Extrel Mass Spectrometry Lab 1

Extrel Mass Spectrometry Lab 1
Getting to Know Your Mass Spec
A mass spectrometer is a gas analyzer. Gaseous
mixtures are introduced to a mass spectrometer,
ionized, filtered based on mass to charge ratios,
and detected. This lab will focus on identifying
and understanding the components of a mass
spectrometer, experimental setup, and basic
data interpretation.
Greg Thier Extrel CMS Pittsburgh, PA
Introduction
There are four main components of a mass spectrometer.
• Sample Inlet
• Ionization Source
• Mass Filter
• Detector
The ionization source, mass filter, and detector are all enclosed in a vacuum chamber. The IQ-2000, an example of a quadrupole mass spectrometer is shown in the image bank to the right.
A sample inlet is responsible for bringing gas into the analyzer. The IQ2000 should be configured for this lab with a 30µm fused silica line running between analysis sample and vacuum chamber. This acts as a very
slight “leak” allowing small amounts of gas to pass into the vacuum
chamber for analysis.
An ionization source is needed to apply a charge to gas particles, creating ions. The ionization source found in the IQ-2000 utilizes electron ionization for this process. Gas enters the ionization source, which features
two yttria coated iridium filaments. Current is run through these filaments causing them to become very hot and emit electrons. Electrons
are propelled from the filament using a voltage bias (giving the electrons
kinetic energy) towards our gas molecules. If the kinetic energy in these
electrons is high enough to electrostatically repel and electron from a
The capillary inlet configuration for the IQ-2000 vacuum chamber and internal
components.
gas molecule, ionization occurs. An ion is a molecule that has a different
number of electrons and protons, leaving it with an overall charge. Gas
particles can be given different charges, depending on how many electrons are lost in this process. These charges (and mass of a gas particle)
will be used to describe an ion’s “mass-to-charge ratio.” The IQ-2000
ionizer also features several lenses (disc-shaped metal plates with applied voltages) that are used to accelerate and focus ions towards the
mass filter. A diagram of our ionizer is shown in the figure above:
The mass filter is responsible for separating ions of different masses (using mass/charge ratios). The IQ-2000 features a quadrupole mass filter.
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A quadrupole is four parallel conductive rods (9.5mm in diameter, approximately 20cm long) with wiring connecting opposite rods. A quadrupole mass filter uses a combination of RF (radio frequency) and DC (direct current) voltages, ramping in magnitude, to “guide” ions towards a
detector. Particular voltage magnitude allows ions of specific mass-tocharge ratios to pass to the detector. Lower voltage magnitudes correspond to lower mass-to-charge ratio ions and higher voltage magnitudes correspond to higher mass-to-charge ratio ions.
Understanding Vacuum Systems
Mass spectrometers need to operate in vacuum systems for two reasons. First, ion-ion interactions need to be limited. Second, the possibility for arcing between high voltage components needs to be minimized.
A detector measures ion current exiting a mass filter. The IQ-2000 uses
a continuous diode electron multiplier detector, featuring a conversion
dynode. In normal operating mode (positive ion detection using a conversion dynode), ions are attracted to the high potential (typically ~
-5kV) of the conversion dynode. Upon striking the dynode, electrons are
ejected from this abundant source and attracted to the electron multiplier. The electrons will strike the wall of this electron multiplier tube several times, each time emitting more electrons. This creates a cascade
effect, and a multitude of electrons are generating ion current from each
ion reaching the detector.
Pre-Lab Questions
This is because at low enough pressures, there are not enough gas
In-Depth Study Questions
is called the “Paschen Law.”
The mean free path of a gas particle is defined as the distance a particle will travel before in interacts with another particle. Lower pressures
yield lower gas densities, increasing the mean free path distance. Increasing this distance can reduce any ion-ion interactions to the point
of negligibility. Additionally, lowering the gas density avoids electrical gas breakdown.
At low enough pressures, high voltages can be placed on a conductor
sitting very close to another conductor without breakdown or “arcing.”
particles to conduct electricity. This phenomenon is dictated by what
1. Why is it important to have the sample inlet tubing diameter very
small?
2. What characteristic of the chamber may cause arcing between the internal components?
3. Why is it necessary to create “ions” before attempting to filter and detect gases?
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Background
The mass spectrometer vacuum system must be at very low pressures
(< 1 x10-5 Torr range) before turning the electronics on. The IQ-2000
uses a two-stage pumping system. There is a small diaphragm pump
connected to the cart. This provides the first stage of vacuum, or a
“rough” vacuum. For this reason, this pump is often referred to as the
“roughing” pump. Connected to the chamber is a turbo molecular
pump. This pump will pull the chamber down to operating vacuum.
The electronics module controlling the IQ-2000 is referred to as the
“5221 card cage.” See diagram below:
The 5221 card cage has several necessary connections.
The processor board supplies the instrument to the PC for instrument
control, has a connection for signal coming out of the detector, and has
a vacuum interlock safety function.
The filament supply supplies our filament current and bias voltage and
has the ability to control a heater (not featured on the IQ-2000).
The Pole DC board supplies the DC voltage for the quadrupole.
The baseboard reads our vacuum chamber pressure from an ion
gauge, and has the ability to command a variety of input/output signals
(not featured on the IQ-2000).
The multiplier supply supplies the multiplier voltage in positive ion
mode (connection J18) and negative ion mode (connection J16 – not featured on the IQ-2000).
The dynode supply supplies the high voltage for the conversion dynode.
The optics supply supplies the specified lens voltages for the ionizer.
The optics raw supply provides the raw +/-120V and +/-430V voltages
for the optics supply.
Diagram of 5221 card cage. For detailed description of each electronics board
see MANUAL
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Activity
Extrel MAX-CS control electronics
Using the diagram above, fill in the table with each connection’s corresponding function.
Function
Diagram Number
Quadrupole Controller DC Supply
1
Filament Voltage and current
2
Preamplifier
3
Software Ethernet
Communication
4
Software USB Communication
5
Multiplier (+) Voltage Supply
6
Multiplier (-) Voltage Supply
7
Ion Gauge
8
Optics Voltage Outputs
9
Dynode Voltage Supply
10
Vacuum Interlock Connection
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Connected to the vacuum chamber and wired to the 5221 card cage is
an ion gauge. The ion gauge uses a hot filament to ionize the residual
gas in the vacuum chamber and the collects and neutralizes the ion created. The current created at the collector is used to calculate the pressure. Note: Pressure readings can change for different gases due to
the difference in ionization characteristics. This hot filament gauge is
called a Bayard-Alpert gauge. (IMAGE)
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Wired to both the 5221 card cage and the vacuum chamber is a quadrupole controller or “QC.” The QC is connected to the Pole DC Supply on
the 5221 card cage. The QC takes the DC voltage and adds RF voltage,
sending both of these to the quadrupole. (IMAGE) Before collecting
data, if the system has been off and/or vented for a long time ( >1 day),
or if the vacuum chamber hardware has been changed and/or cleaned,
the QC needs to be resonated. Resonating the QC will optimize the voltages going to the quadrupole so that maximum voltages may be
achieved. The “oscillator status” on the QC will show if the commanded
scan cannot be achieved in the current resonance state of the QC. [For
more information on resonating the QC, see MANUAL].
1. Turn on the switch labeled “Main Power” located on the back of the
instrument cart. There are two status LEDs on the side of the turbo
pump. These LEDs will blink while the bearings in the turbo pump are
accelerating and stay constant once the bearings have reached maximum speed. Note that the turbo pump will only begin to spin up to
speed after a delay as the roughing pump pulls the chamber pressure
down. (If the turbo pump LEDs do not remain constant, see MANUAL)
2. Allow the system to pump for approximately five minutes, and then
turn on the switch labeled “Electronics.” After approximately one minute, the green “ready” LED on the processor board should come on.
At this point, the electronics are ready to connect to the software.
Lastly, wired to the processor module and the multiplier detector is a
preamplifier. The preamplifier (or “preamp”) takes ion current, sends it
through a gain resistor, and converts is to a signal voltage that can be
read by the software. This voltage will give m/z signals, or “peaks.” (IMAGE)
When the filaments are turned on, we begin heating the iridium wire and
emitting both electrons and photons. The emitted photons cause the filament to “glow” and can be seen through the glass chamber walls. Electron emission is the emission of electrons induced by an electrostatic
field, or the amount of electrons flowing off the filaments. This is measure in milliamps (mA). The electron emission can be read in the Merlin
software in the tune window (IMAGE) under FIL_ON, em_cmd, “emission meter.”
Experimental
Part 1 – System Startup
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4. Double click the “Merlin Automation Data System” shortcut. This will
open up the software package to control the instrument. The default
view for Merlin Automation shows four windows: prof (profile), pict
(picture), list (list), and cent (centroid). You should see a baseline
around 100mV in the profile window (displayed in the top-right corner
of the window. To change the windows viewed in the software, click
the “select views” tool (IMAGE). More software details and exploration will be in lab 2.
5. Open the tune window by clicking the tune tool (IMAGE).
6. In the tune window, highlight “System_Voltages” and click the “on”
Boolean. You should now be able to see several LEDs on you 5221
card cage, as well as a light on the QC.
7. Highlight IG_ON in the tune window and click the “on” Boolean. You
can now check the vacuum system pressure by highlighting “Pressure” and clicking the Update box. NOTE: In order to see a real “readback” in the tune window, you must highlight the particular reading
you need and click the update box.
8. If the pressure is below 10-5 Torr, the filaments can be safely turned
on.
9. Highlight FIL_ON and click the “on” Boolean. The filament in the ionizer assembly should now be able to be seen glowing.
NOTE: By expanding the FIL_ON selection in the tune window, several settings and read-backs can be found. For information on different settings see MANUAL.
10.The multiplier and dynode can now be turned on. Highlight Dynode_On and click the “on” Boolean. Highlight the Multiplier_On and
click the “on” Boolean.
Part - Tuning
11.The instrument will first be tuned to air signals. Make sure the “T” fitting at the end of the sample inlet is open to room air. NOTE: When
tuning, it is important to keep the multiplier detector from becoming
saturated. The bar at the right side of the profile window shows the
level of saturation. Numerically, the detector saturates at 10V. If the
detector becomes saturated, lower the voltage by expanding Multiplier_On, highlighting Multiplier_Voltage, and using the Up/Down arrows to adjust the voltage applied to the multiplier.
Regions of Stability and the effect of Delta-Res and Delta-M on scan line
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12.The instrument first needs to be “hardware tuned.” Using the following guide, hardware tune the instrument until nitrogen and oxygen
signals are shown approximately 1 unit wide, at m/z 28 and 32, respectively.
Each ion will have a “region of stability” depending on the combination
of RF and DC voltages applied, these regions are the triangular shapes
on the graph. The goal is to get a scan line like the one shown in black,
for independent, resolved peaks at every mass along the spectra. Adjusting the hardware (DeltaM and DeltaRes) will affect this scan line according to the graph.
DeltaM / DeltaRes:
Clockwise – Peaks narrow, decrease in height, and move to higher
mass
CounterClockwise – Peaks broaden, increase in height, move to lower
mass
(DeltaM affects low mass resolution more than higher mass resolution,
DeltaRes affects higher masses more than lower masses. )Mass Cal:
High mass gross position DIP switches – “On” moves peaks to lower
mass
Fine Mass Cal: High mass fine mass cal
Linearize offset: Low mass peak resolution and position
DeltaM and DeltaRes adjustments are found on the Pole DC Board
Other tuning parameters are found inside the access panel of the QC
13.Gross lens tuning is done by switching the quadrupole into RF_Only
mode to remove any DC filtering voltage. Highlight quadrupole_1
and select the box next to RF_Only mode. NOTE: Without
14.Move the voltages of the four ionizer lenses (Ion Region, Extractor
lens, Lens 1, and Lens 2) up and down until maximum signal is observed in the profile window.
15.Fine tuning is completed the same way as gross tuning except with
DC filtering voltage. Turn off RF_Only mode and continue tuning,
making smaller voltage adjustments. The peaks should become symmetrical, with noise reduced to a minimum.
Additional software tuning can be adjusted by clicking quadrupole_1
and selecting calibrate. For more advanced tuning adjustments, see
MANUAL.
Part 3 – Leak Checking
16.It is very important for a mass spectrometer to be free of air leaks.
Leak checking the instrument will be done with helium. Before leak
checking, be sure the instrument is tuned properly so that a helium
signal is visible. Change the scan range to m/z 2 to 6.
17.Spray helium into the “T” fitting of the sample inlet. Be sure you can
see a helium peak at m/z 4. If not, the instrument will need to be
tuned more before proceeding.
18.Secure the pFTBA bulb assembly to the end of the sample inlet.
19.Open the toggle valve on the pFTBA bulb assembly.
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20.Spray helium around each fitting of the sample inlet and each potential spot for leaks around the chamber. A leak is found if the helium
signal reappears while spraying the gas around a sealed instrument.
If leaks are found, the fitting, bolt, or adjustment at the leak needs to
be carefully tightened.
22. After you are done tuning the instrument, save your tune file. Use
the following format “YYYYMMDD_[YOURNAME]_Tune.” For example, if John Smith tuned the instrument on January 1, 2015, the tune
file would be named “20150101_JohnSmith_Tune.” The tune files are
saved on the computer under C:\Merlin Automation\tune.
23.The instrument can now be turned off. Start by opening the tune window, and turning the filaments off.
24.Turn the ion gauge off.
25.Turn the system voltages off.
26.Wait for approximately 2 minutes, then turn the main power off.
Thought Questions
Post-Lab Questions
In-Depth Analysis Questions
Caption...
1. Using the cutaway diagram shown below, label the following 4 main
components of the mass spectrometer. Note that the electronics and
data system are not pictured.
A. Sample Inlet
Part 4 – Additional Tuning
B. Ionizer
21.pFTBA is widely used as a mass spectrometer tuning and calibrating
sample because it provides well-known signals over a wide mass
range. With the pFTBA bulb attached and opened, continue to tune
the instrument until a spectrum is obtained showing signals that correspond with the attached peaks. (ATTACH pFTBA Spectrum).
C.Mass Filter
D.Detector
2. On the cutaway diagram shown below, where is the vacuum chamber?
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3. What do you think might stop the turbo pump LEDs from staying solidly lit?
4. When a QC is not properly resonated, would you expect to lose low
mass signal or high mass signal?
5. If you lower the filament emission (em_cmd) in the software from
3.0mA to 1.0mA, what do you think will happen to the “glow” of the
filament? What happens to the intensity of the singals? Try it!
6. Why are electrons emitted from the conversion dynode attracted to a
multiplier with a -1kV potential on it?
7. Knowing that air is composed mainly of nitrogen, oxygen, argon, and
carbon dioxide, what masses did you observe corresponding to
each air component?
8. What component corresponds to a peak at m/z 18?
9. What component corresponds to a peak at m/z 14?
10.What do you think would cause two components with equal partial
pressures to have different intensity peaks on the mass spectrum?
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