Varian 4000 MS User manual

Varian, Inc.
2700 Mitchell Drive
Walnut Creek, CA 94598-1675/USA
©Varian, Inc. 2004-2009 Printed in U.S.A. 03-954032-00:Rev. 4
4000 MS
4000 MS Users Guide
Internal Ionization
www.angeldans.com

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Contents
Overview of Internal Configuration.........................................................................................5
Scan Functions Control MS Processes ......................................................................................................................6
Steps to Create a Mass Spectrum..............................................................................................................................6
Sample Introduction .............................................................................................................................................6
Ionization ..............................................................................................................................................................6
Fragmentation ......................................................................................................................................................7
Ion Storage...........................................................................................................................................................7
Ion Preparation.....................................................................................................................................................7
Ion Analysis..........................................................................................................................................................7
About Internal Electron Ionization...............................................................................................................................7
Forming Ions ........................................................................................................................................................7
Ion Preparation Options .......................................................................................................................................8
Scanning Ions to Collect Mass Spectra ...............................................................................................................8
Library Searching and Data Handling ..................................................................................................................9
About Internal Chemical Ionization.............................................................................................................................9
Forming Reagent Ions..........................................................................................................................................9
Chemical Ionization Reactions in PCI................................................................................................................10
Ion Preparation Options .....................................................................................................................................10
Scanning Ions to Collect Mass Spectra .............................................................................................................11
Library Searching ...............................................................................................................................................11
Selectivity Considerations ........................................................................................................................................11
Type of Matrix ....................................................................................................................................................11
Using EI and PCI to Get More Information ........................................................................................................11
Conversion from External to Internal Configuration .................................................................................................12
Checklist.............................................................................................................................................................12
Conversion from Hybrid to Internal Configuration ....................................................................................................12
Outline ................................................................................................................................................................12
Effects of Hardware Configuration Changes......................................................................................................12
Starting the Instrument .............................................................................................................................................13
Initial Pump down...............................................................................................................................................13
Check the Vacuum Status..................................................................................................................................13
Diagnostic Tests.................................................................................................................................................14
Setting System Temperatures ...........................................................................................................................15
Analysis Temperatures................................................................................................................................15
System Bakeout...........................................................................................................................................15
Startup and Shutdown........................................................................................................................................16
Starting the System .....................................................................................................................................16
Shutting Down the System ..........................................................................................................................16
Adjustment and Tuning of the MS ............................................................................................................................16
Checks and Adjustments ...................................................................................................................................16
RF Tune.......................................................................................................................................................16
Adjusting the RF Ramp ...............................................................................................................................17
Adjusting the RF Ramp ...............................................................................................................................17
Adjusting the Calibration Gas ......................................................................................................................17
CI Gas Adjustment ......................................................................................................................................18

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Air/Water Check...........................................................................................................................................18
Setting Up CI Reagents............................................................................................................................................18
Installing a Liquid Reagent.................................................................................................................................19
Installing a Gaseous Reagent............................................................................................................................20
Auto Tune...........................................................................................................................................................20
Integrator Zero.............................................................................................................................................20
Set Electron Multiplier..................................................................................................................................20
Electron Lens Tuning...................................................................................................................................20
Ion Lens Tuning ...........................................................................................................................................21
RF Full Scale Adjust ....................................................................................................................................21
Mass Calibration..........................................................................................................................................21
Trap Frequency Calibration .........................................................................................................................21
Trap DC Offset Voltage ...............................................................................................................................21
Preparing an MS Method for Data Acquisition .........................................................................................................22
Building a New MS Method................................................................................................................................22
Name the Method ........................................................................................................................................24
Set the 4000 MS Instrument Configuration .................................................................................................24
Select the Acquisition Data Type.................................................................................................................25
Edit Chromatographic Time Segments .......................................................................................................25
Edit the 4000 MS Method Segments .................................................................................................................25
Scan Function Settings................................................................................................................................26
General Parameters Tab .............................................................................................................................26
Ionization Control.........................................................................................................................................27
EI Ionization Parameters .............................................................................................................................27
Setting Parameters for Chemical Ionization ................................................................................................28
Full Scan Parameters ..................................................................................................................................29
Setting Parameters for an MS/MS Method Segment ..................................................................................30
Viewing Method Parameters in Manual Control.................................................................................................31
Activating a Method .....................................................................................................................................31
Displaying Ions ............................................................................................................................................32
Viewing Method Parameters .......................................................................................................................33
Editing a Method in Manual Control ............................................................................................................33
Saving a Method..........................................................................................................................................35
Acquiring Data ..........................................................................................................................................................35
Acquisition ..........................................................................................................................................................35
Status and Control.......................................................................................................................................36
Activating a Method............................................................................................................................................37
Injecting a Single Sample...................................................................................................................................37
Injecting Using a SampleList..............................................................................................................................38
Monitoring the Status of Runs............................................................................................................................39

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Overview of Internal Configuration
The Internal configuration is one of the three operational configurations of the
4000 GC/MS system. In this configuration, it is possible to collect either electron
ionization or positive chemical ionization (EI or PCI) data. Unlike the External
Ionization configuration, it is possible to collect EI or PCI data during different
time segments of a single chromatographic acquisition. However, it is not
possible to collect Negative Chemical (NCI) data in Internal configuration. In
common with the other configurations, it is possible to perform ion preparation
techniques including Selected Ion Storage (SIS) or with optional software and
equipment, Tandem Mass Spectrometry: (Automated Methods Development
(AMD), MS/MS, MSn, and Multiple Reaction Monitoring (MRM). Refer to the 4000
GC/MS Software Operation Manual for on-line help information on setting up
these experiments.
The 4000 GC/MS analyzes the gas-phase ions formed from a sample in terms of
their mass-to-charge (m/z) ratios and their relative abundances in the resulting
spectra. The mass spectrum is a graphical representation of the ion intensities
versus the mass-to charge ratio.
The 4000 GC/MS creates the mass spectrum with an ion trap analyzer. The ion
trap confines the ions within a single region where time-dependent
electromagnetic fields control ion processes.
E.M.
Endcap
Ring Electrode
Transfer
Line Tip
Filament
Endcap
Filament
Electron Gate
Electron Multiplier
H.E.D.

6
Scan Functions Control MS Processes
Scan functions are programmable time sequences for applying voltages to the
external source, lens, and ion trap electrodes. The scan function controls the
variations in time of the RF potential applied to the ring electrode as well as any
supplementary waveforms applied to the endcap electrodes. The 4000 MS
module has two techniques, Electron Ionization (EI) and Chemical Ionization (CI),
for generating sample ions in the external source. Consequently, there are two
basic scan functions to perform electron ionization and chemical ionization (either
positive or negative). The diagram below illustrates the RF voltage profile of a
typical EI scan function. These scan functions are discussed in more detail in the
4000 GC/MS Software Operation Manual.
RF Voltage
Steps to Create a Mass Spectrum
Sample analysis with an ion trap analyzer may be divided into several steps:
Sample Introduction
Sample components are introduced from the transfer line to the ion trap analyzer
through the direct-coupled capillary column.
Ionization
The sample is ionized in the mass spectrometer by one of the following method:
•Electron Ionization (EI): The sample molecules are struck with energetic
electrons removing an electron from a molecular orbital, to create
molecular ion.
•Positive Chemical Ionization (PCI): A reagent gas is introduced in the ion
trap and EI is performed on that gas to form reagent ions. The reagent
ions then undergo ion-molecule reactions with the sample molecules to
create ions of the sample molecules and their fragments.

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Fragmentation
Depending on the structure of the molecular ion and the excess internal energy
remaining after electron impact, there may be further unimolecular decomposition
of some of the molecular ions to form various fragment ions and neutrals.
Unimolecular decomposition happens in picoseconds, the time scale of a few
molecular vibrations, effectively occurring at the same time as ionization.
Ion Storage
The molecular and fragment ions are stored and stabilized in the ion trap cavity,
where they travel in defined orbits governed by voltages applied between the ring
electrode and the endcap electrodes. Helium buffer gas is also present in the
cavity. It buffers the ions into more compact orbits that produce well-resolved
mass peaks as they are scanned out. Helium is used as a buffer gas because it
is light and does not degrade MS resolution. While helium ions are created in the
trap, they are ejected electronically as soon as they are formed.
Ion Preparation
Once ions are stored in the trap they can be manipulated, if desired. Examples of
ion preparation techniques are tandem mass spectrometry (MS/MS) and
selected ion storage (SIS). Advantages associated with ion preparation methods
are similar to those of other sample preparation methods, e.g., reduction of
background noise and increased selectivity.
Ion Analysis
The stored ions are analyzed by ramping the RF voltage applied to the ring
electrode to a high value, during which time ions from low to high mass are
successively destabilized and ejected from the trap. Supplemental dipole and
quadrupole voltages applied to the endcap electrodes improve the mass
resolution of the process. After ejection, the ions strike a conversion dynode,
initiating a signal multiplication process at the electron multiplier.
Each of the areas above is discussed in general in this guide, and in detail in the
4000 GC/MS Software Operation Manual.
About Internal Electron Ionization
Internal electron ionization is the most common mode of operation of the 4000
MS. All of the sample ionization, fragmentation, storage, and scanning steps
occur within the confines of the ion trap. Electron ionization generates fragments
that are specific to the compound, providing fingerprint spectra. It is, however,
not selective and will show ions for all compounds present. EI is sensitive but the
sensitivity can be improved by reducing the interfering ions using ion preparation
techniques.
Forming Ions
In the EI mode, electrons are gated into the ion trap cavity during the ionization
period. These electrons collide with the neutral sample (or Analyte) molecules A,
removing an additional electron to create energetically-excited molecular ions
∗+
A
. Some of the excited molecular ions equilibrate through collisions with

8
helium but others undergo unimolecular decomposition to create various
fragment ions, f
+
i.This set of fragment ions, characteristic of the sample
molecule, makes up the mass spectrum.
−
∗
+
−
+
→+
e
A
e
A
2
Ionization
∗
+
A
(
is excited
)
He
+∗+
→ AA
De-excitation
A →
∗+
11
nf +
+
Equilibration
→
22
nf +
+
→
3
3
n
f
+
+
Fragmentation
The ion trap has a maximum storage capacity beyond which mass resolution and
spectral quality deteriorate. The number of ions created depends on the
ionization time. As the ionization time increases, more ions are created.
Automatic Gain Control (AGC) controls the ionization time to always create an
optimum number of ions in the trap.
The AGC scan-function consists of a prescan and up to six analytical scan
segments. The number of ions detected in the prescan is used to calculate the
ionization time for the analytical scan.
Ion Preparation Options
The 4000 MS can use a combination of waveforms applied to ion trap electrodes
to isolate or remove specific ions once they have been formed and are stored in
the trap.
Options like Selected Ion Storage (SIS) and Tandem Mass Spectrometry
(MS/MS) can be performed on the ions stored in the ion trap before mass
analysis takes place. In SIS, resonant waveforms are applied to eject unwanted
ions within the stored mass range and fill the trap only with ions in the mass
range(s) of interest. In MS/MS, a parent ion is isolated and then dissociated by
energetic collisions with helium buffer gas to form product ions.
The Internal configuration can have SIS, MS/MS, MSn, and Multiple Reaction
Monitoring (MRM) as ion preparation options. SIS is included with all
instruments, while MS/MS, MSn, and MRM are available with the MS/MS option
installed.
Scanning Ions to Collect Mass Spectra
After ionization, trapping, and ion preparation steps, ions are scanned out of the
trap to the conversion dynode and electron multiplier. The ions are analyzed by
applying a radio frequency (RF) voltage to the ring electrode encircling the trap
cavity. As the voltage increases on the ring electrode, ions are sequentially
ejected from the trap according to their mass-to-charge ratio. Supplemental
waveform voltages are applied to the endcap electrodes during the analysis to
improve mass resolution and mass axis stability. Ions strike the conversion
dynode and then electrons are ejected from the conversion dynode, held at
-10 kV, and are repelled to the electron multiplier. The signal is amplified by ~105
by the electron multiplier and sent through an integrator to collect an intensity for
each m/z. MS data are stored as sets of ion-intensity pairs for each m/z over the
acquired mass range. A complete mass spectrum is stored for each analytical

9
scan. There are actually two types of mass scanning in internal EI. First there is a
prescan to count the number of ions formed in a short fixed ionization time. After
a calculation based on the prescan ion count, ions are formed for the ionization
time recommended by the AGC prescan algorithm and the analytical scan is
carried out. The analytical scan can be broken up into up to six segments and the
relative ionization times for the segments can be adjusted to meet tuning
requirements for methods such as those of the US EPA for the compounds
DFTPP and BFB.
Library Searching and Data Handling
The mass spectra collected from the MS are analyzed through Varian MS Data
Review. The identity of most compounds is determined by the comparison of the
collected spectrum with a reference library. The mass and intensity listing is
compared to results collected on other instruments. Such listings include the
NIST library, the Wiley MS library, and the PMW library. Each library has a
different focus, from pharmaceutical to environmental analysis. Custom libraries
can also be generated from results collected on the 4000 MS system.
About Internal Chemical Ionization
Chemical ionization (CI) provides mass spectral data that complement electron
ionization (EI) data for the analysis of complex compounds. The generation of
ions in chemical ionization is a two-step process. A CI reagent gas is introduced
into the ion trap analyzer. The reagent gas is ionized by EI. Then, the sample
molecules are ionized by ion-molecule reactions with the reagent gas ions.
CI is a softer ionization technique than EI. That is, CI imparts less energy to the
sample molecules than does EI. Thus, the ionized sample molecule undergoes
less fragmentation, and an ion indicative of the molecular weight is more likely to
be observed. In addition to molecular weight confirmation, CI mass spectra often
provide other significant structural information that may not be available from EI
mass spectra.
Forming Reagent Ions
In the first step, reagent gas ions are formed as the reagent gas is ionized by
interaction with electrons emitted by the filament. The ion trap operates in a
pulsed mode. The supply of reagent ions is created during the ionization pulse
and consumed during the reaction period to form analyte ions.
In internal mode, the CI reagent can be either liquid or gas. The most common
reagents are methane, methanol, acetonitrile, and isobutane.
Reagent ion formation can be a complex process. For example, when methane is
used as the reagent gas, reagent gas ions are formed as follows:
First, methane is ionized to form two primary ions:
−+•− +→+ e2CHeCH 44 )(
−−+− ++→+ HeCHeCH 34
These primary ions then react very rapidly to form predominantly the secondary
ions, :
++ 525 HCandCH

10
•++• +→+ 3544 CHCHCHCH )(
25243 HHCCHCH +→+ ++
Chemical Ionization Reactions in PCI
In the second step, the reagent gas ions react with sample molecules in the ion
trap to form sample ions. The four principal reactions between reagent gas ions
and sample molecules are as follows:
(A) Proton transfer: +
)RH( + M →(MH) ++ R
(B) Hydride abstraction: +
R+ M →[M-H] ++ RH
(C) Association: +
R+ M →(MR) +
(D) Charge transfer: +
R+ M →+ M+ R
where R+is the secondary reagent gas ion and M is the neutral sample molecule.
For methane CI, proton transfer (A) is the major reaction, and hydride abstraction
(B) is the next most often observed reaction. In both cases the resulting even-
electron ions are often relatively stable, and the observation of strong (M+1) or
(M-1) ions is possible even if the EI spectrum of the same component shows no
molecular ion. The exothermicity of the reactions determines the amount of
energy deposited; therefore the degree of fragmentation can be controlled by the
choice of a suitable CI reagent gas. The proton affinities of some common
reagent gases of this type, known as proton transfer agents or Bronsted acids,
range from 130 kcal/mol to 200 kcal/mol in the following order: methane, water,
isobutane, and ammonia (with ammonia resulting in the “softest” ionization).
Among the common liquid CI reagents, methanol has a proton affinity of 180.3
kcal/mol, while acetonitrile is 1862 kcal/mol. By choosing a suitable reagent gas,
you can obtain high specificity (i.e., less efficient detection of background or
matrix interferences compared to the analyte) as well as molecular weight
information for the compounds of interest.
Association reactions (C) typically have very low reaction rates, and the reaction
products require rapid collisional stabilization. The products of these association
reactions are called adduct ions because the reagent ion has been added to the
analyte. They are typically seen on the 4000 GC/MS in Internal configuration at
much lower abundance then the (M+1) ion, but when (M+29) and (M+41) adduct
ions are observed using methane, they are useful for verifying the molecular
weight.
The charge transfer reaction (D) produces a radical molecular ion (i.e., an ion
with an odd number of electrons) that dissociates quickly, giving EI-like spectra.
However, the energy deposited in the molecular ion and the resulting
fragmentation pattern does not depend on the electron energy of the ionizing
electrons.
Ion Preparation Options
The 4000 MS uses a combination of waveforms and RF to isolate, or remove,
specific ions after they are formed and are stored in the trap. Selected Ion
Storage (SIS) and Tandem Mass Spec (MS/MS) can be performed on the ions
stored in the ion trap before mass analysis takes place.

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Scanning Ions to Collect Mass Spectra
The scanning process for chemical ionization is similar to that for electron
ionization. After ionization, trapping, and ion preparation steps, ions are scanned
out to the conversion dynode and electron multiplier. Mass scanning is
implemented by increasing the RF voltage on the ring electrode; the mass
spectrum is collected in order from low to high mass over the user-designated
scan range. In positive modes, electrons are ejected from the conversion
dynode, held at -10,000 V, and repelled to the electron multiplier. In negative
mode, positive ions are ejected from the conversion dynode, held at +10,000 V,
and repelled toward the electron multiplier. The signal is amplified by ~105by the
electron multiplier and sent through an integrator to collect an intensity for each
m/z. MS data are stored as sets of ion-intensity pairs for each m/z over the
acquired mass range. A complete mass spectrum is stored for each analytical
scan. There is no prescan in internal PCI; the ionization time is calculated based
on the base peak intensity of the previous scan. Ions are formed for this
ionization time and the analytical scan is carried out.
Library Searching
The 4000 MS has small CI libraries generated using internal configuration ion
trap GC/MS systems. The libraries are organized by the CI reagent, which
include methane, methanol, and isobutane.
Selectivity Considerations
Type of Matrix
An advantage of chemical ionization is selectivity. In PCI, hydrocarbons have a
poor response in methane CI. It is easier to locate target compounds in a sample
contaminated with hydrocarbons using methane PCI than using EI. Because of
these selectivity considerations, the time spent to develop a method using the
different ionization and ion preparation options is well spent.
Using EI and PCI to Get More Information
Generating EI and CI data on a single sample gives both the ion-intensity
fingerprint information allowing library searching as well as the molecular weight
information to confirm species identification. Fatty acid methyl ester (FAME)
analysis is an example. Under EI conditions, the FAME fragmentation is
extensive and molecular ion intensity is weak. Using CI, the molecular weight is
obvious and the most intense ion is M+1.
Because the 4000 MS is able to switch between EI and CI in a single run, the
best analytical conditions can be used for a given compound.
NOTE: Wait several seconds to switch between EI and CI. The CI segment
should not be less than 60 seconds wide and the CI peak should be at least 20
seconds into the segment to allow CI reagent stabilization.

12
Conversion from External to Internal Configuration
Converting the 4000 MS from External to Internal configuration involves changing
both the ion source and the column position. The External ion source assembly is
removed from the trap assembly and replaced with the Internal ion source
assembly.
See the 4000 GC/MS Hardware Operation Manual for details.
Checklist
•Remove the analyzer from the MS manifold.
•Change the ion source to internal.
•Move the heat shield to the forward position.
•Add the filament adapter and connect the flex cable.
•Change the transfer line orientation.
•Change the transfer line tip.
•Cut the column to 7 mm.
•Change the transfer line switch to Internal/Hybrid.
•Replace the analyzer in the MS manifold.
Conversion from Hybrid to Internal Configuration
Changing from the Hybrid to Internal configuration only requires changing the ion
source. The column position and transfer line are already directed to the trap and
do not need to be adjusted.
Outline
1. Change the ion source.
2. Move the heat shield to the forward position.
3. Add the filament adapter and connect the flex cable.
Effects of Hardware Configuration Changes
After changing the configuration, for example from External to Internal
configuration, the following occurs when System Control is restarted.
1. System Control compares the current configuration stored in the current
Module Attributes with the configuration reported by the hardware.
2. If these do not match, the Module Attributes are updated (preset) to the
appropriate configuration. A similar process occurs for the default method
(Default.mth).
3. After making the hardware configuration change, new methods will have the
appropriate instrument configuration by default.
NOTE: Presetting the Module Attributes requires performing all Auto Tune
routines, because the prior Auto Tune results are invalid.

13
Starting the Instrument
Initial Pump down
Check the following:
•Check the Vacuum connections.
•Make sure the transfer line is in.
•Make sure the vent valve is fully closed.
•Make sure the column is not broken.
Turn on the power at the main power switch; the roughing pump should stop
gurgling after about 10 to 20 seconds.
If the pump continues to gurgle, then do the following.
1. Check that the analyzer assembly is seated properly on the manifold (there
should be no gaps).
2. Check that the transfer line is in.
3. Check that the vent valve is sealed.
Open System Control and the Startup/Shutdown page opens.
Check the Vacuum Status
The vacuum readings tell a lot about the state of the MS after pump down (and
during operation). Typical operating ranges for the 4000 MS in Internal mode are:
•Speed 100%
•Current 200 – 300 mAmps
•Power 9 – 13 Watts
•Ion Gauge Pressure < 20 μTorr
•Roughing Line < 50 mTorr
If the Pump Spin Speed does not steadily increase, there may be a leak in the
system. Large leaks are indicated by a turbo speed less than 100%. Small leaks
are indicated by an increase in the pump current after 100% is reached, or in the
ion gauge pressure, see “Diagnostics”. Small leaks are diagnosed by changes in
the ion gauge reading and can be pinpointed using the leak check section in the
method Service.mth. For more detail on troubleshooting leaks, see the
Troubleshooting section in the 4000 GC/MS Hardware Operation Manual.

14
Diagnostic Tests
Monitor the current state of the instrument using the Monitoring tab. Monitor the
vacuum system, the electron multiplier, the waveform system, temperatures, and
the ion source.
Perform hardware checks on the 4000 MS using the Diagnostics tab. For more
details on the diagnostic tests, seethe Diagnostics section in the 4000 MS Ion
Trap Software Operation Manual.

15
Setting System Temperatures
Analysis Temperatures
Analysis temperatures are sample dependant. The stability of the compounds
and their volatility affect the temperature choice. For species that are more
fragile, decrease the trap temperature. For example, to obtain molecular ion
information on saturated hydrocarbons, which have unstable molecular ions, set
the trap temperature to 80 °C. However for semi-volatile analysis set the trap
temperature to 220 °C so the heavy PAHs (benzo[ghi]perylene,
dibenz[a,h]anthracene and indeno[1,2,3-cd]pyrene) do not tail.
After changing the temperature setting, allow about one hour for the trap to reach
the new setting. After the setting is reached, allow about two hours for the trap to
stabilize. The temperature of the trap affects mass calibration, and therefore the
trap frequency calibration.
Set the transfer line temperature so there are no cold spot between the GC
column oven and the MS. This is typically about the maximum column
temperature (± 20 °C).
The manifold temperature (typically 50 °C) reduces the effect room temperature
variation may have on the system.
System Bakeout
To remove water adsorbed on the manifold while the 4000 MS was vented,
perform a Bakeout from the Temperatures tab in System Control.
Perform a system bakeout to remove chemical background after running
samples. After doing a bakeout to remove contamination, decrease the
temperature to the analytical temperature.
Typical bake-out settings are:
•Trap Temperature 230 °C
•Manifold Temperature 110 °C
•Transfer Line Temperature 280 °C
•Bakeout time 12 hr
NOTE: You can use shorter bakeout times.

16
NOTE: The transfer line temperature should not exceed the maximum isothermal
temperature limit of the column.
Startup and Shutdown
Starting the System
When the system is first turned on, System Control only operates in
Startup/Shutdown mode. During system startup, observe the increase in Pump
Spin Speed in the Operating Conditions field. The software is locked in the
Startup/Shutdown mode until the speed reaches 100%. You will also see the
temperature readings for heated zones begin to increase in the Operating
Conditions field.
NOTE: Failure to reach 100% pump speed in a reasonable time indicates a
vacuum leak and corrective action should be taken. For details, see the
appropriate Troubleshooting section in the 4000 GC/MS Hardware Operation
Manual.
Shutting Down the System
To shut down the 4000 MS, click the Shut Down button in the upper left corner
of the Startup/Shutdown dialog. The heaters will be turned off and the speed of
the turbo pump will be gradually reduced to 35% of full speed.
After the temperature zones have cooled below 80 °C, turn off the main power by
placing the switch at the rear of system into the OFF (down) position. Manually
vent the system for at least 5 minutes by opening the vent valve on the front
panel one full turn counterclockwise.
NOTE: Retract the transfer line before lifting the analyzer assembly from the
vacuum manifold. Failure to retract the transfer line can cause damage to the
transfer line tip and to the trap assembly.
Adjustment and Tuning of the MS
Checks and Adjustments
RF Tune
Adjust the RF tuning in the Checks and Adjustments tab dialog of Manual Control
after performing one of the following:
•Performing MS maintenance.

17
•Changing the analyzer assembly.
•Changing the MS configuration.
Adjusting the RF Ramp
Adjusting the RF Ramp
To adjust the RF ramp, do the following:
1. Click RF Ramp Adjustment in the Checks and Adjustments tab.
2. Click Start.
3. Use a flathead screwdriver to turn the RF Adjustment screw, inside the front
door of the 4000 MS, either clockwise or counterclockwise until the tuning
display shows a straight line and the intensity is at a minimum. The Status
Bar in the Adjustment Results field should be just below OK.
Adjusting the Calibration Gas
To adjust the calibration gas, do the following:
1. Check the flow of perfluorotributylamine (PFTBA or FC-43) calibration gas
before doing Auto Tune procedures.
2. Click Cal Gas Adjustment in the Checks and Adjustments tab in Manual
Control.
3. Turn the Cal Gas valve inside the front door of the 4000 MS either clockwise
to decrease the flow or counterclockwise to increase the flow. Adjust the flow
so that the status bar in the Adjustment Results field reads OK.

18
CI Gas Adjustment
Before performing chemical ionization, adjust the reagent gas pressure. The next
section explains the set up of the most common reagent gases.
Air/Water Check
Too high a pressure of air or water in the system because of an air leak or a
need to bake out the system will result in poor performance. This checking
routine gives advice on the levels of air and water.
NOTE: The Air/Water Check uses the electron multiplier voltage giving a 105
gain, not the manual setting. After replacing the electron multiplier, auto tune of
Electron Multiplier before performing the Air/Water Check.
Setting Up CI Reagents
Before running CI experiments, adjust the CI gas pressure.
To adjust the CI gas pressure, do the following:
1. Click the Checks and Adjustments tab of the Manual Control window.
2. Select CI Gas Adjustment. Select your CI reagent from the drop down box
in the Parameters section.
3. Click Start below the adjustments selection.
4. The criteria for adjusting the flow of CI reagent into the instrument are shown.
5. After completing this, you must perform a mass calibration and trap function
calibration before beginning your experiments.

19
Installing a Liquid Reagent
To connect a liquid reagent reservoir to the liquid reagent inlet block, do the
following:
1. Connect a liquid reagent reservoir containing the chosen liquid to the
liquid reagent inlet block.
2. Open the CI needle valve 6-7 turns clockwise.
3. Click CI Gas Adjustment to open the CI gas valve solenoids.
4. Allow the vapor flow from the reservoir to equilibrate. If, after several
minutes, there is not enough CI gas entering the trap, open the needle
valve (clockwise).
5. While observing the spectrum, use the Adjust CI Gas, and turn the CI
needle valve to increase or decrease the amount of reagent entering the
trap until the resolution between M and M+1 just starts to degrade.
Details for the three most common reagents can be found under the following
sections in the 4000 GC/MS Software Operation Manual: PCI with CH4, PCI with
CH3CN, and PCI with CH3OH.
Properly Adjusted Methanol Reagent Spectrum
Properly Adjusted Acetonitrile Reagent Spectrum
NOTE: For best results with acetonitrile, use a filament emission current of at
least 20 μA and maintain at least 50% valley between m/z 41 and m/z 42.

20
Installing a Gaseous Reagent
To install a gaseous reagent, do the following:
1. Connect the regulator of the gas cylinder to the back of the instrument using
a 4 mL/min restrictor.
2. See the 4000 MS Ion Trap Hardware Operation Manual for more details.
Auto Tune
Depending on your configuration and settings, you may not see all the available
Auto Tune routings. Perform auto tune after the instrument is first set up and
whenever significant maintenance operations are performed. Also, perform Mass
Calibration and Trap Frequency Calibration whenever the temperature or RF
adjustment is changed.
Auto Tune works the same way in either EI or Hybrid CI modes; you do not need
to run a different automatic setup, tuning, and calibration program for Hybrid CI.
Integrator Zero
Integrator Zero obtains the average value of the signal level from the integrator
circuitry when the filament is off. When the filament is off, the major source of
signal coming is electronic noise. The integrator zero is adjusted so electronic
noise does not create artificial ions, which may create a measurable signal.
Set Electron Multiplier
Set Electron Multiplier determines two settings, the multiplier voltage needed to
achieve a multiplier gain of approximately 105, and the Electron Multiplier voltage
boost for optimum peak intensity and resolution.
Electron Lens Tuning
Electron lens tuning involves measuring the transient behavior of the emission
current immediately after the lenses have been switched on or off. If the lenses
are unbalanced, the emission current will change in time and be proportional to