NOTICE: This document contains references to Varian.

Please note that Varian, Inc. is now part of Agilent Varian 240-MS GC/MS
Technologies. For more information, go to
www.agilent.com/chem. Ion Trap Mass Spectrometer
Pre-installation Instructions

Checklist
NOTE: Do not unpack the boxes.
Place a check in the box after satisfying each requirement as described in the instructions. All requirements must
be met before requesting installation.

NOTE: If the laboratory is not ready for installation when the Varian Representative arrives, Varian, Inc.
reserves the right to invoice for the Representative’s time.

Requirements 
Principal installation site is in compliance with all relevant safety regulations. 
User Representative will be available during the installation and certification period. 
Entrance to the laboratory is at least 92 cm (36 in.) wide. 
Sufficient bench space is available for all components. 
Bench can support system weight. 
Bench does not vibrate. 
Laboratory temperature maintained between 16 and 30 °C. 
Relative humidity maintained between 40 and 80%. 
Laboratory is free of excessive particulate matter. 
Ventilation system is suitable. 
Specified electrical supply and power outlets are installed. 
CI reagent gas (methane, isobutane, or ammonia: 99.99% pure), regulator, and gas lines

are installed.
Helium (99.999% pure), regulator, and gas lines are installed. 
Shipping cartons examined for damage. If there was any damage, the damaged shipping

carton procedure was completed.

Request for Installation

After preparing your site, contact the Customer Service office in your region to schedule installation.

395416500:3 1 of 18 Pre-installation Instructions

Contents
Introduction ...................................................................2 Installation Site Power .......................................... 11
Safety ......................................................................2 Qualified Computer Equipment .................................. 15
Before the Installation ...................................................3 Gas Requirements ..................................................... 15
User Representative................................................3 Chemical Ionization Reagent Gases..................... 15
Entrance ..................................................................3 GC Carrier Gases ................................................. 16
Bench Space and Load ...........................................3 When the GC/MS Arrives ........................................... 17
Vibration ..................................................................8 Inspection.............................................................. 17
Temperature ............................................................8 Unpacking and Installing....................................... 18
Humidity...................................................................8 Spare Parts ................................................................ 18
Particulate Matter ....................................................8 Preventive Maintenance ............................................. 18
Ventilation System...................................................9 Trademark Acknowledgment...................................... 18
Power Requirements ...............................................9

Introduction
The Pre-installation Instructions guide you through each requirement of the checklist. Follow
these instructions to ensure that the installation requires no more than the usual three days.
Have the completed checklist available when you call to schedule the installation. After the
Varian Representative has completed the installation, you can analyze your samples.
This document includes pre-installation instructions for the 431-GC and the 450-GC.
The GC/MS operates reliably under carefully controlled environmental conditions. It is your
responsibility to provide suitable, power sources, operating environment and materials. Using or
maintaining a system outside of the power and operating environment ranges and limits
described in these instructions, may cause failures. The Warranty and Service contract
specifically excludes the repair of failures due to such causes.

All phases of the installation site preparation must conform to

local safety, electrical, and building codes. These codes take
CAUTION precedence over any recommendations in these instructions,
and the customer is responsible for compliance.

Safety
Safety is the most important consideration for instrument use. Determine if the installation site
complies with all relevant safety regulations.

 Check the checklist box: Principal installation site is in compliance with all
relevant safety regulations.

395416500:3 2 of 18 Pre-installation Instructions

Before the Installation
User Representative
Schedule the installation when the User Representative is available, because one of the
important duties of the Varian Representative is to familiarize the User Representative with the
basic functions of the 240-MS GC/MS.

 Check the checklist box: User Representative will be available during the
installation and Varian certification period.

Entrance
Before arranging for delivery of the GC/MS, determine that there is sufficient clearance to move
the shipping container to the installation site. The shipping box is 72 cm (28 in.) wide by 92 cm
(36 in.) long. If you move the instrument using the pallet, you need at least 92 cm (36 in.)
clearance in the in the width of doorways. Allow additional room for maneuvering the shipping
containers around corners or through doors.

The MS, foreline pump, and GC are heavy. To prevent personal

CAUTION injury, use appropriate moving and lifting techniques.

 Check the checklist box: Entrance to the laboratory is at least 92 cm (36 in.)
wide.

Bench Space and Load

Use the following information to plan the layout for your system. The Varian Representative will
unpack the boxes and place the modules on the bench. Figure 1 shows a possible layout for the
240-MS with the 431-GC. Figure 2 shows a possible layout for the 240-MS with the 450-GC.

395416500:3 3 of 18 Pre-installation Instructions

 240-MS with the 431-GC
In Figure 1, the 431-GC is to the left of the MS to allow the transfer line to connect from the GC
to the 240-MS. The bench must be long enough and strong enough to support the weight of the
system and any additional equipment, see Table 1 and Table 2. The bench must be at least 84
cm (33 in.) deep.

Figure 1 Layout of the 240-MS with the 431-GC

Table 1 Bench Space

Bench Monitor and CPU 431-GC 240-MS Total

Length Keyboard

cm 43.8 18.6 33 38 133.4 cm

in. 17.25 7.4 13 15 52.65 in.

Table 2 Bench Load

Bench Load Monitor, CPU 431-GC 240-MS Total

And Keyboard
kg 17.9 23 42 82.9 kg

lb 39.4 51 93 183.4 lb

395416500:3 4 of 18 Pre-installation Instructions

 240-MS with the 450-GC
In Figure 1, the 450-GC is to the left of the MS to allow the transfer line to connect from the GC
to the 240-MS. The bench must be long enough and strong enough to support the weight of the
system and any additional equipment, see Table 3 and Table 4. The bench must be at least 84
cm (33 in.) deep.

Figure 2 Layout for the 240-MS with the 450-GC

Table 3 Bench Space of the 240-MS with the 450-GC

Bench Monitor and CPU 450-GC 240-MS Total

Length Keyboard

cm 43.8 18.6 66 38 166.4 cm

in. 17.25 7.4 26 15 65.65 in.

Table 4 Bench Load of the 240-MS with the 450-GC

Bench Monitor, CPU 450-GC 240-MS Total

Load and Keyboard

kg 17.9 43 42 102.9 kg

lb 39.4 95 93 227.4 lb

Determining Space and Load

The 240-MS GC/MS, except for the foreline pump, belongs on a clean, flat bench. The foreline
pump belongs under the bench. The vacuum line connecting the MS to the foreline pump is 1.2
m long (48 in.) long. The MS ships with a 1.7 m (66 in.) vacuum line attached. To accommodate
the pump vacuum line, the bench should be no higher than 91 cm (36 in.). If your bench is
higher, place a bench that can isolate vibrations under the pump. The bench must support the
22 kg (48 lb) pump. If your bench abuts a wall, drill a 3.8 cm (1.5 in.) diameter hole through the

395416500:3 5 of 18 Pre-installation Instructions

 rear of the bench for the vacuum hose.
Put the PC either on the same bench as the MS or on a separate table. If you put it on a
separate table, position it within 3 m (10 ft) of the rear of the MS to accommodate the length of
the connections. Table 5 has more information.

Table 5 Dimensions and Weights

Instrument Height Width Depth Weight

cm in. cm in. cm in. kg lb
240-MS 46 18 38 15 66 26 42 93
431-GC 46 18 33 13 56 22 23 51
450-GC 53 21 66 26 56 22 43 95
Monitor 36.2 14.3 41 16.1 18.3 7.2 5.7 12.6
CPU 41 16 18.6 7.5 44.5 17.5 11.7 25.8

Allow bench space for other functions see Table 6.

Table 6 Bench Space Allowances

Purpose Recommended Space Allowance

Provide access to the transfer line. Allow at least 30 cm (12 in.) to the left side of the GC/MS.
Provide space for air circulation, gas Allow at least 15 to 30 cm (6 to 12 in.) behind the GC/MS.
lines, and electrical connections.
Dissipate heat and allow for routine Allow at least 76 cm (30 in.) above the GC/MS.
maintenance.

The bench must be at least 84 cm (33 in.) deep to accommodate the system. Use the
Calculation Worksheets, Table 7 and

Table 8, to plan your system.

Table 7 Bench Space Calculation Worksheet for Your System

Bench Monitor and CPU ______GC MS Other Total

Length Keyboard Components

cm 43.8 18.6 ______ 38 ______ ______ cm

in. 17.25 7.5 ______ 15 ______ ______in.

Table 8 Bench Load Calculation Worksheet for Your System

Bench Monitor, Keyboard ______GC MS Other Total

Load and CPU Components

kg 17.9 ______ 42 ______ ______cm

lb 39.4 ______ 93 ______ ______in.

 Check the checklist box: Sufficient bench space is available for all
components.

395416500:3 6 of 18 Pre-installation Instructions

  Check the checklist box: Bench can support system weight.

395416500:3 7 of 18 Pre-installation Instructions

 Vibration
Ensure that the bench for the 240-MS GC/MS is free from vibrations, especially those caused by
equipment in adjoining locations. Because the foreline pump vibrates during operation, put it on
the floor below the MS, not alongside the system on the bench.

 Check the checklist box: Bench does not vibrate.

Temperature
The optimal operating temperature is between 16 and 30 C (61 and 86 F).

NOTE: As laboratory temperature increases, system reliability decreases due to heat generated
by electronic components during instrument use. This heat must dissipate to the surrounding air
for reliable operation.

The airflow around the system must be adequate. The air conditioning system must be capable
of maintaining a constant temperature in the immediate vicinity of the system. Do not place the
system near air ducts, windows, or heating and cooling systems. The average steady-state heat
load of the 240-MS GC/MS is 6,000 Btu, with a possible short-term heat dissipation of 15,000
Btu during startup.
Hot air vented from GC column ovens may contribute to room heating and to the resulting air
conditioning load. Ducting the GC column oven air out of the laboratory reduces this heating
effect.

 Check the checklist box: Laboratory temperature maintained between 16 and

30 °C.

Humidity
The relative humidity of the operating environment must be between 40 and 80%, with no
condensation. Operating the 240-MS GC/MS at a very low humidity may result in the
accumulation and discharge of static electricity, shortening the life of electronic components.
Operating the system at high humidity may produce condensation and result in short circuits. Put
a temperature/humidity monitor in your laboratory.

 Check the checklist box: Relative humidity maintained between 40 and 80%.

Particulate Matter
The laboratory must not have excessive dust, smoke, or other particulate matter. Particulate
matter may block airflow vents causing the electronics to over heat.

 Check the checklist box: Laboratory is free of excessive particulate matter.

395416500:3 8 of 18 Pre-installation Instructions

 Ventilation System
The foreline pump exhausts most compounds introduced into the MS along with oil vapor from
the pump. Check that the ventilation system is suitable for the foreline pump. Consult local
regulations.

 Check the checklist box: Ventilation system is suitable.

Power Requirements
431-GC
The 431-GC requires a separate circuit and the outlet must have adequate amperage capacity
and a reliable ground.
All voltages of the 431-GC are supplied with a standard molded power cord with an IEC60320
“Hot” connector. This power cord can be replaced to suit local power requirements.
Each 431-GC requires a power source capable of providing up to:
 101 V ac ± 10%, 50 or 60 Hz ± 2%, 14 Amps, 1.4 Kilowatts
 120 V ac ± 10%, 60 Hz ± 2%, 11 Amps, 1.3 Kilowatts
 230 V ac ± 10%, 50 Hz ± 2%, 6 Amps, 1.3 Kilowatts
Installation Category: II (per Standard IEC664)
Power supply interruptions/Dips conform to EN61000-4-11: 1994
A voltage drop of 40% maximum, in a timeframe of 20 msec is allowed.

450-GC
The 450-GC requires a separate circuit and the outlet must have adequate amperage capacity
and a reliable ground.

395416500:3 9 of 18 Pre-installation Instructions

 In 230V, 50 Hz countries, the 450-GC is supplied with a standard molded power cord with an
IEC60320 “Hot” connector. This connector plugs into the receptacle on the rear of the GC.
This power cord can be replaced to suit local power requirements. Power cords for North
America and other 120V, 60 Hz applications are terminated in a 3-prong plug that requires a
matching 120 V ac receptacle, see the NEMA 5-20P power plug and outlet in

Figure 3.
Each 450-GC requires a clean power source capable of providing up to:

 101 V ac ± 10%, 50 or 60 Hz ± 2%, 25 Amps, 2.5 Kilowatts

 120 V ac ± 10%, 60 Hz ± 2%, 20 Amps, 2.4 Kilowatts

 230 V ac ± 10%, 50 Hz ± 2%, 10 Amps, 2.3 Kilowatts

Installation Category: II (per Standard IEC664).
Power supply interruptions/Dips conform to EN61000-4-11: 1994.
A voltage drop of 40% maximum, in a timeframe of 20 msec is allowed.

395416500:3 10 of 18 Pre-installation Instructions

 240-MS
The MS requires a separate circuit and the outlet must have adequate amperage capacity and a
reliable ground.
The MS requires a clean power source capable of providing up to:
 90-132V ac, 60 Hz ± 3 Hz, 12 A, 1.5 kW
 180-264V ac, 50 Hz ± 3 Hz, 6 A, 1.5 kW

240-MS GC/MS
The 240-MS GC/MS requires the following:
 One dedicated duplex single-phase power source with earth grounds hard-wired to the
main power panel ground for the GC.
 One dedicated fourplex power source for the MS, computer, and monitor.
 Additional sample preparation devices or test equipment requires a dedicated power.
 Never plug the MS and the GC into the same power source or the power source may
overload. Never use the free outlet on any of the power sources for equipment that
draws more than 2A.

 Within North America, these power sources must be 20A, 100-120V ac 60 Hz  3 Hz.
 Outside North America, power sources must be 10A, 200-240V ac, 50 Hz  3 Hz.

NOTE: 120V and 101V systems are designed for single phase use only.

Installation Site Power

The power supply of the installation site must be either 100-120V ac or 200-240 V ac, and be
stable (free of fluctuations due to slow changes in the average voltage or to changes resulting
from surges, sags, or transients). The voltage must meet IEC 1000-4-5 and IEC 1000-4-11
standards for voltage stability.

NOTE: If the quality of the power is a concern, use an uninterrupted power supply or a power
conditioner, or both.

Table 9 has the current requirements for instruments and components of the 240-MS Ion Trap
GC/MS Mass Spectrometer
Table 9 GC/MS Power Requirements

Instrument or Max Current Draw (AMPS)

Component 100-120V 200-240V
431-GC 11 6
450-GC 20 10
240-MS 10 5
Computer 3 1.5
Monitor 3 1.5
Printer 3 1.5

395416500:3 11 of 18 Pre-installation Instructions

 The power cable from the GC is approximately 2 m (6.7 ft) long and has a National Electronics
Manufacturers Association (NEMA) 5-20P power plug, shown in

Figure 3. NEMA 5-20P plugs are rated at 20A and 120 V ac, see Figure 3.

395416500:3 12 of 18 Pre-installation Instructions

 The power cable from the 240-MS is approximately 2.5 m (8 ft) long and has a National
Electronics Manufacturers Association (NEMA) 5-15P power plug shown in

Figure 3 NEMA 5-15P plugs are rated at 15A and 120V ac.
The power cables for the computer, monitor, and printer are approximately 2 m (7 ft) long. They
have NEMA 5-15P plugs.
Systems shipped outside the United States and Canada have CEE 7/7 plugs. These plugs are
rated at 16A and 230V ac.

Replacing or substituting power cords or plugs must be done

with strict compliance with all regulations, including electrical
CAUTION codes, power cord color coding, and appropriate regulatory
agency certification marks.

395416500:3 13 of 18 Pre-installation Instructions

 Figure 3 NEMA 5-20P, CEE 7/7, and NEMA 5-15P Outlets and Power Plugs

 Check the checklist box: Specified electrical supply and power outlets
installed.

395416500:3 14 of 18 Pre-installation Instructions

Qualified Computer Equipment
If you need to install the Varian MS Workstation software on a computer not purchased
from Varian, you must ensure that the computer is adequately equipped and compatible
with the operation of data system and its communication interfaces of the data system.
Consult the current list of requirements, available at this web site.

http://www.varianinc.com/cgi-bin/nav?products/chrom/gcms/msws_computer_req
The Varian Representative uses only a Varian qualified computer when testing the system
specifications. Varian does not guarantee the function of the Varian MS Workstation software on
other computer hardware or operating systems.

NOTE: Contact your Sales Representative for a list of the currently qualified equipment or more
information.

Gas Requirements
Chemical Ionization Reagent Gases
The Chemical Ionization (CI) mode uses methane, isobutane, or ammonia as a reagent gas. CI
operation consumes about 1 to 2 mL/min of reagent gas. The CI reagent gas should contain less
than 1 ppm water. The reagent gas supply line connects directly to the CI gas inlet using 1/8
inch Swagelok® fittings.
New gas lines typically contain significant amounts of adsorbed water vapor. Pump air through
the gas line to evacuate the water. Use the shortest gas line possible to minimize pumping time.

Methane 99.99% purity

 Use a two-stage, 0-15 psi (0-1 bar) pressure regulator with a stainless steel diaphragm.
 Set the output pressure to the MS between 3 and 5 psi (0.2-0.3 bar).
 Use stainless steel gas lines for methane.
 Flame treat or solvent wash gas lines to remove oil.

Isobutane 99.99% purity

 Use a two-stage, 0-15 psi (0-1 bar) pressure regulator with a stainless steel diaphragm.
 Set the output pressure to the MS between 3 and 5 psi (0.2-0.3 bar).
 Use stainless steel gas lines for isobutane.
 Flame treat or solvent wash gas lines to remove oil.

Ammonia 99.99% purity

 Use a two-stage, 0-15 psi (0-1 bar) pressure regulator with a stainless steel diaphragm.
 Set the output pressure to the MS between 3 and 5 psi (0.2-0.3 bar).
 Use stainless steel gas lines for ammonia.
 Flame treat or solvent wash gas lines to remove oil.

395416500:3 15 of 18 Pre-installation Instructions

 Ammonia, Anhydrous (CAS Number 7664-41-7)
Anhydrous Ammonia gas is highly toxic. Inhalation may cause irritation to eyes and throat and
may cause pulmonary edema, which can result in serious injury or death. Repeated exposure
to Anhydrous Ammonia may cause permanent lung damage.
 Refer to the Material Safety Data Sheet (MSDS) for Anhydrous Ammonia for exposure
control/personal protection, handling/storage, accidental release, first aid, and fire
fighting measure requirements.
 Only use anhydrous ammonia with an appropriate ventilation system for the
instrument, the exhaust from the foreline pump, and the gas cylinder. Use appropriate
safety shutoff valves for the anhydrous ammonia supply and interconnecting lines.
You are responsible for determining and implementing appropriate precautions when
using anhydrous ammonia and for compliance with all governmental regulations. You are
responsible for understanding and adhering to all safe laboratory practices concerning the
use of toxic gases, including anhydrous ammonia.

 Check the checklist box: CI reagent gas, regulator, and gas lines are installed.

GC Carrier Gases
Helium
Helium is required as a carrier gas for the GC, with a minimum of 99.999% ultra-high purity, and
less than 1.0 ppm each of water, oxygen, and total hydrocarbons. The minimum requirement is
one 257 ft3 tank with an Alltech regulator #AL8111, or equivalent tank. Use a two-stage 0-100 psi
pressure regulator with a stainless steel diaphragm.

 Check the checklist box: Helium is at least 99.999% pure and the
appropriate regulator and gas lines are installed.

A carrier gas supply that has greater than 1 ppm oxygen or water
may significantly affect the performance of the GC/MS. It may also
damage components such as the capillary column, filaments, and
multiplier. Verify that your gas suppliers use controlled tanks to
ensure that purity standards are maintained. If you purchase pure
gases in contaminated tanks, your system may become
contaminated and require costly and time consuming repairs.

Optional Carrier Gas Filter

Use the optional carrier gas filters to protect your system from potential contamination and to
ensure optimum performance. For replacement procedures, refer to the instructions enclosed
with the filters. The easy-to-remove gas filter cartridge combines three highly adsorptive
materials in one filter to remove water, oxygen, and organic compounds. Install the carrier gas
filter so that the indicator is visible. Replace the filter when the indicator shows that the filter is
saturated, or after one year of service, depending on which comes first. For replacement
procedures, refer to the instructions enclosed with the filter.

395416500:3 16 of 18 Pre-installation Instructions

When the GC/MS Arrives
Inspection
After the 240-MS 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.
 Blue beads in the Tip (N) Tell arrow point.
Two Tip (N) Tell indicators and labels are affixed to
the exterior of the shipping boxes. Read and follow
the instructions on the label. If the Tip (N) Tell
arrow point is blue, the box was on its side or
tipped in transit, and the instrument may be
damaged.

If no external damage is apparent, sign the receiving documents, “Received but not inspected”
to indicate that the boxes have not been opened.
Varian will not accept liability for damage if you received obviously damaged materials
without noting the damage on the receiving documents.
Do not open any boxes. The Varian Representative opens them during installation. Move
the shipping containers to a warm, dry, secure area near the installation site.
If a shipping carton shows evidence of damage, do the following damaged shipping carton
procedure:
1. Report the conditions to the carrier when you receive the shipment.
2. Note the damage on all copies of the shipping documents.
3. Write a brief description of the damage.
4. Ask the driver to sign next to your comments to signify agreement with the
observations.
5. Contact the appropriate Varian office to report the damage.
Systems are shipped either FOB Varian or FOB Destination. The manner of shipment
determines who is responsible for filing a claim against the carrier if the system was damaged in
transit. Most systems are shipped FOB Varian, so the purchaser and the carrier are responsible
for any damages incurred during shipping. Contact the Varian office for assistance with filing
claims and billing repairs. If the system is shipped FOB Destination, contact the Varian office,
and that office will file a claim against the carrier.

 Check the checklist box: Shipping cartons examined for damage. If there was
any damage, the damaged shipping carton procedure was completed.

395416500:3 17 of 18 Pre-installation Instructions

 Unpacking and Installing
The Varian Representative will contact you to review the Pre-installation Checklist to ensure that
you have satisfied all of the site requirements. The Varian Representative will unpack and install
the instrument and demonstrate fundamental operation and maintenance procedures. The User
Representative must be available during the installation.
The Varian Representative will demonstrate that your system meets the performance
specifications unless there are additional criteria explicitly written into your sales contract.
Plan to analyze your samples only after the installation, which usually takes three days, is
finished.

Spare Parts
The 240-MS Ion Trap Hardware Operation Manual (part number 395416700) lists the spare
parts for routine operation.

Preventive Maintenance
You are responsible for performing routine and preventive maintenance of the GC, MS, data
system, and any other modules. Any instrument problems resulting from a contaminated gas
supply are billable and not included in the Warranty.
Perform regular preventive maintenance to increase the life of the system, to maximize system
operational time, and to optimize system performance. Refer to the 240-MS Ion Trap Hardware
Operation Manual for details. Your Varian Representative will describe and demonstrate these
procedures during the installation.

Trademark Acknowledgment
Microsoft® and Windows® are registered trademarks of Microsoft Corporation. Swagelok® is a
registered trademark of Swagelok Company, Solon, Ohio. Other brand and product names are
trademarks or registered trademarks of their respective holders.

395416500:3 18 of 18 Pre-installation Instructions