269-318900 - Rev A - Nicolet iS5N User Guide

Nicolet iS5 Series Spectrometers
Nicolet iS5N
User Guide
269-318900 Revision A May 2016

© 2016 Thermo Fisher Scientific Inc. All rights reserved.
Microsoft, Windows, and Excel are either trademarks or registered trademarks of Microsoft Corporation in the
United States and/or other countries.
All other trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries.
For U.S. Technical Support, please contact: For International Support, please contact:
Unity Lab Services Thermo Fisher Scientific

Telephone: +1 608 273 5017
Part of Thermo Fisher Scientific
E-mail: [email protected]
5225 Verona Road
Madison WI 53711-4495 U.S.A.
Telephone: 1 800 532 4752
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.
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.
C
Contents
Chapter 1 Welcome. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Conventions Used . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
About the Help System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Finding Other PDF Documents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Ordering Parts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Chapter 2 Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
Electrical and Communication Cabling. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Turning the Power On and Off. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Installing an Accessory. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Installing Integrated Accessories. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Installing Baseplate-Mounted Accessories . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Installing Slide-Mounted Accessories. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Installing Attenuation Screens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Collecting Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Setting Purge Gas Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Aligning Your Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Verifying the Laser Frequency . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Using the iD1 Transmission Accessory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Installing Samples in the iD1 Transmission Accessory . . . . . . . . . . . . . . . . . . 19
Collecting Data With the iD1 Transmission Accessory . . . . . . . . . . . . . . . . . 20
Entering Serial Numbers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Chapter 3 Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23

Maintaining Your Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Running Performance Verification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Cleaning Your Instrument. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Static Electricity Precautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Checking the Humidity Indicators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Replacing the Desiccant. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Regenerating the Desiccant . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Checking and Changing the Purge Gas Filter . . . . . . . . . . . . . . . . . . . . . . . . 35
Thermo Scientific Nicolet iS5N Spectrometer User Guide iii

Contents
Installing or Replacing Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Installing a Purge Kit. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Replacing Sample Compartment Windows . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Replacing the Power Supply . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Replacing the Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Replacing the Laser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Replacing the Detector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Replacing the Electronics Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Replacing Fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Chapter 4 Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .51

Using the Troubleshooting Topics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Hardware Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
PV Test Failed. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
System Suitability Test Failed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Spectral Peaks Appear Shifted in Wavenumber Axis . . . . . . . . . . . . . . . . . . . 56
Fails Laser Frequency Verification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Power Indicator Does Not Light After Power Up . . . . . . . . . . . . . . . . . . . . . 56
Power Indicator Blinks Continuously . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
System Scans Normally but Signal Intensity Is Low. . . . . . . . . . . . . . . . . . . . 57
Spectra Have Noise Spikes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Spectral Baseline Is Not Stable. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Alignment Fails . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Data Cannot Be Collected (or Other Software Problems) . . . . . . . . . . . . . . . 59
Error Messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Computer Cannot Communicate With Instrument . . . . . . . . . . . . . . . . . . . 60
Instrument Temperature Is Out of Specification . . . . . . . . . . . . . . . . . . . . . . 60
OMNIC Cannot Communicate With the Detector . . . . . . . . . . . . . . . . . . . 61
Instrument Is Not Scanning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Laser Voltage Is Out of Specification. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Source Voltage Is Out of Specification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Power Supply Voltages Are Out of Tolerance . . . . . . . . . . . . . . . . . . . . . . . . 62
Humidity Is Too High . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Laser Temperature Is Out of Specification. . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Interferometer Temperature Is Out of Specification . . . . . . . . . . . . . . . . . . . 62
Laser Frequency Is Out of Specification. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .65
iv Nicolet iS5N Spectrometer User Guide Thermo Scientific

1
Welcome
iS5N spectrometer
with iD1 Transmission
accessory installed
The Thermo Scientific Nicolet™ iS™5N Fourier transform near-infrared (FT-NIR)

spectrometer lets you perform chemical analyses of sample materials by collecting data in the
near-infrared spectral range using a variety of transmission and other accessories. The system
has integrated verification features, a powerful software suite, and many other features that
make data collection easy. You can install optional hardware and perform several service and
maintenance procedures yourself. This document, or other provided documentation, contains
the information you need.
Be sure to read the safety guide that came with the system before operating the instrument.
Note We recommend that you maintain seal and desiccation and/or purge your
instrument at all times. Equipment damage due to failure to maintain seal and desiccation
and/or purge is not covered by the warranty. If you have questions about this requirement,
please contact us.
Thermo Scientific Nicolet iS5N Spectrometer User Guide 1

1 Welcome
Conventions Used
Conventions Used
Safety precautions and other important information use the following format:
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.
About the Help System

To view the electronic Help version of this document, choose Spectrometer Help Topics from
the Help menu in OMNIC software.
Finding Other PDF Documents

PDF files of system documentation are on the documentation media provided with your
instrument.
Ordering Parts
To order parts, contact us.
If you need to send the instrument or an accessory to us for repair, call or e-mail us first for
any shipping requirements or other instructions.
2 Nicolet iS5N Spectrometer User Guide Thermo Scientific

1 Welcome
Contacting Us
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: 1 800 532 4752
For International Support, please contact:
Thermo Fisher Scientific

Telephone: +1 608 273 5017
If you have problems with your system, refer to the Troubleshooting information for help, or
call Technical Support.
Note To expedite and assist in problem diagnosis, please be prepared to send us a copy of
your diagnostics log file. The diagnostics log includes a history of important system
parameters and events that occur during system operation. To copy the diagnostics log to
your Windows desktop, start OMNIC software and choose File > Copy Diagnostics File
to Desktop. Attach this file to an e-mail message to our Technical Support group.

2
Operation
This section provides instructions for setting up the Nicolet iS5N spectrometer and installing
accessories.
The spectrometer is designed for indoor use at altitudes up to 2,000 m (6,500 ft). It operates
reliably when the room environment meets these specifications:
• constant temperature between 15 °C and 35 °C (60 °F and 95 °F). Temperature changes
may result in drift in the system response.
• relative humidity (non-condensing): 20-80%
NOTICE The spectrometer must be protected from excessive humidity, since the
beamsplitter, detectors, and other components may corrode with exposure to moisture.
Maintain humidity in the range of 20% to 80% noncondensing. To accomplish this, this
instrument is sealed and desiccated. For additional humidity protection, the optional
purge configuration can be used.
CAUTION If a protective cover on a system component appears damaged, turn off the
system and secure it against any unintended operation.
DANGER Avoid fire and explosion hazard. The white light source inside the
spectrometer is an ignition source. If the use of flammable gases is intended, vent check
valves away from the spectrometer. Provide a fume hood or other active venting system
that is free of spark and other ignition sources and that prevents flammable vapors from
collecting in the atmosphere surrounding the instrument.

2 Operation
Electrical and Communication Cabling
Electrical and Communication Cabling

The illustration below shows the correct cable connections for electrical power and data
communication.
Power
Computer
Computer (USB)
cable
Power cable
Check the Preparing Your Site guide in your 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.
CAUTION Avoid shock hazard. Each wall outlet used must be equipped with a ground.
The ground must be a noncurrent-carrying wire connected to earth ground at the main
distribution box.
NOTICE Do not position the instrument so that it is difficult to operate the power switch
or access the power supply and power cord.

2 Operation
Turning the Power On and Off
 To cable the instrument:
1. Connect the power supply to the spectrometer and to a properly grounded AC power
source.
2. Connect the USB cable to 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
• Setting Purge Gas Controls
• Checking and Changing the Purge Gas Filter
• Static Electricity Precautions
Turning the Power On and Off

To turn the system power on or off, press the power switch on the back of the spectrometer:
Power switch
When the system is powered on, the blue power indicator on the main cover flashes while the
spectrometer warms up and performs diagnostics (about 2 minutes) and then the indicator
stays lit. During initialization, OMNIC software displays the number of seconds remaining
and the Collect menu is disabled; the system cannot collect data until initialization is
completed.
Power indicator

2 Operation
Installing an Accessory
NOTICE Do not place anything on top of the vents at the back of the spectrometer.
Electronic components can overheat if these vents are blocked.
After the spectrometer is installed, you can leave it turned on.
Note To preserve the life of the source, you can turn it off manually in OMNIC software
by choosing Collect (menu) > Experiment Setup, selecting the Bench tab and setting
Source to Off.
If you turn off the source, wait 5 minutes after you turn it back on before taking a sample
measurement.
Related Topics
• Electrical and Communication Cabling
• Troubleshooting
The Nicolet iS5N spectrometer includes the iD1 transmission accessory which accommodates
a wide variety of samples and slide-mounted sample holders for transmission experiments. A
heated version of the transmission accessory, called the iD1H, is available for liquid samples
that require temperature stabilization. Mounting baseplates are available to accommodate a
wide variety of standard accessories from us and other manufacturers. Contact us for details.
All of our integrated accessories and baseplates are easy to install and remove and are
recognized automatically by the software.

2 Operation
Installing Integrated Accessories

To install an integrated iS5N accessory, such as the iD1H transmission accessory shown
below, grasp it as shown below and lower it onto the spectrometer.
These accessories fit over two alignment pins on the spectrometer baseplate and are held in
place by magnets.
Magnets
Alignment pins

2 Operation
If your spectrometer is purged, attach the purge line labeled “Accessory” to the purge inlet on
the back of the accessory. See Installing a Purge Kit for more information.
Purge inlet
Note To remove an accessory, disconnect the purge line if necessary and then grasp the
accessory by the top and bottom (not the sides) and lift it up. When not using an
accessory, store it in a dust-free environment such as a cabinet or box.
Related Topics
• Using the iD1 Transmission Accessory
• Installing an Accessory
Installing Baseplate-Mounted Accessories

Special baseplates are available to accommodate a wide variety of accessories for FT-NIR
sampling.
iD Base Adapter
The iD Base Adapter provides a place to mount large transmission accessories and other
specialized accessories.

2 Operation
For slide-mounted accessories that are too big for the iD1 transmission accessory, a slide
mount that fits the iD base is available.
Slide mount
The iD Base Adapter has two sets of screw holes so the slide mount can be installed facing
either direction. To install the slide mount, position it over the screw holes, and then insert
and tighten the two washers and screws.
Use the height adjustment screw to raise or lower a sample or accessory to align it in the NIR
light beam.
Height adjustment screw
To install an accessory attached to the iD Base Adapter, remove any accessory from the
spectrometer and place the adapter with the attached accessory over the pins on the
spectrometer baseplate. Magnets hold the adapter in the proper position.
Note Avoid installing the iD Base Adapter without an attached accessory. Very strong
magnets hold the adapter in place; you may need to use a tool to pry it free.

2 Operation
Here is the iD Base Adapter and attached slide mount with a card holder installed in the
spectrometer.
Insert attenuation screen here
iD Foundation Adapter
The iD Foundation adapter fits our Foundation Series Swap-Top Modules. For information
about these modules, see the Foundation Series User Guide in your documentation set.
Tighten screws to secure the Foundation accessory
Remove screws and panel for use with a diffuse reflectance accessory
To install the adapter, remove any accessory from the spectrometer and place the adapter over
the pins on the spectrometer baseplate. Magnets hold the adapter in the proper position.

2 Operation
Slide any Foundation Series Swap-Top Module into the holder, rotate the accessory to line up
the notches and pins and then hand tighten the screws (see the image above). For diffuse
reflection accessories, remove the two screws and lower panel to accommodate the sample
slide as shown in the image below.
Related Topics
Installing Slide-Mounted Accessories

The iD1 Transmission Accessory is designed to accommodate gas or liquid transmission cells
and thin film or pellet holders that have a 2 x 3 inch slide mount.

2 Operation
Installing Attenuation Screens
 To install a slide-mounted accessory
1. Slide the accessory into one pair of slots in the iD1 Transmission Accessory.
Choose a pair of slots that will place the center of the accessory at the beam focus
(designated by arrow heads on the accessory housing).
Beam focus
Related Topics
• Installing Baseplate-Mounted Accessories
• Using the iD1 Transmission Accessory
Installing Attenuation Screens

The iS5N spectrometer is configured with a white light source and a highly sensitive detector
for near-infrared measurements. When collecting near-infrared data for most sample types, an
attenuation screen is needed to decrease the light from the source in order to prevent detector
saturation. The kit that comes with the spectrometer contains four screens for this purpose.
Screen Attenuation Recommended Use

A Very light Very strongly absorbing samples such as tablets
B Light Strongly absorbing samples
C or D Moderate or Heavy Most liquid samples (good linearity with open beam)
The spectrometer’s default Gain setting is optimized for data collection with the iD1 accessory
and C screen in place. Changing the attenuation screen will affect the amount of incident
light that reaches the detector, thereby producing a larger or smaller interferogram signal.
Changing the Gain setting can also be used to amplify or reduce the interferogram signal.
Ideally, the (interferogram) signal should be just below 6 volts. If the signal is too low for a

2 Operation
Collecting Data
particular sample, using a higher throughput screen generally results in better performance
than increasing the instrument Gain setting. For highly absorbing samples, try the B screen or
the A screen (or no screen) as long as the signal stays below 6 volts. (To see the interferogram
signal, choose Collect (menu) > Experiment Setup and select the Bench tab.)
Install screens with the labeled text facing right side up. A magnet holds the screen in place.
The location for installing a screen depends on the installed accessory. Here is a guide:
Accessory Location for Installing Attenuation Screens

iD1 Slot furthest to the right inside the accessory
iD1H Slot furthest to the right inside the accessory
iD Base with standard sample Standard sample holder has two card slots. With sample
holder (card holder) holder installed in spectrometer sample compartment,
insert sample card into slot on left; insert screen into slot
on right.
iD Foundation adapter with any Tape screen to spectrometer side wall and then carefully
sample holder slide accessory in place
Collecting Data
For information about collecting data with the spectrometer, see the Nicolet iS5N Quick
Start Guide in the documentation set.
Setting Purge Gas Controls

You can use an appropriate source of purge gas (dry air or nitrogen) to purge the instrument
of moisture and other environmental contaminants. See Installing a Purge Kit for more
information.
For best results the purge gas should be dried to a dew point of -70 °C (-94 °F) or below.

2 Operation
Setting Purge Gas Controls
NOTICE We recommend maintaining seal and desiccation and/or purging the

and/or purge is not covered under the warranty.
WARNING Never use a flammable, combustible, or toxic gas to purge this instrument.
The purge gas must be free of oil and other reactive materials. Heat from the source or
from laser absorption may ignite flammable gases or reactive materials in purge gas. Use
only dried air or nitrogen to purge your instrument.
 To set the purge gas controls
1. Open the main valve to start the flow of purge gas through the regulator.
2. Adjust the pressure regulator for the spectrometer until the gauge indicates the pressure is
5 psig.
Set accessory pressure Set spectrometer pressure
Set accessory flow Set spectrometer flow
3. Set the flowmeter for the spectrometer to 1 scfh (0.47 l/min).

4. If you are using an accessory that is purged, set the purge gas controls for the accessory as
indicated below.
• Accessory pressure, 5 psig
• Accessory flow, 4–10 scfh (1.9–4.7 l/min)
NOTICE Flow rates greater than recommended values can cause vibration which can
affect data quality.

2 Operation
Aligning Your Spectrometer
Related Topics
• Installing a Purge Kit
Aligning Your Spectrometer

The spectrometer can be aligned automatically using OMNIC software. Alignment optimizes
the energy throughput to the detector. Alignment can change slightly over time, particularly
in locations that have large temperature swings or excessive vibration.
 To align the spectrometer
1. From the OMNIC software main screen, choose Collect > Experiment Setup.
2. Select the Diagnostic tab and click Align.
For more information, see OMNIC Help Topics in the Help menu.
Note The spectrometer is aligned automatically each time you run a Performance
Verification (PV) test. We recommend running a PV test at least once a month.
Related Topics
• Verifying the Laser Frequency
• Maintaining Your Instrument
• Troubleshooting
Verifying the Laser Frequency

Use the Laser Verification button on the Diagnostic tab in the Experiment Setup box in
OMNIC software to verify the laser frequency. For optimum system performance, verify the
laser frequency according to the following schedule:
Spectrometer environment Spectrometer state Recommended Schedule

Stable Always powered on every 3 months
Unstable (e.g., temperature or Powered on and off every day or once a week
humidity constantly changing) frequently
Note The laser is verified automatically each time you run a Performance Verification
(PV) test. We recommend running a PV test at least once a month.

2 Operation
Using the iD1 Transmission Accessory
 To verify the laser frequency
1. From the OMNIC software main screen, choose Collect > Experiment Setup.
2. Select the Diagnostic tab and click Laser Verification.
3. Remove any samples from the instrument (you can leave your accessory or sample holder
in place) and choose Start Verification.
When verification is completed, one of the following occurs:
• A message indicates the laser frequency has been verified.
• The newly measured laser frequency appears below the previously measured
frequency and a message indicates the laser frequency has been optimized.
4. Choose OK to finish.
Related Topics
• Aligning Your Spectrometer
• Troubleshooting

The iD1 transmission accessory lets you collect spectra of transmission samples, such as thin
films, liquids in a liquid cell or gases in a gas cell.
Install the module as explained in Installing an Accessory.

2 Operation
Related Topics
• Installing Samples in the iD1 Transmission Accessory
• Installing Integrated Accessories
• Installing Slide-Mounted Accessories
• Collecting Data With the iD1 Transmission Accessory
Installing Samples in the iD1 Transmission Accessory

To install a thin sample such as a film, lift the accessory cover and slide the sample into any of
the narrow slots. Normally a slot at or near the beam focus is used. The beam focus is at the
center of the sample compartment as indicated by the arrows on the sample compartment
housing.
Narrow slot Wide slot
Beam focus
The wide slot provides clearance for certain slide-mounted accessories.
Related Topics
• Installing Integrated Accessories
• Collecting Data With the iD1 Transmission Accessory

2 Operation
Entering Serial Numbers
Collecting Data With the iD1 Transmission Accessory

For information about collecting data with the accessory, see the Nicolet iS5N Quick Start
guide in the iS5N spectrometer documentation set.
Related Topics
• Installing Samples in the iD1 Transmission Accessory

The software stores important settings, serial numbers and installation dates. Update any
corresponding setting, serial number or installation date after replacing components in your
spectrometer.
 To check or update the instrument information
1. Choose Collect (menu) > Advanced Diagnostics. The Diagnostics screen appears.
Verify that all components are working properly. (If a component malfunctions, a red
slash mark appears over the corresponding icon on this screen. See Troubleshooting or
contact us for assistance.)
2. Click the Installation icon. An information screen appears.
Update any pertinent information, enter today’s date and choose Save.

2 Operation
Related Topics
• Troubleshooting

3
Maintenance
This section provides instructions for installing and replacing hardware and maintaining your
instrument.
NOTICE All other maintenance, troubleshooting or repair must be performed by one of

our trained and certified service engineers.
WARNING When performing any of the maintenance procedures, always follow the
safety precautions included in the user guide or Help system and in any of the other
documentation that came with your instrument.
Maintaining Your Instrument

Running Performance Verification
Performance Verification (PV) aligns the spectrometer, verifies the laser frequency, checks the
energy throughput and uses a polystyrene reference card to confirm wavenumber accuracy.
We recommend that the Performance Verification test is run once a month.
Time needed: 6 minutes
Tools needed:
• iD1 transmission accessory
• C screen from the iS5N accessory kit
• Polystyrene reference card from the iS5N accessory kit
Note The polystyrene reference card is good for two years from the instrument’s arrival
date. Contact us to order a reference new card. After you receive the new card, open
OMNIC software and choose View > Configure System Status > Performance
Verification > Configure Standards, select the row for the reference you are replacing
and choose Update. In the Standard Settings box, select Installation Date and enter
today’s date. Choose Yes after the prompt to reinitialize the Performance Verification
standard’s values. Then run Performance Verification and insert the new reference card
after the prompt.

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Before you begin, make sure the spectrometer has been powered on for at least 15 minutes
(one to six hours for best results).
 To run performance verification
1. Make sure the iD1 transmission accessory is installed in the spectrometer sample
compartment.
2. Insert the C screen from the iS5N accessory kit into the card slot furthest to the right
inside the iD1 sample compartment.
(There should not be a sample in the iD1 sample compartment.)
C screen
3. Click the System Status shield in the OMNIC main window.

System Status
The System Status Overview box is displayed.

4. Choose Performance Verification and then choose Run.

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5. Choose Performance Verification and then choose Run.

A message is displayed:
The software performs an alignment to maximize the laser signal and then verifies the
laser frequency.
6. When those are completed, follow the prompt to insert the polystyrene reference card
into the center card slot, close the cover and choose OK to continue.
Polystyrene reference card
Note The iS5N accessory kit includes one polystyrene reference card and four
attenuation screens labeled A through D. Use only the supplied polystyrene reference
and C screen to verify system performance.
After the polystyrene measurement is completed, the overall PV test result is displayed in
the System Status Overview window.
Detailed PV test results are saved automatically.

7. To view or print the results, choose Report (see the previous image).

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8. When you are finished viewing the report, close all open windows except OMNIC.
9. Replace any accessories you removed earlier on the instrument.
The possible overall PV test results are explained below:
Green Shield indicates that all subsystems are operating within specification
and all performance tests passed.
Yellow Shield indicates that the system identified a minor problem, which
should be viewed to determine the possible effects on the quality of the data
collected.
Red Shield warns that the system is out of specification or a sub-system failed.
It can also indicate that the last performance test did not meet specifications.
If your overall performance test result is a yellow shield or red X, see PV Test Failed.
Related Topics
• PV Test Failed
Cleaning Your Instrument

If the outside of the instrument needs cleaning, turn it off (see Turning the Power On and
Off) and disconnect the power supply. Then use a soft cloth that is damp (not wet) and a mild
soap to clean the outside of the instrument.
CAUTION Avoid shock hazard. Do not allow liquid to run into the power supply or the
back of the instrument.
NOTICE
• Do not use harsh detergents, solvents, chemicals or abrasives; these can damage the
finish. Do not allow liquid to contact any windows in the sample compartment.
• Windows can be scratched and ruined very easily. Do not touch or attempt to clean
them. Dust will not affect the signal, but fingerprints can degrade the performance of
the instrument and permanently damage mirrors or windows. If you wish to remove
dust from a mirror or window, blow it off with a gentle stream of clean, dry air or
nitrogen. Never allow any liquid to come into contact with a window or optical
component in the instrument.
Related Topics
• Static Electricity Precautions

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Cleaning the iD1 Transmission Accessory

If the outside of the accessory needs to be cleaned, remove the accessory from the instrument,
and use a soft, damp (not wet) cloth and a mild soap to clean it. Do not use harsh detergents,
solvents, chemicals or abrasives (since they can damage the finish), and do not allow liquid to
contact any windows (such as those in the sample compartment). When you are finished
cleaning the accessory, allow it to dry, and then reinstall it in the instrument.
Static Electricity Precautions

Critical components in the instrument can be permanently damaged by static electricity. To
help prevent such damage, follow these recommendations:
NOTICE
• Before you disconnect the power supply, always discharge any static electricity you
may have accumulated by touching the perforated metal shield over the power supply.
• Do not touch any printed circuit board in the instrument (such as the circuit board
on the detector).
• Do not remove replacement components from their protective packaging until you
are ready to install that component in the instrument.
Related Topics
• Electrical and Communication Cabling
• Troubleshooting
Checking the Humidity Indicators

The instrument is tightly sealed and its optical components are protected by desiccant that
absorbs water vapor. The instrument can also be purged with dry air or nitrogen (see
Installing a Purge Kit).

instrument at all times. Optical damage caused by failure to maintain seal and desiccation
or to purge the spectrometer is not covered under the warranty.
Follow these steps to monitor the humidity level inside the instrument.
Related Topics
• Replacing the Desiccant
• Regenerating the Desiccant
• Troubleshooting

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Checking Humidity When the Instrument is Powered Off

A paper indicator lets you know when to change the desiccant when the instrument is
powered off.
Humidity indicator
As long as the humidity indicator on the instrument is blue, the desiccant is not saturated and
does not need replacement. When the desiccant becomes saturated, the humidity indicator
turns pink and then light pink or almost white. This means you must replace the desiccant
and the humidity indicator. See Replacing the Desiccant for instructions.
NOTICE Check the paper humidity indicator at least once a month when the instrument
is powered off.
Related Topics
• Checking the Humidity Indicators
Checking Humidity When the Instrument is Powered On

When the instrument is powered on, an internal sensor closely monitors the humidity level
inside the instrument and alerts you when the humidity is high.
 To check the internal humidity indicator
1. From the OMNIC software main screen, choose Advanced Diagnostics in the Collect
menu. The Diagnostics screen appears.

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2. Click the Electronics icon. An information screen appears.
3. Verify that the current Internal Humidity value is between 2 and 50%.
Note When the internal humidity is above 50%, OMNIC software displays a
message to replace the desiccant (see Replacing the Desiccant) or increase the purge
flow (see Setting Purge Gas Controls). If the humidity is above a critical level, the
System Status will report an instrument failure.
Related Topics
Replacing the Desiccant

If your instrument is not equipped with a purge kit, or the purge is off, you must monitor the
humidity level inside the spectrometer. Replace the desiccant when the paper humidity
indicator turns pink (can be light pink or almost white) or the software displays a message that
the internal humidity is above 50%. (See Checking the Humidity Indicators for more
information.) Replace the paper humidity indicator each time you replace the desiccant.
Time needed: 5 minutes or less
Tools needed:
• iS5 series desiccant replacement kit (or desiccant canisters that have been regenerated)
• 0.05-inch Hex key
• #2 Phillips head screw driver
• Gloves, finger cots, or laboratory tissue (to handle the humidity indicator)
Note To order parts, contact Technical Support; see Contacting Us.

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WARNING Avoid explosion hazard. Before you open the desiccant compartment, turn off
the instrument power, unplug the power cord and remove all accessories and samples from
the system. Entry of flammable liquids or gases into the desiccant compartment is an
explosion hazard. If such entry occurs, contact us immediately and do not apply power to
the instrument until the condition has been corrected.
NOTICE
• Make sure nothing falls into the instrument while the desiccant cover is removed.
• Replace the desiccant only with replacement parts supplied by us.
 To replace the desiccant
1. Turn off the instrument (see Turning the Power On and Off) and unplug the power cord.
2. Turn off the purge, if applicable, and disconnect the purge line to the instrument and any
installed accessory.
3. Remove any installed accessory and all samples from the instrument (see Removing an
Accessory).
Note You can use either desiccant cartridge (with or without the purge connector) to
maintain the required humidity when the instrument is powered off. The illustrations
below show the nonpurged version of the desiccant cartridge. To see the purged
version, see Installing a Purge Kit. The instructions for replacing the desiccant
canisters are the same for both types of desiccant cartridges.
4. Use the #2 Phillips head screw driver to loosen the two captive screws from the desiccant
cartridge, and lift the cartridge straight up and out of the instrument.

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5. Remove and discard the large O-ring.
Note Be careful not to drop the sealing O-ring into the desiccant compartment.
6. Remove the new O-ring from the kit and install it on the instrument base plate (see the
previous image).
Press (rather than roll) the new O-ring into place to be sure it is properly seated in the
groove.
7. Use the 0.05-inch Hex key to loosen (approximately two turns) the eight screws that hold
the two saturated desiccant canisters to the desiccant cartridge. Remove the canisters.
Note The desiccant canisters can be regenerated. See Regenerating the Desiccant for
details.
Humidity indicator
Desiccant cartridge
Channel
Remove these screws

(4 on each side)
Desiccant canisters

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WARNING The contents of the desiccant canisters (hydrated metal aluminosilicate

molecular sieve) could be harmful if ingested. If you discard the saturated desiccant
canisters, make sure they are properly disposed of.
8. Turn the desiccant cartridge upside down and peel the old humidity indicator off the
window. Discard the used indicator.
NOTICE Always wear lab gloves or finger cots, or use laboratory tissue, when
handling a new humidity indicator. Oil or moisture from skin can discolor the
indicator.
9. Open the sealed packet that contains the new desiccant (must be sealed to maintain the
desiccant) and remove the new humidity indicator.
10. Turn the desiccant cartridge upside down and press the blue indicator onto the window
so that the flat edges of the indicator are aligned with the edges of the cartridge. The text
should be visible through the window when you turn the cartridge right side up.
NOTICE Make sure the indicator is pressed tightly against the window so it does not
come loose in the desiccant compartment when you reinstall the cartridge.
11. Install the new desiccant canisters. See the previous illustration for this step.
Insert the canisters into the channel of the desiccant cartridge and tighten the eight screws
(approximately 2 turns) until they are flush with the cartridge channel.
12. Insert the desiccant cartridge into the spectrometer so that the text on the humidity
indicator can be read by someone standing in front of the instrument.
Make sure the cartridge is seated properly over the O-ring and then secure it using the
two screws.
13. Plug in the power cord to the instrument and turn on the power.
14. Record the desiccant replacement date in OMNIC software.
Start OMNIC software and then choose Advanced Diagnostics in the Collect menu.
The Diagnostics screen appears.

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Click the Installation icon. A diagnostic information screen appears.
Enter today’s date for the desiccant replacement and click Save.
15. Reconnect the purge line to the instrument, if applicable, and turn on the purge.
16. Make sure the system has been on for at least 15 minutes (one to six hours for best
results), and then run the Performance Verification (PV) test.
17. Install any accessories you removed earlier and reconnect the purge, if applicable.
Related Topics
• Regenerating the Desiccant
Regenerating the Desiccant

When the desiccant canisters must be replaced, you can contact us to order new desiccant
canisters, or you can dry and reuse the saturated canisters according to the following
instructions.
Time needed: 3 hours
Tools needed:
• Used desiccant canisters
• Vented oven
• Insulated cloth or hot pad

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Note If you need to replace the humidity indicator, you must order new desiccant
canisters. A new humidity indicator is included with the new desiccant canisters.
NOTICE
• If you plan to dry and reuse saturated desiccant canisters, make sure you have fresh
desiccant canisters to place in the instrument while the saturated canisters dry.
• Do not leave canisters in the oven for more than three hours and do not exceed a
temperature of 150 °C (300 °F). Allow the canisters to cool completely in a dry
environment before you install them in the cartridge.
• Make sure the insulated cloth or hot pad you use to handle the regenerated desiccant
canisters is not contaminated with substances that could be absorbed by the desiccant
and subsequently released into the instrument.
 To regenerate the desiccant
1. Place the saturated desiccant canisters in a vented oven at 150 °C (about 300 °F) for three
hours.
CAUTION Avoid burn hazard. Use an insulated cloth or hot pad to handle the heated
desiccant canisters, and always wait until the canisters have cooled to room temperature
before installing them in the spectrometer.
2. Use an insulated cloth or hot pad to remove the desiccant canisters from the oven.
Place the hot canisters in a dry environment such as a desiccator and allow them to cool
to room temperature. As soon as the canisters reach room temperature, you must either
install them in the instrument or seal them in an airtight container or bag. Otherwise,
they will absorb moisture from the air in the room and quickly become saturated again.
Related Topics

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Checking and Changing the Purge Gas Filter

Check the purge filter occasionally to make sure it is clean and dry. (The illustration below
shows where the purge filter is located.)
If the filter is clean and white, it does not need replacement. If the filter is yellow, or otherwise
discolored, or if it is contaminated with debris or foreign particles, replace the filter.

and/or purge is not covered under the warranty.
Tools needed: iS5 series replacement purge gas filter
 To change the purge gas filter
1. Turn off the purge gas at the main valve. Do not turn down the flowmeter or the pressure
regulator.
2. Remove the plastic bowl that houses the filter and then remove the filter. (You can
unscrew them both by hand.)
Bowl Filter

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Installing or Replacing Hardware
3. Install the new filter and then reinstall the bowl.

4. Open the main valve to turn on the purge flow to the instrument.
Note You may notice increased levels of water and carbon dioxide in spectra collected
immediately after you have had the purge gas turned off. If this interferes with your
data, wait 15 to 60 minutes until purge is completely re-established.
Related Topics

NOTICE The following parts must be replaced only with replacement parts
supplied by us:
• white light source
• desiccant
• sample compartment windows
• power supply
Installing a Purge Kit

Purging protects instrument components from moisture and other environmental
contaminants by maintaining an internal atmosphere of dry air or nitrogen. If you ordered the
purge option, you must install a purge kit.

and/or purge is not covered under the warranty. If you have questions about this
requirement, please contact us.
Set up needed:
• Source of dry air or nitrogen that meets Thermo Scientific specifications for the
Nicolet iS5N spectrometer. See the Preparing Your Site manual in your documentation
set for more information.
Note For best results dry the purge gas to a dew point of -70 °C (-94 °F) or below.

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Tools needed:
• iS5N purge kit with sealed desiccant packet (open just prior to installation)
• 3/4-inch open-ended wrench
• 11/16-inch open-ended wrench
• #2 Phillips head screw driver
• Purge regulator valve (with a 1/4-inch male or 3/8-inch female fitting)
• Teflon® pipe tape
Note To order parts, call Technical Support. See Contacting Us.
WARNING Avoid explosion hazard. Never use a flammable, combustible, or toxic gas to
purge this instrument. The purge gas must be free of oil and other reactive materials. Heat
from the source or from laser absorption may ignite flammable gases or reactive materials
in purge gas. Use only dried air or nitrogen to purge your instrument.
 To install a purge kit
1. Install the regulator valve and either a 1/4-inch male fitting or a 3/8-inch female fitting
on the purge gas source. (Choose a valve and fittings that are appropriate for the purge gas
source.)
2. If you used a 1/4-inch male fitting, proceed to the next step.

If you used a 3/8-inch female fitting on the purge gas source, install the 3/8-inch to
1/4-inch reducing nipple from the purge kit. Wrap the reducing nipple with pipe tape
before you install it, and use an 11/16-inch open-ended wrench to tighten the
connection.

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3. Wrap the reducing nipple or the 1/4-inch male fitting with pipe tape, and then install the
pressure coupling. Use a 3/4-inch open-ended wrench to tighten the connection.
4. Snap the male inlet of the wall plumbing assembly firmly into the pressure coupling.
Refer to this drawing when performing this and subsequent steps:
Pressure coupling
To accessory Pressure regulator Pressure regulator To spectrometer
Flowmeter Wall plumbing assembly Flowmeter
5. Turn off the instrument power, unplug the power cord and remove all accessories and
samples from the system. See Turning the Power On and Off and Removing an Accessory
for instructions.
WARNING Before you open the desiccant compartment, turn off the instrument
power, unplug the power cord and remove all accessories and samples from the
system. Entry of flammable liquids or gases into the desiccant compartment is an
explosion hazard. If such entry occurs, contact us immediately and do not apply
power to the instrument until the condition has been corrected.

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6. Loosen the two captive Phillips head screws from the standard desiccant cartridge, and lift
the cartridge straight up and out of the instrument.
Note If the standard desiccant cartridge is stored in a dry box or sealed bag (you can
use the bag the purge cartridge came in), the cartridge can be reused.
7. Remove and discard the large O-ring.
Note Be careful not to drop the sealing O-ring into the desiccant compartment.
8. Open the purge kit and then open the sealed desiccant packet (must be sealed to keep the
desiccant dry).
9. Remove the O-ring from the packet and install it on the instrument base plate (see the
previous image). Press (rather than roll) the new O-ring into place to be sure it is properly
seated in the groove.
10. Remove the desiccant cartridge with purge fittings from the packet, insert the cartridge in
the desiccant compartment, make sure it is seated properly over the O-ring and then
secure it using the two screws.

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Note the correct orientation of the cartridge (the label on the cartridge should be readable
from the front of the instrument when the cartridge is installed).
Purge inlet Relief valves
Purge Desiccant
Cartridge
11. Connect the right-angle flow coupler from the wall plumbing assembly (labeled “to
spectrometer”) to the purge inlet on the instrument.
12. Install any sampling accessory you removed previously.
13. If the accessory is purged, connect the straight flow coupler from the plumbing assembly
(labeled “to accessory”) to the purge inlet on the installed accessory.
14. Open the main regulator valve and set the purge gas controls as indicated below (see
Setting Purge Gas Controls for details). If you are not purging an accessory, set the
pressure regulator for accessories to zero.
Hardware Pressure (psig) Flow Rate (scfh)

iS5N Spectrometer 5 1
iD1 Transmission Accessory 5 4-10
iD1H Transmission Accessory 5 4-10
iD Foundation Accessory 5 4-10
15. Plug in the power cord to the instrument and turn on the power.
16. Wait 30 to 60 minutes for the instrument to fully purge.
Note If the instrument is powered off without purge, you can use either desiccant
cartridge (with or without the purge connectors) to maintain the required humidity.
Make sure you check the humidity indicator once a month (see Checking the
Humidity Indicators) and replace the desiccant when necessary (see Replacing the
Desiccant).

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Related Topics
Replacing Sample Compartment Windows

Your instrument has windows on both sides of the sample compartment that seal the
spectrometer from moisture and other contaminants in the room atmosphere. The windows
must be installed, even if your system is purged.
The sample compartment windows are made of quartz. The windows should be clear and
clean (no fingerprints).
NOTICE
• Do not allow liquids to come into contact with the sample compartment windows.
• Windows can be scratched and ruined very easily. Do not touch or attempt to clean
them. Dust will not affect the signal, but fingerprints can degrade the performance of
the instrument and permanently damage mirrors or windows. If you wish to remove
dust from a mirror or window, blow it off with a gentle stream of clean, dry air or
nitrogen (Do not use compressed air from a can or contaminants may cause damage.)
• Replace sample compartment windows only with replacement parts supplied by us.
Time needed: 10 minutes
Tools needed:
• iS5 series window replacement tool (provided)
• iS5N sample compartment window replacement kit (contains 2 quartz windows)
• latex gloves
Window replacement tool
Replacement windows

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 To replace sample compartment windows
1. Turn off the instrument power. See Turning the Power On and Off.
Note If your instrument is purged, you can leave the purge on while you replace the
windows to prevent ambient air from entering the spectrometer.
2. Remove any sampling accessory from the instrument. See Installing an Accessory.
3. Line up the three ribs in the window replacement tool with the notches in the rim of the
installed window.
Sample
compartment window
Note The window fittings are tight. Use one hand to stabilize the instrument and the
other to remove the window.
4. Press firmly on the tool and turn it counterclockwise to loosen the window.
5. Remove the tool and continue loosening the window by hand until it releases.
NOTICE Use gloves to handle replacement windows and handle them by the rims.
(Avoid touching the windows even when wearing gloves.)
6. Gently insert the new window into the opening and turn it clockwise until hand tight.
The window should screw in easily at the start; if it doesn’t, remove the window and
restart to avoid stripping the threads.
7. Using the window replacement tool, slowly and firmly turn the window as far as it will go
(you will feel the O-ring compress fully when the window rim contacts the housing).
8. Turn on the instrument power and start OMNIC software.
9. Make sure the window type is properly configured in OMNIC software.
Choose Advanced Diagnostics in the Collect menu. The Diagnostics screen is displayed.

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Enter today’s date for the Purge Windows and choose Save.
11. Replace any accessories you removed earlier on the instrument.
Related Topics
• Troubleshooting
Replacing the Power Supply

Tools needed:
• iS5 series power supply replacement kit
Note To order parts, call our Technical Support. See Contacting Us.
CAUTION Avoid shock hazard.

• Do not attempt to remove the cover of the power supply.
• Do not allow liquid to run into the power supply or the back of the instrument.
• Do not block access to the power supply, AC power cord or power switch.
• Turn off the spectrometer power switch before replacing the power supply.

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NOTICE Replace the power supply only with replacement parts supplied by us.
 To replace the power supply
1. Turn off the instrument power. See Turning the Power On and Off.
2. Disconnect the old power supply from the wall outlet or power strip and from the
instrument power connector.
Power switch
Power
connector
DC power cord Power supply AC power cord
3. Disconnect the AC power cord from the power supply.
Note The power supply replacement kit does not include the AC power cord, which
is specific for the location of your installed instrument. Save the cord and use it with
the new power supply. If the power cord becomes damaged, contact us to order a new
one.
4. Connect your AC power cord to the new power supply.

5. Connect the power supply first to the instrument power connector and then to the wall
outlet or power strip. The wall outlet you use must be equipped with a 3-wire line: live,
neutral, and ground.

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6. Turn on the instrument power and start OMNIC software.

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. If the instrument
does not function normally, turn off the power and check the cable connections between
the power supply, the instrument, and the wall outlet or power strip. If the connectors are
seated properly and the instrument still does not function normally, contact us for
assistance.
7. Enter the serial number for the new power supply in OMNIC software.
Choose Advanced Diagnostics in the Collect menu. The Diagnostics screen is displayed.
Type the serial number for the new power supply, enter today’s date and click Save.
Related Topics
• Troubleshooting

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Replacing the Source

The iS5N spectrometer comes with a tungsten-halogen source that provides approximately
one year of regular use. The source is easy to replace.
Tools needed:
• iS5N source replacement kit
• #1 Phillips head screwdriver (provided with the instrument)
CAUTION Avoid shock hazard. To turn off the spectrometer power switch and unplug the
power cord before replacing an internal component.
CAUTION Avoid burn hazard. The source becomes extremely hot during normal
spectrometer operation. Turn off the spectrometer power and wait at least 10 minutes
before removing a source from the spectrometer.
NOTICE
• Replace the source only with replacement parts supplied by us.
• Never touch a source element with your bare fingers. Skin oils or other deposits on
the element will shorten its life. Always use clean finger cots, gloves, or clean
laboratory tissue when handling a source element.
 To replace the source
1. Turn off the instrument (see Turning the Power On and Off) and unplug its power cord.
2. Disconnect the cables from the back of the instrument.
3. If the spectrometer or an installed accessory is purged, disconnect the purge lines from the
spectrometer and the accessory (quick connect fittings stop the flow automatically). See
Installing a Purge Kit for more information.
4. Remove any installed accessories from the instrument (see Removing an Accessory).
CAUTION Make sure at least 10 minutes have passed since you turned off the instrument
before you perform the next step.

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5. Carefully tip the instrument back until it rests on the four feet on the rear panel.
6. Use a #1 Phillips head screwdriver to loosen the three captive screws that hold the source
in place.
7. Grasp the bale firmly and pull the source straight out of the instrument.
8. Record the serial number for the new source on a piece of paper. You will need to enter it
after the source is installed.

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NOTICE Never touch a source element with your bare fingers. Skin oils or other
deposits on the element will shorten its life. Always use clean finger cots, gloves, or
clean laboratory tissue when handling a source element.
9. Insert the new source.

Make sure the three captive screws are straight and then slowly insert the source into the
cavity until the source mount is flush with the instrument. Tighten the screws to secure
the source and snap the bale into its storage position.
10. Carefully return the instrument to its upright position and reconnect the cables you
removed.
11. If your instrument is not purged, replace the desiccant. See Replacing the Desiccant for
instructions.
12. Plug in the power cord to the instrument, turn on the power switch and start OMNIC
software.
13. Wait until the power indicator stops flashing.
14. Enter the serial number for the new source in OMNIC software.
Choose Advanced Diagnostics in the Collect menu. The Diagnostics screen appears.
Verify that the new source is working properly. (If it does not work properly, a red slash
mark appears over the Source icon on this screen. Contact Technical Support for
assistance; see Contacting Us.)

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Type the serial number for the new source (recorded in step 8), enter today’s date and
click Save.
results), and then align the instrument (see Aligning Your Spectrometer).
16. Run the Performance Verification (PV) test.
17. Replace any accessories you removed earlier.
18. If the system is purged, reconnect the purge lines.
Related Topics
Replacing the Laser

The laser in your instrument is not user-replaceable. If you suspect there is a problem with the
laser, contact us for assistance.
Related Topics
• Troubleshooting
Replacing the Detector

The detector in your instrument is not user-replaceable. If you suspect there is a problem with
the detector, contact us for assistance.
Related Topics
• Troubleshooting
Replacing the Electronics Module

The electronics module in your instrument is not user-replaceable. If you suspect there is a
problem with the electronics module, contact us for assistance.
Related Topics
• Troubleshooting

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Replacing Fuses
The fuses in your instrument are in the power supply and are not user-replaceable. If the fuses
blow, you must replace the power supply (see Replacing the Power Supply). If you need
assistance, contact us.
Related Topics
• Replacing the Power Supply
• Troubleshooting

4
Troubleshooting
Using the Troubleshooting Topics

The troubleshooting topics will help you solve problems with the instrument. These topics are
divided as follows:
Hardware Problems contains topics that address specific hardware problems you may
encounter. Each topic lists steps you can take to try to resolve the problem.
Error Messages contains topics that deal with error messages you may see. Each topic lists
steps you can take if you see such error messages.
To expedite and assist in problem diagnosis, please be prepared to send us a copy of your
diagnostics log file. The diagnostic log includes a history of important system parameters and
events that occur during system operation. To copy the diagnostics log to your Windows
desktop, start OMNIC software and choose File > Copy Diagnostics File to Desktop. Attach
this file to an e-mail message to our Technical Support group. See Contacting Us for e-mail
addresses.
Note If you are having a problem with applications or software, refer to the
documentation that came with your system.
WARNING When performing any of the procedures in the troubleshooting topics, always
follow the safety precautions included in this document or Help system and in any of the
other documentation that came with your instrument.

4 Troubleshooting
Hardware Problems
Hardware Problems
PV Test Failed
1. If the performance verification (PV) test fails, check the following and then rerun PV:
a. Make sure the iD1 accessory is installed correctly in the spectrometer sample
compartment and fully seated on the locator pins.
b. Make sure the C screen from the iS5N accessory kit is installed in the slot furthest to
the right inside the iD1 sample compartment.
c. Make sure the light beam is not blocked by a sample holder or sample.
d. Rerun PV taking care to install the correct polystyrene reference after the software
prompt (leave the C screen in the sample compartment during the polystyrene
measurement):
– For the iD1 accessory, use the polystyrene reference card from the iS5N accessory
kit.
– For the iD1H accessory, use the polystyrene reference cuvette shipped with that
accessory.
2. If PV fails again, take the following action depending upon which portion of the test
failed:
• If a noise level test failed:
– If the instrument is purged with dry air or nitrogen, make sure the purge is set to
the recommended flow rate. See Setting Purge Gas Controls for details. If the
flow rate was set incorrectly, reset it, wait 5 minutes for the flow rate to stabilize
and rerun PV.
– If a noise level test fails again and there are exhaust fans nearby or other
equipment that is causing the table on which the instrument is sitting to vibrate,
move the instrument to a more stable location and rerun PV.
– If a noise level test fails again, choose Collect > Experiment Setup > Diagnostic
> Align, wait for spectrometer alignment to complete and rerun PV.
– If a noise level test fails again, make sure the source is working:
– Choose Collect > Experiment Setup > Bench and make sure the Source
option is set to “White Light.”
– Choose Collect > Advanced Diagnostics. If the Source icon has a red slash,
replace the source. Otherwise, click the Source icon and check that the
source current and voltage are within specifications.
– If the source is on and the current and voltage are within specifications,
remove any sampling accessory from the spectrometer and put your hand in
the light beam. You should see a spot of yellow light that is about 1 cm in
diameter. If you don’t see the light beam, replace the source and rerun PV.

4 Troubleshooting
Hardware Problems
– If a noise level test fails after you have replaced the source, contact Technical
Support.
• If a wavenumber accuracy test failed:
– Choose Collect > Experiment setup > Diagnostic > Laser Verification, wait for
laser verification to complete and rerun PV.
– If a wavenumber accuracy test fails again, visually examine your polystyrene
reference for damage or contamination (the polystyrene reference card for the
iD1 or the polystyrene reference cuvette for the iD1H). If the polystyrene is
obviously dirty or damaged, contact us to buy a replacement reference card or
cuvette and then rerun PV using the new reference card (for the iD1 accessory)
or cuvette (for the iD1H accessory).
Before you run PV, update the installation date for the reference card or cuvette.
In OMNIC software choose View > Configure System Status > Performance
Verification > Configure Standards, select the table row that matches the
standard you are using, choose Update and enter today’s date as the Installation
Date for the standard.
– If a wavenumber accuracy test fails again, contact Technical Support.
• If the slope and/or intercept test failed:
– Close OMNIC software.
– Recycle the power to the iS5N spectrometer.
– Open OMNIC software and rerun PV taking care to install the polystyrene
reference card (for the iD1 accessory) or the polystyrene reference cuvette (for the
iD1H accessory) after the software prompt.
– If the slope and/or intercept test fails again, update the installation date for the
reference card or cuvette (see the instructions above). Then rerun PV.
– If the slope and/or intercept test fails again, contact Technical Support.
System Suitability Test Failed

1. If the System Suitability (SS) test fails, check the following and then rerun SS:
a. Make sure the iD1 or iD1H accessory is installed correctly in the spectrometer
sample compartment and fully seated on the locator pins.
b. Make sure the C screen from the iS5N accessory kit is installed in the slot furthest to
the right inside the accessory sample compartment.
c. Make sure the light beam is not blocked by a sample holder or sample.
d. Rerun SS taking care to install the correct polystyrene reference after the software
prompt.
– For the iD1 accessory, use the polystyrene reference card from the iS5N accessory
kit.

4 Troubleshooting
Hardware Problems
– For the iD1H accessory, use the polystyrene reference cuvette shipped with that
accessory.
2. If SS fails again, take the following action depending upon which portion of the test
failed:
• If a throughput test failed:
– Make sure the C screen from the iS5N accessory kit is installed in the slot
furthest to the right inside the accessory sample compartment.
– Remove any sample from the beam path (leave the C screen installed), choose
Collect > Experiment Setup > Diagnostic > Align, wait for spectrometer
alignment to complete and rerun SS.
– If a throughput test fails again, make sure no sample is in the beam path and
choose View > Configure System Status > System Suitability > Configure >
Collect to collect a new SS reference spectrum. When the collection is
completed, choose OK and rerun SS.
– If a throughput test fails again, contact Technical Support.
• If a contamination test failed:
– Remove any sampling accessory from the instrument and visually examine the
sample compartment windows on the spectrometer for damage or
contamination. (Contamination from fingerprints or other sources can result in
undetermined peaks in the spectra.) If the windows are obviously dirty or
damaged, replace them (see Replacing Sample Compartment Windows) and
rerun SS.
– If the windows look okay but a contamination test fails again, you can remove
the windows and rerun SS (see Replacing Sample Compartment Windows for
more information). If all contamination tests pass, replace the sample
compartment windows (reinstall the old windows to protect the instrument until
the new windows arrive).
– If a contamination test fails after you have replaced the sample compartment
windows, contact Technical Support.
• If a noise level test failed:
– If the instrument is purged with dry air or nitrogen, make sure the purge is set to
the recommended flow rate. See Setting Purge Gas Controls for details. If the
flow rate was set incorrectly, reset it, wait 5 minutes for the flow rate to stabilize
and rerun SS.
– If a noise level test fails again and there are exhaust fans nearby or other
equipment that is causing the table on which the instrument is sitting to vibrate,
move the instrument to a more stable location and rerun SS.
– If a noise level test fails again, choose Collect > Experiment Setup > Diagnostic
> Align, wait for spectrometer alignment to complete and rerun SS.

4 Troubleshooting
Hardware Problems
– If a noise level test fails again, make sure the source is working:
– Choose Collect > Experiment Setup > Bench and make sure the Source
option is set to “White Light.”
– Choose Collect > Advanced Diagnostics. If the Source icon has a red slash,
replace the source. Otherwise, click the Source icon and check that the
source current and voltage are within specifications.
– If the source is on and the current and voltage are within specifications,
remove any sampling accessory from the spectrometer and put your hand in
the light beam. You should see a spot of yellow light that is about 1 cm in
diameter. If you don’t see the light beam, replace the source and rerun SS.
– If a noise level test fails after you have replaced the source, contact Technical
Support.
• If an X-axis (wavenumber) accuracy test failed:
– Choose Collect > Experiment setup > Diagnostic > Laser Verification, wait for
laser verification to complete and rerun SS.
– If an X-axis accuracy test fails again, visually examine your polystyrene reference
for damage or contamination (the polystyrene reference card for the iD1 or the
polystyrene reference cuvette for the iD1H). If the polystyrene is obviously dirty
or damaged, contact us to buy a replacement reference card or cuvette and then
rerun SS using the new reference card (for the iD1 accessory) or cuvette (for the
iD1H accessory).
– If an X-axis accuracy test fails with a new polystyrene reference card or cuvette,
contact Technical Support.
• If a Y-axis (peak height) accuracy test failed:
– Make sure the C screen from the iS5N accessory kit is installed in the slot
furthest to the right inside the accessory sample compartment.
– If a Y-axis accuracy test fails again, visually examine your polystyrene reference
for damage or contamination (the polystyrene reference card for the iD1 or the
polystyrene reference cuvette for the iD1H). If the polystyrene is obviously dirty
or damaged, contact us to buy a replacement reference card or cuvette and then
rerun SS using the new reference card (for the iD1 accessory) or cuvette (for the
iD1H accessory).
– If a Y-axis accuracy test fails with a new polystyrene reference card or cuvette,
choose Collect > Experiment Setup > Bench and make sure the Gain option is
set to “1” and the interferogram peak maximum is 6 volts or less.
– If the Gain was set incorrectly, reset it and rerun SS.
– If the interferogram peak maximum is greater than 6 volts with the C screen
installed and Gain set to “1”, contact Technical Support.

4 Troubleshooting
Hardware Problems
Spectral Peaks Appear Shifted in Wavenumber Axis

1. Run laser verification. See Verifying the Laser Frequency.
2. Contact Technical Support for assistance; see Contacting Us.
Fails Laser Frequency Verification

1. Laser verification requires some water vapor to be present in the sample compartment. If
laser verification fails, remove any accessory from the spectrometer, breath slowly into the
sample compartment and immediately rerun laser verification.
2. If laser verification fails again, contact Technical Support for assistance; see Contacting
Us.
Power Indicator Does Not Light After Power Up

1. Turn the instrument off and check the connections between the instrument and the
power supply.
2. Make sure the power cord is securely connected to the power supply and the power
supply is connected to a properly grounded and working outlet.
3. Check the power cord descriptions and part numbers to make sure the power cord is
appropriate for your local AC power source. Order a new power cord if necessary.
4. Check the ground prong on the power cord. If the ground prong has been removed or is
defective, replace the power cord.
Power Indicator Blinks Continuously

The instrument power indicator blinks for two minutes after power up while the instrument
runs internal diagnostic tests. If the power indicator continues to blink after two minutes,
there is a problem with the internal temperature or humidity. Follow these steps:
1. In OMNIC software, choose Experiment Setup > Diagnostic and click the status icon
that has a red slash for details.
2. If the internal humidity is too high, see Humidity Is Too High.
3. If the internal temperature is out of specification, see Instrument Temperature Is Out of
Specification.

4 Troubleshooting
Hardware Problems
System Scans Normally but Signal Intensity Is Low

1. Make sure the light beam is not blocked by a sample holder or sample.
2. Make sure any accessory you are using is installed correctly. (For more information, see
the instructions that came with the accessory.)
3. Install the iD1 transmission accessory and insert the C screen into the slot furthest to the
right inside the accessory sample compartment (remove any sample), choose Collect >
Experiment Setup > Diagnostic > Align and wait for spectrometer alignment to
complete.
4. If the signal intensity is still low, keep the iD1 accessory installed with the C screen and
no sample and run Performance Verification taking care to install the polystyrene
reference card after the software prompt.
5. If the signal intensity is still low, make sure the sample compartment windows are not the
problem:
a. Remove any accessories from the instrument and visually examine the sample
compartment windows for damage or contamination. If the windows are obviously
dirty or damaged, replace them (see Replacing Sample Compartment Windows).
b. If the windows look okay but the signal intensity is still low, you can remove the
windows (see Replacing Sample Compartment Windows for more information). If
the signal intensity increases, replace the sample compartment windows (reinstall the
old windows to protect the instrument until the new windows arrive).
6. If the sample compartment windows are okay and the signal intensity is still low, make
sure the source is working:
a. Choose Collect > Experiment Setup > Bench and make sure the Source option is
set to “White Light.”
b. Choose Collect > Advanced Diagnostics. If the Source icon has a red slash, replace
the source. Otherwise, click the Source icon and check that the source current and
voltage are within specifications.
c. If the source is on and the current and voltage are within specifications, remove any
sampling accessory from the spectrometer and put your hand in the light beam. You
should see a spot of yellow light that is about 1 cm in diameter. If you don’t see the
light beam, replace the source.
7. If the source is working and the signal intensity is still low, make sure the detector is
working:
a. Choose Collect > Experiment Setup > Diagnostic and select View Reference
Detector.
b. If a normal sized interferogram appears (5 to 6 volt maximum), deselect the reference
detector by clearing the View Reference Detector checkbox.

4 Troubleshooting
Hardware Problems
c. If the signal gets smaller again, there may be a problem with the sample detector.
Contact Technical Support for assistance; see Contacting Us.
Spectra Have Noise Spikes

1. If the instrument is purged with dry air or nitrogen, make sure the purge is set to the
recommended flow rate. See Setting Purge Gas Controls for details. If the flow rate was
set incorrectly, reset it. Wait 5 minutes for the flow rate to stabilize.
2. If there are exhaust fans nearby or other equipment that is causing the table on which the
instrument is sitting to vibrate, move the instrument to a more stable location.
3. Choose Collect > Experiment Setup > Diagnostic > Align and wait for spectrometer
alignment to complete.
4. Make sure the source is working:
a. Choose Collect > Experiment Setup > Bench and make sure the Source option is
set to “White Light.”
b. Choose Collect > Advanced Diagnostics. If the Source icon has a red slash, replace
the source. Otherwise, click the Source icon and check that the source current and
voltage are within specifications.
c. If the source is on and the current and voltage are within specifications, remove any
sampling accessory from the spectrometer and put your hand in the light beam. You
should see a spot of yellow light that is about 1 cm in diameter. If you don’t see the
light beam, replace the source.
d. Contact Technical Support.
5. If sharp spikes are apparent throughout the spectra, you may have problems from
electrical noise.
a. Remove any potential sources of electrical noise emission that are nearby such as
computers or other lab equipment.
b. Your power supply or USB cable may be picking up electrical noise from other
equipment or cables. Reposition the power supply or USB cable.
c. Your AC power source may contain electrical noise. See the Site and Safety guide in
your documentation set for electrical specifications. You may need an AC power
conditioner.
d. Replace the power supply.
e. Contact Technical Support for assistance; see Contacting Us.
Spectral Baseline Is Not Stable

1. Minimize the acoustic noise inside the instrument. If the instrument has the purge
option, lower the purge flow rate until the baseline is stable.

4 Troubleshooting
Hardware Problems
2. Choose Experiment Setup > Diagnostic > Align and wait for alignment to complete.
3. Make sure the environmental conditions (especially vibration) meet the requirements
listed in the Site and Safety guide in your documentation set.
4. Make sure the ambient temperature is not changing dramatically.
5. Check the humidity indicator and replace the desiccant and indicator if needed.
6. Make sure the ambient humidity is not changing dramatically. If it is, consider adding the
purge option (see Installing a Purge Kit).
7. If the power to the instrument was recently turned on, allow 1 to 6 hours for the
temperature to completely stabilize.
Note If you are using purge and the accessory cover was recently opened (or a service
representative opened the main cover), allow the instrument to equilibrate for 1 to
6 hours after the cover is closed.
8. Choose Experiment Setup > Bench, click the Laser icon and check the laser indicators.
If a laser measurement is out of tolerance, contact Technical Support for assistance (see
Contacting Us).
Alignment Fails
1. Make sure any accessories are installed according to the instructions that came with them.
2. Check the sample compartment windows for damage. Contact Technical Support for
assistance if they are not clear or appear to be damaged.
3. Choose Experiment Setup > Diagnostic. If one of the status indicators has a red slash
through it, click the indicator and follow the on-line instructions to resolve the problem.
4. Choose Experiment Setup > Diagnostic > Reset Bench. Make sure the system has been
on for at least 15 minutes (one hour for best results), and then choose Align on the
Diagnostic tab.
5. If no interferogram appears after alignment, select View Reference Detector on the
Diagnostic tab. If the interferogram appears, you may have a problem with the sample
detector. Contact Technical Support for assistance; see Contacting Us.
Data Cannot Be Collected (or Other Software Problems)

1. Make sure the system has completed the initialization period (about 2 minutes after you
power it up). During initialization, the blue power indicator on the front of the
instrument flashes and the OMNIC Collect menu is disabled.
2. Close OMNIC software and turn off the computer. Turn off the instrument power.
Check the computer cable. If it is damaged, replace it. If the cable is loose or

4 Troubleshooting
Error Messages
disconnected, reconnect it. Wait a few seconds and turn on the instrument power. Then
turn on the computer and restart OMNIC software.
3. Choose Experiment Setup > Diagnostic > Reset Bench.
Error Messages
Computer Cannot Communicate With Instrument
1. Check that the computer USB port supports USB version 2.0 and the cable between the
computer and the spectrometer is a high speed USB cable.
2. Open Experiment Setup in OMNIC software, click the Diagnostic tab, and then click
Reset Bench.
3. If the problem continues, close OMNIC software and turn off the instrument power.
Wait a few seconds and then turn on the instrument power. Restart OMNIC software.
4. If the Power indicator on the instrument does not light, make sure the power supply is
connected to the instrument and to a properly grounded wall outlet or power strip.
5. Turn off the computer and then turn off the instrument power. Check the USB data
cable. If the cable is damaged, replace it. If the cable is loose or disconnected, reconnect it.
If the cable looks okay and was properly connected, try connecting it to a different
USB 2.0 port on the computer.
6. Turn on the instrument power. Turn on the computer and restart OMNIC software. You
should hear a sound or receive a message confirming communication with the
instrument.
7. Remove any USB computer accessories that may be interfering with communication with
the spectrometer.
8. Close any applications that might interfere with OMNIC software.
Instrument Temperature Is Out of Specification

1. Make sure nothing is placed on top of the instrument and air can flow freely around it.
2. The ambient temperature may be too high. The ambient temperature should be between
15 °C and 35 °C (between 60 °F and 95 °F). Allow 1 to 6 hours for the spectrometer to
reach temperature equilibrium.

4 Troubleshooting
Error Messages
OMNIC Cannot Communicate With the Detector

If OMNIC software cannot communicate with the detector, contact Technical Support for
assistance; see Contacting Us.
Instrument Is Not Scanning

Note After 1 hour without data collection activity, the interferometer automatically stops
scanning. Any subsequent data collection activity will cause the interferometer to begin
scanning again.
1. Turn on the instrument power (if it is not already on).

2. Start OMNIC software.
3. Make sure the system has been on for at least 15 minutes (one hour for best results), and
then align the instrument (choose Experiment Setup > Diagnostic > Align).
4. Turn off the power to the computer and the instrument. Leave the power off for
15 seconds. Turn on the instrument power. Turn on the computer and restart OMNIC
software.
5. Choose Experiment Setup > Diagnostic > View Reference Detector.
If the instrument scans normally (an interferogram should appear in the Diagnostic
pane), the problem is probably related to the sample or the sample detector. Make sure
that the light beam is not blocked, and check the Diagnostic tab in Experiment Setup to
make sure the detector is recognized. If it is not, contact Technical Support for assistance;
see Contacting Us.
6. Check all of the status indicators on the Diagnostic tab in Experiment Setup. Click any
indicator that has a red slash through it to view diagnostic information about the
component.
If the laser frequency is outside the specified range, contact Technical Support to have the
electronics module replaced. If the laser voltage or current is outside the specified range,
contact Technical Support for assistance.
If the temperature is not in the acceptable range, make sure the cooling vents on the back
of the instrument are not blocked and nothing is stacked on top of the instrument.
Maintain at least 30 cm (12 in) of clearance behind the instrument and 64 cm (25 in) of
clearance above the table. Make sure the ambient temperature is between 15 °C and
35 °C (between 60 °F and 95°F).

4 Troubleshooting
Error Messages
Laser Voltage Is Out of Specification

1. Remove any accessories or samples from the sample compartment.
2. Choose Experiment Setup > Diagnostic > Align and wait for spectrometer alignment to
complete.
Source Voltage Is Out of Specification

1. Make sure the source holder is properly seated in the instrument.
2. Replace the source. See Replacing the Source.
Power Supply Voltages Are Out of Tolerance

1. Choose Experiment Setup > Diagnostic and click the Power icon. Check that the
current value for +12 Volt is within specifications. If it is out of the specified range,
replace the power supply.
2. If other values on the Power diagnostic screen are out of their specified ranges, contact
Technical Support for assistance; see Contacting Us.
Humidity Is Too High

1. If the instrument is equipped with an optional purge kit, check that the purge gas flow is
set properly; see Setting Purge Gas Controls for details.
2. Check the humidity indicator and replace the desiccant and indicator; see Replacing the
Desiccant for instructions.
Laser Temperature Is Out of Specification

1. Make sure the room temperature is between 15 °C and 35 °C (between 60 °F and 95 °F),
and allow the instrument adequate time to stabilize.
Interferometer Temperature Is Out of Specification

1. Make sure the room temperature is between 15 °C and 35 °C (between 60 °F and 95 °F),
and allow the instrument adequate time to stabilize.

4 Troubleshooting
Error Messages
Laser Frequency Is Out of Specification

1. Choose Experiment Setup > Diagnostic > Align and wait for spectrometer alignment to
complete.
2. Choose Experiment Setup > Diagnostic > Laser Verification and wait for laser
verification to complete.

I
Index
A cleaning
iD1 Transmission Module 27
accessory
instrument 26
attaching purge to 10
installing base-plate mounted 10 collecting data 15
installing integrated 9 collecting data with the iD1 20
installing slide-mounted 13 collection failure 59
removing 10 communication cabling 6
storing 10 computer
adapter communication error 60
installing iD base 10 contact information 3
aligning conventions 2
spectrometer 17
alignment failure 59 D
altitude
danger
recommended for instrument 5
volatile solvents 5
attenuation screens
data cable 6
installing 14
data collection 15, 20
data collection failure 59
B desiccant
baseline checking 27
unstable 58 regenerating 33
baseplate mounted accessory replacing 29
installing 10 desiccant indicator
beam focus 19 proper handling 32
desiccation
requirement 1
C
detector
cabling 6 replacing 49
calibrating detector communication error 61
laser 18
documentation 2
caution
burn hazard from hot desiccant canisters 34
burn hazard from hot source 46 E
damaged cover 5 electrical cabling 6
power supply 43 electricity
shock hazard when replacing components 46 static 27
use proper grounding 6 electronics module
using liquids 26 replacing 49

Index: F
error checking 27
computer communication 60 ordering 34
detector communication 61
humidity 62
interferometer temperature 62
I
laser frequency 63 iD base adapter
laser temperature 62 installing 10
laser voltage 62 iD Foundation Adapter
power supply voltage 62 installing 12
scanning 61 iD1 Transmission Module 18
source voltage 62 cleaning 27
temperature 60 collecting data using 20
error messages 60 installing 9
installing sample in 19
indicators
F humidity 27
failure initialization 7
alignment 59 installing
data collection 59 baseplate-mounted accessory 10
laser verification 56 film sample 19
performance test 52 gas cell 13
system suitability test 53 iD base adapter 10
film sample integrated accessories 9
installing 19 power supply 43
filter purge kit 36
purge 35 slide-mounted accessory 13
flow rate 15 source 46
and vibration 16 transmission cell 13
focus 19 installing attenuation screens 14
focus point instrument
for infrared beam 19 aligning 17
Foundation Series accessory altitude range for operation 5
installing 12 cleaning 26
fuses humidity range for operation 5
replacing 50 purging 36
recommended humidity range 5
temperature range for operation 5
G troubleshooting 52
gas cell 19 vent access for 8
installing 13 instrument information
grounding updating 20
how to properly 27 instrument operation
grounding specifications 6 verifying 23
interferometer temperature error 62
H
help L
about 2 laser
humidity calibrating 18
recommended for instrument 5 replacing 49
recommended for operation 5 verifying 17
humidity error 62 laser frequency error 63
humidity indicator laser temperature error 62

Index: M
laser verification failure 56 power supply

laser voltage error 62 replacement parts 44
LED replacing 43
blinks continuously 56 power supply voltage error 62
does not light 56 purge
liquid cell 19 changing the filter 35
low signal 57 for accessories 10
requirement 1
setting 15
M purge gas
maintenance 23 specifications 15
manual conventions 2 purge kit
manuals 2 installing 36
messages
error 60
R
regenerating desiccant 33
N removing
narrow slot 19 an accessory 10
noise spikes 58 replacing
notice desiccant 29
access 6 fuses 50
replacement parts 36 power supply 43
source 46
the detector 49
O the electronics module 49
OMNIC software the laser 49
and instrument initialization 7
operation
verifying 23 S
ordering parts 2 sample
outlet focus 19
power 6 installing film 19
installing in iD1 Transmission Module 19
scanning error 61
P screens
parts installing 14
ordering 2 serial numbers
PDF documents 2 entering 20
PDFs 2 shifting
peaks of peaks in the spectrum 56
shifted 56 signal
performance test failure 52 too low 57
performance verification slide-mounted accessory
running 23 installing 11, 13
Performance Verification test 17 slots
power in iD1 Transmission Module 19
turning on or off 7 solvents
power indicator 7 warning 5
blinks continuously 56 source
does not light 56 replacing 46
power outlet source voltage error 62
specifications for 6 specification

Index: T
for purge gas 15 explosion hazard from open desiccant compartment 30

specifications for performing maintenance 23
for power outlet 6 open desiccant compartment 38
spectrometer purge gas 16, 37
aligning 17 wide slot 19
cleaning 26
installing integrated accessory in 9
laser 18
power 7
purging 15, 36
troubleshooting 52
spectrum
noise spikes in 58
shifted peaks 56
unstable baseline 58
static electricity precautions 27
storing
an accessory 10
Swap-Top Module
installing 12
system suitability test failure 53
T
technical support 3
Technical Support contact information 3
telephone numbers 3
temperature
recommended for instrument 5
temperature error 60
transmission cell
installing 13
troubleshooting 51
U
unstable baseline 58
using
iD1 Transmission Module 18
V
vents
access to 8
verifying laser 17
vibration
and flow rate 16
W
warming up the instrument 7
warning
desiccant harmful if swallowed 32

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Nicolet iS5 Series Spectrometers

269-318900 Revision A May 2016

Unity Lab Services Thermo Fisher Scientific

WARNING Avoid an explosion or fire hazard. This instrument or accessory is not

Chapter 3 Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23

Thermo Scientific Nicolet iS5N Spectrometer User Guide iii

Installing or Replacing Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Chapter 4 Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .51

iv Nicolet iS5N Spectrometer User Guide Thermo Scientific

The Thermo Scientific Nicolet™ iS™5N Fourier transform near-infrared (FT-NIR)

Thermo Scientific Nicolet iS5N Spectrometer User Guide 1

Note Contains helpful supplementary information.

Tip Provides information that can make a task easier.

About the Help System

Finding Other PDF Documents

2 Nicolet iS5N Spectrometer User Guide Thermo Scientific

Unity Lab Services

For International Support, please contact:

Thermo Fisher Scientific

Thermo Scientific Nicolet iS5N Spectrometer User Guide 3

Thermo Scientific Nicolet iS5N Spectrometer User Guide 5

Electrical and Communication Cabling

6 Nicolet iS5N Spectrometer User Guide Thermo Scientific

 To cable the instrument:

Turning the Power On and Off

Thermo Scientific Nicolet iS5N Spectrometer User Guide 7

After the spectrometer is installed, you can leave it turned on.

8 Nicolet iS5N Spectrometer User Guide Thermo Scientific

Installing Integrated Accessories

Thermo Scientific Nicolet iS5N Spectrometer User Guide 9

Installing Baseplate-Mounted Accessories

10 Nicolet iS5N Spectrometer User Guide Thermo Scientific

Height adjustment screw

Thermo Scientific Nicolet iS5N Spectrometer User Guide 11

12 Nicolet iS5N Spectrometer User Guide Thermo Scientific

Installing Slide-Mounted Accessories

Thermo Scientific Nicolet iS5N Spectrometer User Guide 13

 To install a slide-mounted accessory

Installing Attenuation Screens

Screen Attenuation Recommended Use

14 Nicolet iS5N Spectrometer User Guide Thermo Scientific

Accessory Location for Installing Attenuation Screens

Setting Purge Gas Controls

Thermo Scientific Nicolet iS5N Spectrometer User Guide 15

NOTICE We recommend maintaining seal and desiccation and/or purging the

 To set the purge gas controls

Set accessory flow Set spectrometer flow

3. Set the flowmeter for the spectrometer to 1 scfh (0.47 l/min).

16 Nicolet iS5N Spectrometer User Guide Thermo Scientific

Aligning Your Spectrometer

 To align the spectrometer

Verifying the Laser Frequency

Spectrometer environment Spectrometer state Recommended Schedule

Thermo Scientific Nicolet iS5N Spectrometer User Guide 17

 To verify the laser frequency

Using the iD1 Transmission Accessory

Install the module as explained in Installing an Accessory.

18 Nicolet iS5N Spectrometer User Guide Thermo Scientific

Installing Samples in the iD1 Transmission Accessory