Molecular Devices SpectraMax iD3 User manual

5054747 B
May 2017
SpectraMax® iD3 Multi-Mode Microplate
Reader
User Guide

SpectraMax iD3 Multi-Mode Microplate Reader User Guide
2 5054747 B
This document is provided to customers who have purchased Molecular Devices equipment, software,
reagents, and consumables to use in the operation of such Molecular Devices equipment, software,
reagents, and consumables. This document is copyright protected and any reproduction of this
document, in whole or any part, is strictly prohibited, except as Molecular Devices may authorize in
writing.
Software that may be described in this document is furnished under a non-transferrable license. It is
against the law to copy, modify, or distribute the software on any medium, except as specifically
allowed in the license agreement. Furthermore, the license agreement may prohibit the software
from being disassembled, reverse engineered, or decompiled for any purpose.
Portions of this document may make reference to other manufacturers and/or their products, which
may contain parts whose names are registered as trademarks and/or function as trademarks of their
respective owners. Any such usage is intended only to designate those manufacturers’ products as
supplied by Molecular Devices for incorporation into its equipment and does not imply any right and/or
license to use or permit others to use such manufacturers’ and/or their product names as trademarks.
Each product is shipped with documentation stating specifications and other technical information.
Molecular Devices products are warranted to meet the stated specifications. Molecular Devices makes
no other warranties or representations express or implied, including but not limited to, the fitness of
this product for any particular purpose and assumes no responsibility or contingent liability, including
indirect or consequential damages, for any use to which the purchaser may put the equipment
described herein, or for any adverse circumstances arising therefrom. The sole obligation of Molecular
Devices and the customer's sole remedy are limited to repair or replacement of the product in the
event that the product fails to do as warranted.
For research use only. Not for use in diagnostic procedures.
The trademarks mentioned herein are the property of Molecular Devices, LLC or their respective owners. These trademarks may not
be used in any type of promotion or advertising without the prior written permission of Molecular Devices, LLC.
Patents: http://www.moleculardevices.com/productpatents
Product manufactured by Molecular Devices, LLC.
1311 Orleans Drive, Sunnyvale, California, United States of America 94089.
Molecular Devices, LLC is ISO 9001 registered.
©2017 Molecular Devices, LLC.
All rights reserved.

5054747 B 3
Contents
Safety Information 5
Warnings, Cautions, Notes, and Tips 5
Before You Operate the Instrument 8
Chapter 1: Introduction 11
Computer Integration 11
Applications 12
Optics 12
Microplate Controls 13
Temperature Regulation 13
Injectors 14
Chapter 2: Unpack and Setup the Instrument 17
Contents of the Package 18
Unpack the Instrument 20
Remove Transport Locks 23
Remove Transport Locks - Alternate 25
Connect Instrument Cables 29
Turn the Instrument On and Off 31
Get the Instrument On Your Network 32
Install the QuickSync Tool 35
Injector Assembly and Maintenance 37
Chapter 3: Home Page 43
Protocol Libraries 44
Quick Read 46
External Shake Settings 46
Microplate Chamber Temperature Settings 48
Injector Maintenance - Wash and Prime 49
Maintenance Page 61
Change User 67
Load and Unload Microplates 68
Chapter 4: Protocols 69
View Protocol Settings 69

SpectraMax iD3 Multi-Mode Microplate Reader User Guide
4 5054747 B
Define Protocol Settings 71
View Protocol Results 82
Chapter 5: Read Modes and Read Types 89
Endpoint Read Type 89
Kinetic Read Type 89
Spectrum Read Type 90
Absorbance Read Mode 90
Fluorescence Intensity Read Mode 94
Luminescence Read Mode 98
Chapter 6: Maintenance and Troubleshooting 103
Clean Injector and Accessories 103
Preventive Maintenance 104
Replace Fuses 104
Clean the Instrument 106
Before You Move the Instrument 106
Troubleshooting 123
Obtain Support 124
Appendix A: Instrument Specifications 125
Measurement Specifications 125
Computer System Specifications 128
Physical Specifications 129
Injector Specifications 130
Appendix A: System Diagrams and Dimensions 133
Appendix B: Electromagnetic Compatibility 137
Index 139

5054747 B 5
Safety Information
Information about the safe use of the SpectraMax® iD3 Multi-Mode Microplate Reader
instrument includes an understanding of the user-attention statements in this guide, the
safety labels on the instrument, precautions to follow before you operate the instrument,
and precautions to follow while you operate the instrument.
Read and observe all warnings, cautions, and instructions. The most important key to safety
is to operate the instrument with care.
WARNING! If the instrument is used in a manner not specified by Molecular
Devices, the protection provided by the equipment might be impaired.
Warnings, Cautions, Notes, and Tips
All warning symbols are framed within a yellow triangle. An exclamation mark is used for
most warnings. Other symbols warn of other types of hazards such as temperature, pinch,
biohazard, or electrical as is described in the text of the warning.
When warnings and cautions appear in this guide, be careful to follow the specific safety
information related to them.
The following user-attention statements can display in the text of Molecular Devices®user
documentation. Each statement implies a particular amount of observation or
recommended procedure as described:
WARNING! A warning indicates a situation or operation that could cause
personal injury if precautions are not followed. Some warnings can have a
different symbol on the left, such as electric shock or biohazard warnings. The
definition of the symbol is included in the text of the warning.
CAUTION! A caution indicates a situation or operation that could cause damage to
the instrument or loss of data if correct procedures are not followed.
Note: A note calls attention to significant information.
Tip: A tip provides useful information or a shortcut, but is not essential to the
completion of a procedure.

SpectraMax iD3 Multi-Mode Microplate Reader User Guide
6 5054747 B
Symbols on the Instrument
Each safety label on the instrument contains an alert symbol that indicates the type of
potential safety hazard. The following table lists the alert symbols on the instrument.
Symbol Indication
This symbol indicates that you must consult the product documentation.
This symbol indicates a potential lifting hazard. To prevent injury, use a minimum of
two people to lift the instrument. For information about the weight of the instrument,
see Physical Specifications on page 129.
This symbol indicates a potential pinch hazard.
This symbol indicates a potential biohazard.
This symbol indicates a potential heat hazard.
This symbol indicates an electrostatic sensitive device (ESD). Observe precautions for
handling electrostatic sensitive devices.
Table 3-1: Instrument Label Alert Symbols
Note: This equipment has been tested and found to comply with the limits for a Class
A digital device, pursuant to part 15 of the FCC Rules. These limits are designed to
provide reasonable protection against harmful interference when the equipment is
operated in a commercial environment. This equipment generates, uses, and can
radiate radio frequency energy and, if not installed and used in accordance with the
instruction manual, may cause harmful interference to radio communications.
Operation of this equipment in a residential area is likely to cause harmful interference
in which case the user will be required to correct the interference at their own
expense. Changes or modifications made to this equipment not expressly approved
by the party responsible for compliance may void the FCC authorization to operate
this equipment.

Safety Information
5054747 B 7
The following sticker appears on the back of your instrument.
Symbol Indication
This symbol indicates the location of a fuse.
This symbol indicates that you must consult the product documentation.
This symbol indicates the instrument serial number.
This symbol indicates the instrument manufacture date.
This symbol indicates you should consult the instructions for use.
This symbol indicates CSAcertification.
This symbol signifies European technology conformity.
This symbol signifies that the instrument complies with Australian radio
communication requirements.
Table 3-2: Instrument Label Symbols

SpectraMax iD3 Multi-Mode Microplate Reader User Guide
8 5054747 B
Symbol Indication
This symbol on the product is required in accordance with the Waste Electrical and
Electronic Equipment (WEEE) Directive of the European Union. It indicates that you
must not discard this electrical or electronic product or its components in domestic
household waste or in the municipal waste collection system.
For products under the requirement of the WEEE directive, contact your dealer or
local Molecular Devices office for the procedures to facilitate the proper collection,
treatment, recovery, recycling, and safe disposal of the device.
This symbol indicates the environmental friendly use period.
This symbol indicates there is an authorized representative in the European
community.
This symbol indicates the instrument manufacturer.
This symbol indicates the manufacturer catalog number.
Table 3-2: Instrument Label Symbols (continued)
Before You Operate the Instrument
Make sure that everyone involved with the operation of the instrument has:
Received instruction in general safety practices for laboratories.
Received instruction in specific safety practices for the instrument.
Read and understood all Safety Data Sheets (SDS) for all materials being used.
Electrical Safety
To prevent electrically related injuries and property damage, properly inspect all electrical
equipment before use and immediately report all electrical deficiencies. Contact Molecular
Devices technical support for servicing of equipment that requires the removal of covers or
panels.
WARNING! HIGH VOLTAGE. Within the instrument is the potential of an
electrical shock hazard existing from a high-voltage source. All safety instructions
must be read and understood before proceeding with the installation,
maintenance, and servicing of all modules.

Safety Information
5054747 B 9
Do not remove the instrument covers. To prevent electrical shock, use the supplied power
cords only and connect to a properly grounded wall outlet. Use only multi-plug power strips
that are provided by the manufacturer.
To ensure sufficient ventilation and provide access for disconnecting power from the
instrument, maintain a 20cm to 30cm (7.9in. to 11.8in.) gap between the rear of the
instrument and the wall.
Turn the instrument power off when the instrument is not in use.
In the event that you need to change the instrument fuses, see Replace Fuses on page 104.
Chemical and Biological Safety
Normal operation of the instrument can involve the use of materials that are toxic,
flammable, or otherwise biologically harmful. When you use such materials, observe the
following precautions:
Handle infectious samples based on good laboratory procedures and methods to
prevent the spread of disease.
Observe all cautionary information printed on the original containers of solutions before
their use.
Dispose of all waste solutions based on the waste disposal procedures of your facility.
Operate the instrument in accordance with the instructions outlined in this guide, and
take all the required precautions when using pathological, toxic, or radioactive materials.
Splashing of liquids can occur. Therefore, take applicable safety precautions, such as
using safety glasses and wearing protective clothing, when working with potentially
hazardous liquids.
Observe the applicable cautionary procedures as defined by your safety officer when
using hazardous materials.
Observe the applicable cautionary procedures as defined by your safety officer when
using flammable solvents in or near a powered-up instrument.
Observe the applicable cautionary procedures as defined by your safety officer when
using toxic, pathological, or radioactive materials.
WARNING! Never use the instrument in an environment where potentially
damaging liquids or gases are present.
CAUTION! Use of organic solvents can cause harm to the optics in the instrument.
Extreme caution is recommended when using organic solvents. Always use a plate lid
and do not place a plate containing these materials in the microplate chamber for
prolonged periods of time. Damage caused by the use of incompatible or aggressive
solvents is NOT covered by the instrument warranty.

SpectraMax iD3 Multi-Mode Microplate Reader User Guide
10 5054747 B
CAUTION! When you use aggressive or corrosive reagents, you should turn the Auto
Eject Plate setting on the Maintenance page Reader Settings tab to the On position.
See Reader Settings Maintenance on page 64.
WARNING! BIOHAZARD. Depending on your usage, the injectors can have
biohazardous material in and on them. Always use the personal protective
equipment (PPE) prescribed by your laboratory.
Moving Parts Safety
The instrument contains moving parts that can cause injury. Under normal conditions, the
instrument is designed to protect you from these moving parts.
To prevent injury due to moving parts, observe the following:
Never try to exchange labware, reagents, or tools while the instrument is operating.
Never try to physically restrict the moving components of the instrument.
Keep the instrument work area clear to prevent obstruction of the movement. Provide
clearance in front of the instrument of 18 cm (7.1 in.) for the microplate drawer.
The instrument has adjustable optics to define the read height, or z-height. In a top
read, the read height is the gap between the lens and the top of the microplate, or the
top of the lid if the microplate is lidded.
CAUTION! To prevent damage to the instrument, the height of the microplate must
not exceed 22mm, including the lid if the microplate is lidded.
Transport locks are placed on the transport slide and on the microplate drawer to protect
the instrument from damage during shipment. You must remove the transport locks before
you power on the instrument. See Remove Transport Locks on page 23.
To move the microplate drawer into or out of the instrument, always use the icon on the
touchscreen or the controls in the software. See Load and Unload Microplates, see page 68.
When your instrument is equipped with the SpectraMax®Injector System with
SmartInject™, the injectors in the instrument enable you to deliver a reagent to the wells of a
microplate. Follow the instructions in this guide for injector use and maintenance. See
Injectors on page 14.
WARNING! Do not attempt to access the interior of the instrument unless
instructed to do so. The moving parts inside the instrument can cause injury. Do
not operate the instrument with any covers or panels removed.
Note: Observe all warnings and cautions listed for all external devices attached to or in
use during the operation of the instrument. See the applicable user guide for the
operating and safety procedures of that device.

5054747 B 11
Chapter 1: Introduction
The SpectraMaxiD3 Multi-Mode Microplate Reader from Molecular Devices is a
monochromator-based, multi-mode plate reader. The touchscreen interface provides
integrated instrument control, data display, and the ability to export results for statistical
data analysis.
The instrument supports the following read modes:
UV and Visible Absorbance (ABS), see Absorbance Read Mode on page 90.
Fluorescence Intensity (FL), see Fluorescence Intensity Read Mode on page 94.
Luminescence (LUM), see Luminescence Read Mode on page 98.
For each read mode, you can setup and run the following read types:
Endpoint Read Type on page 89
Kinetic Read Type on page 89
Spectrum Read Type on page 90
CAUTION! To prevent damage to the instrument, the height of the microplate must
not exceed 22mm, including the lid if the microplate is lidded.
Computer Integration
All software required to run basic non-injector reads is installed in the instrument and is
accessible from the touchscreen. You must use a computer running SoftMax® Pro Software
to operate the instrument for advanced acquisition settings and for protocols that use the
SpectraMax Injector System.
Optional integration of the instrument with a computer enables you to export data over
your intranet or to a USB flash drive in an Excel format for further analysis.
You can use SoftMax Pro Software to have the instrument collect data from one or more
microplates and store the data in a single file, using the same or different instrument settings
for different microplates. Assays that require a read in two or more read modes or read types
can be combined in a single experiment and run with a single command in the SoftMax Pro
Software, by defining separate microplate reads and enabling Auto Read. For information on
the acquisition and analysis capabilities of the SoftMax Pro Software, see the SoftMax Pro
User Guide.
Note: When you use a computer running the SoftMax Pro Software to operate the
instrument, the instrument touchscreen is locked.
When you use SoftMax® Pro GxP Software to operate the SpectraMaxiD3 Multi-Mode
Microplate Reader and you log on as a user with the Sign Statements permission, two
additional icons appear on the GxP tab.
1

SpectraMax iD3 Multi-Mode Microplate Reader User Guide
12 5054747 B
Users with the Sign Statements permission click GxPMode On to lock the
instrument touchscreen and operate the instrument from the computer running the
SoftMax Pro Software in GxP mode. This locks the instrument touchscreen for all users
and the instrument must be operated from a computer running SoftMax Pro GxP
Software.
Users with the Sign Statements permission click GxPMode Off to release the lock
from the instrument touchscreen and allow users to perform reads from the instrument.
Note: The instrument remains locked until the Sign Statements user clicks GxPMode
Off to stop the GxP mode. You cannot use the Instrument Connection dialog to
disconnect from an SpectraMax iD3 instrument that is locked in GxP mode.
The SpectraMax iD3 software version 1.0 is compatible with SoftMax Pro Software version
7.0.1.
The SpectraMax iD3 software version 1.1 is compatible with SoftMax Pro Software version
7.0.2.
To update the SpectraMax iD3 software, please contact Technical Support.
Applications
The high sensitivity and flexibility of the instrument make it useful for applications in the
fields of biochemistry, cell biology, immunology, molecular biology, and microbiology.
Typical applications include ELISA, nucleic acid, protein, enzymatic type homogeneous and
heterogeneous assays, microbial growth, endotoxin testing, and pipettor calibration.
Application notes with specific application protocol suggestions can be found in the
Information Center and the Knowledge Base on the Molecular Devices web site at
www.moleculardevices.com.
Optics
The 2x2 monochromators permit individual optimization of wavelengths for both excitation
and emission in fluorescence readings. Mirrored optics shape the light, and a height-
adjustable objective lens focuses the beam into the sample volume. PMT Gain can be set to
automatic, high, medium, or low.
Dynamic Range
The dynamic range of detection is approximately from 10-6 to 10-12 molar fluorescein.
Variations in measured fluorescence values are virtually eliminated by internal compensation
for detector sensitivity, photomultiplier tube voltage and sensitivity, and excitation intensity.
The photometric range is 0.000 to 4.000ODs with a resolution of 0.001OD.
CAUTION! Never touch the optic mirrors, lenses, filters, or cables. The optics are
extremely delicate, and critical to the function of the instrument.

Chapter 1: Introduction
5054747 B 13
CAUTION! Use of organic solvents can cause harm to the optics in the instrument.
Extreme caution is recommended when using organic solvents. Always use a plate lid
and do not place a plate containing these materials in the microplate chamber for
prolonged periods of time. Damage caused by the use of incompatible or aggressive
solvents is NOT covered by the instrument warranty.
Microplate Controls
Microplates up to a height of 22mm can be placed in the microplate drawer of the
instrument. A camera detects the height of a microplate in the microplate drawer and
confirms that the height is consistent with the microplate type you select and that the plate
is positioned properly on the microplate drawer.
Depending on the application, the instrument can read 6, 12, 24, 48, 96, and 384-well
microplates. For micro-volume measurements, the instrument supports SpectraDrop 24-well
Micro-Volume Microplates and SpectraDrop 64-well Micro-Volume Microplates. See Set Plate
Format and Plate Type on page 72.
CAUTION! To prevent damage to the instrument, the height of the microplate must
not exceed 22mm, including the lid if the microplate is lidded.
Shake
A shake feature can be operated independently from a protocol to permit the contents of
the wells in a microplate to be mixed outside of the microplate chamber for visual inspection.
This makes it possible to do kinetic analysis of solid-phase, enzyme-mediated reactions. See
External Shake Settings on page 46.
You also define shake settings as part of each protocol. The process related to the shake
setting depends on the read mode you select. See Set Shake on page 81.
Temperature Regulation
The temperature inside the microplate chamber can be maintained at 5°C (9°F) above
ambient to 65°C (149°F). See Microplate Chamber Temperature Settings on page 48.
The temperature sensors detect the temperature of the air inside the chamber, not the
temperature of the samples in the microplate. If you use the instrument to warm the
samples, use a seal or lid on the microplate to prevent evaporation of the sample. The seal or
lid also helps to maintain a uniform temperature. It can take an hour or more for a prepared
sample to equilibrate inside the microplate chamber. You can speed up equilibration by
prewarming the sample and the assay reagents to the desired temperature before you place
the microplate in the chamber. Validate the data quality to determine whether the seal or lid
can stay on the microplate for the read.

SpectraMax iD3 Multi-Mode Microplate Reader User Guide
14 5054747 B
Injectors
When your instrument is equipped with the SpectraMax Injector System, the injectors in the
instrument enable you to deliver a reagent to the wells of a microplate. You use the injectors
to deliver a specific volume of reagent to initiate a reaction that occurs rapidly and results in
a luminescent or fluorescent signal that must be detected quickly. The injector system is
method independent which means you can run injector protocols for all read modes:
Absorbance, Luminescence (all wavelength), Luminescence Monochromator, Fluorescence
Intensity top, and Fluorescence Intensity bottom.
Note: You must use a computer running SoftMax Pro Software to operate the
instrument for advanced acquisition or injector protocols.
Before you use the injectors or do maintenance operations, make sure that you are familiar
with the safety information in this guide. See Safety Information on page 5.
Figure 1-1: Hood open to display injectors

Chapter 1: Introduction
5054747 B 15
The SoftMax Pro Software can set up the instrument to inject and read well by well to reduce
signal loss. To define the settings for a read with injection, you must use the Acquisition View
on the Settings dialog. See the SoftMax Pro Software application help for details.
The Injector Maintenance page enables you to wash and prime the injectors. See Injector
Maintenance - Wash and Prime on page 49.
WARNING! BIOHAZARD. Depending on your usage, the injectors can have
biohazardous material in and on them. Always use the personal protective
equipment (PPE) prescribed by your laboratory.

SpectraMax iD3 Multi-Mode Microplate Reader User Guide
16 5054747 B

5054747 B 17
Chapter 2: Unpack and Setup the Instrument
Before you unpack and setup the SpectraMax®iD3 Multi-Mode Plate Reader instrument,
prepare a dry, flat work area that has sufficient space for the instrument and required cables.
See Instrument Specifications on page 125
All software required to run basic non-injector reads is installed in the instrument and is
accessible from the touchscreen. You must use a computer running SoftMax Pro Software to
operate the instrument for advanced acquisition settings and for protocols that use the
SpectraMax Injector System.
You can export data to a computer over your intranet, through a direct Ethernet cable, or to
a USB flash drive in an Excel format for further analysis.
Unpack the instrument and save the original packaging. See Unpack the Instrument on
page 20.
Remove the transport locks from the transport slide and microplate drawer. See Remove
Transport Locks on page 23.
Connect the instrument cables. See Connect Instrument Cables on page 29.
Turn on the instrument power. See Turn the Instrument On and Off on page 31.
Get the instrument onto your network. See Get the Instrument On Your Network on
page 32.
Optionally, install the SoftMax® Pro Software on a computer to operate the instrument.
You must use the SoftMax Pro Software to run injector reads. See the SoftMaxPro User
Guide. The SoftMax Pro Software installation automatically installs the QuickSync®tool.
You can choose to install only the QuickSync tool. See Install the QuickSync Tool on page
35.
Note: When you use a computer running the SoftMax Pro Software to operate the
instrument, the instrument touchscreen is locked.
2

SpectraMax iD3 Multi-Mode Microplate Reader User Guide
18 5054747 B
Contents of the Package
The package contains the instrument plus a box that contains the tools and accessories
required to install the instrument.
Illustration Part
Number
Description
5054744 Installation guide
YW 000
006
Hex key, 2.0mm
YW 000
012
Holex HEXAGONballhead bolt driver 3 mm
5052189 CAT6 Ethernet cable, 2meter (6.56foot)
4400-
0002 or
4400-
0036
Power cord, 115 V
or Power cord, 230 V
5056338 Near Field Communication (NFC)sticker (NTAG 213, 180
byte) Stick sticker to an item to use as your swipe tool. Not
the NFC key fob.
5056339 Near Field Communication (NFC)key fob (NTAG 213, 180
byte). Do not put an NFC sticker on the key fob.
5048887 SoftMax Pro Software with Product Key and QuickSync tool
Table 2-1: Package Contents

Chapter 2: Unpack and Setup the Instrument
5054747 B 19
When your instrument has the SpectraMax Injector System the package also contains the
following.
Illustration Part Number Description
5055247 Injector Nozzle
5044164 Tubing
5055251 Bottle Holder
5044165 Bottle Adapters
5044163 Waste Plate
Cannot order from Molecular Devices
Wide-neck bottle, HDPE
50mL capacity
36mm square by 68mm high
24mm diameter inside neck
Recommended supplier: VWR (215-0440)
Bottles
Cannot order from Molecular Devices
Strip wells, polystyrene
1x8, clear, flat-bottomed
Recommended supplier: Greiner Bio-One (762001)
Strip well
Table 2-2: Package Contents
For a complete list of the contents of the package, see the enclosed packing list.

SpectraMax iD3 Multi-Mode Microplate Reader User Guide
20 5054747 B
Unpack the Instrument
The packaging is designed to protect the instrument during transportation.
Transport locks are placed on the transport slide and the microplate drawer to protect the
instrument from damage during shipment. You must remove the transport locks before you
power on the instrument.
WARNING! LIFTING HAZARD. To prevent injury, use a minimum of two
people to lift the instrument.
Note: Retain the shipping box and all packaging materials for future transport needs.
Do not use tools that can damage the packaging or the instrument.
CAUTION! When transporting the instrument, warranty claims are void if damage
during transport is caused by improper packing.
To unpack the instrument:
1. Check the box for visible damage that occurred during transportation. In case of
damage, inform the supplier immediately and keep the damaged packaging.
CAUTION! Keep the box upright. Do not tip or tilt the box or place it on its side.
2. With the box facing up as indicated on the packaging, use a box cutter to carefully cut
open the side of the box labeled Open Here.
Figure 2-1: Open the box