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DS2 Operators Manual
DS2 Operators Manual
Operator’s Manual
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.
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
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.
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
Washer Specifications
Wash Buffers 2 x 2L
Input connector for external Clean fluid bottle must be provided (any size)
clean fluid bottle provided
Incubator Specifications
Instrument Capacity
Number of Plates 2
Number of Assays/Run 12
Number of 24 x 2 mL tubes
Standards/Controls
The system cover encloses the workspace, the arm and the pipette module.
The cover should be closed during operation to prevent accidents.
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.
Cover
Handle
System Cover
Cover Resting
Point
Indicator Light
Power Switch
Workspace Components
Incubation
Chamber
Reading
Optics
Pipetting/
Washing Area
Wash Head
Barcode Incubator
Scanner Door Lever
Sliding Cover
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)
Wash Head Verifies that wash head assembly has been picked up
Detection or ejected.
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
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
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
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
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
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.
Absorbance Module
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.
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
Neat Fluids Fluid name and type, pipetting profile, load settings
(location, bottle type).
(Sample and
Reagent Fluids)
Wash Fluids Fluid name and load position
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
Worklist Execution
The Optical Density results for each sample ID in the worklist are analyzed
according to the criteria specified in the assay.
Results Reporting
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
Caution, biohazard
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.
Chapter 3 – Installation
Unpacking
Packing List for DS2 Installation
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.
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
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.
Cooling
Fan
Power Cord
Connector
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.
Timeline
Toolbar Incubator
Temperature
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.
• Database Maintenance
• System Configuration
• User Notification
• Absorbance Filter
• Import/Export
• ESP Calibration
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.
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.
Edit
Consumables
DELETE
COPY EXIT HELP
Delete Add Edit Copy Exit Help
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.
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.
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.
OD Limits
Numerical
Conversion
Enter Laboratory
Information
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.
2. Click the Enable LIS Support checkbox to activate the LIS option
within Matrix.
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
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.
Sender
E-mail
Address
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:
E-mail
Addresses
E-mail
Message
Body
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.
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.
Import/Export
Assay and OD data files may be imported or exported for use in other DS2
instruments or in other software applications.
Click to
Browse
Import Selection
Import
Note: Plate Data files must have the *.XDB extension. Assay files
must have the *.XML extension
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.
and the user is prompted to select the most appropriate action in order to
correct the problem (see Figure 29).
Error
Recovery
Options
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.
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.
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.
Time Assay
Range
5. Click Apply.
Well Calculation
Selection Method
Plates
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.
Number of
Fluid Name Volume Transfers
Run Button
Message
Center
(operator
prompts)
Select Bottle
Type
Click Accept
Bottle
Description
Operator Instructions
4. Click Accept
Number
Calibration Point
Enter Next
Decreasing
Weight
Programming
Toolbar
Report
Format
SetUp
Creating An Assay
The Assay Title Page
1. Select File > Assay Editor from the menu bar
• 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
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.
• 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.
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
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
Function
Buttons
Report Format
1. Click on the Report Formats tab.
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.
Source of
data being
reported
Matrix or
Table
Option
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
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.
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.
icon which is currently highlighted will have blue font. Text describing all other
operations will have black font.
Programming Toolbar
Text
Detailing
Assay
Creation
Dispense Operation
Defining Dispense Parameters
Dispense Icon
Select
Reagent
Select
Wells
Enter
Volume
• 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
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:
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.
• 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.
Definition Tab
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.
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.
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.
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.
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.
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
Well Fill Verification is used to track accurate pipetting of fluids into specified wells based on
their OD readings.
Filter
Selection
Selected
Wells
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
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.
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.
Wash Operation
A wash operation can consist of Purge, Dispense, Fill, Aspirate, Clean and Soak settings.
Operation Description
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.
Volume to Dispense
per cycle
Number of Cycles
Specify Fluid
Purge
Volume
Clean
Volume
• 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.
• 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.
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.
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.
• 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.
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.
Wavelength
Shake Time
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.
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
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
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.
See Appendix C for function descriptions and examples which can be entered into Quality
Control Equations.
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.
Ratio Icon
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.
Condition Expression
Results Flagging Tab
Function List
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.
See Appendix D for possible mathematic and function entries which can be used to write
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.
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.
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.
Value Limit
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.
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
7. Units can be entered as mg/ml, µg/ml, etc. by entering the desired units in the Units
box.
Axes
Selection
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.
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.
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
4. Any scaling options that are not compatible with the chosen curve fit type will be
disabled.
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
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
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.
Equation
Entry
Add, Move,
Delete Buttons
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
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)
Figure 73. Auto Difference Mode Equation applied to spreadsheet (Row A-B)
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.
Assay Name
(required)
Assay
Category
(optional)
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.
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.
Sample Batch
Name/Identifier
Enter number of
samples
Use Pattern to
specify root of
sample IDs
Assign
Sample IDs
Rack
Location
Assays
Added
Assay
Selection
Sample
Checkbox
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.
Edit Dilution
Button
Enter
Dilution
Change
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.
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
7. Click the Accept button if no editing or assay additions are needed. The Timeline
will go from inactive to active status.
Start Line
Assay
Operations
Load
Consumables
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.
Wells Tested
Remaining Tips
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.
Report
Button
Plate ID
• 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
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.
Code 39 Standard 2 of 5
Code 93 Interleaved 2 of 5
Quick Disconnect
Wash Buffer Container
Quick Disconnect
Waste Container
Liquid Level
Sense
Connection
Wash Buffer
container
Wash Buffer
Container B
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.
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.
6. Place the waste container on the system and reconnect the quick disconnect
fittings and the liquid level sensor.
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.
Next
Button
Assay
Rack Active Category
Indicator Assay
Saved
Assays
Omit
Sample
Checkbox
Done
Button
Click the
Accept Button
to Start the
Run
Assay Steps
Grayed Out
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.
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.
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.
3. To view the entire Timeline (as displayed above), click on the icon.
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
Daily Maintenance
1. Empty and clean the tip waste container.
Weekly Maintenance
1. Empty the wash buffer containers and rinse them several times
with deionized water.
Six-month Maintenance
1. Replace the dispense tubing.
2. Replace the aspiration tubing.
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
Bulb
Filter Wheel
Tweezers
Bulb
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
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.
3. Firmly grasp the exterior filter housing with a pair of needle nose
pliers.
4. Push the filter into the spring-loaded slot.
Wash Buffer
Bottle A
Wash Buffer
Bottle B
Waste Container
Tip Waste
Door
Pump/Valve
Assembly
Wash Head
Aspirate Tube
Wash Head
Manifold
Wash Head
Dispense Tube
Thumb Nut
Vacuum
Switch
Waste
Fitting
Wash Head
Manifold
Aspirate Tube
Vacuum
Line
Dispense Tube
Pinch Valve
Pump Outlet
Bottle A Tube
90° Fitting
Grommet
Bottle C Tubing Pinch Valves
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
Cradle
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.
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.
Limited Warranty
Warranty and Special Provisions
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).
Sample
Tip Boxes
Rear
Hole
Front
Reader Hole
Cover
Handle
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.
8. Close the reader cover with the spigot pin still inserted in the handle.
Click Get Values. Click Next.
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.
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
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.
Y Right
Datum
X Bottom
Rack 2
Rack 1
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
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.
Barcode
Hole
Wash Head
Waste Hole
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.
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.
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.
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
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.
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.
X Bottom
rd
3 Position
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.
Y Right
2nd Position
Datum
st
1 Position
X Bottom Delrin
rd
3 Position Collar
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.
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.
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
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.
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.
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.
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
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:
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.
A
b
s
o
r
b
a
n
c
e
Concentration
Concentration
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.
Equation C-5 is a quadratic equation, Equation C-6 is a cubic equation, and Equation C-7
is a quartic equation.
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
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).
Absorbance
Concentration
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.
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.
Absorbance
Concentration
Sigmoid Fit
Many immunoassays are characterized by an S-shaped or sigmoid curve fit (Figure C-8).
Absorbance
Concentration
Figure C-8: Sigmoid Curve
C-11
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.
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.
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.
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.
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.