NOTICE: Varian, Inc.
was acquired by Agilent
Technologies in May 2010. This document is provided
as a courtesy but is no longer kept current and thus
will contain historical references to Varian. For more Varian, Inc.
information, go to www.agilent.com/chem. 2700 Mitchell Drive
Walnut Creek, CA 94598 USA
4000 GC/MS
Pre-Installation Instructions
Use these instructions to prepare your site for the installation of the 4000 GC/MS. After you have
prepared the site, and your 4000 GC/MS has been delivered, please contact your local Varian,
Inc. office to schedule the installation of your 4000 GG/MS.
For additional information about the GC refer to the CP-3800 GC Pre-Installation Instructions.
The Varian 4000 GC/MS has been designed to operate reliably under carefully controlled
environmental conditions. It is your responsibility to provide a suitable location, power source,
and operating environment. Operating or maintaining a system in operational conditions outside
of the power and operating environment limits described below could cause failures of many
types. The repair of such failures is specifically excluded from the Warranty and Service contract
conditions.
The Varian 4000 GC/MS is tested according to Safety Standard EN 61010-1 and EMC Standard
61326-A1+A2, which is comprised of Electrical Immunity and Susceptibility Standards.
CAUTION
All phases of the installation site preparation must conform to local safety, electrical,
and building codes. These codes take precedence over any recommendations in these
instructions, and compliance to them is the responsibility of the customer.
Contents
Space and Weight Requirements ..................................................................... 2
Power Requirements......................................................................................... 3
Operating Environment ..................................................................................... 5
Temperature/Humidity .............................................................................. 5
Particulate Matter...................................................................................... 6
Vibration.................................................................................................... 6
Exhaust System ........................................................................................ 6
Gas Requirements ............................................................................................ 6
GC Carrier Gases ..................................................................................... 6
CI Reagent Gases (with CI option only).................................................... 7
Other Gases.............................................................................................. 7
Gas Lines.................................................................................................. 7
Capillary Columns ............................................................................................. 7
Solvents and Materials...................................................................................... 7
Network Requirements...................................................................................... 8
System Requirements / Qualified Computer Equipment................................... 8
Inspection.......................................................................................................... 8
Unpacking and Installation ................................................................................ 9
Parts and Supplies.................................................................................... 9
Preventive Maintenance.................................................................................... 9
Trademark Acknowledgment ............................................................................ 9
03-914997-00:3 1 of 9 4000 GC/MS Pre-installation Instructions
Space and Weight Requirements
Before arranging for delivery of the 4000 GC/MS to your facility, please make sure that all
passages to the site of installation are at least 91.5 cm (36 in.) wide. Allow additional room for
maneuvering the shipping container around corners and/or through doors.
Table 1 identifies the space and weight requirements of the 4000 GC/MS components. The 4000
GC/MS is intended to sit on a workbench that is wide enough and deep enough to accommodate
these components, and sturdy enough to support their combined weight. Varian recommends the
layout shown in Figure 1, and the space allowances in Table 2.
Table 1 Dimensions and Weights of the 4000 MS System Components1
Height Width Depth Weight
Instrument in. cm in. cm in. cm lb. kg
4000 MS 18 44 15 37 26 66 89 40
CP-3800 GC 21 53 26 66 22 56 95 43
CP-8400 AutoSampler / CP-8410 16 41 9 23 18 46 20 9
AutoInjector (sits on top of GC)
Tekmar 3000 Purge and Trap 19 48 9 23 18 46 37 17
Archon Purge and Trap AutoSampler 17 43 22 55 21 53 80 36
Tekmar ALS-2016 27 69 15 38 15 38 35 16
Genesis Headspace AutoSampler 22 56 28 71 18 46 110 50
MS Workstation (computer with 20 51 17 43 21 53 35 16
monitor, approximate values)
1
Rounded up to nearest unit.
Table 2 Spatial Set-up Requirements for 4000 GC/MS
Recommendations Purpose Recommended Distance
Allow adequate space to the right of Permit access to the transfer line ~ 61 cm (24 in.)
the GC/MS. and turbomolecular pump. See
Figure 1.
Allow adequate space behind the Provide clear space for air 15 to 30 cm (6 to 12 in.)
system. circulation, gas lines, and electrical
connections.
Allow vertical clearance above the Dissipate heat and allow for routine ≥102 cm (40 in.)
GC/MS. maintenance.
Allow additional bench space beside Enable mouse operation. 20 cm x 20 cm (8 in. x 8 in.)
the Workstation keyboard
03-914997-00:3 2 of 9 4000 GC/MS Pre-installation Instructions
Figure 1 Recommended System Layout
The 24.5 kg (54 lb) mechanical pump belongs on the floor beneath the workbench on which the
4000 GC/MS system sits. To accommodate the pump, the workbench should be no higher than
91 cm (36 in.); if you use a higher table, be sure to place a suitable stand or support under the
table to elevate the pump. If your bench adjoins a wall, you will either need to drill a 38 mm
(1.5 in.) diameter hole through the bench to accommodate the vacuum hose, or to place a
suitable shelf above the 4000 GC/MS for the pump.
The cable between the computer and MS cannot be longer than five meters (16.4 feet) without
adding powered hubs or extension cables which could affect performance.
Power Requirements
You are responsible for providing two dedicated fourplex single-phase power sources with earth
grounds hard-wired to the main power panel ground. Within North America and Japan these
power sources must be 20A, 90-130 Vac, 60 Hz ±3 Hz, and outside these locations they must be
10A, 180-260 Vac, 50 Hz ±3 Hz. One of these fourplex power sources is for the mass
spectrometer, computer, monitor, and printer. The other fourplex power source is for the gas
chromatograph. If you have additional sample preparation devices or test equipment, we
recommend a separate dedicated power source for their operation.
Care must be taken to ensure that sources of radio frequency interference (RFI) and
electromagnetic interference (EMI) are not placed on the same power line, or share the same
ground plane, since this can degrade the performance of the GC. Equipment such as motors,
solenoids, fluorescent light fixtures, and radio communication transmitters should be isolated
from the instrument and connecting cables as much as possible.
The power cable from the GC is approximately 2m (6 ft) long and fitted with National Electronics
Manufacturers Association (NEMA) 5-20P power plugs. The NEMA 5-20P power plug and
corresponding outlet are shown in Figure 2(a). NEMA 5-20P plugs are rated at 20A and 120 Vac.
03-914997-00:3 3 of 9 4000 GC/MS Pre-installation Instructions
The power cable from the mass spectrometer is approximately 2.5m (8 ft) long and fitted with US
Standard National Electronics Manufacturers Association (NEMA) 5-15P power plugs. The
NEMA 5-15P power plug and corresponding outlet are shown in Figure 2(b). NEMA 5-15P plugs
are rated at 15A and 120 Vac.
Systems shipped outside the United States, Canada, and Japan are fitted with CEE 7/7 plugs;
these are rated at 16A and 230 Vac. The CEE 7/7 plug and outlet are shown in Figure 2(c).
Figure 2 NEMA 5-20P, NEMA 5-15P, and CEE 7/7 Power Plugs and Outlets
The power cables for the computer, monitor, and printer are approximately 2m (6 ft) long. They
are fitted with NEMA 5-15P plugs.
With a 120V power source, the maximum amperage requirements for each of the 4000 GC/MS
components are as follows:
Component Amperes
Mass Spectrometer 12
CP-3800 Gas Chromatograph 20
CP-8400 AutoSampler 0.5
Computer 3
Monitor 2
Laser Printer 3-4
NOTE: With a 230V power source, the maximum amperage requirement of each of the
above components is one-half of the amperage given above.
Never plug the mass spectrometer and the gas chromatograph into the same power
source as you may overload the fourplex power source. Never use the free outlet on each of the
power sources for equipment drawing more than 2A.
The quality of the power supplied to your 4000 GC/MS is very important. The power must be
90-130 Vac, 60 Hz ±3 Hz (180-260 Vac, 50 Hz ±3 Hz outside North America), and it must be
stable, i.e., it must be free of fluctuations due to slow changes in the average voltage or to
changes resulting from surges, sags, or transients.
03-914997-00:3 4 of 9 4000 GC/MS Pre-installation Instructions
Under normal operating conditions the MS unit draws about 600 watts of power. Under bake out
conditions this can increase to 1000 watts. The GC can draw up to 2.5 kilowatts of power but
usually will average half that amount even when using demanding methods.
Slow, average voltage changes are gradual, long-term changes in the average root mean square
(RMS) voltage level, with typical durations greater than 2 seconds.
• Sags and surges are sudden changes in average RMS voltage level, with typical
durations between 50 μsec and 2 seconds.
• Transients (or impulses) are brief voltage excursions of up to several thousand volts
with durations of less than 50 μsec.
Constant high line voltage or surges in voltage may produce overheating and component failures.
Constant low line voltage or sags in voltage may cause the system to function erratically, or even
to cease functioning. Transients, even of a few microseconds duration, may cause electronic
devices to fail catastrophically or degrade sufficiently to significantly shorten device lifetime. It is
important to establish the quality of the line power in your laboratory prior to installation of the
4000 GC/MS.
Occasionally, you may encounter line power sources of unacceptable quality; such power
sources may adversely affect the operation of the 4000 GC/MS. The 4000 GC/MS is tested under
EMC Standard 61326-A1 + A2. If voltage conditions exceed those standards, additional power
conditioning or surge protection is advised. You may want to contact a specialist in power
conditioning services.
To protect against power failures, an Uninterruptible Power Supply (UPS) can be used. The
amount of power drawn depends on instrument operating conditions but 4KVA should be
sufficient under typical acquisition conditions, at normal line voltage. Greater power may be
drawn during system power up or bakeout. The UPS should have a switchover time of 20 ms. or
less.
Operating Environment
You are responsible for providing an acceptable operating environment. Attention paid to the
operating environment will ensure the continued peak performance of your 4000 GC/MS.
Temperature/Humidity
The optimum operating temperature is between 18° and 21 °C (65° and 70 °F).
As laboratory temperature increases, system reliability decreases. All electronic
components generate heat while operating. This heat must be dissipated to the
surrounding air if the components are to operate reliably.
The turbomolecular pump temperature cutoff control protects the bearing and prolongs the pump
lifetime. If the laboratory temperature is significantly above 27 °C (80 °F), the pump cutoff
temperature could be reached causing the pump to shut down.
There must be good air flow around the system. Your air conditioning system must be capable of
maintaining a constant temperature (within operational limits) in the immediate vicinity of the
system. The average steady-state heat load of the 4000 GC/MS is 6000 BTUs/hour.
Hot air vented from the GC column oven may contribute to room heating and to the resulting air
conditioning load. Ducting the GC column oven air out of the lab should reduce this heating
effect.
03-914997-00:3 5 of 9 4000 GC/MS Pre-installation Instructions
The relative humidity (RH) of the operating environment must be between 40 and 80%, with no
condensation. Operating a 4000 GC/MS at very low humidity will result in the accumulation and
discharge of static electricity shortening the life of electronic components. Operating the system
at high humidity will produce condensation and result in short circuits.
Varian recommends that your laboratory be equipped with a temperature/humidity monitor. This
will ensure that your laboratory is always in conformance with temperature and humidity
specifications.
Particulate Matter
Take necessary precautions to minimize particulates in the laboratory environment. A layer of
dust on the electronic components could act as an insulating blanket, and reduce heat transfer to
the surrounding air.
Vibration
Ensure that lab benches are free from vibrations, e.g., those caused by equipment in adjoining
locations. Because the mechanical pump vibrates during operation, you should install it on the
floor beneath the 4000 GC/MS, rather than alongside the system on the workbench.
Exhaust System
It is your responsibility to provide an adequate exhaust system. Most compounds introduced into
the mass spectrometer will eventually be exhausted from the mechanical pump, along with the
small amounts of oil vapor that these pumps characteristically emit. Therefore, the pump outlets
should be connected to a fume exhaust system. Consult local regulations for the proper method
of exhausting the fumes from your system.
Gas Requirements
GC Carrier Gases
Helium
Minimum 99.998% ultra-high purity, with less than 1.0 ppm each of water, oxygen, and total
hydrocarbons. One 257 ft3 tank with an Alltech regulator #AL8111, or equivalent tank and
regulator.
NOTE: The presence of >1 ppm oxygen or water in the carrier gas supply may significantly
affect the performance of the 4000 GC/MS; it may also damage such components as the
capillary column, filaments, and multiplier. Varian recommends that you verify that your
gas suppliers use controlled tanks; this will ensure that purity standards are maintained. If
you purchase pure gases in contaminated tanks, you may end up with a contaminated
system requiring costly and time consuming repair.
Use of a carrier gas filter is required for optimum performance and to protect your system from
potential contamination. Your GC Accessory Kit includes a GC/MS Gas Clean Oxygen/Moisture
filter (part number CP-17973) and filter base. This easy-to-remove gas filter cartridge combines
three highly adsorptive materials in one filter to remove water, oxygen, and organic compounds
to purify the GC/MS gas. Carrier gas filters should be installed in a location where the indicator is
visible. The filter should be replaced when the indicator shows that the filter is saturated. For
replacement procedures, refer to the instructions enclosed with your filter.
03-914997-00:3 6 of 9 4000 GC/MS Pre-installation Instructions
CI Reagent Gases (with CI option only)
Methane gas is required for External Ionization CI system installation. Only Methanol is required
for Internal Ionization CI. Similar purity is recommended for other CI gases used with customer
applications.
Methane
99.99% purity. One lecture bottle with a two-stage pressure regulator which has a stainless steel
diaphragm, and a 0 to 100 psi output gauge.
Other Gases
See the CP-3800 GC Pre-Installation Instructions for information on gases required for Cryogenic
options.
Gas Lines
Methane and isobutane supply lines connect directly to the CI gas inlet without any terminating
fittings. For other gas line requirements see the CP-3800 GC Pre-Installation Instructions.
Capillary Columns
The 4000 GC/MS accommodates the following GC fused-silica capillary columns:
• Narrow bore: 0.25 mm ID; length ≥15 m (50 ft)
• Wide bore: 0.32 mm ID; length ≥30 m (100 ft)
Solvents and Materials
When the FSR uses the OFN standard to demonstrate sensitivity in EI mode, its concentration
must be reduced. The FSR can accomplish this by doing a split style injection or by diluting the
OFN standard. If you require the OFN standard to be diluted you must provide 2,2,4-
trimethylpentane (isooctane), high purity grade solvent (99.5%) and clean materials as described.
Isooctane: To minimize impurities that would adversely affect the sensitivity specification test
purchase 2,2,4-trimethylpentane from one of the following vendors and provide a new, unopened
bottle for the installation.
• EMD Chemicals, OmniSolv® 2,2,4-trimethylpentane, Catalog Number TX1389-6,
http://www.emdchemicals.com
• Acros Organics, 2,2,4-trimethylpentane (ECD tested for pesticide analysis),
Product Number 326620010, http://www.acros.com
Materials: Provide the following materials for diluting the OFN standard.
• 10 mL volumetric flask
• 1 mL volumetric pipette
Provide the following solvents for operation and maintenance
• Methanol, HPLC grade
• Acetone, HPLC grade
NOTE: Handle and store all solvents in accordance with standard safety procedures.
03-914997-00:3 7 of 9 4000 GC/MS Pre-installation Instructions
Network Requirements
If you are planning to connect your GC/MS to a company network, you will need to provide a
10BaseT (Ethernet) connection to the back panel of the CP-3800 GC. In addition, the company
network must allow TCP/IP communications to be routed across it from the GC to the 4000
GC/MS Workstation. For basic Ethernet cabling information, please refer to the CP-3800 GC
Operator's Manual, included on the MS Workstation CD. Any hardware, adapters, cables,
configuration and setup work required to convert from the company network wiring type to
10BaseT wiring will need to be provided by you or your network administrator. This hardware
must comply with the IEEE 802.3 standard.
System Requirements / Qualified Computer Equipment
If you are planning to install the Varian MS Workstation software on a computer that was not
purchased from Varian, it is your responsibility to ensure that this computer is adequately
equipped and compatible with the operation of the data system and its communication interfaces.
Please consult the current list of requirements, available on-line at:
http://www.varianinc.com/cgi-bin/nav?products/chrom/gcms/msws_computer_req
For a list of the currently qualified equipment and/or if you have difficulties accessing this site,
contact your Sales Representative.
Inspection
When your 4000 GC/MS arrives, carefully inspect the exterior of the shipping cartons for
evidence of any damage that might have occurred during shipment. Inspect the cartons for the
following:
• Water stains
• Cuts, punctures, or deep indentations
• Crushed corners or excessively abraded edges
If one or more of the above conditions are evident on any of the shipping cartons, report the
conditions to the carrier at time of receipt.
Systems are shipped either FOB Varian or FOB Destination. The manner of shipment
determines who has responsibility for filing a claim against the carrier if the system is damaged in
transit. Most systems are shipped FOB Varian, and in this instance any damages incurred in
shipment are the responsibility of the purchaser and the carrier. Contact Varian Service for
assistance with claims filing and billing for repairs if necessary. If the system is shipped FOB
Destination, contact Varian Order Processing who will file a claim against the carrier. Note,
however, that Varian will not accept liability for damage if you receive obviously damaged
materials but do not make note of the damage on the receiving documents.
When your 4000 GC/MS arrives, move it indoors to a protected place and call Varian Service to
schedule your installation.
03-914997-00:3 8 of 9 4000 GC/MS Pre-installation Instructions
Unpacking and Installation
A Varian Field Service Representative will unpack and install the 4000 GC/MS once it has arrived
and you have prepared the installation site. At the time of installation, the Field Service
Representative will demonstrate the fundamentals of operation and maintenance. To take full
advantage of this on-site visit, please arrange to have your system operator available during the
installation.
At the time of installation, the Field Service Representative will demonstrate that your system
meets the performance specifications written into your sales contract. Please do not make plans
to analyze samples with the system until after the installation has been completed and you have
accepted the conditions of delivery.
Parts and Supplies
The 4000 GC/MS Hardware Operation Manual provides a list of parts and supplies for routine
operation.
Preventive Maintenance
You will be responsible for performing routine and preventive maintenance of the gas
chromatograph, mass spectrometer, and data system.
Please note that it is essential that you perform regular preventive maintenance. By performing
this maintenance, you will increase the life of the system, increase system uptime, and enjoy
optimum system performance. Please refer to the 4000 GC/MS Hardware Operation Manual for
details. Your Varian field service representative will also describe and demonstrate these
procedures at installation time.
Trademark Acknowledgment
Microsoft and Windows are registered trademarks of Microsoft Corporation. Other brand and
product names are trademarks or registered trademarks of their respective holders.
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