Thermo Scientific Nicolet iS5 LS User manual

Nicolet iS5 Series FT-IR Spectrometers
Nicolet iS5 LS
User Guide
269-299800 Revision B September 2014

© 2014 Thermo Fisher Scientific Inc. All rights reserved.
All trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries.
For U.S. Technical Support, please contact:
Unity Lab Services
Part of Thermo Fisher Scientific
5225 Verona Road
Madison WI 53711-4495 U.S.A.
Telephone: [phone]
E-mail: [e-mail]
For International Support, please contact:
Thermo Fisher Scientific
Telephone: [phone]
E-mail: [e-mail]
Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
product operation. This document is copyright protected and any reproduction of the whole or any part of this
document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.
The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document supersede
all previous information received by the purchaser.
Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or error-
free and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might
result from any use of this document, even if the information in the document is followed properly.
This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This
document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of
Sale shall govern all conflicting information between the two documents.
For Research Use Only. This instrument or accessory is not a medical device and is not intended to be used
for the prevention, diagnosis, treatment or cure of disease.
WARNING Avoid an explosion or fire hazard. This instrument or accessory is not
designed for use in an explosive atmosphere.

Thermo Scientific Nicolet iS5 LS User Guide iii
C
About the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Finding Information about Your System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
About the Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Operating the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Setting Up the Instrument. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
System Status. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Operating Precautions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Cleaning the Sample Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Instrument Performance Tests. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Collecting Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Maintaining the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
General Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Installing or Replacing Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Troubleshooting the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Resolving Common Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Troubleshooting Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .57
Contents

Thermo Scientific Nicolet iS5 LS User Guide 1
1
About the Instrument
The Thermo Scientific™ Nicolet™ iS™5 LS FT-IR analyzer lets you perform transmission
analyses of liquids, gels and films in the mid-infrared spectral range. The system has integrated
verification features, a software suite designed for quality control (QC) applications, and
many other features that make sampling and data handling easy.
You can perform minor service and maintenance procedures yourself. This document, or
other provided documentation, contains the information needed.
Figure 1. Nicolet iS5 LS FT-IR analyzer
The instrument is sealed and desiccated to help prevent damage to the optics or other internal
components due to humidity or corrosive solvents.
NOTICE Be sure that all persons operating this system read the site and safety manual
first.
NOTICE Keep the instrument sealed and desiccated at all times and check the humidity
indicator regularly. Equipment damage due to failure to maintain seal and desiccation is
not covered by the warranty. If you have questions about this requirement, contact us.

1
About the Instrument
2Nicolet iS5 LS User Guide Thermo Scientific
Finding Information about Your System
We recommend first using the documentation provided with qPro software when you have a
question. The qPro Operator application includes a complete Help system for the instrument
and software. The electronic documentation contains PDF files of supporting documents that
are not in the help system such as the site and safety guide.
Conventions Used
Safety precautions and other important information use the following format:
About the Software
The spectrometer can be operated using the Thermo Scientific™ qPro™ Operator software.
qPro Operator provides features for loading and updating workflows and exporting data. It
also allows password protected access to system tools and diagnostics. The workflows are
created using the qPro Developer application which is included in the qPro Developer suite.
Contents
•Finding Information about Your System
•About the Software
•Contacting Us
WARNING Indicates a hazardous situation which, if not avoided, could result in death or
serious injury.
CAUTION Indicates a hazardous situation which, if not avoided, could result in minor or
moderate injury.
NOTICE Follow instructions with this label to avoid damaging the system hardware or
losing data.
Note Contains helpful supplementary information.
Tip Provides information that can make a task easier.

1
About the Instrument
Thermo Scientific Nicolet iS5 LS User Guide 3
Contacting Us
For U.S. Technical Support, please contact:
Unity Lab Services
Part of Thermo Fisher Scientific
5225 Verona Road
Madison, WI 53711-4495 U.S.A.
Telephone: [phone]
E-mail: [e-mail]
For International Support, please contact:
Thermo Fisher Scientific
Telephone: [phone]
E-mail: [e-mail]
If you have problems with your system, refer to the troubleshooting information for help. If
the troubleshooting information doesn’t help you solve the problem, call or e-mail Technical
Support using the information provided above.
If you need to send the instrument to us for repair, call or e-mail us first for any shipping
requirements or other instructions.
and Excel
Note To expedite and assist in problem diagnosis, please be prepared to send us a copy of
your diagnostics log. The diagnostics log includes a history of important system
parameters and events that occur during system operation. The information can be
downloaded to the computer or portable media and sent to our Technical Support group.
For more information, find the “Retrieving the Diagnostic Log” topic in the
qPro Operator Help system.

Thermo Scientific Nicolet iS5 LS User Guide 5
2
Operating the Instrument
This section explains how to set up the Nicolet iS5 LS analyzer and use it to analyze a basic
sample.
Figure 2. Nicolet iS5 LS FT-IR analyzer
This instrument is designed for indoor use at altitudes up to 2,000 m (6,500 ft). It operates
reliably at a constant temperature between 15 °C and 35 °C (60 °F and 95 °F).
The instrument is sealed and desiccated to help prevent damage to the optics or other internal
components due to humidity or corrosive solvents.
Contents
•Setting Up the Instrument
•Operating Precautions
•Cleaning the Sample Windows
•Instrument Performance Tests
•Collecting Data
Sampling arm in
closed position

2
Operating the Instrument
6Nicolet iS5 LS User Guide Thermo Scientific
For optimum instrument stability, the sampling arm should remain closed except when
cleaning it or loading a sample. Keeping the arm closed also allows background measurements
to occur automatically.
Setting Up the Instrument
This section covers these topics:
•Electrical and Communication Cabling
•Turning the Power On and Off
Electrical and Communication Cabling
The illustration below shows the correct cable connections for electrical power and data
communication.
Figure 3. Electrical and communication cabling for the Nicolet iS5 LS analyzer
Check the Site and Safety Information guide in your electronic documentation set for electrical
and other system requirements before you connect the power cord. The wall outlet must be
equipped with a 3-wire line: live, neutral, and ground.
NOTICE Keep the instrument sealed and desiccated at all times and check the humidity
indicator regularly. Equipment damage due to failure to maintain seal and desiccation is
not covered by the warranty. If you have questions about this requirement, contact us.
Power
Communication
Communication
(USB) cable
Power cable

2
Operating the Instrument
Thermo Scientific Nicolet iS5 LS User Guide 7
To cable the instrument
1. Connect the power supply to the power receptacle on the back of the spectrometer and to
a properly grounded AC power source.
2. Connect the USB cable to the USB receptacle on the back of the spectrometer and to a
USB 2.0 port on the computer.
(Do not use a USB auxiliary port or hub.)
Related Topics
•Turning the Power On and Off
Turning the Power On and Off
To turn the instrument power on or off, press the power switch on the back panel. For best
performance, we recommend that you leave the instrument powered on continuously.
Figure 4. Power switch for the Nicolet iS5 LS analyzer
WARNING To ensure a good ground connection and avoid shock hazard, do not use an
outlet that has ground connected to a conduit ground. The ground must be a
non-current-carrying wire connected to earth ground at the main distribution box.
WARNING Do not block access to the power supply, AC power cord or power switch.
Power switch

2
Operating the Instrument
8Nicolet iS5 LS User Guide Thermo Scientific
After the instrument is powered on, the blue power indicator on the main cover flashes while
the instrument warms up and performs diagnostics (about 2 minutes) and then the indicator
stays lit. The system cannot collect data until initialization is completed.
Figure 5. Power indicator for the Nicolet iS5 LS analyzer
Related Topics
•Electrical and Communication Cabling
•Troubleshooting the Instrument
Note If the System Status indicator in the qPro Operator main window has a red “X,”
check that the computer USB cable is securely connected to the spectrometer and the
computer and the instrument driver was installed from the software media.
NOTICE
• Do not block the vents at the back of the instrument. Electronic components can
overheat if these vents are blocked.
• Do not place containers of liquids on top of the instrument. Spilled liquids can enter
the vents or other openings and cause damage.
Power indicator

2
Operating the Instrument
Thermo Scientific Nicolet iS5 LS User Guide 9
System Status
The System Status icon in the qPro Operator main window tells you the current status of the
instrument.
Figure 6. System Status icon in the qPro Operator application
Click the system status icon to check the performance of key instrument components such as
the laser or source.
Figure 7. System Status report for the Nicolet iS5 LS analyzer
Status indicator

2
Operating the Instrument
10 Nicolet iS5 LS User Guide Thermo Scientific
If a component status is red (failed), see the “Troubleshooting the Instrument” section of the
instrument user guide or contact us for assistance.
Related Topics
•Troubleshooting the Instrument
•Operating the Instrument
Operating Precautions
To prolong the life of your instrument and eliminate the possibility of spectral interference
caused by volatile solvent vapors, follow these precautions:
• When cleaning sample windows, avoid using excessive force or you may damage or crack
the windows.
• Do not block the vents at the back of the analyzer. Electronic components can overheat if
these vents are blocked.
• Do not place containers of liquids on top of the analyzer. Spilled liquids can enter the
vents or other openings and cause damage.
• Do not use chlorinated solvents or materials that may produce HCl or HF vapors with or
near the analyzer. These solvents may severely damage the instrument.
• Do not leave solvent on the sample windows for longer than 2 minutes.
WARNING Prevent fire and explosion. The infrared source inside the instrument is an
ignition source. If you are using volatile solvents, provide a fume hood or other active
venting system that is free of spark and other ignition sources and prevents flammable
vapors from collecting in the atmosphere surrounding the instrument.
NOTICE Read the safety guide that came with this instrument before operating the
instrument.

2
Operating the Instrument
Thermo Scientific Nicolet iS5 LS User Guide 11
Cleaning the Sample Windows
Make sure the sample windows are clean before taking reference and sample measurements
with the instrument, and especially before you run the instrument performance tests or
perform any maintenance steps. The instrument has two windows that must be cleaned. One
is inside the sample cup where you load samples. The other is on the sampling arm.
Figure 8. Sample window locations for the Nicolet iS5 LS analyzer
Materials required:
• Small volume of isooctane or other appropriate solvent
• Small, clean dropper bottle or pipette
• Clean, dry, lint-free laboratory wipes (unscented and lotion-free)
• Powder-free nitrile gloves
Lower sample window
(inside sample cup)
Upper sample window
Upper sample window
CAUTION Avoid chemical exposure. Isooctane is a chemical irritant. When handling
isooctane:
• avoid contact with skin and eyes
• avoid inhalation of vapor or mist
• wear gloves that provide adequate protection
NOTICE When cleaning sample windows, avoid using excessive force or you may damage
or crack the windows.

2
Operating the Instrument
12 Nicolet iS5 LS User Guide Thermo Scientific
To clean the sample windows
1. Raise the sampling arm a small amount, place a clean, dry lint-free laboratory wipe
between the two windows and then lower the arm to soak up most of the sample material.
Discard the soiled wipe.
2. Raise the arm and use a clean wipe to gently clean the upper sample window and
surrounding area.
Take care to use a clean portion of the wipe on the last swipe of the window. Discard the
soiled wipe.
Figure 9. Gently clean upper sample window
3. Use a clean wipe to gently clean the sample cup and lower window.
Take care to use a clean portion of the wipe on the last swipe of the window. Discard the
soiled wipe.
Figure 10. Gently clean lower sample window
4. If necessary, place a few drops of cleaning solvent onto a clean wipe and use it to
thoroughly clean both windows and the area around them. Discard the soiled wipe.
5. Gently lower the sampling arm.

2
Operating the Instrument
Thermo Scientific Nicolet iS5 LS User Guide 13
Instrument Performance Tests
Two workflows are provided to verify instrument performance:
•Daily Performance Test, makes several measurements to verify instrument operation.
•Calibration Check, uses hexadecane to verify wavelength accuracy and sample pathlength.
The performance tests start by verifying that the sample windows are clean. See “Cleaning the
Sample Windows” for detailed instructions.
Daily Performance Test
The Daily Performance Test workflow makes several measurements to verify instrument
operation. No special materials are required. We recommend that you run the Daily
Performance Test workflow at least once each day before you analyze your first sample. The
test can be run more often as needed to satisfy your company’s internal protocols.
Before you run the Daily Performance Test, the instrument should be powered on for 4 to
6 hours and the qPro Operator software should be running. The sampling arm should be
closed.
To continue from one screen to the next in the workflow, click the button.
To run the Daily Performance Test workflow
1. Make sure the sample windows are clean and dry.
2. From the qPro Operator main screen, click the Diagnostics category in the left pane and
then click Daily Performance Test.
Figure 11. Diagnostics category in qPro Operator software
Diagnostics category Daily Performance Test workflow

2
Operating the Instrument
14 Nicolet iS5 LS User Guide Thermo Scientific
The workflow shows its historical results.
3. Make sure the sampling arm is closed and click continue.
4. Make sure Run a new performance test is selected and click continue to start the
workflow.
Follow the instructions in the workflow.
When the workflow is completed, the software displays the report. If the instrument
passed, a green check mark appears to the right of each test result and the operator can
proceed. Here is an example.
Figure 12. Example Daily Performance Test report
Sampling arm in
closed position

2
Operating the Instrument
Thermo Scientific Nicolet iS5 LS User Guide 15
5. If your instrument passed the performance test, click continue to complete the workflow.
If your report includes a red “X,” rerun the Daily Performance Test workflow. If the
instrument fails again, the resolution depends on which test has the red X. For more
information, refer to the Performance test failed topic in the Troubleshooting section of
the instrument user guide.
6. To print the report, click the Print button.
Related Topics
•Calibration Check
•Instrument Performance Tests
Calibration Check
The Calibration Check workflow uses hexadecane to verify wavelength accuracy and sample
pathlength. We recommend that you run the Calibration Check workflow at least once a
week. The test can be run more often as needed to satisfy your company’s internal protocols.
Before you run the calibration check, the instrument should be powered on for 4 to 6 hours
and the qPro Operator software should be running. The sampling arm should be closed.
To continue from one screen to the next in the workflow, click the button.
Materials required:
• Small volume of 99% hexadecane (available from us)
• Small, clean dropper bottle or pipette
• Clean, dry, lint-free laboratory wipes (unscented and lotion-free)
• Powder-free nitrile gloves
Note To retrieve data from a Daily Performance Test workflow, use Data Hub.
CAUTION Avoid chemical exposure. Hexadecane is a chemical irritant. When handling
hexadecane:
• avoid contact with skin and eyes
• avoid inhalation of vapor or mist
• wear gloves that provide adequate protection

2
Operating the Instrument
16 Nicolet iS5 LS User Guide Thermo Scientific
To run the Calibration Check workflow
1. Make sure the sample windows are clean and dry.
2. From the qPro Operator main screen, click the Diagnostics category in the left pane and
then click Calibration Check.
Figure 13. Diagnostics category in qPro Operator software
The workflow shows its historical results.
3. Make sure the sampling arm is closed and click continue.
4. Make sure Run a new calibration check is selected and click continue to start the
workflow.
Note
• Use only 99% or higher grade hexadecane for the calibration check.
• Hexadecane solidifies below 18 °C (64 °F). Let it warm to room temperature (or
apply gentle heat) to liquefy before use with the analyzer.
• Do not sample hexadecane directly from its original container. Pour into a clean,
labeled container and use that container for the calibration checks.
Diagnostics category Calibration Check workflow