ThermoFisher Scientific iS20 with OMNIC User manual

iS20 with OMNIC
Paradigm software
FTIRSpectrometer
USER GUIDE
269-3627 00 Revision A July 2023

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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.
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Table of contents
Table of contents 3
Conventions used 5
Contacting us 6
Operation 7
Turning the power on and off 7
Indicators and buttons 8
Installing a Smart Accessory 9
Measuring data with the instrument 10
Measuring data with the module 10
Setting the purge gas controls 11
Aligning your spectrometer 14
Verifying the laser frequency 14
Cooling a detector 15
Installing or replacing hardware 18
Installing a purge kit 18
Installing a sample compartment extension kit 21
Installing baseplate-mounted accessories 23
Installing slide-mounted accessories 23
Installing other accessories 25
Replacing the power supply 25
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Table of contents

Table of contents
Changing the source 28
Installing sidewall adapters 31
Maintaining your instrument 32
Cleaning your instrument 32
Static electricity precautions 32
Maintaining detector dewar 33
Checking the humidity indicator 34
Replacing the humidity indicator 35
Replacing the desiccant 37
Regenerating the desiccant 39
Checking and changing the purge gas filter 40
Troubleshooting 44
Instrument problems 44
Error messages 48
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Conventions used
Safety precautions and other important information use the following format:
DANGER
Avoid hazard. Indicates a hazardous situation which, if not avoided, will
result in serious injury or death.
WARNING
Avoid hazard. Indicates a hazardous situation which, if not avoided,
could result in serious injury or death.
CAUTION
Avoid hazard. 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.
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Conventions used

Contacting us
Contacting us
For Technical Support, please contact us.
If you have problems with your system, refer to the Troubleshooting information for help, or call
Technical Support.
Ordering parts
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.
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Operation
The Thermo Scientific™ Nicolet™ iS20™ spectrometer has integrated validation features, a powerful
software suite, and many other features that make it easy for you to collect data. This document
contains detailed information about performing such procedures.
Turning the power on and off
To turn the system power on or off, press the power switch on the power supply.
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Operation

Operation
Indicators and buttons
The status indicators for the instrument are located on the touch panel, which is on the main cover of
the instrument. The panel also has buttons that allow you to operate the instrument.
Note With the release of OMNIC Paradigm software, functionality of the Background, Sample,
Workflow, and Stop buttons has been streamlined into the OK/Enter button. As such, some of the
following definitions are meant for older OMNIC software and are now superseded by the
OK/Enter button. The same functionality can also be achieved directly from OMNIC Paradigm
software.
For more information, see "Collecting a spectrum" in the iS20 for Paradigm Getting Started guide
as well as the latest OMNIC Paradigm User Guide in the Thermo Fisher Knowledge Base.
Figure 1-1: iS20 Touch Panel
A
Background button. Acquires a background spectrum, which shows the
response of the instrument when no sample is present. (OMNIC software
only.)
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B
Sample button. Measures the current sample installed in the instrument
sample compartment. The sample data is ratioed with the background data,
which leaves only the signals from the sample. (OMNIC software only.)
C
Workflow button. Can be used to assign a software workflow (macro) to the
touch panel for automated operations with the instrument. (OMNIC software
only.)
DStop button. Can be used to cancel a message box displayed in OMNIC
software. (OMNIC software only.)
EOK/Enter button. Can be used to confirm a message box displayed in OMNIC
software.
FHumidity indicator.The humidity indicator monitors the level of humidity inside the
spectrometer. The status is indicated by the color of the indicator.
G
Scan bar. Provides instrument status information. Scan states:
lSolid-pulsing green light: Instrument is ready for use.
lMoving green light: Data collection is in progress.
lSolid-pulsing yellow light: Scheduled maintenance required.
lQuick-pulsing red light: Instrument requires attention. Check status in OMNIC
Paradigm software.
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
accessory lock (located on the top of the instrument at the back edge of the sample compartment) so
that it holds down the accessory.
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Operation

Operation
Figure 1-1: Install transmission 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 box or cabinet. For
information about installing other kinds of accessories, see Installing other accessories
Measuring data with the instrument
For information about measuring data with your instrument, please see the Nicolet iS20 for
Paradigm Getting Started guide.
Measuring data with the module
You must use Thermo Scientific™ OMNIC Paradigm software™ to measure data. OMNIC Paradigm
software can be started by using the OMNIC Paradigm shortcut on your system desktop. For
additional information, please consult the associated documentation or our knowledge base at
https://knowledge1.thermofisher.com/.
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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 °C (-94 °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.
CAUTION
Avoid hazard. Never use a flammable gas to purge your instrument. The
purge gas must be free of moisture, oil, carbon dioxide, and other react-
ive or infrared-absorbing materials. To prevent laser damage, use only
dry air or nitrogen to purge your instrument.
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Operation

Operation
1. Open the shutoff valve.
Figure 1-1: Open purge 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).
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Figure 1-2: Adjust purge pressure
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.
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Operation

Operation
Figure 1-3: Set purge flowmeter
Aligning your spectrometer
Your instrument can be aligned automatically using OMNIC Paradigm 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.
Note The instrument is aligned automatically each time you run a performance verification (PV)
test. We recommend running a PV test at least once a month.
To align the spectrometer, go to Acquire Data>Diagnostics > Align Spectrometer in OMNIC
Paradigm software.
Verifying the laser frequency
For optimum system performance, verify the laser frequency according to the following schedule:
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Spectrometer
environment Spectrometer state Recommended Schedule
Stable Always powered on Every 3 months
Unstable (e.g.,
temperature or humidity
constantly changing)
Powered on and off
frequently
Every day or once a
week
Note The laser is verified automatically each time you run a PV test. We recommend running a PV
test at least once a month.
❖ To verify the laser frequency and calibrate the laser
1. In OMNIC Paradigm software, go to Acquire Data > Diagnostics > Laser Calibration.
2. In the Laser Calibration dialog box, select Start to calibrate the laser.
When the system is finished, a message indicates whether the frequency was changed and
displays the new frequency.
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:
lProtective clothing and eye wear
lA small plastic laboratory funnel
lA one-liter, metal vacuum bottle
lLiquid nitrogen
Note A detector dewar should maintain its insulating vacuum for several years. If the vacuum
leaks, the insulation will lose effectiveness.
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Operation

Operation
WARNING
Avoid freeze burn hazard.Liquid nitrogen is extremely cold and
potentially hazardous. 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 to spray out.
To prevent injury, always follow standard laboratory safety practices and
wear protective clothing and eyewear when you use liquid nitrogen.
Avoid letting liquid nitrogen come into contact with your skin.
1. Open the detector dewar cover and remove the plastic stopper from the dewar.
Figure 1-1: Open detector dewar
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 cools 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.
4. Fill the funnel and let it drain completely two or three times. Wait until the vapor plume disappears
and then repeat until the dewar is filled.
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Figure 1-2: Filling detector dewar
5. Remove the funnel.
6. Wait until the vapor plume disappears, and then replace the plastic stopper and close the dewar
cover.
7. Wait 20 minutes, and then repeat the preceding steps to make sure the dewar is completely filled.
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Operation

Installing or replacing hardware
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.
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:
lA 3/4 inch open-ended wrench
lAn 11/16 inch open-ended wrench
lA shutoff valve with a 1/4 inch male or 3/8 inch female fitting
lPipe tape
Note For best results, the purge gas should be dried to a dew point of -70 °C (-94 °F) or below. To
order parts, contact us.
WARNING
Avoid hazard. Never use flammable gas to purge your instrument. The
purge gas must be free of moisture, oil, carbon dioxide, or infrared-
absorbing materials. To prevent laser damage, use only dry air or nitro-
gen to purge your instrument.
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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.)
Figure 1-1: Purge shutoff valve
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.
Figure 1-2: Purge-reducing nipple
3. Wrap the reducing nipple or the 1/4 inch male fitting with Teflon pipe tape, then install the
pressure coupling. Use a 3/4-inch, open-ended wrench to tighten the connection.
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Installing or replacing hardware

Installing or replacing hardware
Figure 1-3: Connect pressure coupler
4. Install the purge filter, pressure regulator and flow meter, and snap the assembly into the
pressure coupling.
Figure 1-4: Connect purge
5. Connect the purge kit to your instrument, set the purge gas controls, and snap the flow coupler
into the back of the instrument.
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