11. Click on the Optimizations tab.

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Figure 54: The Optimizations Tab

12. Select an option by checking the checkbox to the left of each option. When
diluting in the microplate, the bottom three options are unavailable.

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Options

Option Description
Use new tip for dispense of sample A new sample tip will be used to pipette
each well.
Multishot for dispense sample The same sample tip will be used for
replicates. If fluid for more than one
dispense can be aspirated at one time,
the required number of dispenses will be
aspirated at once and pipetted into the
required wells.
Share dilution wells for microplate replicates Only one dilution will be made for an
(volume will be scaled) individual sample. The dilution will be
used for all replicates on the plate
Share dilution wells across multiple assays Only one dilution will be made for an
(volume will be scaled) individual sample. The dilution will be
used for replicates in all assays on the
current worklist that share a common
sample diluent.
Force level detect before transfer (uses new If selected, a liquid level sense is
tip) performed on each deep well prior to
pipetting the sample to the plate.
Choosing this option will increase the
pipetting time from the deep well strip to
the plate.

6. Click on the Pipette/Mixing tab.

a. Enter the desired speed profile (speed that pipetting takes place).
b. Enter the number of desired mix cycles (the number of times the dilution
mixture will be aspirated and dispensed to ensure thorough mixing before
final pipetting).
Note: Mixing Cycles can only be set for deep well strips. Mixing functions are not
available for dilutions taking place in microplates.

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Figure 55: Pipetting/Mixing Tab

7. By clicking on the View / Edit Pipette Order button, the user can program
which wells will be pipetted to the plate first. For example, if the user
intends to pipette a negative control in the beginning of the plate (NC1),
then samples, then a negative control at the end of the plate (NC2), then
the pipetting order must indicate this sequence. In addition, if the pipetting
order is changed from the default order indicated by the software, the user
must select Use new tip for dispense of sample when pipetting diluted
controls or Use new tip when pipetting directly from the vial to the plate to
ensure the pipetting order is followed.
8. Max post pipette time is the acceptable amount of time that a plate can sit
prior to the next scheduled event being performed once pipetting is
completed. This feature is useful when pipetting plates in parallel, so that
one plate is not inactive for extended periods of time while operations are
being performed on the other plate.

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Pipetting without Dilution

The Pipette Operation pipettes a specified fluid into selected wells. To pipette a control,
standard, or specimen directly from the vial to the plate:
1. Click and drag the Pipette icon onto the assay programming bar.
2. Click on the desired (target) well.
3. Select the desired Neat fluid from the drop down list.

• To add a new neat fluid, click the fluids button.

● Define the Neat Volume by entering the volume (in µl) into the text box. The
Neat Volume is the volume of neat fluid which will be pipetted directly into the
microplate well.

Figure 56: Pipette Test Samples

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4. Select Multishot Allowed and/or Use New Tip. If Multishot is selected, fluid will
be aspirated in one tip to dispense all replicates of an individual test sample or
reagent (up to the volume capacity of the tip). If neither option is selected, if
replicates are present on the microplate pipetting template, the same tip will be
used to dispense all replicates, but multishot will not take place.
5. Select ESP Plus Parameter (Electronic Signature tracking to ensure pipetting
was done properly) if desired. In order for an ESP Plus Parameter to be
available in the drop-down list, an ESP calibration must be performed for the
sample type and the calibration values must be saved (Tools>ESP Calibration).
6. See the “Setting Dilution Parameters” section of this manual for information on
selections in the Plate Options area.
7. Click Validate to save the information.

Fluid to
Pipette

Target
Well
Use new Multishot
tip allowed

Figure 57: Pipette Standards and Controls

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Well Fill Verify Operation

Well Fill Verification is used to track accurate pipetting of fluids into specified wells based on
their OD readings.

Well Fill Verify

Icon

Filter
Selection

Selected
Wells

Figure 58: Well Fill Verification Operation

Setting Well Fill Verify Parameters
1. Click and drag the Well Fill Verify icon to the programming toolbar to add it to the
assay sequence.
2. Select the wells for the well fill verify operation by clicking on the desired wells. A
yellow √ will appear in selected wells.
3. Select the test and reference Absorbance Wavelengths the plate will be read at.
Usually a single wavelength is suitable.
4. Well fill verification can be accomplished in several different ways. The user can:
a. Select the Enabled check box for OD Test. The absorbance from each
selected well will be expected to fall within the specified OD range.
i. To test that each OD falls within a range, check the High OD check
box, enter the highest acceptable OD for each well and enter the lowest
acceptable OD for each well. The user may choose to enter a High OD
value only and leave the low OD value blank. It is also acceptable to
uncheck the check box for the High OD and enter only the lowest
acceptable OD for each well. Select Increment if the previous well fill

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verification results should be subtracted from the active set before

performing the test.
b. Select the Enabled check box for Median Test. Set high and low margins as
percentages around the median. Matrix will calculate the mean OD from the
group of wells, and then calculate an acceptance range based on the entered
percentages.
5. Well fill verification parameters may be entered for more than one group of wells.
To create parameters for more than one group of wells, select a new group
number from the drop down list, select the wells to be included in the new group,
and enter in the verification parameters that apply to these wells.
6. If Blanking on A1 is enabled, the OD from well A1 will be subtracted from all the
other wells before the verification is performed.
7. The user may add a shake step before reading takes place to ensure that no
bubbles interfere with the reported OD. The user can specify a shake time of up to
9 seconds.
8. If any of the wells fail the defined well fill verification criteria, the software will stop
and an alert message will display which requires user interaction to continue.
Therefore it is very important that the user return to the DS2 when a well fill
verification is taking place to ensure no user interaction is required to continue the
timeline.

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Incubate/Shake Operation

The incubate/shake operation specifies a temperature and duration for plate incubation
during an assay, and also allows for shaking. For ambient (up to 25o C) incubations, the
plate will stay outside the incubation chamber. For higher temperatures the plate will move
into the Incubation chamber.

Incubation Icon

Figure 59: Incubate/Shake Operation Screen

Incubate/Shake Settings

1. Drag and drop the Incubation Operation Icon into the Programming Toolbar.
2. Define the Duration by clicking on hours, minutes, or seconds, then clicking on
the up and down arrows. Incubation durations can last up to 23 hours, 59
minutes and 59 seconds.
3. Set the Shortest and Longest duration allowed for incubation. The incubation
duration may be modified from the specified duration to fall within the given
shortest and longest limits by Matrix in order to best-fit assay operations.

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4. Set the Temperature. Matrix will monitor the temperature of the incubation
chamber, showing the current temperature in the upper right corner of the
Timeline.
5. If the temperature selected is Ambient, the user may choose to time the
incubation starting with the first transfer of specimen to the plate by checking the
Start from first transfer to plate checkbox. This check box can only be selected
when ambient temperature incubation is chosen and when there are no
operations inserted in the program between the pipette operation and the
incubation operation (for example, no dispense may be present between the
pipette operation and the incubation operation).
6. Select the radio button for the desired shaking option. The default for shaking
while incubating is off or Do not shake. The user may choose to:
a. Perform a short initial shake by selecting the Initial Shake radio button
and specifying a shaking time.
b. Shake the entire incubation time by selecting the Shake for entire
duration radio button.
7. Select the Speed at which the shaking will take place, (Low, Medium or High).
8. Click Validate to save the settings.

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Wash Operation

A wash operation can consist of Purge, Dispense, Fill, Aspirate, Clean and Soak settings.

Summary of Wash Operations

Operation Description

Purge Dispenses fluid from the dispense wash pins while

the wash head is positioned over the purge tray. A
purge is carried out at the beginning of a wash
protocol to fill the lines to the wash head with the
correct wash buffer and to remove any air bubbles in
the tubing lines.

Clean Dispenses fluid from the clean line from the dispense
wash pins while the wash head is positioned over the
purge tray. A Clean cycle is carried out at the end of
the wash protocol to prevent buffers from crystallizing
inside the tubing lines and causing blockages.
Dispense Aspirates the contents of the well and then dispenses
a specified amount of fluid into the wells. If a bottom
wash is specified, the wash head is then lowered to
the bottom wash position. The fluid will be aspirated
from the bottom of the wells as wash fluid is being
dispensed.
Fill Allows the user to fill the wells with a specific volume.
Aspirate Removes the contents of a well by positioning the
wash pins at the aspiration height in the well and
aspirating the liquid from the wells.
Sweep The aspiration pins move from side to side inside the
well during aspiration.
Super The aspiration pins move in a four-step X pattern
Sweep across the well during aspiration.
Soak The contents of the wells sit for the specified number
of seconds after each dispense cycle. Once the soak
cycle is complete, the fluid is aspirated.

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Volume to Dispense
per cycle
Number of Cycles

Specify Fluid

Purge
Volume

Clean
Volume

Figure 60: Wash Operation Parameters Screen

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Setting Wash Parameters

1. Drag and drop the Wash Operation Icon into the programming toolbar.
2. Set the number of Wash Cycles to be performed, according to the assay
protocol. The number of cycles can be 1 – 9.
Note: The plate frame must contain whole strips for a wash operation to be performed.
Dummy wells may be used to fill in empty spaces to create a whole strip.
3. Select to wash the plate Stripwise or Platewise.

• If washing Stripwise, all cycles are completed on one strip before moving to
the next strip. For example: 3 cycles are programmed with a 5 second soak
after each aspirate-dispense cycle. The DS2 will aspirate and dispense the
first strip, wait 5 seconds, and then repeat this cycle 2 more times on the first
strip prior to performing any cycles on the second strip.

• If washing Platewise, each cycle is completed on all strips on the plate

before another cycle begins. Using the same example scenario as the
stripwise mode, the washer will aspirate/dispense into the first strip, move to
the second strip and so on down the plate, soak the whole plate for 5
seconds, then begin the second cycle.
4. Constant Timing can be set if the time the wash operation lasts should be kept
consistent regardless of number of strips (samples) processed on a given day.
Matrix will add waiting time when washing partial plates in order to simulate the
time to wash a complete plate.
EX: 3 strips on the plate are being washed in strip mode. After finishing the third
strip, the washer will step through the remaining nine columns as if a whole plate
were being washed for three cycles per strip. The wash head will then be parked. If
cycles are performed in plate-wise mode, the washer will complete the first cycle and
stay stationery over the third strip for the time it would take to aspirate / dispense the
remaining nine strips. The washer then moves back to the first strip for the second
cycle, and continues in this manner for the rest of the number of cycles programmed.
5. Do Final Aspirate is used to empty wells before the next operation is performed.
If Do Final Aspirate is not checked, wash solution will remain in the wells
following the wash step.

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6. Select a Sweep Mode if extra aspiration is required to completely empty the

wells of droplets of wash buffer before the next operation is performed. Sweep
mode options are:

• None- normal aspiration will take place.

• Sweep – Normal aspiration takes place, then the aspirate pins move once
across the well in a right to left motion to remove wash buffer which may be
pooled at the well edges.

• Sweep on last cycle only – Sweep takes place only on the last programmed
cycle.

• Super sweep – Normal aspiration takes place, then the aspirate pins move
across the well in an x-patterned aspiration.

• Super sweep on last cycle only – Super sweep takes place only on the last
programmed cycle.

 Note: Select No Sweep and disable bottom washing whenever a C-

bottom, U-bottom, or V-bottom plate is being used.

 Note: Sweep should be used carefully to avoid scratching the bottom

of the microwells.

7. Set the Purge volume and select the desired wash buffer.

• Purging fills the tubing lines with the specified wash buffer prior to beginning
the wash cycle.

• Purging prevents the first few strips from getting air or bubbles dispensed into
them.
8. Set the Clean volume and select the desired clean fluid.

• Note: A fluid must be added to the Washerfluid database with the load
position specified as the “clean line” in order for options to appear in the drop
down list.

• Cleaning uses fluid from the external bottle attached to the rear of the DS2
(bottle C) to clean the tubing lines following the last wash cycle.

• A cleaning routine should be performed before the DS2 is shut down, or

periodically during the day. Cleaning ensures that particulates in wash buffers
do not cause blockages in the wash head pins.
9. Set a soak time in seconds by entering the desired time into the Soak between
cycles for data entry field.

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10. The Synchronize Soak Delay from Transfer Timings check box can be
enabled to minimize OD drift across the plate due to differing incubation times
between the strips.

• The DS2 will synchronize column soak time based on the time taken to
transfer samples to the microplate. For example, if pipetting takes 15
minutes, and plate washing takes 3 minutes, the first samples will be
incubated for the correct amount of time, while the later samples would
incubate a shorter amount of time. This timing problem can be resolved by
synchronization.

• There must be a Pipette step in the assay preceding the Wash operation in
order for the synchronization checkbox to be enabled.

• There cannot be any operations in between the wash and the pipette
operation in order for the synchronization option to be available. The only
exception to this rule is the incubation operation. The incubation operation
may be inserted into the timeline in between the pipette and wash operation;
however the Start from first transfer to plate option must be enabled.

• The synchronization check box is only enabled in strip-wise washing mode.

11. Enter the Dispense volume by using the up and down arrow keys. Dispense
volumes may be from 50 to1000 µL.

• Choose the wash buffer from the washerfluid database drop-down list.

• To add a wash buffer to the washerfluid database, click on the Fluids button.
Follow the prompts to name and define the fluid. The user may select either
the A or B bottle location, but it is recommended not to specify a location if
multiple wash solutions will be used on the instrument.
12. Use Bottom Wash if fast washing is required.

• Bottom wash will squirt bursts of buffer into the well, while aspirating at the
same time. Bottom wash can save time and buffer if used instead of an extra
wash cycle. Bottom wash may be used with either plate or strip washing
mode.

• Specify the number of Cycles and the Volume of wash buffer to use by using
the up and down arrow buttons next to the associated parameter. 0 - 5
bottom wash cycles may be programmed using 0-1000 µL.
13. Check the Fill check box to dispense fluid. The dispense and bottom wash
options must be set to zero for the Fill option to become available. Fill may be
used in either strip or plate-wise mode.

• The Fill operation may be used if a long soak time is needed. Program the
Fill in the Wash operation, then program an Incubation operation for the
length of time needed, then program another Wash operation into the assay.

• Fill may also be used for well fill verification to test the washer dispense
accuracy.

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14. Check Aspirate if wells only need to be emptied of fluid and do not need
washing. The Aspirate checkbox does need not be checked if wells are being
washed normally.

Read Operation

The Read operation allows the user to choose the appropriate wavelength filters for use
with the assay and instructs the DS2 to read the absorbance of each well containing
fluid.

Setting Read Parameters

1. Drag the Read Operation Icon into the programming toolbar.

2. Select the Primary Test Filter and the Primary Reference Filter (if dual
wavelength mode is used). To change the default filter wavelength settings, use
the Tools > Absorbance Filter menu. To install new filters, refer to the Service
and Maintenance section of this manual.
Read Icon

Wavelength
Shake Time

Figure 61: Read Operation Parameters Screen

Wavelengths: Wavelengths for OD readings are determined by the specific filters installed
in the reader. The correct wavelength values must be entered for the installed filters in the
Absorbance Filters menu for valid results.
If using single-mode, a primary test filter wavelength must be entered. If using dual mode,
both filter wavelengths must be entered.
Dual Wavelength Mode:

The dual wavelength mode can be used if necessary to reduce errors caused by dirt and
scratches on the bottom of the wells as these artifacts tend to scatter radiation equally,
regardless of wavelength.

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The choice of test and reference wavelengths for the dual wavelength mode depends on the
particular enzyme/substrate reaction being tested. However, the following rules should
usually be followed:

1. The test wavelength (λt) should be at or near the maximum absorbance of the
reaction product.

2. The reference wavelength (λr) should lie outside the absorbance band of the
reaction, but not far removed.

The Reader subtracts the absorbance at the reference wavelength (λr) from the absorbance
at the test wavelength (λt) to minimize the effect of background noise.

405 nm λt λr 690 nm
FILTER WAVELENGTH

Figure 62: Dual Wavelength Selection

Shake Time: The shake time (in seconds) is performed prior to reading the plate. Plate
shaking may be used to eliminate air bubbles from the sample and to give the sample an
even meniscus.
Blank Mode: Wells to be used as blanks are specified in the microplate pipetting template.
If there are no blank wells specified, Matrix will use air as the reference level for 100%
transmission.
If more than one well is selected to be a blank in the microplate pipetting template, the ODs
of the average of the wells will be subtracted from all other wells on the plate.

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Quality Control Operation

Quality Control Operation equations are used to ensure that an assay has worked properly
and that the data generated can be accepted. The QC equations place criteria on the raw
OD data, or data generated by a curve fit, threshold, ratio or spreadsheet operation.
1. Well ODs are accepted or rejected using criteria such as comparison against a
control well or against a numerical value.
2. QC equations may be applied to any Well Type that has been defined in the
template. If the QC equation fails, the user may elect to suppress all data from
being output to subsequent operations.
3. Quality Control operations are context sensitive, as some QC equations may only
be applicable to the results of a Curve Fit operation or to the results of a
Threshold operation.

Quality
Control Functions Report
Icon List Options

Equation
Bar

Figure 63: Quality Control Operation Screen

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Setting Parameters for the Quality Control Operation

1. Drag the Quality Control Operation icon into the programming toolbar.
2. Double click on the desired Function to add it to the equation. Functions are
used to generate the equations. Continue to add functions until the equation is
defined.
a. Mathematical functions (such as +, -, =, >, <) may be typed into the equation
box.
3. Type in a Fail Message if desired. This message will be displayed in the report
when the equation criteria have not passed.

4. Click on the Add button to add the equation to the list of quality control
acceptance criteria.
5. Click on the Clear button to reset the Equation and Fail boxes so additional
equations can be created.
6. To change an equation already added to the list, highlight the equation to be
edited, make the desired changes in the equation text box, and click Change.
7. To remove an equation from the list, highlight the desired equation and click
Remove.
8. The Quality Control equation checks will be performed in the order they appear in
the list. Therefore if one equation depends on another equation taking place first,
the equation which must be performed first must appear in the list before the
dependent equation (for example: the “I” function equation must appear closer to
the top of the list than the “valid” function equation). To change the order of the
equations, highlight the desired equation and click Move Up or Move Dn.
9. Options for QC Report handling include the default reporting of all QC results
(Full QC Report). If the QC fails, all other results can be suppressed by checking
the Suppress results if QC fails checkbox. This feature may be important if
data is automatically being exported from Matrix into other files. QC results can
also be related to an individual reagent lot by checking the Lot specific
checking of control values checkbox (the Request or Require kit lot data
checkbox must be enabled in the Assay Title Page screen for the lot information
to be available for reporting).
10. Select options for Pos/Neg, Curve Fit, and/or Auto Outlier Removal, if the options
are available. A Curve Fit or Threshold operation must to be included in the
programming toolbar before Quality Control Operation icon in order for these
choices to be enabled.

Quality Control Functions

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See Appendix C for function descriptions and examples which can be entered into Quality
Control Equations.

Typical Quality Control Equations

Example: the template includes 4 NCs and 3 PCs

1. If any NC OD value is greater than 25% higher or lower than the mean OD value of all
the NC’s, it must be rejected, enter:

0.75*NC<=NCi<=1.25*NC
2. If the test must be rejected if one of the NC OD value fails the first Quality Control
equation, enter:
valid(NC)>=3
3. If the average OD value of the Negative Controls must be more than 0.5 OD, enter:
NC>0.5
4. If the average OD value of the Positive Controls must be greater than 20% of the
average OD value of the Negative Controls, then write:
PC>0.2*NC
5. If the average Negative Control OD value must be less than half of the average PC
OD values, enter:
NC<PC/2
6. If the CV% of the Negative Control must be less than 15%, enter:
CV(NC)*100<15

Ratio Operation

The Ratio equation is used to convert raw data using mathematical equations, which often
expresses sample results as a ratio of a control value. Ratio calculations are frequently used
in competitive inhibition assays or when detecting an increase in some factor over a normal
baseline value. Every value on the plate is fed into the equation and the resulting values are
reported and passed on to subsequent operations. Ratio operations can also be used to
multiply wells on the plate by a correction factor, or to perform any calculation which is
required for further data processing.
EX: In the equation “Sample/PC”, all sample OD values will be converted to a ratio of the
average OD value of the Positive Controls.
Results from the ratio equation may be flagged with a user defined “result” or “flag” by
clicking on the Results Flagging tab.
EX: In the equation “Sample>NC then SICK” data calculated from the “Sample/PC” equation
will be flagged based on whether the results are higher or lower than the calculated negative
control value.

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Ratio Icon

Figure 64: Ratio Operation Screen

1. Drag the Ratio Operation icon into the programming toolbar.

2. To create a Ratio equation, double-click on the Functions which will make up the
working components of the equation.

3. Common arithmetic functions, such as addition (+), subtraction (-), multiplication (*),
or division (/), etc. may be typed into the equation box.

4. Enter the Units the data is to be reported in, such as “mg/dL”.

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Condition Expression
Results Flagging Tab

Figure 69: Ratio Results Flagging Screen

Figure 62: Ratio Results Flagging Screen

Function List

Figure 65: Results Flagging for the Ratio Operation

5. Click on the Results Flagging tab in order to specify a phrase that either replaces a
numerical result or is displayed next to a result. The phrase will be initiated whenever
the numerical result meets the criteria programmed. Results Flagging is optional and
should not be used if an LIS is being used.

• The Condition is the Results Flagging expression, such as “Sample>NC”. If

text is to be reported instead of a numerical result, it can be typed into the
Result box. Use of a Flag indicates the entered text will be reported along
with the numerical result. Either a Result or a Flag can be entered, but not
both.

• Examples of Results Flagging:

o The text “20 mg/dL” may be displayed instead of the actual numeric
value whenever a test result is less than 20 mg/dL if the text string is
entered into the Result field.
o A flag of “Abnormal Low” might be displayed along side the numeric
result if the result is less than 20 mg/dL and the text string is entered
into the Flag field.

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Ratio Function Entries

See Appendix D for possible mathematic and function entries which can be used to write
Ratio equations.

Typical Ratio Equations

1. To convert all sample OD values to a ratio of the average OD of the Positive Control
replicates, enter the equation: Sample/PC.

2. To convert all values into larger numbers than the OD units, enter an equation such
as: sample/0.25.

3. Using an equation such as PC/(NC-BLK) (Positive Control divided by the Negative

Control minus Blank well ODs) will cause DS Matrix to replace all values on the plate
with the result of this calculation.

4. There are two methods to multiply all values on the plate by a correction factor:

• Sample*CustomVariable
• Sample*VariableX (where X is replaced by an integer)

When these equations are entered, the user will be prompted at the beginning of the
load wizard to enter the value for the variable.

 Note: Check the Ratio radio button when setting up the Report
Format in an assay to have ratio information included on the report
in either a Matrix or Table format.

 Note: When creating ratio equations, use the Well Symbols from
the Template to create the equations.

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Threshold Operation

The Threshold Operation converts raw OD data into symbols denoting positive and/or
negative results which fall above or below a user defined threshold. In order to use this
operation, Threshold limits must be defined.
A negative OD limit is set using the “–” data label and a positive limit set using the “+” data
label. These positive and negative limits are required to use the limits function. Three
additional positive results levels (++, +++, and ++++) are also available, but not required.
Threshold limits may be entered directly into the equation textbox as absolute numbers. A
result that falls above or below the value entered will be recorded as positive (+) or negative
(-) symbol instead of the actual value. The value entered for the threshold limit may be
based off of raw data, ratio, curve fit or spreadsheet output.
If the – value is lower than or equal to the + value then results below the –value are
negative and results above the + value are positive.
If the – value is higher than the + value, then results below the + value are positive
and results above the – value are negative.
Alternatively, conditions may be introduced into the limits equations. For example, test
sample OD readings may be compared to control OD readings or the average of a number
of samples to determine if they are a positive or negative result.
DS Matrix leaves a grey zone when there is a gap present between the values programmed
for the – and + equations.
The user can change threshold labels to any descriptive words or numbers. For example,
the default “-“ label may be changed to “Negative” by clicking on the text box and typing in
the desired text.

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Functions

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Well type limit

Value Limit

Figure 66: Threshold Operation Screen

Entering Threshold Equations

1. Drag and drop the Threshold Operation icon into the programming
toolbar.
2. Enter absolute values (OD, concentration, etc.) for the positive and negative limit
levels (if values are being used from another operation (such as a curve fit), that
operation must appear in the programming toolbar before the Threshold
Operation).
3. Alternatively, the user may double-click on a function in the Functions list box to
enter this function. Arithmetic operators may be entered.
EX: PC*2 for level +++
4. In the Label column, change the default labels to words or other labels as
desired.
5. When all equations and labels have been entered, click Validate.
The DS Matrix program ensures each equation is valid and contains no errors. If any of the
equations are not valid, the DS Matrix program will display an error message. If this occurs,
edit the equation as required for correctness.

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Curve Fit Operation

In the Curve Fit operation, DS Matrix software constructs a standard curve graph using OD
values from standards of known concentrations.

From the graph, the concentrations of test samples are determined by finding the
concentration that corresponds to a given OD reading. Concentration data is always plotted
on the X-axis, and OD data is always plotted on the Y-axis.
To use the Curve Fit operation, standards of increasing concentrations must be included in
the assay template.
Only one curve fit operation can be programmed into any given assay. To test data using
more than one curve fit, another assay must be created. When the Report is generated from
the first assay, data can be recalculated and another curve fit generated by clicking on the
New Assay button in the report viewer toolbar and generating a report using different a
different assay.

Specify
Standard
Concentration

Standard
Concentrations

Figure 67: Curve Fit Concentration Entry

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Entering Standard Concentrations

1. The plate template is displayed in the Curve Fit Operation Standards tab screen.
2. To enter Standard Concentrations permanently into the assay, select the Now
radio button. If standard concentrations will be changed frequently, the user may
select the At run time radio button to enter standard concentration values at run
time. To enter the standard concentrations using the Now radio button, enter the
concentration for Standard 1 (S1) into the Concentration Entry box. Click on the
Standard 1 well(s). A small box will appear in the lower right of the well, showing
what concentration was entered for that standard.
3. Enter the concentration value for the second standard in the Concentration Entry
box .Click on the wells for the Standard 2 to set the concentration for Standard 2
(S2). Continue this process until all standards have an associated concentration.
• Note: If performing a log/log curve fit, a standard with a concentration of
zero should not be defined in the curve fit operation.
4. To increment each standard concentration by a specific amount, click the Addititive
Factor radio button and enter the number to be added.
EX: Standard 1 (S1) has a concentration of 1 and an Additive Factor of 2 is used. The next
standard (S2), upon clicking the well, will automatically be assigned a value of 3. The next
standard selected will be assigned a value of 5 and so on until all standards have an
assigned concentration.
5. A Multiplication Factor can be used to increment each successive standard by a
specified amount. Click on the Multiplication Factor radio button and enter the
multiplication factor. The first standard must be greater than 0 for this feature to work
properly.
EX: If the first standard (S1) has a concentration of 2, and the Multiplication Factor is 4,
then the next standard well selected (S2) will automatically be assigned a concentration of
8.
6. A Variable Standard Multiplier can be used for standards entry. The Multiplier
Factor radio button must be selected and the Variable Standard Multiplier box
must be checked.
a. The first standard concentration must be greater than zero.
b. Click on the first set of standard wells (S1) to enter the first concentration.
Enter the multiplier for the next standard in the Multiplier box, then click on
the second set of Standard wells (S2). Enter a third multiplier for the third set
of standard wells. Click on the third set of standard wells (S3) Continue until
all standards have an assigned concentration.
EX: If the concentration of the first standard (S1) is 1, and the first multiplier is 2, then the
first standard (S1) will have a concentration of 1 and the second standard (S2) will have a
concentration of 2. If a multiplier of 4 is then entered the third standard (S3) will have a
concentration of 8.

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7. Units can be entered as mg/ml, µg/ml, etc. by entering the desired units in the Units
box.

Axes
Selection

Figure 68: Curve Fit Type Selection Screen

Fit Selection
1. Click on the Fit Type tab in the Curve Fit operation.
2. Highlight the type of regression DS Matrix should use to generate the graph. See
Appendix C for equations defining curve fits.

Fit Type Description

Linear Linear polynomial regression

Quadratic Quadratic polynomial regression

Cubic Cubic polynomial regression

Quartic Quartic polynomial regression

Polygon Point to point straight line fit

Cubic Spline Smooth curve cubic spline fit

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Sigmoid S-shaped curve fit with four definable parameters

Log/Logit S-shaped curve fit with definable parameters

Akima Smooth curve which passes through all data points

Calculation Options
1. Check the Average the standard replicates checkbox to have the mean of the
standard replicates used to generate the curve, rather than individual replicate
points. Averaging the replicates will make the graph easier to interpret.
2. Data can be extrapolated beyond the lower and higher ends of the graph if the
Extrapolate the data checkbox is checked. Extrapolation is usually valid
scientifically if a linear regression curve fit is used, but not if a sigmoidal fit is
used.

Calculation Option Description

Average the Standard Replicate values for standards are

Replicates averaged before they are used in curve
fitting.

Extrapolate the Data The graph is extended beyond the plotted

data points by extending the curve.

3. There are 4 axes options for data plotting. To select an Axis Scaling option, click
on its corresponding radio button.

Axes Selection
Axes Scaling X-Axis Y-Axis

Lin/Lin Linear Linear

Log/Log Logarithmic Logarithmic

Log/Lin Logarithmic Linear

Auto Selected by Matrix Selected by Matrix

4. Any scaling options that are not compatible with the chosen curve fit type will be
disabled.

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EX: If a Sigmoid fit type is highlighted, the axes selections will be disabled, but the Sigmoid
Parameters options will be active.
5. All four of the Sigmoid, S-shaped curve Sigmoid Parameters are user-definable.
To define a parameter, check the box for the desired parameter and type a
number in the textbox. If no options are selected, Matrix will set the A parameter
to the lowest standard concentration and the D parameter to the highest standard
concentration. Matrix will then define the other standard points to obtain an S-
shaped curve.
6. The number entered for maximum Iterations is the maximum number of times
Matrix software will attempt to construct a satisfactory plot before aborting the
operation. The default value of 20 is suitable for most applications , however the
minimum allowable number of iterations is 1 and the maximum number of
iterations is 29999.

Graphing Options

Graph Title

Axis Labels

Figure 69: Options for Graph Scaling

1. Click on the Graph tab in the Curve Fit operation. By default, a graph will always be
produced based on the regression chosen.
2. Enter a title for the graph (if desired) by entering the title in the Title textbox.
3. Titles can also be entered for the vertical and horizontal axes by entering the desired
titles in the “Label:” text boxes.
4. By default Matrix will use Auto Scaling to determine the best fit for the vertical and
horizontal axes based on the range of data.
5. If Manual scaling is chosen, the user can then define the minimum and maximum
numbers to be used to define the axis when the curve fit is displayed graphically. In
the Minimum box the lowest value for either the standard concentration or OD may

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be entered. In the Maximum box a higher OD or standard concentration may be

entered. Tick Marks will divide the axis evenly between the min and max entered
numbers, incrementing by the value entered into the text box.

Results Flagging
1. Click on the Results Flagging tab in the Curve Fit operation.
2. Results Flagging equations are used to specify criteria for generating a text flag
when the specified results are encountered.
The Condition is the Results Flagging equation.
The Result is the text to be reported instead of the numerical value.

Results Flagging Tab

Equation
Entry

Add, Move,
Delete Buttons

Figure 70: Results Flagging Tab

The Flag is the text to be reported along with a calculated numerical value.
3. An unlimited number of Results Flagging expressions can be defined for an assay.

The Spreadsheet Operation

The spreadsheet operation allows the user to create a table or matrix of data generated by
adding or subtracting well values from one another. The user can manually input the calculation
to be performed on a well by highlighting the well and entering an equation (For example: B2-
C2). Using Auto Difference Mode allows the user to select options which can be applied to the

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whole spreadsheet. A custom functionality is also built into the spreadsheet operation (Boolean
Function Assay). This functionality should only be used by those performing certain assays.
Spreadsheet
Operation
Spreadsheet Icon

Equation Entry

Figure 71: Spreadsheet Operation Screen

1. Click on the Spreadsheet Operation Icon and drag it into the programming
toolbar.
2. Highlight a cell in the spreadsheet and enter a calculation or formula for that
individual well, for example A1 – H12. (This will take the incoming data
reduction result from the well at H12 and subtract it from the incoming data
reduction result from the well at A1.) The resulting value will be the output for
that cell. This result will be passed to the next data reduction step.
3. Use the buttons to facilitate spreadsheet equation entry:
• Select the Cut button to remove a calculation from a cell, and then use
the Paste button to paste the calculation into the desired cell.
• Select Copy to copy a formula, and Paste to move the formula from one
cell to another (the calculation cells will offset to reflect the selected cell).
• Select Delete to remove a calculation from a cell and permanently
remove the calculation from the spreadsheet.
• Clear All will remove calculations from all cells in the spreadsheet
operation.
4. Alternatively, the user may select the Auto Difference Mode button and
select a formula to be applied across the entire spreadsheet. Auto Difference
Mode offers the user pre-programmed automatic subtraction equations (see
table: Auto Difference Equations)

Table: Auto Difference Equations

Equation Calculation performed

Rows A-B A-B C-D E-F G-H
Rows B-A B-A D-C F-E H-G

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Rows B-C * B-C D-E F-G

Rows C-B * C-B E-D G-F
Columns 1-2 1-2 3-4 5-6 7-8 9-10 11-12
Columns 2-1 2-1 4-3 6-5 8-7 10-9 12-11
Columns 2-3 * 2-3 4-5 6-7 8-9 10-11
Columns 3-2 * 3-2 5-4 7-6 9-8 11-10
Halves 1-7 A1-A7............H6-H12
Halves 7-1 A7-A1............H12-H6
Halves 2-7 * B2-B7............G6-G11
Halves 7-2 * B7-B2............G11-G6
Halves A-E A1-E1............D12-H12
Halves E-A E1-A1............H12-D12
Halves B-E * B2-E2.............B11-E11
Halves E-B * E2-B2.............E11-B11

* These options ignore Columns 1 and 12, Rows A and H.

Figure 72. Selecting an Auto Difference Mode Equation

Figure 73. Auto Difference Mode Equation applied to spreadsheet (Row A-B)

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Results Flagging
4. Click on the Results Flagging tab in the Spreadsheet operation.
5. Results Flagging equations are used to specify criteria for generating a text flag
when the specified results are encountered.
The Condition is the Results Flagging equation.
The Result is the text to be reported instead of the numerical
value.
The Flag is the text to be reported along with a numerical value.
6. An unlimited number of Results Flagging expressions can be defined for an assay.

Saving an Assay Program

1. When all of the operations in an assay have been programmed, click on File > Save
As from the main Matrix toolbar.
2. Type in an Assay Name (required) and Category (optional). Assays may be
grouped into categories for ease of retrieval.
3. Click OK.

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Assay Name
(required)

Assay
Category
(optional)

Figure 74: Save Assay As Dialog Box

Modifying an Assay
1. Select File > Assay Editor from the main Matrix menu bar. Select File >
Open from the Assay Editor menu bar. The Open dialog box is displayed
(See Figure 75).
2. Select the assay to be modified from the drop-down list, and then click OK.
3. Modify the assay operations and/or data reduction steps as desired.
4. After modifying assay settings, save the changes to the assay using File >
Save.

Figure 75: Open Assay File Dialog Box

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 Chapter 6 – The Worklist

Chapter 6 – The Worklist

Creating a Worklist
A Worklist is created to define which assays will be run on which specific specimens. The
worklist specifies the samples that are to be run, their location in the sample rack, and the
assay(s) to be run on each sample.

 Note: A worklist can be created only after at least one assay has
been created. The worklist can include assays run on one or two
different microplates.
Up to 12 assays can be run on one plate if the assays have the
same incubation, reading, washing, and shaking specifications.
 Only one worklist can be open at a time, although multiple
worklists may be entered on the Timeline.

To Create a New Worklist

1. Select File > Worklist Editor from the Matrix menu bar, or a prior saved worklist
can be opened by clicking on File> Recent Worklists.
2. Select a new or saved Sample Batch from the drop-down list. A sample batch is
defined by its size (the number of samples entered, up to 100) and by the sample
IDs assigned to the physical location of the sample tubes. Once a Sample Batch
has been defined, it is saved, and can be edited up until the time worklist
processing begins. The Matrix software default name for a batch is Sample
Batch followed by the next available sequential number. This name can be
changed by the user.
3. When creating a new worklist, select the Number of samples by clicking on
sample tubes or by changing the number in the Number of Samples text box.
The rack locations containing tubes will turn green and unused rack positions will
remain gray.

Assigning Sample IDs

4. Sample identification can be auto-assigned or barcoded. If sample identification
is automatically assigned, the name will default to be the sample batch number
followed by a sequential number. For example: if a sample batch named ”SAM”
is being run, the sample IDs will be auto-assigned as SAM-1, SAM-2, etc. Click
Assign to assign the specimen IDs,
OR
5. If the user wants the specimen ID to begin with text other than the sample batch
name, then the user should check the Use Pattern checkbox. Matrix will use the
text entered in the Use Pattern textbox for all sample IDs, followed by sequential
sample numbering. For Example: If the pattern ABC is entered, the sample IDs
will be ABC-1, ABC-2, ABC-3, etc. Click Assign to assign the specimen IDs.

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6. Click the Next button.

Entering Sample IDs by Bar Code

1. Click the Scan Bar Codes radio button. The Verify Bar Codes checkbox is
checked by default. When the checkbox is enabled, test sample tube barcode
labels will be read twice to ensure accurate scanning and positioning.
2. Click Next. The “please load samples now” dialog box displays. Load the sample
racks, and click OK when done. Samples may also be loaded prior to creating a
worklist.
3. The robotic arm will move to the scanner. When prompted, pull out the sample
rack and push it back in so the scanner can read each bar code label.

4. Click the button when done.

5. The samples rack screen will display with the samples ID from the scanned bar
codes. A red arrow shows which rack the tubes are in. If a bar code has been
properly read, the tube circle will be green. For a missed barcode, the tube circle
will be red.
6. Attempt to re-scan barcodes which did not enter successfully. If scanning
continues to be unsuccessful, manually enter the sample ID where the tube circle
is red. The tube circle will turn orange after the ID has been manually entered.
7. Select the assays that will be run and click Done (for more information see the
“Choose Assay” section of this manual).
8. If the verify ID checkbox was enabled, the sample rack screen will prompt the
user to “Re-scan”. Rescan the sample rack. The software will ensure the
barcodes scanned match the first barcode entry. Any tube positions with mis-
matched barcodes will turn red.

9. Click the button when done.

10. Sample IDs will appear on the report when the assay specifies that data
reduction operation data should be displayed in a Table format (instead of a
Matrix format) and the Sample ID option is checked.

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Sample Batch
Name/Identifier
Enter number of
samples
Use Pattern to
specify root of
sample IDs
Assign
Sample IDs

Figure 76: Worklist Sample ID Entry Screen

Rack
Location
Assays
Added

Assay
Selection

Sample
Checkbox

Figure 77: Worklist Select Assay Screen

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Choose Assay
1. After the sample ID assignment is complete, click the NEXT button.
2. Choose the assay to be run, then either click on the Add Assay button or double
click on the assay name. An orange strip of check boxes will appear next to the
sample IDs.
3. Add additional assays as needed.
4. By default Matrix assumes that all samples are going to be tested using the
assays chosen. By unchecking the checkbox next to an individual sample ID, the
sample will not be tested using that assay.
5. Once the Sample Batch has been assigned to an Assay, it is called the Worklist.
6. To save a worklist (optional), go to File > Save Worklist after selecting the assay
but before clicking the Done button.

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Modifying the Dilution Ratio at Runtime

1. Open a worklist or create a new worklist by clicking on File > Worklist Editor
from the Matrix main menu. A worklist can also be opened by clicking on File >
Recent Worklists (only saved worklists will appear in this list).
2. The assay selected in the worklist must be programmed to perform a dilution
step and the box must be checked for Allow Sample Dilutions to be Changed
at Run Time.

Option to dilute samples at

runtime must be enabled
(checked)

Figure 78: Pipette Operation Screen

3. Click on the Dil or Dilution Button as shown in Figure 79.

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Edit Dilution
Button

Enter
Dilution
Change

Figure 79: Runtime Dilution Change Screen

Modifying the Dilution Ratios

1. Original dilution parameters will show in the left column of the Set Dilution
window.
2. Type in modified parameters for running assay. Only the volume of diluent can
be changed at runtime, not the volume of sample. Change the dilution for each
individual test sample as required.

3. Click OK. The sample dilution button (Dil) for the sample ID will turn green.
4. The Revert button erases any edits made and the test sample dilution will be
performed according to the original dilution values.
5. Once the assay is selected, dilutions are modified (if required) and the Done
button is clicked, DS Matrix sets up a schedule of assay events.

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6. At the top of the Timeline are buttons which allow changes to the Timeline
Schedule. Active buttons will flash, while inactive buttons will remain greyed out..

Pause Play
Edit
Zoom Abort Skip Plate Add Start
Assay

Figure 80: Timeline Buttons

Button Symbol Action Status

Accept Essentially a start button, Timeline Flashing

is acceptable. Once accept is
clicked the timeline cannot be
changed and will begin
processing.

Edit Allows the sample batch and Flashing

assay to be changed on a
scheduled plate

Add Allows a second worklist to be Flashing

scheduled

Fit Next Allows the user to change the Not

scheduling of a second worklist Flashing -
added to the timeline. disabled

Pause Stops the Timeline at the current Not

operation until the Play button is Flashing -
clicked. disabled

Abort Stops the Timeline and displays a Not

Yes / No dialog box for aborting a Flashing -
plate or the entire Worklist enabled

Play Resumes the Timeline from the Not

point the Pause button was Flashing -
clicked. disabled

Skip Advances the Timeline by Not

skipping wait times in the Flashing –
schedule. Not all wait times can disabled
be skipped.

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Zoom IN Opens up Timeline for closer view Not

Flashing -
enabled

Zoom Out Backs out Timeline for broader Not

view Flashing -
enabled

Position Changes Timeline position and Not

zoom on the screen for the Flashing -
optimal view. enabled

7. Click the Accept button if no editing or assay additions are needed. The Timeline
will go from inactive to active status.

• Note: All reagents and consumables must be ready to load on the

DS2 when the Accept button is clicked. Items such as tips may be
loaded before clicking accept. Waste may be emptied prior to
clicking accept. All reagents (as much as possible) should be in the
appropriate vial and ready to load on the DS2 when prompted. If the
load procedure is not performed within the specified timeframe,
timeline conflicts may occur.
8. The Load Samples wizard appears followed by the Load Consumables wizard
when the assay reaches the start line. The Wizard will request that the sample
racks, plates, controls, standards, diluents, reagents, and wash buffers are
loaded. The system will complete the wizard by prompting the user to empty the
waste containers. The wizard will indicate racks and positions into which fluids
should be placed according to what is programmed into each assay operation.
9. Clicking the Abort button allows the user to stop the entire worklist.
10. Once the consumables are loaded, the Skip button on the main menu bar may
be clicked to skip the wait time before the first assay operation.

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Monitoring Run Status

Timeline View
The Timeline View Window displays the scheduled timing of all assay operations.
The Timeline View shows the user when events will occur (such as loading
consumables), how much time is remaining until worklist/assay completion, and
the current assay step.
Current Accept Button
Time

Start Line

Assay
Operations

Load
Consumables

Figure 81: Timeline View Window

Checking Consumables Status

1. For a report on the status of consumables during a run, click on the button
at the bottom right of the Timeline window.
a. Consumables include all fluids (excluding samples), tips (sample and
reagent), plates, washer fluids, and deep-well strips.
2. The Consumables Status Screen (See Figure 82) will display the name of the
reagent, the reagent volumes, the number of tips left, and which assay is
running.

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Assay File Name

Wells Tested

Remaining Tips

Figure 82: Consumables Status Screen

3. To show the status of a different neat fluid (reagent), click the buttons
beside the fluid tube. To show the status of a wash buffer, click the Washer
Fluids Tab directly under the fluid tube.
4. The plate layout shows the wells being tested. At the top of the plate layout is the
file name of the assay being run.
The Report

After a plate is finished testing, reports become available to view, save and print. The list of
recent reports can be seen on the main DS Matrix screen.

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Report
Button

Plate ID

Figure 83: Retrieve Report

1. To see the Report immediately after a plate is finished, click on the

button. The report for the last completed plate is displayed.
2. To review previous plate data, double click on the desired plate ID or highlight
the desired plate ID and click the report button.
3. To sort plate reports or to find the data for a plate tested on a specific date, click
the View All Reports button.

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Figure 84: Sort Reports Screen

4. Uncheck the Show All box, and change the range of dates to search for the
desired reports. Click the Submit button.
5. Highlight the desired report in the list and click the Open button to display the
Report. Information included is displayed according to how the report was
formatted when the assay was created.

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Figure 85: Report Page One

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Figure 86: Report Viewer Toolbar

6. At the top of the report screen is the Report Viewer Toolbar. From this toolbar
the Report may be edited and printed. The report view, font type, and font size
can be changed. Most reports will be multiple pages. To scroll through the
different pages and review all results, use the Page Up and Page Down buttons.
7. Outliers can be removed by clicking the Outlier Removal button. This feature is
especially useful to redraw curve fits if one standard replicate or an entire point
has an OD that is too high or too low.

• Highlight the well to be removed by clicking on it, and then check the
checkbox associated with the selected well. Click OK and the data will be
recalculated. More than one well can be removed at the same time

Figure 87: Outlier Removal

• Matrix may automatically remove outliers when certain calculations are

used. To restore the outliers and keep the original data, click Outlier
Removal and then click the Restore All button or uncheck the checkbox
associated with the well.
8. To reanalyze the data with a different curve fit, threshold levels, or ratio equation,
click the New Assay button.

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• Note: An assay with the desired operations must be created previously in

the Assay editor and saved in the assay database to reanalyze data using
this feature.

Figure 88: Selecting New Assay for Data Reduction

9. Select the desired assay with the new data reduction from the drop down list
(See Figure 88).
10. Click OK. The data will be reanalyzed and displayed with the following warning
(See Figure 89):
“WARNING! Results may have been reproduced using different settings to the
original assay.”

Figure 89. Warning on Report

The reanalyzed data can be printed, but it cannot be saved.

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Chapter 7 – Starting the Run

General Considerations
Sample Types

1. Biological samples such as serum, plasma, urine, or spinal fluid are typically
analyzed. Adequately prepared, stool and tissue homogenates can be run on the
DS2.
2. Sample IDs may be manually entered by the operator or read from barcode labels
on the sample tubes.

Using Barcode Labels

1. When using an ink jet label maker, large dot spacing may increase the number of
missed scans. Test the labels before using them in an assay. Print quality is very
important to reliable scans.
2. Ensure the barcode density selected is between .005” and .013”.
3. The Vertical Scanner can read test tube barcodes up to 85 mm in length, including
the 5 mm Quiet Zone on each side of the barcode. However, the readable barcode
length may vary, depending upon the code type and barcode density. The user
should test barcodes to ensure a specific barcode topology can be reliably scanned.
4. Check that the barcode Quiet Zone is sufficiently wide at both ends of the barcode
label. This distance must be at least 5 mm from the actual barcode to the end of the
label. Be sure that the Quiet Zone is not reduced; otherwise a missed scan could
occur.
5. The test tube barcode that is to be scanned must be properly aligned The barcode
label must be visible through the sample rack slot.
6. Check that the digits, letters, and other characters are correct for the barcode
symbology that is being used. Also, use the correct number of data digits for a
specific barcode symbology.
SUPPORTED BAR CODES
Codabar Code 128

Code 39 Standard 2 of 5

Code 93 Interleaved 2 of 5

MSI/Plessy UPC / EAN / JAN

7. Symbologies with poor internal verification or partial decodes (such as Interleaved 2

of 5, Standard 2 of 5, and MSI/Plessey) should be avoided if possible.
8. Be sure that the barcode scanner module window is clear, clean, and not scratched.

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Preparing the System

Filling the Wash Buffer Containers
1. Disconnect the wash buffer container and remove it from the system.
a) To remove the wash buffer container, disconnect the wash line by
pressing on the metal tab of the quick disconnect fitting and pull
gently on the wash line. Disconnect the liquid level sense connection
by removing it from the connector socket (See Figure 90).

Quick Disconnect
Wash Buffer Container

Quick Disconnect
Waste Container
Liquid Level
Sense
Connection
Wash Buffer
container

Wash Buffer
Container B

Figure 90: Wash Buffer Container B

2. Remove the top cap of the wash buffer container and fill it with the desired
wash solution.

 Note: The wash buffer containers can hold up to two

liters. DO NOT OVERFILL.

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3. Replace the wash buffer container in its storage location. Reconnect the liquid
level sense connection and the quick disconnect fitting.
4. Repeat Steps 1 through 3 for the second wash buffer container if necessary.

Emptying the Waste Container

1. Two Quick Disconnect fittings connect the liquid and vacuum lines to the Liquid
Waste Container (see Figure 90). Disconnect each one by pressing on the metal
tab of the quick disconnect fitting and gently pulling on the line.
2. Disconnect the level sensor Float Switch Connector (see Figure 90) by pulling it
out of the connector socket.
3. Remove the waste container cap and discard the waste in accordance with local
regulations.

Note: Do not remove the Liquid Waste Container cap when the
 container is in the DS2. Always remove the container first, stand it
upright on the bench with the cap pointed up, then remove the cap.

4. Rinse the waste container with DEIONIZED or distilled water. Discard the rinse
water.

 Note: The waste container can be disinfected with 70%

ethanol, followed by thorough rinsing with distilled or
deionized water.

5. Replace and tighten the waste cap.

 Note: Be sure that the waste cap is securely tightened.

A vacuum leak will occur if the cap is not properly
tightened and will cause the software to report a
vacuum error condition.

6. Place the waste container on the system and reconnect the quick disconnect
fittings and the liquid level sensor.

Starting the Run

Starting the Run
1. Display the worklist to be run by selecting File > Worklist Editor from the main Matrix
screen. A dialog box is displayed prompting selection of a batch or group of test samples
for the assays to be run.

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Figure 91: Sample Batch Selection

2. Select a previously used sample batch or select to create a new sample batch (<new
sample batch>). Click the OK button. The Worklist Editor screen will be displayed.
3. When creating a new sample batch, select the samples that will be run by clicking on
individual tubes or by specifying the number of samples in the text box. By clicking the
last tube in a sample rack, the entire rack of tubes can be selected.

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Next
Button

Figure 92: New Worklist Screen

4. Enter the Sample Batch ID or use the default name.
5. Create the sample IDs by selecting to have the DS-Matrix software auto-assign
individual sample IDs (using the sample batch id or a pattern) or by selecting to bar code
scan the sample IDs..
6. Click the Cancel button to abort and restart the worklist. Click Next to accept the sample
IDs.

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Assay
Rack Active Category
Indicator Assay

Saved
Assays
Omit
Sample
Checkbox

Done
Button

Figure 93: Assay Selection Screen

7. Select the assay category (if any) or All Assays in the drop-down list.
8. Select the assay(s) to be run by highlighting the desired assay and clicking the Add
Assay button or by double clicking on the desired assay. A pale orange strip will appear
next to the Sample IDs with the name of the assay at the top. If the check box next to a
sample ID is checked, then the sample will be run with the assay.

 Note: The checkbox can be used to omit an individual

sample from the run without editing the sample batch
list.
9. To remove an assay, click on the red X at the very top of the orange assay strip. To view
the previous screen, which will allow number of samples to be changed, click Previous.

• Note: When more specimens are added by returning to a previous

screen, new sample IDs created must be selected to be run on any
previously assigned assays. The checkboxes for any added sample IDs
will not be automatically selected with previously added assays.
10. To abort the worklist, click Cancel, which will bring up a box verifying the worklist is to be
aborted.
11. Click Done when assay selection is completed. The Timeline screen will be
displayed.

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The Timeline and Load Wizard

1. The Timeline Screen with the assay steps scheduled, but grayed out, is
displayed once an assay has been assigned to the worklist.
2. The operator must click Accept to start the run. Edit, Add and Accept buttons
will be flashing.

 Note: Prior to accepting the timeline, the user

should have all reagents, samples, and
consumables lined up and ready to load on the
instrument. Items such as tips or sample tube
racks should be loaded prior to clicking accept.
Failure to load reagents promptly can lead to
timeline conflicts.

Click the
Accept Button
to Start the
Run
Assay Steps
Grayed Out

Figure 94: Timeline Screen

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3. After the timeline has been accepted, the software will prompt the user to load
sample tube racks and consumables. (Sample tube racks may be loaded prior to
clicking the Accept button.)
4. The Load Tube Rack Screen will display the number of samples in the Worklist,
along with a diagram of the DS2 with tube racks highlighted. This prompts the
operator to load the appropriate sample racks.

Figure 95: Load Tube Rack Screen

5. Load the sample racks and click the Green Check button.

Loading Consumables
1. After loading the samples, the load consumables wizard begins. The first screen
of the load wizard is a table which lists the reagents, standards and controls
required for the run. The software will prompt the operator to load them in the
appropriate position with the appropriate volume. Where possible, reagents
should be in the appropriate bottles prior to clicking the Accept button.
2. After an item is loaded in the designated position with the designated volume and
any required information is entered, click the button to display the next
prompt.

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Figure 96: Load Consumables Screen

3. Click the button to abort the run.

4. The next screen prompts the operator to load plates and enter plate identifiers. A
default plate identifier (Test_x_x) is assigned by the software, but this plate
identifier can be changed by the user. The plate identifier will assist the user to
identify which report they wish to view upon assay completion. The software also
prompts the operator to check the status of the clean line, load the wash buffer
into the wash container and check the status of the waste containers.
5. After all consumables have been loaded, the run starts.

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Timeline View – Run Status

The Timeline View Screen displays the scheduled timing of individual assay functions.
These time estimates are continuously updated as more runtime information is available to
the DS2.

Assay Steps and

Time Estimates

Figure 97: Timeline View Screen

Using the Timeline View

1. To expand the Timeline View, click on the icon.

2. To condense the Timeline View, click on the icon.

3. To view the entire Timeline (as displayed above), click on the icon.

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Checking Consumables Status

1. For a report on the status of consumables during a run, click on the Status
button.
2. The Consumables Status screen will be displayed with the tube types, fluids, and
plate types that are being used in the run. During the run, the consumables status
is updated as fluids and tips are used.
Tube Types Plate Types

Neat Fluids
Tab

Figure 98: Consumables Status Screen

Generating a Run Report

1. To view a report on a completed plate, select the desired plate identifier from the
recent tests list, and click on the button.
2. The report can be viewed and printed from the View Report screen by clicking
the Print button.

 Note: A printer driver must be installed for Reports to

be viewed and printed using the Matrix software.

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Figure 99: View Report Screen

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Chapter 8 – Routine Service and Maintenance

Chapter 8 – Routine Service and Maintenance

Routine Maintenance Procedures

 Note: Performing maintenance to the DS2 may expose the

operator to hazardous moving parts. Contact DYNEX for
proper safety precautions to avoid possible injury.

The following periodic maintenance procedures are required for the

DS2 Automated ELISA System:

Daily Maintenance
1. Empty and clean the tip waste container.

Warning: While the DS2 alone does not present a

biohazard, the samples that are used and all parts and
consumables in contact with the samples must be
considered biohazardous. Always wear protective gloves
when handling potentially infectious substances.

2. (As needed) Empty and clean the liquid waste container.

 Note: If desired, the waste tip container and the liquid

waste container can be disinfected with 70% ethanol.
The containers must be thoroughly rinsed with
deionized water before replacing, as residual alcohol
fumes may affect the results of ELISA assays.
3. Clean all external surfaces using a towel moistened with 70%
alcohol. Remove residual alcohol with a cloth dampened with
distilled water.
4. Clean the pipette spigot using a non-fibrous towel moistened with
70% alcohol. Remove residual alcohol with a cloth dampened
with distilled water.
5. Purge the washer with 50 ml of deionized or distilled water from
the clean fluid line.

Weekly Maintenance
1. Empty the wash buffer containers and rinse them several times
with deionized water.

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Six-month Maintenance
1. Replace the dispense tubing.
2. Replace the aspiration tubing.

 Note: The dispense tubing and aspiration tubing may

need to be replaced more frequently than every six
months, depending upon the frequency of use and the
severity of operating conditions.
Contact DYNEX TECHNOLOGIES for information on
replacement tubing.

3. Check the cover. The DS2 cover should be able to be opened 8

inches (approximately 203mm) without falling. If the cover drops
instantly above this height then the gas spring should be
replaced.

Cleaning and Decontamination

The DS2 Automated ELISA System is constructed from materials that resist
chemical attack.
Spills should be cleaned as soon as possible. If you need to decontaminate
the DS2 Automated ELISA System (for example: before servicing the
instrument or following a spill), clean the system and then decontaminate it
as described below.

CAUTION: Always disconnect the power cable before

cleaning.

To Clean the System

1. Clean external surfaces with a cloth moistened with mild
laboratory detergent.

 Note: If needed, dilute the laboratory detergent according

to the manufacturer’s instructions before using.

 Note: If there is any doubt about the compatibility of

cleaning agents with parts of the DS2, contact DYNEX
Technologies.

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To Decontaminate the System

1. Wipe the surfaces with a cloth moistened with a 70% (v/v)
solution of alcohol.

 Note: Remove residual alcohol from surfaces with a

cloth moistened with deionized water. Residual alcohol
may affect the results of ELISA assays.

 Note: If there is any doubt about the compatibility of

decontamination agents with parts of the DS2, contact
DYNEX Technologies.

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Replacing the Absorbance Module Bulb

CAUTION: The optics assembly may be hot. Allow at least
five minutes for the instrument to cool before opening the
optics assembly.

Be careful when removing the filter access panel, as there

is a possibility that the bulb may be broken.

Failure to follow the bulb replacement procedures as

described may result in personal injury.

To Replace a Bulb
1. Remove the filter / bulb access panel from the rear of the DS2 by
unscrewing the two screws (one at the top and one at the bottom
of the panel).

Filter
Access
Panel

Figure 100: Filter Access Panel of DS2

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2. The bulb is mounted on the left hand side of the optical

assembly.
Lamp

Bulb

Filter Wheel

Figure 101: Optical Assembly

CAUTION: Gloves are necessary to prevent skin oils

from damaging the lamp. Gloves are also worn as a
safety precaution should the glass bulb accidentally
break.

3. Put on a pair of rubber or latex gloves.

4. Grasp the bulb with plastic tweezers and pull the bulb out of its
socket (see Figure 102).

 IMPORTANT: Use a gloved finger to prevent the bulb from

bumping into the metal sidewalls of the enclosure during removal.

5. Obtain a replacement bulb (Dynex part number 50200410).

6. Grasp the bulb tines with plastic tweezers and align the tines with
the corresponding holes in the lamp socket.
7. Firmly insert the bulb into the lamp socket.
8. Replace the filter access panel.

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Tweezers

Bulb

Figure 102: Removing the Bulb

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Replacing an Absorbance Module Filter

CAUTION: The optics assembly may be hot. Allow at least

five minutes for the DS2 to cool after turning off the system
before opening the optics assembly.

Also, be careful when removing the filter access panel, as

there is a possibility that the bulb may have broken.

To Remove a Filter
1. Remove the filter access panel from the rear of the DS2 by
unscrewing the two screws (one at the top and one at the bottom
of the filter access panel).
2. Remove the filter access panel. The filters are mounted on the
filter wheel as shown in Figure 103.
3. Locate the filter that is to be removed. Note: absorbance filter
405 must stay in slot one on the filter wheel or the DS2 will fail
the self-test on start-up.
4. Firmly grasp the exterior filter housing with a pair of needle nose
pliers.
5. Pull the filter out of the spring-loaded slot.
6. Replace the filter access panel.
7. Go to the Matrix main menu toolbar and select the Tools menu.
Select Absorbance Filter and change the wavelength in the
position the filter was removed from to 0.
8. Click OK to save the changes.

Needle Nose
Pliers

Screws
Grasp Filter

Filter Wheel

Figure 103: Removing a Filter

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To Install a Filter
1. Remove the filter access panel from the rear of the DS2 by
unscrewing the two screws (one at the top and one at the bottom
of the panel). Remove the filter access panel. The filters are
mounted on the filter wheel.
2. Locate the filter position in which the filter will be installed.

 Note: If a new filter is installed in a previously empty

position or if the filter is replacing a filter of a different
wavelength, the wavelength of the new filter must be
entered in the main menu: Matrix Tools > Absorbance
Filter

 IMPORTANT: The 405 nm filter must be installed in

Filter Position 1.

3. Firmly grasp the exterior filter housing with a pair of needle nose
pliers.
4. Push the filter into the spring-loaded slot.

 IMPORTANT: The bottom groove of the filter must be

firmly seated in the filter wheel. If the groove is aligned
with the springs on the filter wheel then the filter has
been installed incorrectly and will cause invalid
instrument performance.

5. Replace the filter access panel.

6. Go to the main Matrix Tools > Absorbance Filter menu and
type in the wavelength of the installed filter in the corresponding
position data entry field.

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Replacing the Tubing

To Replace the Tubing
1. Open the door at the front of the DS2.

 Note: The door is hinged at the bottom. When opening,

prevent the door from dropping all the way forward.

Wash Buffer
Bottle A

Wash Buffer
Bottle B

Waste Container

Tip Waste
Door

Figure 104: Door and Wash Buffer Containers/Waste Containers

2. Disconnect the two Wash Buffer Containers and the Waste

Containers. Remove the Wash Buffer containers, the Waste
Container and the Tip Waste Container.

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Chapter 8 – Routine Service and Maintenance

3. Behind the Tip Waste Container is the Pump/Valve Assembly

that controls the washer dispense and aspiration functions.

Pump/Valve
Assembly

Figure 105: Pump / Valve Assembly

DS2® System Operator’s Manual 161

 Chapter 8 – Routine Service and Maintenance

4. Disconnect the Wash Head Tubing from the Wash Head

Manifold, and unscrew the Manifold Thumb Nut as shown below.
The black thumb nut is on the underside of the DS2 platform.

Wash Head
Aspirate Tube

Wash Head
Manifold
Wash Head
Dispense Tube

Thumb Nut

Figure 106: Tubing Schematic

162 DS2® System Operator’s Manual

Chapter 8 – Routine Service and Maintenance

5. Disconnect the Aspirate and Dispense tubes from the Wash

Head Manifold.
6. Remove the Dispense Tube from the Pinch Valve and disconnect
it from the Pump Outlet.
7. Disconnect the other end of the Aspirate tube from the Waste
Fitting.

Vacuum
Switch

Waste
Fitting

Wash Head
Manifold

Aspirate Tube

Vacuum
Line

Dispense Tube

Pinch Valve
Pump Outlet

Figure 107: Tubing Schematic

DS2® System Operator’s Manual 163

 Chapter 8 – Routine Service and Maintenance

8. Disconnect tubing from fittings for Wash Buffer containers A and

B.
9. Gently pull the 90° fitting out of the Grommet and disconnect the
Bottle C tubing.
10. Remove the tubes from the pinch valves and then disconnect
them from the pump inlet.

Bottle A and B Bottle B Tube

Tube Fittings

Bottle A Tube
90° Fitting

Grommet
Bottle C Tubing Pinch Valves

Figure 108: Tubing Schematic

164 DS2® System Operator’s Manual

Chapter 8 – Routine Service and Maintenance

11. Insert the replacement tubing for the Pump Valve Assembly in
the reverse order of removing the tubing (steps 10 – 4).
12. Lift the Wash Head off its cradle and replace the twin bore tube.
13. Connect the free end of the tube to the Wash Head Manifold.
Ensure the Wash Head is oriented as shown below.

Wash Head

Twin Bore Tube

Cradle

Figure 109: Wash Head Fitting

14. Flip the Wash Head over.

Figure 110: Wash Head Fitting

DS2® System Operator’s Manual 165

 Chapter 8 – Routine Service and Maintenance

15. Rotate the Wash Head 90 degrees clockwise before

locating it onto back onto the cradle.

Figure 111: Wash Head Fitting

16. Remove and replace the tubing on the two Wash Buffer
containers and the Waste container.

Wash Buffer
Container Tubes

Waste Container
Tubes
Figure 112: Container Tubing

17. Connect the two Wash Buffer Containers and the Waste
Container to the DS2. Place the Tip Waste Container in it’s
proper location.

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Chapter 8 – Routine Service and Maintenance

Cleaning the Wash Head Assembly

CAUTION: Always disconnect the power before servicing.

To Remove the Wash Head Assembly

1. Grasp the wash head assembly and lift it up from the cradle.
2. Move the wash head assembly and tubing clear of the DS2. If
necessary, remove the wash tubing and waste tubing.

To Clean the Wash Head Assembly

1. Pass the Cleaning Wire through the inside of each aspirate pin
and dispense pin on the wash head.

 Note: There are two sizes of Cleaning Wires. One is for

the aspirate pin, and the other is for the dispense pin.

2. If necessary, reconnect the wash tubing and waste tubing, and

run a PURGE to rinse any material from the pins.

 Note: Dynex recommends performing a final purge with

deionized water at the end of every run. This can be
programmed into the final wash step in an assay.

To Replace the Wash Head Assembly

1. Position the wash head assembly back in the cradle.

Requesting Service
If the DS2 needs service, contact the Vendor from whom the system
was purchased or contracted for. The Vendor will troubleshoot,
assess the situation, and work with Dynex to find a solution to the
service issue.

DS2® System Operator’s Manual 167

Chapter 8 – Routine Service and Maintenance

Limited Warranty
Warranty and Special Provisions

DYNEX TECHNOLOGIES products are fully guaranteed for one year

against defects in parts, materials, and workmanship. Defective parts and
materials will be replaced or, at the discretion of DYNEX TECHNOLOGIES,
repaired at no charge for a period of one year and labor required for such
replacement or repair will be provided at no charge for a period of one year,
provided that the products are utilized and maintained in accordance with
the instructions in the applicable operating and servicing manual, and
provided further that the products have not, as determined solely by DYNEX
TECHNOLOGIES, been subject to misuse or abuse by the Customer or
other parties unrelated to DYNEX TECHNOLOGIES. DYNEX
TECHNOLOGIES makes no warranty, expressed or implied, as to the
fitness of any product for any particular purposes other than those purposes
described in the applicable operating and servicing manual, nor does
DYNEX TECHNOLOGIES make any other warranty, whether expressed or
implied, including merchantability, other than those appearing on the face
hereof. Where DYNEX TECHNOLOGIES guarantees any product, whether
under this Warranty or as a matter of law, and there is a breach of such
guarantee, the Customer’s only and exclusive remedy shall be the
replacement or repair of defective parts and materials, as described above.
This shall be the limit of DYNEX TECHNOLOGIES liability. Furthermore,
DYNEX TECHNOLOGIES shall not be liable for incidental or consequential
damages. Failure of the Customer to notify DYNEX TECHNOLOGIES of a
claimed defect by registered mail within thirty days of the discovery thereof
shall constitute a waiver of any claim for breach of warranty.
When a product is required by DYNEX TECHNOLOGIES to be installed by
a DYNEX TECHNOLOGIES engineer or technician, the period of this
Warranty shall begin on the date of such installation, provided, however,
that any use of the product prior to such installation shall, at the sole
election of DYNEX TECHNOLOGIES, void this Warranty. When installation
by DYNEX TECHNOLOGIES personnel is not required, the period of this
Warranty shall begin on the date of shipment from DYNEX
TECHNOLOGIES. The period of this Warranty shall begin as described
above whether or not the product has been installed or shipped pursuant to
a purchase order, and any trial period shall be deducted from the Warranty
period that would otherwise apply under a subsequent placed purchase
order for that product.
Limitation of Liability. Notwithstanding anything to the contrary contained
herein, the liability of SELLER (whether by reason of breach of warranty,
breach of contract, tort, or otherwise), including without limitation under any
indemnification provision contained herein, shall be limited to replacement of
goods returned to DYNEX TECHNOLOGIES which are shown to DYNEX
TECHNOLOGIES reasonable satisfaction to have been nonconforming or to
refund the purchase price, or, if not paid, to a credit amount of the purchase
price therefore.

168 DS2® System Operator’s Manual

Chapter 8 – Routine Service and Maintenance

THE FOREGOING WARRANTIES ARE EXCLUSIVE AND ARE GIVEN

AND ACCEPTED IN LIEU OF ANY AND ALL OTHER WARRANTIES,
EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION, THE
IMPLIED WARRANTY OF MERCHANTABILITY AND THE IMPLIED
WARRANTY OF FITNESS FOR A PARTICULAR PURPOSE. NEITHER
PARTY SHALL BE LIABLE TO THE OTHER FOR ANY INCIDENTAL,
INDIRECT, SPECIAL, OR CONSEQUENTIAL DAMAGES.

DYNEX Technologies Contact Information

DYNEX Technologies, Inc.

14340 Sullyfield Circle
Chantilly, VA 20151-1621
Tel: 703 631-7800
800 288-2354
Fax: 703 631-7816
Email: customerservice@dynextechnologies.com
techservice@dynextechnologies.com
www.dynextechnologies.com

DS2® System Operator’s Manual 169

Appendix A – Arm Calibration Tool

Appendix A – Arm Calibration Tool

The Arm Calibration Tool is only available if the Matrix plug-in software has
been installed. This Tool should only be used by a trained technician.

1. Double Click the Arm Calibration Tool icon or select the program
using Start>All Programs>Dynex Technologies>DS-Matrix>Arm
Calibration Tool.

2. A window with a picture of the DS2 (cover open) and several buttons
appears. Click the Arm Calibration button. The Arm Calibration
Wizard screen appears with a window instructing the user that a
Calibration Tool, a Dynex Microtiter plate, and a black delrin stepped
collar will be needed to complete this procedure.

3. Insert all five Sample Racks and both Reagent Racks into the rack
carriers.

4. The brass Calibration Tool should not be on the spigot. Detach and
remove the brass calibration tool if it is attached to the spigot. Click
Next.
Consumables Rack Position

5. Insert the spigot into the rear hole located on the top edge of the
consumables rack between the sample (blue) tip and deep well strip
areas. On the dialog, click “Get Values” for the frame marked Rear
Consumables Hole. Values will appear in the X,Y,Z boxes (See
Figure A-1).

Figure A-1. Arm Calibration Tool Software

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Appendix A – Arm Calibration Tool

Sample
Tip Boxes

Rear
Hole

Front
Reader Hole
Cover
Handle

Figure A-2: Consumables Rack and Reader Cover Positions

6. Move the spigot to the front hole of the tips rack top edge. Click Get
Values in the Front Consumables Hole frame. Values will appear
in the X, Y, Z boxes. Click Next.

Reader Cover Positions

7. Insert the Spigot into the hole in the top of the handle on the Reader
Cover. Open the reader cover. Click Get Values.

8. Close the reader cover with the spigot pin still inserted in the handle.
Click Get Values. Click Next.

Sample Tip Rack Positions

9. Take the tip out of the reader cover hole and gently move the arm up
and back to home position. Load a box of blue sample tips into the
sample tip rack. Load clear reagent tips into the reagent tip racks.

DS2® System Operator’s Manual 171

Appendix A – Arm Calibration Tool

10. Place the spigot fully into the tip marked Datum in Rack 1 (rear
sample tip rack) as shown in the Figure A-3. Ensure the spigot is
securely inserted into the tip and click Get Values.
Y Right
Datum

Rack 1

X Bottom

Rack 2

Figure A-3: Sample Tip Rack Positions

11. Repeat step 10 for the tip locations marked “Y Right” and “X Bottom”
after reinserting the spigot into the appropriate tips as indicated by
the black circles in Figure A-4.

12. Repeat the entire procedure for Rack 2 (front sample tip rack). Click
Next.
Reagent Tip Rack Positions

13. Ensure clear reagent tips are loaded into both racks in the positions
shown in the following illustration.

172 DS2® System Operator’s Manual

Appendix A – Arm Calibration Tool

Y Right

Datum

X Bottom

Rack 2
Rack 1

Figure A-4: Reagent Tip Rack Positions

14. Insert the spigot fully into the tips located in the reagent tip locations
indicated in Figure A-5 below. Click Get Values for the frames
marked “Datum”, “Y Right” and “X Bottom” for both sample racks.
Click Next.
Bar Code Reader Position

15. Ensure there is a Barcode Reader installed on the DS2. Otherwise

skip this step.

16. Move the Barcode Reader to the far left position until it clicks into it’s
home position. Insert the Spigot fully into the Barcode Reader hole.
Do not force the spigot or compress the spring. Click Get Values in
the frame labeled Barcode Position. Click Next.

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 Appendix A – Arm Calibration Tool

Barcode
Hole

Wash Head
Waste Hole

DS2 Front Left

Figure A-5: Bar Code Reader, Tip Waste, and Wash Head Positions

Tip Waste Hole Position

17. Mount a clear reagent tip on the end of the Spigot. Move the Spigot
and tip to the Waste Hole. Center the tip over the hole. Push the
spigot down until the pins are as far down as possible without
engaging the spring/eject mechanism in the spigot.

18. Click Get Values for the frame marked Waste Position. Remove the
reagent tip. Click Next.

Washer Pickup Position

19. Insert the spigot fully into the wash head assembly. Engage and
latch the pins on the Spigot into the catches on the wash head
assembly. Click Get Values in the Washer Pickup frame. Remove
the Wash Head assembly from the Spigot. Click Next.

20. A message dialog box will come up which invites the user to save or
to cancel the calibrations done so far. Ensure that the calibration tool
is not present on the spigot and click Next to save the values and
initiate a self-test.

21. The DS2 will home the arm.

Washer with Microplate Positions

22. Manually open the Reader Cover. Click Present Upper Plate
Carrier. Insert a standard microplate into the plate carrier.

23. Engage and latch the Wash Head Assembly with the spigot. Be
careful not to compress the wash head.

24. Center the long aspirate pins in the wells in Column 1. Click Get
Values for the frame marked Upper Plate Datum.

25. Center the aspirate pins in the wells in Column 12. Click Get Values
for the frame marked Upper Plate Y Right.

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Appendix A – Arm Calibration Tool

26. Move the Spigot with the Wash Head Assembly attached back to the
home position. Click Present Lower Plate Carrier. Insert a standard
microplate into the plate carrier. Repeat the procedure in steps 24
and 25 to Get Values for Columns 1 and 12 for the lower plate
carrier.

27. Park the Wash Head Assembly in its carrier and remove it from the
Spigot. Click Next.

Calibration Tool
Holding Screw
Flat Side

Figure A-6: Calibration Tool

28. Mount the brass Calibration Tool onto the Spigot. The flat sides of
the calibration tool must be to the left and right on the Spigot. Use a
hex wrench to tighten the Holding Screw to hold the Calibration Tool
in place. Click Next.

Plate Carrier Positions

29. Click Present Upper Plate Carrier, and follow the prompts to clear
the arm and insert a plate.

30. Insert the Calibration Tool into well A1, click Get Values.

31. Insert the Calibration Tool into well A12, Get Values. Repeat using
well H1.

32. Move the Spigot and the calibration tool free of the plate carriers.
Click Present Lower Plate Carrier, and follow the prompts to clear
the arm and insert a plate.

33. Repeat Get Values for wells A1, A12 and H1 for the lower plate
carrier. Click Next.

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 Appendix A – Arm Calibration Tool

Sample Rack Positions

Rack 1 Rack 2
Y Right
nd
Datum 2 Position
st
1 Position

X Bottom
rd
3 Position

Figure A-7: Sample Rack Positions

34. Insert the Calibration Tool fully into Sample Tube position 1 in Rack
1. There should be no sample tube in the rack and the Tool should
go all the way down to the bottom of the sample rack. Click Get
Values for the Datum position. Repeat for the Y and X positions. (Y-
position is the first sample tube location on Rack 5. X-position is the
last sample tube location on Rack 1.) Click Next.

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 Appendix A – Arm Calibration Tool

Reagents Rack Positions

Rack 1 Rack 2

Y Right
2nd Position
Datum
st
1 Position

X Bottom Delrin
rd
3 Position Collar

Figure A-8: Reagents Rack Positions

35. Put the black Delrin Collar firmly into position 1 on the large tube
Reagent Rack. There should not be a reagent tube in this location.

36. Insert the Calibration Tool into the collar as far as it will go. Click Get
Values.

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Appendix A – Arm Calibration Tool

37. Repeat the procedure in steps 35 and 36 with the first tube position
on Rack 2 (Y-Right position). Click Get Values.

38. Repeat the procedure in steps 35 and 36 with the last small reagent
tube position on Rack 1 (X-Bottom position). Click Get Values. Click
Next.

Control Rack Positions

39. There should be no tubes in the control racks. The Delrin Collar is no
longer needed for calibration and should be stored.

Y Right
nd
Datum 2 Position
st
1 Position

X Bottom
rd
3 Position

Rack 1 Rack 2

Figure A-9: Control Rack Positions

40. Insert the Calibration Tool into the bottom of Datum position on
Control Rack 1, Click Get Values, and repeat the procedure for Y-
right and X- bottom positions as shown in Figure A-9.

41. Repeat the procedure for all three positions on Control Rack 2. Click
Next.

Calibration Finished

42. Remove the Calibration Tool from the Spigot by loosening the small
holding screw using a Hex wrench.

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Appendix A – Arm Calibration Tool

43. The calibration is complete. To save all settings, click OK, otherwise
click cancel, which will revert the settings back to the original values.

44. The DS2 will return the Spigot to home position, and move the plate
carriers into position.

45. Select to test for wash head detection.

46. The DS2 will home the arm.

Arm Speed

To review or change the settings for the speed of the Spigot Arm movement,
a Dynex-issued password is required. Only factory trained service personnel
are authorized to perform this procedure.

Click Exit.

DS2® System Operator’s Manual 179

Appendix B – Labware Specifications

Appendix B – Labware Specifications

I. Specifications
Type Max Height Internal External Bottom
Volume mm Diameter Diameter Shape
mL mm mm
Controls & 2000 44.45 8.69 10.3 V
Standards
Vial
Deep Well 2000 39.8 7.4 8 V
Strip
Large 25000 89.2 22.45 25.4 V
Reagent
Tube
Small 15000 75.9 17.6 20.5 V
Reagent
Tube
Sarstedt 10000 92 14.41 16 Flat
Monovette
12x75 4000 74.4 9.7 11.9 U
Sample Test
Tube

II. Consumables Ordering Information

Item Number Description Unit
65910 Blue Sample Tips, 300µl, 108/box 4 box pack
65921 White Reagent Pipette Tips, 108/box 4 box pack
62910 Deep Well Strips, 250/box Box
62920 Reagent Tubes, 25 ml, 10/pack Pack
62930 Small Reagent Tubes, 15 ml, 10/pack Pack
65940 Control/Standards Vials w. Caps, Pack
33/pack
394000100 Purge Tray, Microplate Form 3 Pack
III. Microplate Ordering Information
Item Number Description Quantity / Box
1000 Immulon® Medium binding, untreated 40
polystyrene, 96-well flat bottom
immunoassay plates
1010 Immulon® 2HB, High binding, treated 40
polystyrene, 96-well flat-bottom
immunoassay plates
1011 Immulon® 2HB, High binding, treated 40
polystyrene, 96-well “U”-bottom plates

180 DS2® System Operator’s Manual

 Appendix B – Labware Specifications

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DS2® System Operator’s Manual 181

Appendix C – Curve Fit Equations

Appendix C – Curve Fit Equations

DS-Matrix allows the user to select from nine mathematical relationships to determine the
concentration of the compound of interest. In this appendix, each of the curve fits is defined.

Linear Regression
A Linear Regression is used to put a "best fit" straight line through a set of data points.
Equation C-1 describes a linear relationship between the measured variable and the
concentration of the compound of interest:

Y = mX + b
C-1 where: m = the slope
b = the y-intercept defining the line
X = the value for the concentration
Y = the value for measured variable (O.D.)

The linear regression formulae for determining the best straight line through a series of data
points are provided in Equations C-2 and C-3:

m = NΣxiyi -ΣxiΣyi C-2

NΣxi2-_(Σxi)2

C-3 b = Ymean – m (Xmean)

The linear regression coefficient, R, is defined by Equation C-4:

R = (NΣxiyi -ΣxiΣyi)2 C-4

(NΣxi2 −(Σxi)2)(NΣyi2 −(Σyi)2)

The linear correlation coefficient (R) is used to determine how well the line fits through the
points of the graph. Since the linear correlation coefficient can be either positive or negative,
the value of R2 is normally reported. When comparing two sets of data (fits), the fit with the
larger value for R2 is a better fit for the data set; if R2 =1, all data points lie along the line of
best fit and if R2=0, the data points are highly scattered and there is a poor correlation.

Once the linear relationship best fit has been established for a set of known standards, the
concentration of an unknown sample can be determined via equation C-1.

An example of a linear relationship is presented in Figure C-1.

182 DS2® System Operator’s Manual

 Appendix C – Curve Fit Equations

A
b
s
o
r
b
a
n
c
e

Concentration

Figure C-1: Linear Regression Fit

Absorbance

Concentration

Figure C-2: Polygon Fit

DS2® System Operator’s Manual 183

Appendix C – Curve Fit Equations

Polygon Fit
A Polygon Fit of the data involves joining successive data points using straight lines in a
connect-the-dots fashion as shown in Figure C-2.

Quadratic, Cubic and Quartic Regression

Polynomial regressions are similar to a linear regression (equation C-1), but use
quadratic, cubic and quartic equations to relate the observed OD to the concentration.

Equation C-5 is a quadratic equation, Equation C-6 is a cubic equation, and Equation C-7
is a quartic equation.

Quadratic Equation: Y = a +bX + cX 2 C-5

Cubic Equation: Y = a +bX + cX 2+ dX 3 C-6

Quartic Equation: Y = a +bX + cX 2+ dX 3+ eX4 C-7

The procedures used to fit these functions to experimental data are similar to that for linear
regression and have a similar mathematical derivation. A polynomial regression tends to
minimize the deviations of the data points from the polynomial equation. The squaring
(cubing, etc.) of the deviations tends to minimize them since positive and negative
deviations tend to cancel out.

The regression coefficient is handled in a similar manner as with a linear relationship. When
R2 = 1, all the data points have been fitted to the curve, when R2 = 0, the data points are
scattered.

Examples of Quadratic and Quartic fits are shown in Figure C-3 and C-4 respectively.
Absorbance

Concentration

Figure C-3: Quadratic Fit

184 DS2® System Operator’s Manual

 Appendix C – Curve Fit Equations

Figure C-4: Quartic Fit

DS2® System Operator’s Manual 185

Appendix C – Curve Fit Equations

Cubic Spline Curve Fitting

When a Cubic Spline Curve fit is used, a curve is passed through all the data points and a
smoothing is function applied. Equations C-8 to C-10 are then used to determine the
concentration of the sample.

C-8

C-9

C-10

The Cubic Spline Curve Fit is not a best fit algorithm as it assumes that each data point is
correct. If the data is erratic, if it is known that the data has significant errors or if the
concentration/absorbance has many inflection points, this method can lead to significant
errors in the reported concentration.

At high concentrations, the Cubic Spline Curve Fit may break up (Figure C-5). In some
cases, a semi-log or log-log axis (instead of a linear fit) will improve the quality of the data.
Absorbance

Concentration
Figure C-5: Cubic Spline Curve Fit

Akima Fit
The Akima fit constructs a smooth curve through the data points. The fitted curve appears
smooth and approximates a manually drawn curve (Figure C-6).

186 DS2® System Operator’s Manual

 Appendix C – Curve Fit Equations

Absorbance

Concentration

Figure C-6: Akima Fit

The Akima Curve Fit involves applying a set of polynomials to the data points, which
determines the slope of the curve at each point .The Akima Fit is based on the assumption
that each data point is determined by five points, the point of interest and two points on
either side of it.

Extrapolation of Non-Linear Curves

In many instances, a data point is observed outside the range of the curve that is used to
determine the concentration. The analyst should note that some curve fit functions may not
behave as expected if they are extrapolated beyond the range defined by the data points.

For example, the readings for a set of Standards increase in a non-linear fashion with
increasing concentration for a given test (right side of curve in Figure C-7) and the user
determines that a quadratic curve fit might give the best fit for such data. However, at
concentrations lower than the concentration of the lowest Standard, the curve may turn
sharply upwards as shown in the left side of the curve.

DS2® System Operator’s Manual 187

Appendix C – Curve Fit Equations

Absorbance

Concentration

Figure C-7: Non-Linear Curve Fit

Sigmoid Fit
Many immunoassays are characterized by an S-shaped or sigmoid curve fit (Figure C-8).
Absorbance

Concentration
Figure C-8: Sigmoid Curve

The sigmoid curve is described by equation C-11:

C-11

where: a is the minimum response

188 DS2® System Operator’s Manual

 Appendix C – Curve Fit Equations

b is the shape factor (determines the gradient of the curve)

c is the response midway between the maximum (d) and the minimum
response
d is the maximum response

The above definition assumes that b has a positive value. If b is negative, the definition of
parameters a and d are reversed.

Matrix uses an algorithm for estimating the four parameters and determining the best fit for
the sigmoid curve. The curve requires at least four standards (data points), one for each of
the four parameters. It is recommended that at least eight Standards are defined on a plate
to ensure satisfactory statistical significance.

The Sigmoid Curve Fit algorithm is iterative, requiring many complex calculations. Matrix
may take some time to process the results. If the curve cannot be drawn or data cannot be
processed, a Windows® “Illegal Operation – Shut Down” error message will occur. If this
happens, examine your data carefully to determine if the number of Standards should be
altered or a different type of curve fit should be used.

Log – Logit Curve Fit

The Log – Logit Curve Fit is the Rodbard’s Four Parameter fit, similar to the Sigmoidal fit.
It also uses auto- or manually-assigned parameters to calculate the graph.

Using Logarithmic Axes Fitting

In most instances, linear scales are used to plot the concentration (X axis) and the OD
measured variable (Y axis). Alternatively, a semi-log fit or a log-log axes fit can be used.
The following example equations relate to linear regression fits, but Semi-Log and Log-Log
Axes fits may be used with all the other selectable curve fits.

Semi-Log Fit

When a semi-log fit is used, the X axis presents log (power of 10) concentration. To obtain
the concentration of a sample, equation C-12 is used.

Concentration = antilog (y-c)/m C-12

Log-Log Fit

When a log-log fit is used, the X axis represents the log of the concentration (concentrations
in powers of 10) and the Y axis represents log of the OD (measured variable). To obtain the
concentration of a sample, equation C-13 is used.

antilog Concentration = antilog (y-c)/m C-13

DS2® System Operator’s Manual 189

Appendix C – Curve Fit Equations

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190 DS2® System Operator’s Manual

 Appendix D – Equation Functions

Appendix D – Equation Functions

Entries for Quality Control Equations

SYMBOL FUNCTION COMMENT
0-9 Numeric entry
+ Addition Standard Arithmetic operator
- Subtraction Standard Arithmetic operator
/ Divide Standard Arithmetic operator
* Multiplication Standard Arithmetic operator
** To the power of Standard Arithmetic operator
((( ))) Parenthesis Max 6 levels
Log Base 10 logarithm
Ln Natural logarithm
Exp Inverse natural
logarithm
CV(well type) Coefficient of variation
SD(well type) Standard deviation
Median© Median If all values in a group are listed,
the median is the value in the
middle of the list. If the list
contains an even number of
values, the median if the mean of
the middle two. The group of
values may be a well type, or a
sample, if it contains replicates.
Custom Variable Can be used to prompt for entry
of a variable number at run time
> Greater than
< Less than
>= Greater than or equal to
<= Less than or equal to
== Must be equal to
MIN or MAX Represents the highest or lowest
value on the plate or within a
group of values. The group may
be a well type or a sample if it
contains replicates.
EX: MIN(PC)= the lowest value
of all the Positive Control
samples
MIN= the lowest value on the
plate

DS2® System Operator’s Manual 191

Appendix D – Equation Functions

T,T1,T1.1 Referenced Well Types T represents the mean of all the

Test values
T1 represents the mean of the
replicates of Test1
T1.1 is the value of the first
replicate of Test 1
T1.2 is the value of the second
re[plicate if Test 1
I Each sample of a well EX: 0.74*C<Ci<1.25*C means
type each Control sample must be
within 25% of the mean of the
Controls or that well is removed
from the calculations. Should be
accompanied by a Valid
statement
Valid( ) A Valid( ) expression indicates
that a specified number of values
within a group must pass other
QC equations otherwise the data
fails QC. The group of values
may be a Well Type or a sample
with replicates.
EX: valid(PC)>=3 means the
number of valid Positive Controls
must be greater than or equal to
three or QC is failed.
= Assignment An assignment expression
indicates that, depending on
certain criteria, a well type,
sample or replicate should be
assigned a value.
EX: If NCi<0.0 then NCi=0.0
Thus, if every NC value is less
than 0.0, then let every NC be
assigned a value of 0.0
If {condition} Conditional EX: If PC<0.2 then NC>0.5 else
then Requirement NC>0.1
{expression} Means If the average PC value is
else less than 0.2 then the average
{expression} NC value must be more than 0.5
else the average NC value must
be more than 0.1.
If these conditions are not met,
the data fails QC

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 Appendix D – Equation Functions

Verify (value, Expression Indicates that a specified number

limit, mode) of values within a group must be
within specified limits or the data
fails QC.
Value represents a well type
checked for the number of
verified samples within that
group or number of verified
replicates within a specified
sample.
Limit determines the range into
which values must fall in order to
be verified.
A limit may be a number.
EX: If the value is PC, the mode
is 0 and the limit is 0.2, such that
every PC sample is within 0.2 of
the average of all the group
values.
A limit may be a percentage.
EX: If the value is PC, the mode
is 0 and the limit is 20%, then
every PC sample must be within
20% of the average of all the
group values.
A Limit may be a standard
deviation.
EX: If the value is PC, the mode
is 0 and the limit is 1.5SD, then
the standard deviation of all the
PC samples must be within 1.5
SD.

EX: Verify(T,10%,2>=3
Means the number of verified
Test samples must be greater
than or equal to 3. A verified Test
sample falls within 10% of the
mean of all other Test samples.

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Appendix D – Equation Functions

Following
Threshold
POS / NEG Well Label The user can require that a
specific (default or user defined)
threshold Well Type be labeled
All samples within the Well Type
must fall into the required result
range or the Well Type will fail
QC and a warning will be
displayed in the results.

Following Curve Fit

Min R-squared R-squared may be used to
determine how closely the
Min Slope standards fit a linear regression
Max Slope curve fit. QC may fail if they R-
squared is below a specified
Min Y-Intercept value.
Max Y-intercept Min slope / Max slope may be
used to define the change in Y
over the change in X within a
certain range
Min Y-intercept / Max Y-intercept
may be used to keep the data on
the y-axis in the correct place or
else the curve fit fails, meaning
there is not enough
discrimination in response

194 DS2® System Operator’s Manual

 Appendix D – Equation Functions

Entries for Ratio and Threshold Equations

SYMBOL FUNCTION COMMENT
Sample Value of every well on Represents the value of every
the plate well on the plate regardless of
Well Type
EX: sample/10
0-9 Numeric entry
+ Addition Standard Arithmetic operator
- Subtraction Standard Arithmetic operator
/ Divide Standard Arithmetic operator
* Multiplication Standard Arithmetic operator
** To the power of Standard Arithmetic operator
((( ))) Parenthesis Max 6 levels
Log Base 10 logarithm
Ln Natural logarithm
Exp Inverse natural
logarithm
MIN or MAX Represents the highest or lowest
value on the plate or within a
group of values. The group may
be a well type or a sample if it
contains replicates.
EX: MIN(PC)= the lowest value
of all the Positive Control
samples
MIN= the lowest value on the
plate
CV(well type) Coefficient of variation
SD(well type) Standard deviation
Median( ) Median If all values in a group are listed,
the median is the value in the
middle of the list. If the list
contains an even number of
values, the median if the mean of
the middle two. The group of
values may be a well type, or a
sample, if it contains replicates.
Custom Variable User defined variable
VariableX Different variable to use each
time run is done

DS2® System Operator’s Manual 195