Varian 4000 GCMS Reference guide

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Varian, Inc.
2700 Mitchell Drive
Walnut Creek, CA 94598-1675/USA
4000 GCMS SYSTEM
Installation Procedures
.

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Contents
Introduction...............................................................................................................................5
Section 1. System Unpacking / Checking / Set Up ................................................................7
1.1 Unpacking / Parts Checking .................................................................................................................................7
1.2 System Set Up On Bench.....................................................................................................................................8
1.3 GCMS Plumbing and Purging ..............................................................................................................................9
1.4 Column Installation Into the MS............................................................................................................................9
Section 2. GC/MS Power Up ..................................................................................................11
2.1 Initial Power Up ..................................................................................................................................................11
2.2 Quick Check of Air / Water .................................................................................................................................16
2.3 Checking for High Mass Noise ...........................................................................................................................20
2.4 System Conditioning...........................................................................................................................................21
Section 3. Preliminary Tuning ...............................................................................................23
3.1 System Monitoring..............................................................................................................................................23
3.2 RF Ramp Adjustment .........................................................................................................................................24
3.3 Dipole Adjustment ..............................................................................................................................................26
3.4 Air Water Check .................................................................................................................................................28
3.5 Cal Gas Adjustment............................................................................................................................................29
Section 4. Auto Tuning...........................................................................................................31
4.1 Internal Auto Tuning ...........................................................................................................................................31
4.2 External Auto Tuning ..........................................................................................................................................32
Section 5. Achieving Internal EI Specifications...................................................................35
5.1 Methodology .......................................................................................................................................................35
5.2 OFN Acquisition..................................................................................................................................................36
5.3 Library Search and Signal to Noise Calculation.................................................................................................36
5.4 Customer Familiarization....................................................................................................................................49
Section 6. Achieving Internal CI Specifications...................................................................51
6.1 Install Liquid CI ...................................................................................................................................................51
6.2 Adjust Liquid CI Reagent Flow ...........................................................................................................................52
6.3 Methodology .......................................................................................................................................................53
6.4 BZP Acquisition ..................................................................................................................................................54
6.5 Signal-to-noise Calculation.................................................................................................................................54

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Section 7. Achieving External EI Specifications..................................................................55
7.1 Methodology .......................................................................................................................................................55
7.2 OFN Acquisition..................................................................................................................................................56
7.3 Library Search and Signal-to-noise Calculation .................................................................................................56
Section 8. Achieving External PCI Specifications ...............................................................57
8.1 Install Gaseous CI ..............................................................................................................................................57
8.2 Adjust Gaseous CI Reagent Flow ......................................................................................................................57
8.3 Methodology .......................................................................................................................................................59
8.4 BZP Acquisition ..................................................................................................................................................59
8.5 Signal-to-noise Calculation.................................................................................................................................60
Section 9. Achieving External NCI Specifications...............................................................61
9.1 Methodology .......................................................................................................................................................61
9.2 DFB Acquisition ..................................................................................................................................................61
9.3 Signal-to-noise Calculation.................................................................................................................................62
Appendix A. 4000 MS Installation Specifications and Test Samples.................................63

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Introduction
This installation procedure represents a stepwise guide to setting up the 4000
GCMS system, meeting product specifications, and carrying out basic customer
familiarization.
The 4000 MS has several modes of operation. It is not desirable to test all of
these modes at installation. The customer needs to decide what will be the
standard mode or preferred mode of operation when the system is sold. The
system will be shipped in the preferred mode. Install and test the system using
the preferred mode. Additional ionization mode demonstrations may be sold. If
so, these ionization modes should also be demonstrated. Under normal
circumstances, the 4000 MS installation should be complete within 2-3 days on
site. Demonstration of additional ionization modes will increase the time needed
to install a system.
A Typical MS Installation
1. System unpacking, setup and checking 2 hours
2. Power up, pump down, initial customer familiarization 4 hours
3. Verification of GC/MS System Operation 2 hours
4. EI ionization mode demo 1 hours
5. Additional customer familiarization 4 hours
Option Installation
1. Autosampler installation, check out, familiarization 1.5 hours
2. CI ionization mode demo, familiarization 1.5 hours
Installation results should be entered into the Installation Tracking Database.
The following should be determined before arriving at an installation site:
The CSR should be aware of whether the customer has met the important site
requirements outlined in the Pre-Installation Document. A phone call should be
placed with the customer to pre-qualify the site. The critical site requirements
are bench space and load, power, temperature, humidity, carrier gas purity
(helium) and CI gas purity (external only, methane). The specific requirements
are clearly outlined in the 4000 Pre-Installation Document.
It is also important to determine, before going on site, whether the customer
desires to use the existing system PC or the PC included with the MS upgrade. If
the customer provides the PC, then the set up of this computer should be a
billable call, and not charged to installation. In addition, Varian assumes no
liability for configuration or operational problems associated with the customer's
computer.

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NOTE: Test samples are not shipped overseas with the system. Before going on
site to do an installation, ensure you have all the necessary samples, or that they
have been shipped to the customer from a local Varian office. Installation
engineers outside of the USA should confirm the availability of test samples from
their home office as much as 2 weeks in advance. For US shipments the
samples are shipped with the system.

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Section 1. System Unpacking /
Checking / Set Up
1.1 Unpacking / Parts Checking
Unpack the entire system, and check thoroughly for missing parts and shipping
damage. Use caution when unpacking the MS - the transfer line is not a handle,
lifting the instrument using the transfer line can result in damage to the
analyzer.
NOTE: The Cal Gas (FC-43 P/N 03-920353-00) is shipped uninstalled in an
ampule. The Cal Gas must be installed during the installation. Aliquot
approximately 0.5 mL of the FC-43 into the Cal Gas vial and install into the MS.
The remaining FC-43 can be stored in the vials provided in the accessory kit.
Do not overfill the Cal Gas vial installed in the MS. Overfilling can result in
FC-43 contamination that interferes with Cal Gas adjustments.
Before setting up and starting the GC/MS system, check that all parts and kits
have been delivered, and are complete. Review with the customer the contents
of the accessory kits and their functions.
Report all shipping damage or missing parts to the Customer Service department
(Phone: [phone], Fax: [phone], email: [email protected]),
Varian, 2700 Mitchell Drive, Walnut Creek, CA, 94598.
Shipping damage or missing items should also be noted on the installation
checklist and in the Installation Tracking Database.

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1.2 System Set Up On Bench
Set the 3800 GC and 4000 MS onto the bench. The GC and MS should initially
be well separated to allow easy access. Remove the turbo pump shipping
restraint and analyzer shipping restraints from the 4000 MS. Remove shipping
restraints from the GC such as the metal dowel at the rear of the GC. The
removed restraints and brackets should be retained in case the system needs to
be transported in the future.
Connect the roughing hose to the roughing pump. Connect the roughing pump
power cord to the LINE VOLTAGE PUMP ONLY connector at the rear of the MS.
To minimize vibration, the roughing pump should not be on the bench with the
GCMS.
Connect the GC-to MS sync cable under the GC top cover at J6 ANALOG OUT
and at the rear of the MS at J9 SYNC.
Connect the USB cable to the rear of the MS at J7 USB and to a USB port on the
PC.
Connect the Ethernet cable to the GC and to the PC. Be sure to connect the
Ethernet cable using the side connector of the Tee and NOT the terminal end.
Install the new column shipped with the system into the 1177 injector (or 1079 if
no 1177 is installed) but to prevent contamination do not connect to the MS
transfer line until after initially conditioning the column in the GC oven.
Uninstall the empty Cal Gas vial from behind the MS front door by loosening the
two mounting screws and twisting the vial while pulling down. Fill the vial with
approximately 0.5 mL of the FC-43 (03-920353-00) provided in the 4000 MS
Accessory Kit. Re-install the partially (less than half) filled vial into the MS and
tighten the mounting screws. The vial must be inserted far enough into the
pneumatic block to engage the o-ring. Store the remaining FC-43 in the vials
provided in the accessory kit. Be careful not to overfill the Cal Gas vial to avoid
FC-43 contamination that can interfere with system performance.

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1.3 GCMS Plumbing and Purging
Use 1/8” brass tubing to plumb 99.995% helium to the back of the GCMS
system. Install the Gas Clean Filter assembly. For an external mode 4000 MS,
Tee the helium output line after the Gas Clean Filter assembly so helium can be
delivered to the GC and the MS. The 4000 MS (in External Mode only) uses
helium Damping Gas that will need to be plumbed into the MS. This MS Damping
Gas is typically installed by teeing off the helium line to the GC and MS after the
Gas Clean Filter assembly. Verify that the helium line pressure is set to 80 psi. at
the cylinder regulator. Ensure the cylinder contains at least 500 psi. of helium.
Before connection to the GC/MS, purge the helium line from the cylinder for 10
minutes at maximum flow. Connect one end of the Tee to the inlet on the back of
the GC, the other to the inlet on the back of the MS. The GC pneumatics need to
purge for at least 1/2 hour to remove any water or air that may have entered
during shutdown.
NOTE: The MS pneumatics (in External Mode) will also need to be purged as
described in Section 2 of this document
The column shipped with the system must be installed to achieve the best results
for acquisitions associated with the installation. If an 1177 injector is installed on
the GC, use the 1177 to pass the sensitivity specifications. Condition the injector
and column one time before installing into the MS to prevent column bleed from
contaminating the MS. Condition the injector at 230 °C with a high split ratio
(e.g., 50:1). Condition the column starting at 50 °C, ramping at 5 degrees/minute
up to 300 °C, and hold for 60 minutes unless this exceeds the maximum
allowable operating temperature for the column phase.
1.4 Column Installation Into the MS
Column installation into the 4000 MS transfer line depends on the ionization
mode of the MS and is described in the 4000 Hardware Operation Manual. Note
the ionization mode in which the instrument was shipped and install the column
accordingly.
NOTE: Be sure to leave a significant service loop of column detached from the
column cage so the GC and MS can be easily separated.
At this point the GC and MS can be pushed together on the bench. Ensure that
the transfer line column nut is visible inside the GC oven and the transfer line
rubber boot is inside the hole on the GC side panel.

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Section 2. GC/MS Power Up
Ensure that the GC and MS are plugged into separate isolated outlets as
specified in the 4000 Pre-installation Document.
2.1 Initial Power Up
Turn on the GC. Open System Control and bring the GC online.
Turn the Service Switch underneath the MS top cover to ON. Turn on the main
circuit breaker at the rear of the MS. The mechanical pump will run loudly initially,
but should run quietly within 30 seconds. If the mechanical pump continues to
run loudly, turn off the main circuit breaker and check the system for obvious
leaks. Common sources of large leaks at this point are the vacuum hose
connections to the turbo or roughing pumps, the manifold or transfer line O-rings,
and the column connection into the transfer line.

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Found New Hardware Wizard
Because the PC has not been connected to the MS the Windows XP operating
system may launch the Found New Hardware Wizard when first turning on the
MS. Configure the MS as new hardware by clicking through the pages of this
wizard as shown in the following screen captures.
Select No, not this time and click Next.
Figure 2.1

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Select Install the software automatically (Recommended) and click Next.
Figure 2.2

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Click Finish to close the wizard.
Figure 2.3

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Open System Control
Open System Control and if necessary to start the pumps click the Start Up
button on the Startup/Shutdown tab. Monitor the Pump Spin Speed and Current
from Startup/Shutdown (refer to Figure 2.4). Normally, the turbo should run up to
100% in about 1 minute. Current is usually less than 300 mA when the turbo
reaches 100%.
Figure 2.4
4000 MS in External Mode
The 4000 MS in External Mode is equipped with Damping Gas. Once the
vacuum is established but before heating up the Getter, the MS pneumatics
should be purged by turning on the Damping Gas flow in Startup/Shutdown (refer
to Figure 2.4, click Turn On for Pneumatics). Set the Damping Gas Flow to 4
mL/min on the Module Attributes tab in Manual Control (refer to Figure 2.5, enter
4.0 mL/min and click Activate Changes) and purge the MS for approximately 20
minutes. After purging the MS pneumatics, set the Trap Damping Gas Flow as
appropriate for the external EI acquisition, for the external PCI acquisition, or the
external NCI acquisition. The appropriate Damping Gas flow rates can be found
embedded in the names of the test data files from the Test Files CD included
with the system, and also in the Module Attributes section of the Data File
Information dialog of each external data file. After purging and setting the
analytical damping gas flow rate, turn on the Getter heater (click Turn On for
Getter Control).

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Figure 2.5
2.2 Quick Check of Air / Water
It is important to monitor the progress of the manifold pump down before initiating
a bakeout. Once the Pump Spin Speed reaches 100%, check for the presence of
a massive water peak (18 and 19 m/z, unlikely to be resolved) and the absence
of a nitrogen peak (28 m/z). Only turn the trap on for a short period of time
(<5 seconds) so the filaments and multiplier are not adversely affected.
NOTE: This check of air water may not give usable results until after auto tuning
the system.
Go to Manual Control and click the Active Segment tab. Enter a Mass Range of
15 to 45 m/z (refer to Figure 2.6, Full Scan Parameters tab). Also enter a Fixed
Ionization Time of 100 microseconds for internal mode or 5000 microseconds for
external mode (refer to Figure 2.7, Ionization Control tab). Click Activate
Changes. Alternatively, one can use segment 1 of
C:\VarianWS\4000Service\4000 MS (Int or Ext) Service.mth.
This is a quick check to confirm the absence of a m/z 28 signal. The m/z 28
signal should not be present due to the massive intensity of the 18/19 signal
before bakeout. Presence of a m/z 28 signal can indicate a leak or contaminated
gas.

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Figure 2.6

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Figure 2.7

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Turn on the ion trap briefly, take a quick glance at the spectrum, and then turn
off the ion trap. If the system is pumping down as expected, there should be one
large off scale peak on the display centered around 19 m/z and a smaller
(typically 10-50% full scale) peak around 32 m/z. There should not be a
significant 28 m/z peak visible. (Refer to Figure 2.8.) If there is the system has a
leak which needs to be found and fixed. If the system has a significant leak, the
baseline will be flat, or there will be one large, broad peak from about 15 - 35
m/z. If this is the case, then the leak should be found and corrected before
progressing any further with the installation. After the system has been pumping
for > 30 minutes the intensity of the 18/19 m/z signal will decrease and the 28
m/z signal should appear.
Figure 2.8

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2.3 Checking for High Mass Noise
Before baking out the system it should be checked for high mass noise (HMN).
NOTE: This check for HMN may not give usable results until after auto tuning the
system.
On the Full Scan Parameters tab in Manual Control (refer to Figure 2.9) enter a
Mass Range of 50 to 1000 m/z. On the Ionization Control tab turn off the fixed
ion time option (turned on in section 2.2) by un-checking the Fixed Ionization
Time check box (refer to Figure 2.7) and click Activate Changes. Alternatively,
one can use segment 2 of the C:\VarianWS\4000Service\4000 MS (Int or Ext)
Service.mth. Turn on the trap and click on the words Ion Source to turn off the
ion source. The RF and Multiplier should remain on (green is on, black is off). In
this configuration (refer to Figure 2.9) the Base Amount (monitored in the upper
right corner of the spectral window) should equal 1 or 2. In addition, no spiking
above the baseline should be observed. If the Base Amount is significantly > 2
and spiking is observed, the system should be shut down and trap should be
blown free of debris using a compressed inert gas. In a persistent case, the trap
cavity may require repeated efforts to free it of debris. If so, the surrounding area,
including the vacuum manifold and the center tube of the transfer line may also
need to be blown free of debris using a compressed inert gas.