Thermo Scientific Nicolet iS50 GC-IR User manual

FT-IR Spectrometers
Nicolet iS50
Getting Started
269-277300 Revision A June 2012

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Thermo Scientific Getting Started with the Nicolet iS50 Spectrometer 1
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.
This document explains the features of your spectrometer and takes you through a basic
sample collection. These topics are covered:
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.
Contents
•When to open the shipping box
•An introduction to the instrument
•The procedure for collecting a spectrum
•System options
•Performance checks
•Maintenance
•Important documents
•Contact information
• The instrument warranty
•Troubleshooting information
NOTICE Be sure that all persons operating this system read the site and safety manual
first.

Getting Started
When can I open the shipping box?
2Getting Started with the Nicolet iS50 Spectrometer Thermo Scientific
When can I open 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.

Getting Started
What are the features?
Thermo Scientific Getting Started with the Nicolet iS50 Spectrometer 3
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
Help available through the Help menu in the OMNIC™ software.
1- Desiccant access cover
2- Humidity indicator
(under access cover)
8- Right external beam port
9- Emissions port
(left back)
3- Sample compartment
4- Sample compartment Touch Point
5- Protective windows or purge shutters
7- iS50 ATR module (optional)
6- Sample compartment Accessory and Purge ports (inside)
10 - Beamsplitter access door
11 - Detector access cover
13 - Power switch
7 - ATR Touch Point)
8- Left external beam port
(left front)
12 - Nitrogen fill port

Getting Started
What are the features?
4Getting Started with the Nicolet iS50 Spectrometer Thermo Scientific
Spectrometer Features
1Your 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.
2The humidity indicator monitors the level of humidity inside the spectrometer. The
status is conveyed by the color of the indicator:
3You 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
Blue - good
Light blue - Buy replacement desiccant
Pink or white - Change desiccant
White - Call for service
Smart Accessories TGA accessory iS50 Raman module

Getting Started
What are the features?
Thermo Scientific Getting Started with the Nicolet iS50 Spectrometer 5
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
4The 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. Touch Points are
explained in the “How do I collect a spectrum?” chapter of this document and in the
spectrometer and OMNIC software Help.
5Whenever 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.
6The 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.
7The 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.
8The 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.

Getting Started
What are the features?
6Getting Started with the Nicolet iS50 Spectrometer Thermo Scientific
9The 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.
10 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 software.
11 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.
12 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
spectrometer Help for instructions and important safety information.
13 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).

Getting Started
What are the features?
Thermo Scientific Getting Started with the Nicolet iS50 Spectrometer 7
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 damage 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.
Purge In
Auxiliary Signals
DC PowerComputer
Microscope Accessory
Left Accessory
Sample Compartment Accessory
Right Accessory

Getting Started
What are the features?
8Getting Started with the Nicolet iS50 Spectrometer Thermo Scientific
Back Panel Connectors
•Auxiliary 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.
•Accessory (left/right) - 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).
•Computer USB 2.0 - Connects to the USB cable from the system computer.
•DC Power - Connects to the power supply for the instrument.
•Microscope 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.
•Purge 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.
•Sample Compartment Accessory USB 2.0 - 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.

Collecting a Spectrum
How do I collect a spectrum?
Thermo Scientific Getting Started with the Nicolet iS50 Spectrometer 9
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 collect a spectrum?
The following procedure takes you through the data collection process for the four commonly
used techniques using the sample compartment beam path: 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 software.
Next, make sure the sample holder or sampling accessory you want to use is installed and
ready for the background collection (see the table below).
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 software, please see the spectrometer Help and the
OMNIC help (both are available through the Help menu in OMNIC software) or their
PDF versions on your documentation media.
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.

Collecting a Spectrum
How do I collect a spectrum?
10 Getting Started with the Nicolet iS50 Spectrometer Thermo Scientific
To select the sample compartment beam path and load its default workflow, 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.
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 Place a gold mirror face down on the accessory.

Collecting a Spectrum
How do I collect a spectrum?
Thermo Scientific Getting Started with the Nicolet iS50 Spectrometer 11
The workflow is user-configurable and defines everything from the background and sample
collections to quantitative analysis and spectral search. For the purposes of this getting started
exercise, we will assume the default workflows and settings are in place.
After you press a Touch Point, the Touch Point LED lights and a message is displayed while
the instrument collects a few scans to determine stability with the new configuration. When
the stability test is completed, another message may appear while the instrument runs a
performance test.
When the performance test is completed, press the Touch Point again to start the workflow.
A message asks you to enter a spectrum title.
Enter a title for your sample spectrum and choose OK (or press the Touch Point to accept
the default title). A message tells you to prepare for the background collection.

Collecting a Spectrum
How do I collect a spectrum?
12 Getting Started with the Nicolet iS50 Spectrometer Thermo Scientific
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 background collection.
As the collection proceeds, the background data appear in the OMNIC main window. When
background collection is complete, a message asks whether to add the spectrum to a window.
Choose Yes (or press the Touch Point) to add the background spectrum to an OMNIC
window, or choose No to continue without adding the spectrum to a window. The
background spectrum is saved even if you don’t add it to a window.
Next, install a sample:
If you have… You should…
The standard sample holder and
baseplate
Slide a sample into place. A good first sample is a plastic
bag or any polymer film.
The iS50 ATR module or an
ATR accessory
Place the sample 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.
If your spectrometer includes the optional purge
shutters, you will hear them open and a message
asks you to wait until the purge has stabilized.
After a few seconds, the message goes away and
the background collection starts.

Collecting a Spectrum
How do I collect a spectrum?
Thermo Scientific Getting Started with the Nicolet iS50 Spectrometer 13
Now, press the Touch Point to collect a sample spectrum.
When the data collection is complete, the sample spectrum is displayed. Here is an example of
a typical sample spectrum.
A DRIFTS accessory Fill the cup with a sample and level the surface with a
spatula. A good first sample is a ground aspirin tablet
diluted to 3-5% 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.
If you have the optional purge shutters, you will hear them
open again and see the message to wait until the purge has
stabilized. After a few seconds, the sample collection starts.

Collecting a Spectrum
How do I collect a spectrum?
14 Getting Started with the Nicolet iS50 Spectrometer Thermo Scientific
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 Analyze menu in
OMNIC software. For more information, find
“Comparing Spectra with QCheck” in the OMNIC
Help.
You can also configure your workflow to run QCheck
automatically. For more information, find “Touch Point
Setup” in the OMNIC Help.

Collecting a Spectrum
How do I collect a spectrum?
Thermo Scientific Getting Started with the Nicolet iS50 Spectrometer 15
If you want to… You can…
Identify an unknown material Use the OMNIC Search feature. For more information,
find “Setting Up a Spectral Search” in the OMNIC Help.
You can also configure your workflow to run Search
automatically. For more information, find “Touch Point
Setup” in the OMNIC Help.
Alternatively, after the workflow is completed, you can
use the OMNIC Specta search features shown below to
perform a search of the sample spectrum. This software
includes our unique multi-component search feature for
identifying the spectra of mixtures, a 9,000 compound
spectral database, and features for using the spectra on
your computer’s hard drive as a library. Refer to the
software help in the OMNIC Specta Help menu for
more information.

Collecting a Spectrum
How do I collect a spectrum?
16 Getting Started with the Nicolet iS50 Spectrometer Thermo Scientific
If you want to… You can…
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 Analyze menu in
OMNIC software to select and run the method. For
more information, refer to the OMNIC Help and the
help system in TQ Analyst software.
You can also configure your workflow to run Quantify
automatically. For more information, find “Touch Point
Setup” in the OMNIC Help.

Taking the Next Steps
What options are available?
Thermo Scientific Getting Started with the Nicolet iS50 Spectrometer 17
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.
For more information, search for the module or accessory name in the spectrometer or other
help, available from the Help menu in OMNIC software. (For information about additional
modules and accessories, contact our sales representative in your area.)
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.

Taking the Next Steps
What options are available?
18 Getting Started with the Nicolet iS50 Spectrometer Thermo Scientific
iS50 Raman module Provides integrated tools for FT-Raman sampling. This
module easily slides into the spectrometer sample
compartment and includes an integrated sample stage
and USB video camera. The module can be used for
screening drugs, studying crystals, and other
applications. For more information, find “iS50 Raman
Module” in the spectrometer Help.
iS50 GC-IR module Interfaces seamlessly between the Nicolet iS50
spectrometer and a compatible gas chromatograph for
GC-IR analysis of mixtures, especially stereoisomers. The
module mounts on the right side of the spectrometer. For
more information, find “iS50 GC-IR Module” in the
spectrometer Help.
Contact our representative in your area for compatible
brands and models for the gas chromatograph.
Continuμm infrared microscope Allows you to identify particles as small as
10 micrometers and perform many operations such as
surface analyses and chemical mapping. The microscope
module mounts on the right or left side of the
spectrometer. For more information, see the microscope
Help or find the Continuμm User Guide on your
Nicolet iS50 documentation media.