Agilent Technologies Varian 325-MS LC/MS User manual

Varian 325-MS LC/MS
Quadrupole Mass Spectrometer
Pre-installation Instructions
9300015500 Rev. C 1of 14 Pre-installation Instructions
Checklist
NOTE: Do not unpack the shipping cartons.
Check off each checklist box after satisfying each requirement as described in the instructions. All requirements
must be met before requesting installation.
NOTE: If the site is not ready for installation when the Varian Representative arrives, Varian, Inc.
reserves the right to invoice for the Representative’s time.
REQUIREMENTS ;
Installation site complies with all relevant safety regulations. 
User Representative will be available during the installation and certification period. 
Entrance to the installation site is at least 92 cm (36 in.) wide. 
Bench space is available for all components. 
Bench can support system weight.
325-MS with 460-LC at least 114 kg (250 lb)
325-MS with HTS PAL at least 103 kg (231 lb)

Bench does not vibrate. 
Exhaust system is suitable (2 L/min foreline pumps and separate 12 L/min for source). 
Temperature maintained between 16 and 30 °C, (61-86 °F). 
Relative humidity maintained between 20 and 80%. 
Installation site is free of excessive particulate matter. 
Specified electrical supply and power outlets are installed. 
Nitrogen gas (at least 99% pure), regulator, and gas lines installed. 
Air (less than 0.1 ppm hydrocarbons), regulator, and gas lines installed. 
Argon (greater than 99.0%), regulator, and gas lines installed. 
Materials and solvents of specified grade are on site. 
Shipping cartons examined for damage. If there was any damage, the conditions were reported. 
Requesting Installation
After preparing the site, contact the Customer Service office to schedule installation.

9300015500 Rev. C 2of 14 Pre-installation Instructions
Contents
Introduction ...................................................................2
Safety ......................................................................2
Before the Installation ...................................................3
User Representative................................................3
Entrance ..................................................................3
Bench Space and Load ...........................................3
Vibration ..................................................................6
Exhaust System.......................................................7
Temperature ............................................................7
Humidity...................................................................8
Particulate Matter ....................................................8
Power Requirements .............................................. 8
Installation Site Power ............................................ 9
Qualified Computer Equipment............................. 10
Gas Requirements ................................................ 10
Argon .................................................................... 11
Materials and Solvents ......................................... 11
When the LC/MS Arrives............................................ 13
Inspecting the Shipping Cartons........................... 13
Unpacking and Installing....................................... 14
Spare Parts ................................................................ 14
Preventive Maintenance............................................. 14
Introduction
The Pre-installation Instructions are a guide for each requirement of the checklist. Follow these
instructions to ensure that the installation requires no more than the usual three days. The
requirements in this document must be complete before scheduling an installation. Have the
completed checklist available to schedule the installation. The Varian Representative will install
your instrument, run the installation checks and tests; and once it‘s performance is accepted,
samples can be analyzed.
After meeting all of these requirements, contact the Customer Service office in your
region to schedule the installation.
The LC/MS operates reliably under carefully controlled environmental conditions. You must
provide suitable power sources, operating environment, materials, and solvents. Failures may
occur if you use or maintain the system outside of the power and operating environment ranges
and limits described in these instructions. The Varian Warranty and Service contract specifically
excludes the repair of failures due to such causes.
CAUTION
All phases of preparing the installation site must conform to
local safety, electrical, and building codes. These codes take
precedence over any recommendations in these
instructions. 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: Installation site complies with all relevant safety
regulations.

9300015500 Rev. C 3of 14 Pre-installation Instructions
Before the Installation
User Representative
Schedule the installation when the User Representative will be available. One of the important
duties of the Varian Representative is to familiarize the User Representative with the basic
functions of the LC/MS.
;Check off the checklist box: User Representative will be available during the
installation and certification period.
Entrance
Before arranging delivery of the LC/MS, determine that there is sufficient clearance to move the
shipping cartons to the installation site. The largest shipping carton is 72 cm (28 in.) wide by
92 cm (36 in.) long. If the cartons are to be moved with the pallet, at least 92 cm (36 in.)
clearance is needed. Allow additional room for maneuvering the shipping containers around
corners and through doors.
;Check the checklist box: Entrance to the installation site is at least 92 cm
(36 in.).
CAUTION
The MS, foreline pump, and LC are heavy. To prevent
personal injury, use appropriate moving and lifting
techniques.
Bench Space and Load
Use the following information to plan the layout of your LC/MS. The Varian Representative will
unpack the cartons and put the modules on the bench.
Figure 1 shows a possible layout for the LC/MS with the 212-LC pumps and the 460-LC
AutoSampler. Tables 1 and 2 provide information about the bench.
Figure 2 shows a possible layout for the LC/MS with the 212-LC pumps and the HTS PAL
AutoSampler. Tables 3 and 4 provide information about the bench.
The bench must be strong enough to support the weight of all modules, wide enough for all
modules, and at least 84 cm (33 in.) deep for the MS.

9300015500 Rev. C 4of 14 Pre-installation Instructions
212-LC and the 460-LC
Figure 1 shows a possible layout for the LC/MS with the 212-LC pumps and the
460-LC autosampler.
Figure 1 Suggested Layout with 212-LC and 460-LC
Table 1 and Table 2 list the dimensions and weights of the modules in Figure 1.
Table 1 Bench Width with the 460-LC
Bench
Width 212-LC 460-LC 325-MS CPU Monitor and Keyboard Total
cm 26 30 53.5 18.7 51 180 cm
in. 10.5 12 21 7.4 20 71 in.
Table 2 Bench Load with the 460-LC
Bench
Load 212-LC 460-LC 325-MS CPU
Monitor and
Keyboard Total
kg 14.5
without cooling 19
with cooling 21 61 11.5 5.5 without cooling 111.5 kg with cooling 113.5 kg
lb 32
without cooling 42
with cooling 46 134 25.3 11.5 without cooling 245 lb
with cooling 250 lb

9300015500 Rev. C 5of 14 Pre-installation Instructions
212-LC and HTS PAL
Figure 2 shows a possible layout for the LC/MS with 212-LC pumps and CTC HTS PAL
autosampler.
Figure 2 Suggested Layout with 212-LC and HTS PAL
Table 3 and Table 4 give the dimensions and weights of the modules in Figure 2.
Table 3 Bench Width with the HTS PAL
Bench
Width 212-LC 325-MS CPU
Monitor and
Keyboard Total
cm 26 53.5 18.7 51 150 cm
in. 10.5 21 7.4 20 59 in.
Table 4 Bench Load with the HTS PAL
Bench
Load 212-LC 325-MS and HTS PAL CPU Monitor and Keyboard Total
kg 14.5 71 11.5 5.5 102.5 kg
lb 32 162 25.3 11.5 231 lb
Additional Bench Considerations
The system requires a clean, flat bench. The bench must have enough space for the modules,
the mouse, solvent bottles, and such, see Table 5. The bench must be strong enough to
support the weight of the modules. The area under the bench must be large enough for the
foreline pumps. If the bench is against a wall, drill a hole in the back of the bench large enough
for the vacuum tubing of the foreline pumps. See Table 8 for information about the length of the
power cord, serial cable, and vacuum hoses for the MS40+ foreline pumps.
Plan to put the monitor and keyboard on the same bench as the LC/MS. If the plan is to use a
separate bench, position it within 3 m (10 ft) of the rear of the LC/MS. The CPU can go on or
under the bench.

9300015500 Rev. C 6of 14 Pre-installation Instructions
Table 5 Additional Bench Space Requirements
Function Space Allowance
Provide space for air circulation, gas
lines, and electrical connections. 15 to 30 cm (6 to 12 in.) behind the system.
Dissipate room heat and allow for
routine maintenance. At least 76 cm (30 in.) above the system.
Provide space for solvent bottles. At least 30 cm (12 in.) to side of the LC.
Please refer to the Varian LC Systems Pre-installation Instructions, part number 391483100, for
information about LC modules.
Use Table 6 and Table 7 to determine the required width of the bench and the weight the
bench must support for your configuration.
Regardless of configuration, the depth of the bench depends on the clearance between the
bench and the wall to accommodate the vacuum hoses for the foreline pumps.
•If the distance between the bench and the wall is greater than or equal to 10.2 cm
(4 in.) then the bench must be at least 84 cm (33 in.) deep. The vacuum hoses will have
sufficient room to connect the MS to the foreline pump.
•If the distance between the bench and the wall is less than10.2 (4 in.) then the bench
must be at least 94 cm (37 in.) deep. To accommodate the vacuum hoses, two 5.8 cm
(2.3 in.) holes must be drilled into the bench on the left side and to the rear of the MS
location.
Table 6 Bench Width Worksheet
Bench
Width ___-LC Auto-
sampler Other Components 325-MS CPU
Monitor and
Keyboard Total
cm ______ ______ ______ 53.5 18.7 51 ___cm
in. ______ ______ ______ 21 7.4 20 ____in.
;Check the checklist box: Bench space is sufficient.
Table 7 Bench Load Worksheet
Bench
Load ___-LC Auto-
sampler Other Components 325-MS CPU
Monitor and
Keyboard Total
kg ______ _______ ______ 61 11.5 5.5 ____kg
lb ______ ______ ______ 134 25.3 11.5 ____lb
;Check the checklist box: Bench can support system weight.
325-MS with 460-LC at least 114 kg (250 lb)
325-MS with HTS PAL at least 103 kg (231 lb)
Vibration
Ensure that the benches are free from vibrations, especially those caused by equipment in
adjoining locations. Because the foreline pump vibrates during operation, it belongs on the floor
below the LC/MS, not a on the bench with the LC/MS.
;Check the checklist box: Bench does not vibrate.

9300015500 Rev. C 7of 14 Pre-installation Instructions
MS40+ Foreline Pumps
The 325-MS uses two MS40+ foreline pumps. See Table 8 for more information.
Table 8 MS40+ Foreline Pump Details
Item Information
Diameter of hole in bench, if needed 5.8 cm (2.3 in.)
Width 29.7 cm (11.75 in.)
Depth 41.8 cm (16.5 in.)
Height 22.8 cm (9 in.)
Vacuum hose length 1.8 m (6 ft)
Power cord length 2.5 m (8 ft)
Serial cable length 2.7 m (9 ft)
Dedicated circuits Varian recommends:
1 circuit for each pump which can provide 200-240V ac,
50-60 Hz, 10A
If required both pumps can use a single circuit which can
provide 200-240V ac, 50-60 Hz, 20A
Power cord plug CEE 7/7 or NEMA 6-15P
Exhaust System
Do not put the foreline pumps in an enclosed space. Foreline pumps exhaust most compounds
introduced into the MS and small amounts of oil vapor.
Provide an adequate fume exhaust system for the outlet of each foreline vacuum pump. Each
foreline pump must be vented at least 2 L/min. The API spray chamber must be vented at least
20 L/min to a separate vent line. Ensure that the exhaust system does not pull a vacuum on the
API chamber. Consult local regulations for the proper method of exhausting the fumes.
;Check the checklist box: Exhaust system is suitable.
Temperature
The optimal operating temperature is between 16 and 30 °C (61-86 °F).
NOTE: As installation site temperature increases, system reliability decreases due to heat
generated by electronic components during operation. This heat must dissipate to the
surrounding air for reliable operation.
The airflow around the system must be adequate. The air-conditioning system must maintain a
constant temperature (within the operational limits) around the system. Do not place the system
near air ducts, windows, or heating and cooling systems. The average steady-state heat load
for the MS alone is 6,000 Btu, with a possible short-term heat dissipation of 15,000 Btu during
startup.
;Check the checklist box: Temperature maintained between 16 and 30 °C
(61-86
° F).

9300015500 Rev. C 8of 14 Pre-installation Instructions
Humidity
The relative humidity of the operating environment must be between 20 and 80%, with no
condensation. Operating the LC/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 create condensation and result in short circuits.
Varian recommends using a combination temperature and humidity monitor at the installation
site.
;Check the checklist box: Relative humidity maintained between 20 and 80%.
Particulate Matter
Your installation site must not have excessive dust, smoke, or other particulate matter.
Particulate matter may block airflow vents causing the electronics to overheat.
;Check the checklist box: Installation site is free of excessive particulate matter.
Power Requirements
212-LC
The 212-LC requires 85-264V ac; 47-63 Hz; 60 Watts 100 VA
460-LC
The 460-LC requires 95-240V ac± 10%; 50 - 60 Hz; 200 VA.
325-MS
The 325-MS requires a separate circuit, and the outlet must have adequate amperage capacity
and a reliable ground. The power source must be clean and capable of providing up to
200-240V ac, 50/60 Hz ±3 Hz, 1.0 kW.
325-MS LC/MS
The 325-MS LC/MS requires the following:
•325-MS: One circuit for the MS, 10A, 200-240V ac.
•MS40+: Varian recommends one dedicated circuit for each pump, which can provide
200-240V ac, 50-60 Hz, 10A. If required, both pumps can use a single circuit that can
provide 200-240V ac, 50-60 Hz, 20A.
•Other modules: See the user manual.
Table 9 LC/MS Power Requirements
Module Max Current Draw (Amps)
200-240V ac
325-MS 10A
2 each MS40+ foreline pumps 1 circuit for each pump which can provide10A
If required both pumps can use a single circuit which can
provide 20A

9300015500 Rev. C 9of 14 Pre-installation Instructions
Use a separate dedicated power source for HPLC modules and additional instruments and
equipment. Never plug the mass spectrometer and the chromatograph 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. Figure 3 displays the power cords and Table
10 provides more information.
Figure 3 Outlets and Power Plugs
Table 10 Power Cords
Power Cord 325-MS MS40+ Foreline Pumps
Length 1 each 2.5 m (8 ft) 2 each 2.5 m (8 ft)
Type 1 each CEE 7/7 or
1 each NEMA 6-15P
2 each CEE 7/7 or
2 each NEMA 6-15P
The power cables for the CPU, monitor, and printer are approximately 2.13 m (7 ft) long. They
have NEMA 5-15P plugs.
CAUTION
Replacing or substituting power cords or plugs must be done
with strict compliance with all regulations, including electrical
codes, power cord color coding, and appropriate regulatory
agency certification marks.
Installation Site Power
In the United States, the power supply to the installation site must be 200-240V ac for the MS
and the foreline pump and 100-120V ac for the LC, autosampler, computer, printer and other
modules. In Europe, the power supply to the site must be 200-240V ac.
All power supplies must 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
EN/IEC 61000-4-5 and IEC 61000-4-11 standards for voltage stability.

9300015500 Rev. C 10 of 14 Pre-installation Instructions
A measured ground to neutral potential of greater than 3V ac or V dc indicates grounding
problems that may need correction. Evaluate any power source suspected of having noise
problems with a recording-type power line monitor before operating the system.
NOTE: If there is concern about the quality of the power, install an uninterrupted power supply,
or a power conditioner or both. The maximum power consumption is 3600 VA.
;Check the checklist box: Specified electrical supply and power outlets are
installed.
Qualified Computer Equipment
If the Varian MS Workstation software is to be installed on a computer not purchased
from Varian, the customer is responsible to ensure that the computer is adequately
equipped and compatible with the operation of the data system and its communication
interfaces. Please check the current list of requirements, available at the following web
site.
http://www.varianinc.com/cgi-bin/nav?products/chrom/gcms/msws_computer_req
Varian does not guarantee the function of the Varian MS Workstation software on
computer hardware or operating systems that do not meet the specified requirements.
NOTE: Contact your Sales Representative for a list of qualified equipment or for more
information.
Gas Requirements
Nitrogen
A nitrogen gas supply that can provide up to a maximum of 20 L/min of gas regulated at 80 psi
is sufficient for vESI or APCI operation for one LC/MS. The nitrogen must be at least 99% pure
with less than 0.1 ppm hydrocarbons and less than 1% oxygen. It must be clean and dry with a
−40 °C dew point. Use a nitrogen generator, or liquid nitrogen boil-off to supply the nitrogen
gas. The Varian Warranty does not cover MS problems caused by poor gas quality. It is the
responsibility of the customer to conform to all regulations regarding the installation and
operation of the gas system. The nitrogen supply uses ¼ in. connectors.
;Check the checklist box: Nitrogen gas (at least 99% pure), regulator, and gas
lines are installed.
Air
A compressed air gas supply, capable of providing up to 3 L/min of gas regulated to 80 psi with
a two-stage regulator, is required as a nebulizing gas for negative vESI. The customer is
responsible to conform to all regulations for the installation and operation of the gas system.
The air must be clean and dry, with less than 0.1 ppm total hydrocarbons, including methane,
and have a −40 °C dew point. The air supply uses ¼ in. connectors.
;Check the checklist box: Air (less than 0.1 ppm hydrocarbons), regulator, and
gas lines are installed.

9300015500 Rev. C 11 of 14 Pre-installation Instructions
Argon
Argon is required as a collision gas for MS/MS work. The argon supply uses 1/8 in. connectors.
Use a two-stage 0-100 psi pressure regulator with a stainless steel diaphragm. The purity of the
argon must be greater than 99.0%.
;Check the checklist box: Argon (greater than 99.0%), regulator, and gas lines
are installed.
Materials and Solvents
The Varian Representative will prepare solutions to tune and evaluate the LC/MS. Please
supply the materials on Table 11 and the solvents on Table 12.
Table 11 Materials
Quantity (each) Material
2 50 mL clean and new volumetric flask
2 1 L clean and new bottle for mobile phase reservoirs
1 1 L or larger bottle for LC/MS waste
2 10 mL clean and new volumetric flask
2 100 mL clean and new volumetric flask
1 Pipette 100 to 1000 µL and tips
1 Pipette 20 to 200 µL and tips
1 50 mL clean and new volumetric flask (for optional APCI)
1 500 mL clean and new volumetric flask (for optional APCI)
Table 12 Solvents for vESI or APCI
Quantity (each) Solvent
2 4-liter bottle LC/MS grade or better water, new and unopened
2 4-liter bottle LC/MS grade or better, acetonitrile, new and unopened

9300015500 Rev. C 12 of 14 Pre-installation Instructions
The following illustrate how critical LC/MS grade solvents are for optimum performance. The MS
is sensitive enough to detect impurities in HPLC solvents, which can cause a very noisy
baseline.

Figure 4 Signal-to-Noise Ratio with HPLC Grade Solvents

Figure 5 Signal-to-Noise Ratio with LC/MS Grade solvents
Additional tubing is required to complete installation. Most of this tubing is included in the
accessory kits of the LC modules. Additional tubing (PEEK™ or stainless steel) may be required
for installation of special valves or modules. For most analytical HPLC systems, use 1/16 in. OD
tubing with an ID of 0.005 in. To prevent peak broadening use at least 0.005 in ID downstream
of the sample injector and autosampler. Keep tubing as short as possible to prevent peak
broadening and to minimize run time.
;Check the checklist box: Materials and solvents of specified grade are on site.

9300015500 Rev. C 13 of 14 Pre-installation Instructions
When the LC/MS Arrives
Inspecting the Shipping Cartons
Do not open any shipping cartons. The Varian Representative opens them during
installation. Move the shipping cartons to a warm, dry, and secure area near the
installation site.
After the instrument arrives, carefully inspect the exterior of the shipping cartons for evidence of
any damage that could have occurred during shipment. Inspect the cartons for the following:
•Water stains.
•Cuts, punctures, or deep indentations.
•Crushed corners or excessively abraded edges.
•Arrow point on the Tip N Tell™ indicator is blue.
•ShockWatch® indicator tube is red.
Tip N Tell ShockWatch
One indicator is on the
exterior. Read and follow the
instructions on the label. If the
Tip N Tell arrow point is blue,
the carton was on its side or
tipped in transit and
instrument damage may have
occurred.
One indicator is on the exterior. Read and follow the instructions on the
label. If the tube on the ShockWatch indicator is red, the carton was
dropped in transit and instrument damage may have occurred.
The instrument label may be yellow, purple, or red, depending on the
sensitivity of the instrument to impact that exceeds a specified G-level
force.
If no external damage is apparent, write “Received but not inspected” on the receiving
documents to indicate that the cartons were not opened.
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 any damages incurred in shipment are the
responsibility of the purchaser and the carrier. Contact the Varian office for assistance with filing
claims and billing repairs. If the system ships FOB Destination, contact the Varian office, and
that office will file a claim against the carrier.

9300015500 Rev. C 14 of 14 Pre-installation Instructions
Varian will not accept liability for damage if obviously received damaged materials were
received without noting the damage on the receiving documents.
;Check the checklist box: Shipping cartons inspected for damage. If there was
any damage, the conditions were reported.
Unpacking and Installing
The Varian Representative will review the Pre-installation Checklist with the customer to ensure
that the site requirements were met. The Varian Representative will unpack and install the
instrument and demonstrate the fundamental operation and maintenance procedures. The User
Representative must be present during the installation.
The Varian Representative will demonstrate that the system meets the performance
specifications, which are on the data sheet and any additional criteria explicitly written into the
sales contract.
Plan to analyze samples only after the installation is complete and the conditions of delivery
accepted. The process requires at least three days.
Spare Parts
Please refer to the 325-MS LC/MS Quadrupole Hardware Manual, part number 9300017200,
which has a list of spare parts for routine operation.
Preventive Maintenance
The customer is responsible for performing routine and preventive maintenance of the LC,
autosampler, MS, and data system. If using a nitrogen generator, perform the preventive
maintenance to ensure that the nitrogen supply is clean and dry. Any instrument problems
resulting from a contaminated gas supply are billable and not included in the Varian Warranty.
Perform regular preventive maintenance to increase the life of the system, to maximize system
uptime, and to optimize system performance. Please refer to the 325-MS LC/MS Quadrupole
Hardware Manual, part number 9300017200, for details. The Varian Representative will
describe and demonstrate these procedures during the installation.
Trademark Acknowledgment
Microsoft® and Windows® are registered trademarks of Microsoft Corporation. PEEK™ is a
registered trademark of the Victrex PLC Company, Lancashire, England. Other brand and
product names are trademarks or registered trademarks of their respective holders.