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.