Thermo Scientific Nicolet iS10 Guide

Using Your Nicolet iS10 Spectrometer

The information in this publication is provided for reference only. All
information contained in this publication is believed to be correct and
complete. Thermo Fisher Scientific shall not be liable for errors
contained herein nor for incidental or consequential damages in
connection with the furnishing, performance or use of this material. All
product specifications, as well as the information contained in this
publication, are subject to change without notice.
This publication may contain or reference information and products
protected by copyrights or patents and does not convey any license
under our patent rights, nor the rights of others. We do not assume
any liability arising out of any infringements of patents or other rights
of third parties.
We make no warranty of any kind with regard to this material,
including but not limited to the implied warranties of merchantability
and fitness for a particular purpose. Customers are ultimately
responsible for validation of their systems.
© 2008 Thermo Fisher Scientific Inc. All rights reserved. No part of
this publication may be stored in a retrieval system, transmitted, or
reproduced in any way, including but not limited to photocopy,
photograph, magnetic or other record, without our prior written
permission.
For Technical Support, please contact:
Thermo Fisher Scientific
5225 Verona Road
Madison, WI 53711-4495 U.S.A.
Telephone: [phone]
E-mail: [email protected]
World Wide Web: http://www.thermo.com/spectroscopy
For International Support, please contact:
Thermo Fisher Scientific
Telephone: [phone]
E-mail: [email protected]
World Wide Web: http://www.thermo.com/spectroscopy
Windows is either a trademark or a registered trademark 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.
269-233700, Rev A

Table of Contents
Welcome....................................................................................................................1
Questions and concerns.............................................................................................1
Conventions used in this help system ..........................................................................1
Warranty information................................................................................................2
Purge/desiccation requirement ...................................................................................2
Finding PDF documents .............................................................................................3
Ordering parts..........................................................................................................3
Safety .......................................................................................................................4
Safety precautions....................................................................................................4
Safety labels............................................................................................................4
Safety and electrical symbols .....................................................................................5
Indicators and buttons ..............................................................................................6
Dangerous contaminants ...........................................................................................7
Using liquid nitrogen .................................................................................................7
Using corrosives and solvents.....................................................................................7
Checking the power supply ........................................................................................8
Operation...................................................................................................................9
Turning the power on and off .....................................................................................9
Installing a Smart Accessory ......................................................................................9
Collecting data with the instrument .............................................................................9
Collecting data with the module..................................................................................9
Setting the purge gas controls.................................................................................. 10
Aligning your spectrometer ...................................................................................... 11
Cooling a detector .................................................................................................. 11
Service .................................................................................................................... 14
Installing or replacing hardware................................................................................ 14
Installing a purge kit ............................................................................................ 14
Installing a sample compartment extension kit......................................................... 17
Installing baseplate-mounted accessories ................................................................ 18
Installing slide-mounted accessories....................................................................... 18
Installing other accessories ................................................................................... 19
Replacing the power supply................................................................................... 20
Replacing or changing the source ........................................................................... 21
Installing sidewall adapters ................................................................................... 23
Maintaining your instrument..................................................................................... 24
Cleaning your instrument...................................................................................... 24
Static electricity precautions.................................................................................. 24
Maintaining detector dewars.................................................................................. 25
Checking the humidity indicator ............................................................................. 25
Replacing the humidity indicator ............................................................................ 26
Replacing the desiccant ........................................................................................ 27
Regenerating the desiccant ................................................................................... 28
Checking and changing the purge gas filter.............................................................. 29
Troubleshooting ........................................................................................................ 33
Using the troubleshooting topics ............................................................................... 33
Hardware problems................................................................................................. 33
The status indicators do not light when you turn on your instrument ........................... 33
The Scan indicator flashes intermittently ................................................................. 34
The Scan indicator does not flash (the instrument is not scanning).............................. 34
The system scans normally but the signal intensity is very low ................................... 35
The baseline is not stable...................................................................................... 35
The alignment fails............................................................................................... 36
There is a problem selecting an external detector in a microscope............................... 36
Data cannot be collected (or other software problems) .............................................. 36

Error messages ...................................................................................................... 37
The computer cannot communicate with the instrument ............................................ 37
The instrument temperature is out of specification.................................................... 37
OMNIC cannot communicate with the detector ......................................................... 37
The instrument is not scanning .............................................................................. 38
The MCT detector is warm.....................................................................................38
The laser voltage is out of specification ................................................................... 39
The source voltage is out of specification................................................................. 39
The power supply voltages are out of tolerance ........................................................ 39
Index ...................................................................................................................... 40

Thermo Fisher Scientific Using Your Nicolet iS10 Spectrometer 1
Welcome
The Thermo Scientific Nicolet™ iS™10 spectrometer has integrated validation features, a
powerful software suite, and many other features that make it easy for you to collect data. It
was designed to allow you to install optional hardware and perform several service and
maintenance procedures yourself, and this help system, or printed documentation, contains
detailed information about performing such procedures.
If you are using the electronic help version of this document, you can access information by
double-clicking the book in the Contents tab that interests you, and then double-clicking the
topic you want to read. There is also an Index tab where you can search for topics by phrase
or keyword, and there is a Find tab that allows you to search for specific words.
Questions and concerns
In case of emergency, follow the procedures established by your facility. If you have questions
or concerns about safety or need assistance with operation, repairs or replacement parts, you
can contact our sales or service representative in your area or visit our web site at
www.thermo.com/spectroscopy.
Conventions used in this help system
This help system includes safety precautions and other important information presented in the
following format:
Note: Notes contain helpful supplementary information.
Notice: Follow instructions labeled "Notice" to avoid damaging the system hardware or losing
data.
Caution: Indicates a hazardous situation which, if not avoided, could result in minor or
moderate injury.
Warning: Indicates a hazardous situation which, if not avoided, could result in death or
serious injury.
Danger: Indicates a hazardous situation which, if not avoided, will result in death or
serious injury.

Warranty information
Thermo Fisher Scientific warrants that each product we sell you is free from defects in labor
and materials and shall conform to its product specifications as defined in the product user
documentation. If the product does not function as warranted during the warranty period, we
will repair or replace it without charge. If in our judgment we are unable to do so, you may
return it to us and we will refund your money.
This warranty replaces all other warranties, expressed or implied, including the implied
warranties of merchantability and fitness for a particular purpose and any other obligations or
liabilities on the part of Thermo Fisher Scientific whether in contract, warranty, negligence or
otherwise. Thermo Fisher Scientific shall not be liable for and disclaims all consequential,
incidental and contingent damages.
Warranty period
The system warranty period is 12 months in the U.S.A. and Canada. The warranty period
begins on the date of installation or 30 days from the date of invoice, whichever is sooner.
The system warranty period for products sold outside the U.S.A. and Canada is 12 months
from the date of installation or 14 months from the date of shipment, whichever is sooner.
Limit of warranty
Misuse, accident, modification, unsuitable physical or operating environment, improper
maintenance, or damage caused by a product for which we are not responsible will void the
warranty. Certain components may have separate warranty periods as stated in the product
user documentation. Consumables are not covered under warranty.
Items not covered by warranty
We do not warrant uninterrupted or error-free operation of a product. We provide certain non-
Thermo Fisher Scientific products on an "as is" basis. Non-Thermo Fisher Scientific
manufacturers or suppliers may provide their own warranties to you. A separate software
warranty is provided with the software user documentation.
Purge/desiccation requirement
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 under the warranty. If you have questions about this requirement, please contact us.
2 Using Your Nicolet iS10 Spectrometer Thermo Fisher Scientific

Finding PDF documents
PDF files of your instrument documentation are installed on the hard drive of the system
computer when the software is installed. To access these PDFs:
1.—Click the Start button on the Windows®taskbar.
2.—Click All Programs.
3.—Click the Thermo Scientific OMNIC™ folder.
4.—Click the Documentation folder.
5.—Choose the PDF file you want to open.
Ordering parts
To order parts, contact us.
Thermo Fisher Scientific Using Your Nicolet iS10 Spectrometer 3

Safety
Safety precautions
The United States Department of Health and Human Services warns against improper laser
use, as follows:
Warning: Use of controls or adjustments or performance of procedures other than those
specified in your printed and electronic documentation may result in hazardous radiation
exposure. Do not alter or attempt to remove the laser head from its protective housing or
attempt to remove the shields that surround the laser head. Exposure to laser energy and
high voltage may result.
Warning: Never stare directly into the laser beam or at its bright reflection. Avoid skin
contact with the laser beam or its bright reflection. Never tamper with the laser head.
Exposure to laser light or high voltage may result.
Warning: When operating your instrument, use only equipment (such as power supplies
and lasers) supplied by us. Use of equipment (such as power supplies and lasers) not supplied
by us can result in permanent damage to the instrument and may create a safety hazard.
Safety labels
The safety labels on your instrument are shown below. To order new labels, contact us.
4 Using Your Nicolet iS10 Spectrometer Thermo Fisher Scientific

Safety and electrical symbols
The following safety and electrical symbols may be used on this product:
Symbol Description Indication
Black graphical
symbol inside a
yellow triangle
with a black
triangular band
This is a warning symbol. The
graphic in this symbol is used to
alert the user to potential
hazards.
Black graphical
symbol inside a
red circular band
with a red
diagonal bar
This is a prohibition symbol. The
graphic in this symbol is used to
alert the user to actions that
shall not be taken or shall be
stopped.
White graphical
symbol inside a
blue circle
This is a mandatory action
symbol. It is used to indicate that
an action shall be taken to avoid
a hazard.
Black graphical
symbol inside a
yellow triangle
with a black
triangular band
This is the general warning sign.
Failure to heed the safety
precautions could result in
personal injury.
White graphical
symbol inside a
blue circle
This is the general data loss or
property damage symbol and is
not related to personal injury.
Failure to heed these precautions
can result in irreparable damage
to property or permanent data
loss.
Thermo Fisher Scientific Using Your Nicolet iS10 Spectrometer 5

Symbol Indication
Alternating current
Earth terminal or ground
Protective conductor terminal
Fuse
Power on
Power off
Indicators and buttons
The status indicators for the instrument are located on the operations panel, which is on the
main cover of the instrument. This panel also has buttons that allow you to operate the
instrument.
1) Humidity indicator
2) Power indicator
3) Scan indicator
4) Macro button
5) Background button
6) Sample button
7) OK/Enter button
8) Stop button
6 Using Your Nicolet iS10 Spectrometer Thermo Fisher Scientific

Dangerous contaminants
Biohazards or radioactive materials and infectious agents:
Instruments, accessories, components or other associated materials may not be returned to
us or other accessory manufacturers if they are contaminated with biohazard or radioactive
materials, infectious agents, or any other materials and/or conditions that could constitute a
health or injury hazard to employees. Contact us if you have questions about decontamination
requirements.
Using liquid nitrogen
Some detectors must be cooled with liquid nitrogen before use. The following symbols remind
you to wear protective clothing when using liquid nitrogen.
Warning: Liquid nitrogen is extremely cold and therefore potentially hazardous. When
filling the detector dewar, be careful not to contact the liquid nitrogen with your skin. Wear
protective gloves and splash-proof goggles and follow standard laboratory safety practices.
Warning: To avoid hazardous equipment damage or contact with liquid nitrogen, make
sure any dewar or container you use to hold liquid nitrogen can do so safely without breaking.
Using corrosives and solvents
Caustic or corrosive agents:
Instrument components may be degraded by exposure to caustic or corrosive agents or their
vapors. Materials such as hydrochloric acid and hydrofluoric acid are particularly corrosive and
may accelerate the degradation of the metallic components in your instrument. Damage can
also occur if the concentration level of corrosive gasses in the air is excessively high due to
improper sampling techniques.
To maintain the instrument in safe working condition, do not use caustic agents, such as
acetone or chlorinated solvents, when cleaning or operating your instrument. Damage to the
instrument caused by the use of caustic agents is not covered by the warranty.
Volatile solvents:
You can use your instrument to analyze samples dissolved in solvents, but you must follow the
guidelines listed below. These measures will help prolong the life of your instrument and will
eliminate the possibility of spectral interference caused by volatile solvent vapors.
Thermo Fisher Scientific Using Your Nicolet iS10 Spectrometer 7

–—Use sealed sample holders.
–—Do not leave exposed solvent in the sample compartment for longer than necessary.
–—Do not leave the solvents near the instrument.
–—Be sure that your work space is properly ventilated.
Solvents containing halogenated hydrocarbons:
The pyrolysis of chlorinated solvents, perfluorochlorinated solvents, and other solvents by an
infrared source or by excessive heating caused by laser absorption may produce hydrochloric
acid (HCl), hydrofluoric acid (HF), phosgene (COCl2), or other hazardous compounds.
Warning: Materials such as hydrochloric acid, hydrofluoric acid and phosgene are highly
toxic. If you regularly use solvents containing halogenated hydrocarbons, your work area must
be properly ventilated, and your system must be purged while the solvents are in use.
Damage to your system due to pyrolysis of halogenated hydrocarbons and/or exposure to
other corrosive or caustic agents is not covered by the warranty.
Checking the power supply
Danger: Your instrument is powered by an external power supply that accepts a variety of
AC power sources and adjusts automatically to maintain a consistent VDC output. To avoid
injury, only a qualified person using the appropriate measuring device should check the line
voltage, current and frequency.
8 Using Your Nicolet iS10 Spectrometer Thermo Fisher Scientific

Operation
Turning the power on and off
To turn the system power on or off, press the power switch on the power supply.
Installing a Smart Accessory
To install a Smart Accessory™ in the sample compartment, lower the accessory into the
sample compartment and press gently downward until the accessory locks in place. Then
rotate the stabilizer arm (located on the top of the instrument at the back edge of the sample
compartment) so that it holds down the accessory.
Note: If you want to remove a Smart Accessory, simply reverse the steps in this procedure.
When you are not using an accessory, store it in a dust-free environment like a cabinet or box.
Note: For information about installing other kinds of accessories, see "Installing other
accessories".
Collecting data with the instrument
For information about collecting data with your instrument, please see the getting started
manual that came with the instrument.
Collecting data with the module
You must use OMNIC to collect data. OMNIC can be started by using the OMNIC shortcut on
your system desktop. For additional information, please see the OMNIC help (available
through the Help menu in OMNIC) or the printed documentation that came with the system
microscope or spectrometer.
Thermo Fisher Scientific Using Your Nicolet iS10 Spectrometer 9

Setting the purge gas controls
You must connect a source of purge gas (dry air or nitrogen) to purge your instrument of
moisture and other environmental contaminants. For best results the purge gas should be
dried to a dew point of -70 degrees C (-94 degrees F) or below. Use the following instructions
to set the purge gas controls.
Notice: 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 under the warranty. If you have questions about this requirement, please contact
us.
Warning: Never use a flammable gas to purge your instrument. The purge gas must be
free of moisture, oil, carbon dioxide and other reactive or infrared-absorbing materials. To
prevent laser damage, use only dried air or nitrogen to purge your instrument.
1.—Open the shutoff valve.
2.—Adjust the pressure regulator until the gauge indicates that the pressure is between 0.7
and 1.4 bar (70 to 140 kPa, or 10 to 20 psig).
10 Using Your Nicolet iS10 Spectrometer Thermo Fisher Scientific

Notice: Flow rates greater than 10 scfh can cause vibration that can affect data quality. We
recommend keeping the flow rate at approximately 10 scfh.
3.—Set the flowmeter to 10 scfh.
Aligning your spectrometer
Your instrument can be aligned automatically using OMNIC. To align your instrument, use the
Align button on the Diagnostic tab of the Experiment Setup dialog box (which is available
through the Collect menu in OMNIC). For more information, refer to the electronic software
help for OMNIC.
Cooling a detector
If you have an MCT detector, you must cool it with liquid nitrogen before you can collect data.
Time needed: 40 minutes or less
Tools needed: Protective clothing and eyewear
A small plastic laboratory funnel
A one-liter, metal vacuum bottle
Liquid nitrogen
Note: A detector dewar should maintain its insulating vacuum for several years. If the
vacuum leaks, the insulation will lose effectiveness.
Note: Your MCT detector, when cooled according to the following procedure, should remain
cool for approximately six hours.
Thermo Fisher Scientific Using Your Nicolet iS10 Spectrometer 11

Warning: Liquid nitrogen is extremely cold and can be hazardous. When you use liquid
nitrogen, always follow standard laboratory safety practices, and make sure your dewar is
made to use with liquid nitrogen. Wear protective clothing and eyewear, and avoid letting
liquid nitrogen come into contact with your skin.
1.—Open the detector dewar cover and remove the plastic stopper from the dewar.
Warning: Make sure you pour the liquid nitrogen slowly when you fill the vacuum bottle or
the detector dewar. Pouring too quickly can cause liquid nitrogen spray out. Wear protective
clothing and eyewear, and follow standard laboratory safety practices to prevent injury.
2.—Fill the metal vacuum bottle with liquid nitrogen.
Notice: Do not spill liquid nitrogen on or near the detector window. If the window’s O-ring
seal is cooled very rapidly, the dewar may lose its vacuum and expose the detector element to
damaging atmospheric pressure.
3.—Insert the funnel into the detector dewar, and pour the liquid nitrogen slowly into the
funnel. (A small amount of liquid nitrogen typically spills out of the funnel. This will not
harm your instrument.)
Fill the funnel and then let it drain completely two or three times. Wait until the vapor
plume disappears and then repeat until the dewar is filled.
12 Using Your Nicolet iS10 Spectrometer Thermo Fisher Scientific

4.—Remove the funnel.
5.—Wait until the vapor plume disappears, and then replace the plastic stopper and close the
dewar cover.
6.—Wait 20 minutes, and then repeat the preceding steps to make sure the dewar is
completely filled.
Thermo Fisher Scientific Using Your Nicolet iS10 Spectrometer 13

Service
Installing or replacing hardware
Installing a purge kit
Purging your instrument protects the internal components from moisture and other
environmental contaminants by maintaining an internal atmosphere of dry air or nitrogen. If
your instrument is not already equipped to purge, you must install a purge kit. To install a
purge kit, use the following procedure.
Notice: 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 under the warranty. If you have questions about this requirement, please contact
us.
Time needed: 30 minutes or less
Tools needed: A 3/4 inch open-ended wrench
An 11/16 inch open-ended wrench
A shutoff valve (with a 1/4 inch male or 3/8 inch female fitting)
Pipe tape
Note: To order parts, contact us.
Note: For best results the purge gas should be dried to a dew point of -70 degrees C
(-94 degrees F) or below.
Warning: Never use a flammable gas to purge your instrument. The purge gas must be
free of moisture, oil, carbon dioxide and other reactive or infrared-absorbing materials. To
prevent laser damage, use only dried air or nitrogen to purge your instrument.
1.—Install a shutoff valve and either a 1/4 inch male fitting or a 3/8 inch female fitting on the
purge gas source. (Choose a shutoff valve and fittings that are appropriate for the purge
gas source.)
14 Using Your Nicolet iS10 Spectrometer Thermo Fisher Scientific

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 that was included with your purge kit. Wrap the reducing nipple with
Teflon pipe tape before you install it, and use an 11/16 inch open-ended wrench to tighten
the connection.
3.—Wrap the reducing nipple or the 1/4 inch male fitting with Teflon pipe tape, and then
install the pressure coupling. Use a 3/4 inch open-ended wrench to tighten the connection.
Thermo Fisher Scientific Using Your Nicolet iS10 Spectrometer 15

4.—Install the purge filter, pressure regulator and flowmeter, and then snap the assembly into
the pressure coupling.
5.—Connect the purge kit to your instrument, set the purge gas controls, and then snap the
flow coupler into the back of the instrument.
16 Using Your Nicolet iS10 Spectrometer Thermo Fisher Scientific