Thermo Scientific iS5N Series User manual

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

Thermo Scientific Nicolet iS5N Spectrometer User Guide iii
C
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
Contents

Contents
iv Nicolet iS5N Spectrometer User Guide Thermo Scientific
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

Thermo Scientific Nicolet iS5N Spectrometer User Guide 1
1
Welcome
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.
iS5N spectrometer
with iD1 Transmission
accessory installed

1Welcome
Conventions Used
2Nicolet iS5N Spectrometer User Guide Thermo Scientific
Conventions Used
Safety precautions and other important information use the following format:
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 o rd e r p a r t s , 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.
WARNING Indicates a hazardous situation which, if not avoided, could result in death or
serious injury.
CAUTION Indicates a hazardous situation which, if not avoided, could result in minor or
moderate injury.
NOTICE Follow instructions with this label to avoid damaging the system hardware or
losing data.
Note Contains helpful supplementary information.
Tip Provides information that can make a task easier.

1 Welcome
Contacting Us
Thermo Scientific Nicolet iS5N Spectrometer User Guide 3
Contacting Us
For U.S. Technical Support, please contact:
Unity Lab Services
Part of Thermo Fisher Scientific
5225 Verona Road
Madison, WI 53711-4495 U.S.A.
Telephone: [phone]
E-mail: [e-mail]
For International Support, please contact:
Thermo Fisher Scientific
Telephone: [phone]
E-mail: [e-mail]
If you have problems with your system, refer to the Troubleshooting information for help, 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.

Thermo Scientific Nicolet iS5N Spectrometer User Guide 5
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.

2Operation
Electrical and Communication Cabling
6Nicolet iS5N Spectrometer User Guide Thermo Scientific
Electrical and Communication Cabling
The illustration below shows the correct cable connections for electrical power and data
communication.
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.
Power
Computer
Computer (USB)
cable
Power cable
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.