Thermo Scientific Nicolet iS50 GC-IR User manual

Nicolet iS50 Spectrometer
Getting Started
Congratulations on your purchase! The Thermo Scientific NicoletiS50 spectrometer is our
highest performance FT-IR spectrometer with integrated features for carrying out a wide range of
experiments and applications. The system includes performance verification features, a powerful
software suite, and many other features that make it easy for you to collect data and get the
answers you need.
Note The optional ValPro™ Qualification is a comprehensive system qualification package that
can be used instead of, or in addition to, performance verification. If you purchased ValPro
Qualification for your spectrometer, please refer to your ValPro documentation for more
information.
269-3516 00 A Revision A
February 2022 ThermoFisher Scientific
All rights reserved.

This document explains the features of your spectrometer and takes you through a basic sample
collection. These topics are covered:
Nicolet iS50 SpectrometerGetting Started 1
When can I unpack the shipping box? 3
What are the features? 4
Collecting a Spectrum 12
Taking the Next Steps 18
NOTICE
Be sure that all persons operating this system read the site and safety manual first.
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Nicolet iS50 SpectrometerGetting Started

When can I unpack the shipping box?
Your spectrometer will be unpacked and installed by a service representative, but if necessary,
you can unpack the shipping box beforehand. Wait 24 hours for the boxes to come to room
temperature before you open anything!
NOTICE
To avoid causing permanent damage to optical components inside your spectrometer or in
separate packaging, wait 24 hours for the shipping boxes to come to room temperature before
you open anything, especially the plastic wrapping that protects the spectrometer. If a
protective wrap is opened before the contents reach room temperature, moisture may
condense on the optics and cause permanent damage. The warranty does not cover damage
to optical components caused by unpacking the shipping box before it has reached room
temperature. Please see “"What about the warranty?"” in the “"Taking the Next Steps"” section
for more information.
CAUTION
Avoid risk of personal injury. Your instrument cannot be lifted safely by a
single person. Lifting or moving the instrument requires two people. Use
proper lifting techniques when lifting or moving the instrument or other
system components.
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Nicolet iS50 SpectrometerGetting Started
When can I unpack the shipping box?

What are the features?
The following image shows the main features of your spectrometer. Below the image, you will find
descriptions of these features. For additional information, please see the spectrometer user
manual.
ANitrogen fill port The nitrogen fill port is used to fill the vacuum dewar of an MCT
or InSb detector with liquid nitrogen before you collect data if one
of those detectors is installed. Before you attempt to fill the
dewar, please review “Cooling a Detector” in the user guide for
the spectrometer for instructions and important safety
information.
Table 1-1: iS50 Spectrometer Features
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Nicolet iS50 SpectrometerGetting Started
What are the features?

BHumidity indicator The humidity indicator monitors the level of humidity inside the
spectrometer. The status is conveyed by the color of the
indicator:
CDesiccant access
cover
Your spectrometer is protected from excessive humidity by
desiccant located in a compartment below the desiccant access
cover. Use the humidity indicator (see below) to monitor the
moisture level inside the spectrometer and replace the desiccant
as soon as it becomes saturated. For information about
replacing the desiccant, find “Replacing the Desiccant” in the
spectrometer Help.
Leave the desiccant in the spectrometer even if you purchased
the optional purge kit so the system is protected in the event of a
power failure or if the purge is turned off. For information about
purging your spectrometer, refer to your spectrometer Site and
Safety Guide.
DPower switch The power switch turns the spectrometer on and off. Two
indicator lights next to the power switch tell you the status of the
spectrometer:
System status (steady blue - ready; flashing yellow - error with a
component).
System scan (blinking blue - scanning; off - not scanning or
sleep mode).
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Nicolet iS50 SpectrometerGetting Started
What are the features?

EProtective
windows or purge
shutters
Whenever the sample compartment cover is open or off, the
spectrometer is protected from environmental humidity and
other chemical vapors by two windows (or two purge shutters, if
this option is installed). These windows or shutters isolate the
optics in the spectrometer. You still, however, need to be careful
when using or cleaning the spectrometer to avoid damaging the
optics or the windows, if installed. Never attempt to clean the
sample compartment windows.
FBeamsplitter
access door
The beamsplitter access door lets you access the beamsplitter
compartment where you can easily remove and install
beamsplitters by releasing and engaging a latch. The
compartment also has a storage area for up to two additional
beamsplitters.
Notice: Beamsplitters are sensitive to moisture and must be
stored in a desiccated environment. To preserve the integrity of
your beamsplitters, leave them in their shipped configuration or
packaging until you have reviewed the instructions for handling
them. For more information, find “Handling Beamsplitters” in the
spectrometer Help.
If your spectrometer has the optional iS50ABX (Automatic
Beamsplitter eXchanger), the beamsplitter compartment is
replaced with a tower where up to three beamsplitters can be
installed and interchanged using OMNIC Paradigm software.
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Nicolet iS50 SpectrometerGetting Started
What are the features?

GSample
Compartment
You can use the sample compartment for transmission sampling
and with many different accessories and modules including:
Smart Accessories™
• A wide range of these accessories and techniques can be
used including:
• Diffuse Reflection Infrared Fourier-Transform Spectroscopy
(DRIFTS)
• Attenuated Total Reflection (ATR)
• Specular Reflection (SR)
• Temperature controlled accessories
Large baseplate-mounted accessories
The sample compartment is large enough to accommodate
specialized accessories including:
• Thermal Gravimetric Analysis (TGA) interface
• iS50 Raman module
• Multi-pass (long pathlength) gas cells
• Other accessories
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Nicolet iS50 SpectrometerGetting Started
What are the features?

HiS50 ATRmodule
(optional)
The optional built-in iS50ATR module offers convenient,
reproducible Attenuated Total Reflection (ATR) sampling with
the NicoletiS50 spectrometer. The ATR module includes all-
reflective diamond optics, a dedicated broad-band detector,
extended spectral range and our signature Touch Point
operation.
IATR
Touchpoint
JRight and left
external beam
ports
The right and left external beam ports can be used to send the
infrared beam to external modules connected to the
spectrometer such as the iS50NIR module, the iS50GC-IR
module, the iS50Research module, or the Continuµm FT-IR
microscope. The external modules allow specialized sampling
while leaving the main sample compartment available for
transmission or other techniques. Each module has an
associated Touch Point that allows you to configure the
spectrometer and run experiments without needing to interact
with the computer.
Note: The left external beam port can also be used to send the
collimated beam from an external source such as a Synchrotron
beam line, directly into the interferometer (the beam bypasses
the aperture). Optional hardware is required.
KSample
compartment
touch point
The sample compartment Touch Point allows you to configure
the spectrometer for the installed sample, sampling module or
accessory and then run experiments without needing to interact
with the computer. Other Touch Points are available for
sampling modules that mount in or alongside the spectrometer.
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Nicolet iS50 SpectrometerGetting Started
What are the features?

LSample
compartment
Accessory and
Purge ports
(inside)
The sample compartment Accessory and Purge ports are used
to connect accessories that have detectors or power needs,
such as the sample shuttle, and accessories that require purge.
MDetector access
cover
The detector access cover allows access to the detector
compartment where a standard TGS detector and up to two
additional detectors may be installed.
Notice: Detectors are sensitive to static electricity. To preserve
their integrity, leave them in their shipped configuration or
packaging until you have reviewed the instructions for handling
them. For more information, see “Removing a Detector” and
“Installing a Detector” in the spectrometer Help.
NEmissions port
(left back)
The emissions port on the left side of the spectrometer can be
used to send light from an external source through the aperture
and into the interferometer, allowing high resolution studies of
external emissions.
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Nicolet iS50 SpectrometerGetting Started
What are the features?

What is on the back panel?
The following image shows the connectors that are on the back panel of your spectrometer:
NOTICE
Improper or unsafe cabling can cause damager to system hardware and may create a safety
hazard. We are not responsible for damage or injury resulting from improper or unsafe cabling.
Refer to your spectrometer Site and Safety Guide for details.
AAuxiliary
signals
Can be used to connect the remote start cable or iS50Hub. This
port is also used by service personnel to check the function of the
spectrometer.
Table 1-2: Back panel connectors
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Nicolet iS50 SpectrometerGetting Started
What are the features?

BLeft accessory The left and right Accessory ports are for connecting components
and enhanced applications modules that mount on the left and
right side of the spectrometer. Examples include the iS50GC-IR
module (right), the iS50NIR module (left), and the Continuµm™
FT-IR microscope (right or left).
CRight accessory
DComputer Connects to the USB cable from the system computer.
EDCPower Connects to the power supply for the instrument.
FSample
compartment
accessory
Connects the cable from the USB video camera that comes with
some accessories that mount in the spectrometer sample
compartment such as the iS50Raman module. The other end of
the cable connects to any USB 2.0 port on the computer.
GPurge In Connects to a purge gas supply if your spectrometer includes a
purge kit. Before you attach a purge source, review “Installing a
Purge Kit” in the spectrometer Help for instructions and important
safety information.
HMicroscope
accessory
Connects the Touch Point cable for an FT-IR microscope or other
accessory that mounts on the right or left side of the spectrometer.
The other end of the cable connects to the Touch Point assembly.
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Nicolet iS50 SpectrometerGetting Started
What are the features?

Collecting a Spectrum
To collect a sample spectrum, you must first collect a reference (or background) spectrum that
shows the response of the system when no sample is present. Once you have the background
spectrum, you can collect data with a sample in place. The sample data is then ratioed with the
background data, which leaves only the signals from the sample.
How do I measure a sample?
The following procedure walks you through measuring and analyzing samples using four
commonly used techniques: transmission, Attenuated Total Reflection (ATR), Diffuse Reflection
Infrared Fourier-Transform Spectroscopy (DRIFTS), and Specular Reflection (SR).
For more information, please refer to the other documentation that came with your spectrometer.
Begin by starting the OMNIC Paradigm software.
Note The software may display various prompts during collection. If any prompts appear,
follow the instructions shown on the screen. For additional information about preparing the
system and using OMNIC Paradigm software, please see the spectrometer and software user
guides and tutorials at www.knowledge1.thermofisher.com
Step 1:Prepare to measure the background
Make sure the sample holder or sampling accessory you want to use is installed and ready for the
background collection (see the table below).
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Nicolet iS50 SpectrometerGetting Started
Collecting a Spectrum

If you have ... You Should ...
The standard sample holder
and baseplate (included with
the iS50spectrometer)
Install the baseplate by placing it in the sample
compartment over the alignment pins.
Make sure no samples that would block the beam are
installed in the accessory.
The iS50 ATR module or an
ATR sample compartment
accessory
Make sure the pressure device is not in contact with the
crystal. Clean the crystal with a clean, soft cloth or a white
paper napkin. If needed, you can dampen the cloth or
napkin with water, mild soap, or alcohol for the iS50ATR
module. (If you are using a sample compartment ATR
accessory, check the documentation that came with it for
cleaning agents that are compatible with your accessory
and the type of crystal it has.)
Do not pour liquids directly onto the sampling area; if
additional solvent is needed to clean the crystal, use a
pipette or dropper.
A DRIFTS accessory Make sure the slider is pushed in to the second cup (the
one closer to the handle). This positions the gold alignment
mirror in the beam.
A Specular Reflection
accessory, such as the Smart
SAGA accessory
Place a gold mirror face down on the accessory.
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Nicolet iS50 SpectrometerGetting Started
Collecting a Spectrum

To select the sample compartment beam path and load the related settings, press the Touch
Point next to the sample compartment.
If you are using the iS50 ATR module, press the Touch Point next to that module.
You can customize and save measurement settings for each of the Touch Points.
For the purposes of this getting started exercise, we will assume the default settings are in place.
Step 2:Measure the background
When the software switches to the settings for the main sample compartment, press the Touch
Point again to start the measurement.
If there is not a current background measurement, the software prompts you to measure the
background. Make sure your sample holder or accessory is set up for a background collection
(refer to the previous table) and then press the Touch Point to start the measurement.
If your system has purge shutters, the software will display a purge delay message when needed.
When the software shows the background preview, press the Touch Point to measure the
background.
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Nicolet iS50 SpectrometerGetting Started
Collecting a Spectrum

Step 3:Measure your sample
Place the sample in the sampling accessory.
If you have ... You Should ...
The standard sample holder
and baseplate (included with
the iS50spectrometer)
Slide a sample into place. A good first sample is a plastic
bag or any polymer film.
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Nicolet iS50 SpectrometerGetting Started
Collecting a Spectrum

If you have ... You Should ...
The iS50 ATR module or an
ATR sample compartment
accessory
Place the samlpe on the crystal and apply pressure (turn
the handle clockwise until it clicks). A good first sample
might be a credit card, an old CD, or a piece of plastic. For
liquids, no pressure is needed.
A DRIFTS accessory Fill the cup with a sample and level the surface with a
spatula. A good first sample is a ground asprin tablet
diluted to 3 to 5 % in KBr powder. You do not need to
overfill the cup.
A specular reflection
accessory
Place the sample upside down on the accessory. A good
first sample is a piece of shiny metal, like aluminum, with a
thin coating of vegetable oil. Add a drop of oil, and then
wipe the metal with a cloth so that a thin layer of oil
remains.
When the sample is in place, press the Touch Point to collect a sample spectrum.
When the data collection is complete, the sample spectrum is displayed.
Finally, you can verify, identify, and quantify your data:
If you want to ... You can ...
Verify the purity or
quality
of your sample
Use the QCheck tool available from the Identify menu in OMNIC
Paradigm software. See the OMNIC Paradigm User Guide for
details.
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Nicolet iS50 SpectrometerGetting Started
Collecting a Spectrum

If you want to ... You can ...
Identify an unknown
material
Use a correlation search to identify a single component or use
multi-component search to identify components in a mixture. For
details on setting up and running a search, see the OMNIC
Paradigm User Guide.
Quantify the amount of
a component in your
sample
Use the features in the TQ Analyst™ software to create a
quantitative method, and then use the Quant Setup and Quantify
features available from the Identify menu in OMNIC Paradigm
software to select and run the method. For more information, see
the OMNIC Paradigm User Guide and the help system in TQ
Analyst software.
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Nicolet iS50 SpectrometerGetting Started
Collecting a Spectrum

Taking the Next Steps
Now that you are familiar with your spectrometer and have collected a sample spectrum, you are
ready to explore other options and learn where you can find additional information.
What options are available?
Many applications modules and accessories that expand what you can do with your spectrometer
are available. The following is a list of some of these modules and accessories.
This accessory or module
...
Does this ...
iS50 ATR module Allows reproducible attenuated total reflection (ATR)
sampling with the spectrometer without needing to use the
main sample compartment. For more information, find “iS50
ATR Module” in the spectrometer Help.
iS50 NIR module Provides two near-infrared sampling options in a compact
module that attaches to the left side of the spectrometer. The
two options are an integrating sphere for diffuse reflection
measurements of materials contained in vials or blister
packs, and ports for connecting a diffuse reflection fiber optic
probe, such as the optional Thermo Scientific SabIR™ probe,
for remote sampling. For more information, find “iS50 NIR
Module” in the spectrometer Help.
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Nicolet iS50 SpectrometerGetting Started
Taking the Next Steps

This accessory or module
...
Does this ...
RaptIRFTIRmicroscope Allows you to identify particles and perform operations such
as surface analyses and chemical mapping.
The microscope module mounts on the right or left side of the
spectrometer.
Extra sources The spectrometer can have up to three light sources
(infrared, white light, and external emission) that let you
collect spectra in the mid-IR to far-IR range or in the visible to
near-IR range.
Note: Spectrometers with the optional emission accessory
can use an external source.
Extra detectors The spectrometer has a fixed DTGS detector that is always
present. The fixed detector has the standard potassium
bromide (KBr) window or an optional cesium iodide (CsI)
window.
If your spectrometer includes the optional three-position
detector mirror, up to two additional detectors may be
installed in the detector compartment of your spectrometer.
The detector mount closest to the back of the spectrometer
can be used for a variety of cooled and room temperature
detectors. The front mount fits room temperature detectors
only. You can change the front and back detectors yourself.
Notice: Detectors are sensitive to static electricity. To
preserve the integrity of your detectors, leave them in their
shipped configuration or packaging until you have reviewed
the instructions for handling them. For more information, find
“Changing a Detector” in the spectrometer user guide.
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Nicolet iS50 SpectrometerGetting Started
Taking the Next Steps

This accessory or module
...
Does this ...
Extra beamsplitters The spectrometer requires a beamsplitter for operation. The
type of beamsplitter installed depends on your spectrometer
configuration. Up to two additional beamsplitters can be
stored in the beamsplitter compartment. An Automatic
Beamsplitter eXchanger (ABX) is also available (see below).
Notice: Beamsplitters are sensitive to moisture and must be
stored in a desiccated environment. To preserve the integrity
of your beamsplitters, leave them in their shipped
configuration or packaging until you have reviewed the
instructions for handling them. For more information, find
“Manually Changing a Beamsplitter” in the spectrometer user
guide.
iS50 ABX Allows up to three beamsplitters to be mounted inside the
spectrometer and interchanged with the press of a button.
For more information, see“Using the iS50ABX” in the
spectrometer user guide.
Automated purge shutters Software controlled metal shutters located on both sides of
the sample compartment. The shutters are normally closed to
seal the spectrometer optics. They can be opened using an
option in OMNIC software, or configured to open
automatically for data collection. For more information, find
“Using Purge Shutters” in the spectrometer Help.
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Nicolet iS50 SpectrometerGetting Started
Taking the Next Steps