MDS SCIEX API 4000 LC/MS/MS Technical manual

http://www.appliedbiosystems.com
API 4000 LC/MS/MS
Site Planning Guide
P/N 1002198D
May 2002

This document contains information proprietary and confidential to MDS SCIEX,
a division of MDS Inc., and is for customer use in the operation and maintenance
of MDSSCIEX equipment or isfor vendor use inthe specification, fabrication, and
manufacture of MDS SCIEX designed component parts. Any other use, disclosure
to third parties, or reproduction of the information contained herein is strictly
forbidden, except as MDS SCIEX may authorize in writing.
Equipment that may be described in this document is protected under one or more
patents filed in the United States, Canada, and other countries. Additional patents
are pending.
Software that may be described in this document is furnished under a license
agreement. It is against the law to copy, modify, or distribute the software on any
medium, except as specifically allowed in the license agreement. Furthermore, the
license agreement may prohibit the software from being disassembled, reverse
engineered, or decompiled for any purpose.
Portions of this document may make reference to other manufacturers’ products,
which may contain parts that are patented and may contain parts whose names are
registered as trademarks and/or function as trademarks. Any such usage is intended
only to designate those manufacturers’ products as supplied by Applied
Biosystems/MDS SCIEX for incorporation into its equipment and does not imply
any right and/or license to use or permit others to use such product names as
trademarks.
All products and company names mentioned herein may be the trademarks of their
respective owners.
Applied Biosystems/MDS SCIEX makes no warranties or representations as to the
fitness of this equipment for any particular purpose and assumes no responsibility
or contingent liability, including indirect or consequential damages, for any use to
which the purchaser may put the equipment described herein, or for any adverse
circumstances arising therefrom.
Applied Biosystems/MDS SCIEX is a joint venture between Applera Corporation
and MDS SCIEX, the instrument technology division of MDS Inc.
For Research Use Only. Not for use in diagnostic procedures.
Equipment built by MDS SCIEX, a division of MDS Inc.,
at 71 Four Valley Dr., Concord, Ontario, Canada. L4K 4V8.
MDS SCIEX and Applied Biosystems are ISO 9001 registered.
© 2001, 2002 Applied Biosystems/MDS SCIEX, Joint Owners.
All rights reserved.
Printed in Canada.
ISO
900
1
REGISTERED
COMPANY

API 4000 Site Planning Guide Table of Contents
iii
Table of Contents
AboutthisManual ........................................................1
InternationalStandards ...................................................2
FederalCommunicationsCommissionCompliance.................................. 2
InternationalCompliance ...................................................... 2
CustomerSiteSetupCheckList.............................................3
CustomerResponsibilities...................................................... 3
The API 4000 Instrument ..................................................6
Introduction................................................................. 6
Connections................................................................. 7
SystemRequirements .....................................................8
WeightsandDimensions....................................................... 8
RoomDimensions............................................................ 9
OperatingEnvironment....................................................... 10
ElectricalRequirements ...................................................... 11
GasRequirements ........................................................... 12
ExhaustRequirements........................................................ 15
DrainVesselConsiderations................................................... 16
ComputerCommunicationsCableLayoutRequirements............................. 17
AnalystComputerSystemRequirements ......................................... 17
RecommendedSupplies ...................................................... 18
Customer-SuppliedEquipmentandFacilities ................................19
Solvents................................................................... 19
Gases..................................................................... 19
Electrical .................................................................. 19
Regulators ................................................................. 20
Ventilation................................................................. 20
AppendixA.............................................................21
Line Voltage Conditioning . . . ................................................. 21
LineInputCircuits .......................................................... 21

Table of Contents API Site Planning Guide
iv

API 4000 Site Planning Guide About this Manual
1
About this Manual
This site planning guide contains information intended to familiarize customers with the
necessary preparations and procedures for installing the API 4000 product and associated
peripherals.
The site planning guide contains detailed descriptions of the requirements for laboratory
layout and required customer supplies.
Within the scope of this manual, the following conventions are used:
WARNING! Indicates an operation that may cause personal injury if precautions
are not implemented.
WARNING! Indicates an operation that may involve flammable compounds.
CAUTION! Indicates an operation that may cause damage to the instrument if
precautions are not implemented.
NOTE: Emphasizes significant information in a procedure or description.

International Standards API 4000 Site Planning Guide
2
International Standards
Federal Communications Commission Compliance
This equipment has been tested and found to comply with the limits for a Class A digital
device, pursuant to Part 15 of the Federal Communications Commission Compliance
(FCC) rules. These limits are designed to provide reasonable protection against harmful
interference when the equipment is operated in a commercial environment. This
equipment generates, uses, and can radiate radio frequency energy and, if not installed and
used in accordance with the operator’s manual, can cause harmful interference to radio
communications. Operation of this equipment in a residential area is likely to cause
harmful interference in which case you will be required to correct the interference at your
own expense. Changes or modifications not expressly approved by the manufacturer could
void your authority to operate the equipment.
International Compliance
API 4000 LC/MS/MS instruments are in compliance with the following standards:
• EN 61326-1:1997
• EN 61010-1, EN 61010-2-061
• Class A of CISPR publication 11 and EN 55011:97
• IEC 1000-3-3, IEC 1000-4-2, IEC 1000-4-3,
IEC 1000-4-4, IEC 1000-4-5, IEC 1000-4-6, IEC 1000-4-8, and
IEC 1000-4-11
• CE Mark Declaration of Conformance is included with the instrument
• CSA C22.2 No. 1010.1-92, CSA C22.2 No. 1010.1-2-061:1995
• UL 3101-1
•FCC15AClassA

API 4000 Site Planning Guide Customer Site Setup Check List
3
Customer Site Setup Check List
Customer Responsibilities
Customer name _____________________________________________________________
Purchase Order number _____________________________________________________________
Customer Service Representative
Name and number _____________________________________________________________
Date _____________________________________________________________
Requirement OK Preinstallation Action Required
Lab Requirement and Supplies
A moveable bench for the API system or a
fixed bench with 1 m (3.3 ft) of rear clearance
and sufficient space underneath for the
roughing pump(s).
A bench for the data acquisition workstation,
located within 2 m (6.6 ft) of the main console.
One liter (1 L) quantities of HPLC or MS
grade methanol, acetonitrile, and water.
Tubing fittings required to connect any LC
equipment to the API unless the equipment
was sold by Applied Biosystems or was part of
an Applied Biosystems designed and
distributed workstation.
Space for benches and supplies
Gas Requirement
(three separately regulated gas lines with shut off valves and fittings)
Gas 1 and Gas 2 – Zero grade air, delivery
pressureat100psig,flowsupto17L/min.
Source exhaust pump – Oil-free air at
<50psig,flowsupto6L/min(airorN
2)
Curtain and CAD Gas – UHP nitrogen
(99.999%) or gas generators with impurities
that are known not to negatively impact
performance, delivery pressure at 60 psig,
flowsupto5L/min.

Customer Site Setup Check List API 4000 Site Planning Guide
4
Requirement OK Preinstallation Action Required
Environmental Requirements
API 4000 mass spectrometer: ambient
temperature of 15 °C to 30 °C (stable within
±2 °C) and relative humidity from 20 to 80%,
noncondensing.
Roughing pump(s): ambient temperature of
15 °C to 30 °C (stable within ±2°C) and
relative humidity from 20 to 80%,
noncondensing.
Venting Requirements
Two positive flow vents with 3.2 cm (1.25 in)
OD smooth fitting located within 1.5 m (5 ft)
of the roughing pump(s) outlets or two mist
filters.
One positive flow vent with sufficient tubing
to loosely couple the vent to the source exhaust
drain vessel supplied by Applied Biosystems/
MDS SCIEX.
Safety Requirements
Gas cylinders mounted to meet local safety
standards.
Gas delivery lines as required by local safety
standards.
Ventilation requires a vent to remove gases
from ion source exhaust.
Preparation of Samples
Test samples should be ABD P/N 401936
received and refrigerated.
Data Acquisition Workstation
Data acquisition workstation from Applied
Biosystems/MDS SCIEX.
Power Requirements
Two separate, 220 VAC (207-242 VAC),
15 amp circuits at 50/60 Hz, each with two
NEMA 6-15R receptacles (four in total)
located no more than 1.8 m (6 ft) from the
bench. These service the API 4000 mass
spectrometer and the roughing pump(s).

API 4000 Site Planning Guide Customer Site Setup Check List
5
Comments
The following sign-off acknowledges that the Site Planning Guide has been read and that
the site has been prepared and set up according to the specifications in this document, with
the limitations noted in the Preinstallation Action Required column.
Customer Signature ________________________________________
Title _____________________________________________________
Date _____________________________________________________
NOTE: Extra charges will apply if the site is not set up to specification or extra parts are
required.
Customer Service Representative Responsibilities
The Customer Service Representative for site set up and installation will:
1. Supply all fittings, plugs, tubing, and cables required to connect the API system to the
lab vents, electrical receptacles, and regulators, provided they are within the
maximum distances specified in this site planning guide.
2. Test and qualify the API system to the specifications in the installation test documents.
3. Assemble and set up any Applied Biosystems/MDS SCIEX benches, if ordered with
the instrument.
4. Only set up Applied Biosystems/MDS SCIEX supplied and manufactured LC
equipment.
5. Only connect and ensure RS-232 communications with peripheral devices unless they
are part of a workstation.
The Customer Service Representative for site set up and installation will not:
1. Supply regulators, shut off valves, electrical receptacles, solvents, or gases.
2. Supply LC fittings or tubing unless the equipment was sold by Applied Biosystems or
was part of an Applied Biosystems designed and distributed workstation.

The API 4000 Instrument API 4000 Site Planning Guide
6
The API 4000 Instrument
The API 4000 LC/MS/MS instrument, in addition to housing a mass spectrometer,
provides connection panels for gas inputs and exhaust, and electronic interfaces for the
data acquisition system.
Introduction
The API 4000 LC/MS/MS instrument is a Liquid Chromatography (LC) Mass
Spectrometer (MS), which incorporates an Atmospheric Pressure Ionization (API) ion
source.
API 4000 mass spectrometer– front view
API 4000 mass spectrometer–rear view

API 4000 Site Planning Guide The API 4000 Instrument
7
Connections
Electric power, gas, and exhaust connections to the instrument are located on the two rear
bulkheads, which are positioned on the rear corners of the mass spectrometer.
The gas and vacuum panel is located on the back of the instrument, closest to the ion
source housing. This panel contains the connections for the curtain gas supply,
Gas 1/Gas 2 supply, source exhaust supply, and source exhaust waste out. See the Gas and
Vacuum Panel figure below.
Gas and vacuum panel
The interface connection panel contains the connections for the main power connection
(207-242 VAC at 50/60 Hz), the Analyst computer interface, an RS-232 interface, and an
Auxiliary I/O port; see the Interface Connection Panel figure below.
Interface connection panel

System Requirements API 4000 Site Planning Guide
8
System Requirements
Weights and Dimensions
The API 4000 mass spectrometer is 130 cm (53 in) long by 50 cm (20 in.) wide by 52 cm
(21.5 in.) high. This instrument weighs approximately 136 kg (299.2 lb), excluding the
roughing pump(s) and the Line Adjustment Transformer (LAT) option.
The customer should supply a bench capable of supporting a minimum weight of 242 kg
(529 lb). The minimum suggested bench is 75 cm (30 in.) wide by 150 cm (60 in.) long by
75 cm (30 in.) high. In addition, the bench should have wheels for optimum operation and
service access. The optional API custom bench is the recommended bench. See the
Suggested bench height figure.
The roughing pump weighs approximately 36 kg (79 lb) and is 28 cm (11 in.) high by
16.5 cm (6.5 in.) wide by 50.8 cm (20 in.) long. For API 4000 instruments with two
roughing pumps, each pump weighs approximately 25 kg (55 lb) and is 50 cm (20 in.)
high by 24 cm (10 in.) wide by 52 cm (20.5 in.) long. The pump(s) should be located
underneath the API instrument on the mounting or damping plates included with the
special bench, but may be positioned on the floor within 1.5 m (5 ft) of the unit.
The Line Adjustment Transformer (LAT) option weighs approximately 15 kg (33 lb) and
is 20 cm (8.2 in.) high by 20 cm (8.2 in.) wide by 27.5 cm (11.5 in.) long. The Line
Adjustment Transformer (LAT) option should be located behind the instrument bench or
on the special bench shelf.
Suggested bench height

API 4000 Site Planning Guide System Requirements
9
Room Dimensions
At the time of service, the customer must provide the Customer Service Representative
with adequate access around the instrument. Provisions should be made for clearance of
approximately 1 m (3.3 ft) to any one side of the unit, as necessary.
NOTE: The custom bench option is the recommended bench. Use of wall-mounted, or
fixed benches will require custom installation.
For purposes of soundproofing, it is highly recommended that a softwall be located 1 m
behind the instrument or that you order a soundproof panel.
Suggested Room Layout
While the recommendations for room layout are flexible, the recommendations for
operating conditions should be followed as closely as possible to ensure proper and safe
equipment operation.
Top view of the suggested room layout

System Requirements API 4000 Site Planning Guide
10
Operating Environment
The site environment should be kept clean and generally dust-free. High standards of
cleanliness are expected. The instrument should be located in an area that is:
• Free of smoke and corrosive fumes
• Not prone to excessive vibration
• Out of direct sunlight
• Away from radiators
Mass Spectrometer
This instrument complies with Pollution Degree 2; Installation Category 2, Electrical
Insulation requirements. To ensure the proper operating conditions for the instrument, the
environmental conditions must be maintained within ±2 °C in the range of 15 °C and
30 °C (59 °F to 86 °F) with a relative humidity between 20 and 80% noncondensing.
An air conditioning unit with a capacity of 2550W (8700 Btu/h) is required for this API
system including the mass spectrometer, roughing pump(s), and the heat load from the
TurboIonSpray or Nebulizer heater.
Operation of the instrument above 2000 m (6500 ft) above sea level is not recommended.
Roughing Pump(s)
To ensure proper operation of the roughing pump(s), the ambient temperature must be
maintained between 15 °C and 30 °C (59 °F to 86 °F), with a relative humidity of 20 to
80% noncondensing.
NOTE: It is important that the roughing pump(s) not be put in an enclosed area. Without
proper ventilation, it will fail prematurely or shut down from overheating, and cause
severe damage to the instrument.

API 4000 Site Planning Guide System Requirements
11
Electrical Requirements
Applied Biosystems/MDS SCIEX recommends using two separate, 220 VAC
(207-242 VAC), 15 amp circuits at 50/60 Hz to supply power to the following items:
•APImainconsole
• Rouging (backing) pump
The Line Adjustment Transformer (LAT) option, P/N WC014179 is the recommended
means of supplying the required voltage if the 207-242 VAC at 50/60 Hz specification
cannot be met. If the line voltage fluctuates by more than 5% during a 24 hour period and
falls out of specified values, a power conditioner may be needed. Refer to Appendix A.
In North America, use 6-15R receptacles and 6-15P plugs. Outside of North America, use
local standardized power receptacles and plugs. A minimum of three electrical outlets are
required for the computer equipment. Consult the respective manufacturer’s
documentation for specifications.
Various outlets are required for LC pumps, autosamplers, Analog-to-Digital Converter
boxes and ultraviolet (UV) detectors. The respective manufacturers’ specifications contain
this information.

System Requirements API 4000 Site Planning Guide
12
Gas Requirements
The API 4000 instrument requires several types of input gas. The recommended purities
and pressures of these input gases should be adhered to for proper operation of the
instrument. The stated gas purities are given as required at the instrument.
NOTE: When switching gas sources while the instrument is running, ensure that a steady
supply is available as back up. If gas flow stops, the instrument will shut down.
Curtain/CAD Gas Supply
The gas supply for curtain and CAD gas requires an input of UHP (99.999%) nitrogen,
with an input pressure of 60 psig and flows up to 5 L/min.
Gas 1 and Gas 2
The gas supply for the Gas 1/Gas 2 connection requires an input of zero air or UHP
nitrogen with an input pressure of 100 psig to a maximum of 105 psig and flows up to
17 L/min. Nebulizer and sheath gas are derived from this input. The gas is internally
divided and controlled to provide one flow for TurboIonSpray nebulizer gas and heater
(turbo) gas, or APCI probe nebulizer gas, and a second flow for cooling and sheath gas.
Source Exhaust Supply
The source exhaust supply requires a regulated input of clean, dry, oil-free air at up to
50 psig and flows up to 6 L/min for the source exhaust (venturi) pump.
Component Gas Delivery (psig) Gas Purity Flow
Curtain and CAD
gas N260 psig max UHP N2(99.999%) 5 L/min
Gas 1 and Gas 2 Zero air/N2100psig Zeroair 17L/min
Source exhaust Clean, dry oil-
free air or N2
50 psig Clean, dry oil-free
air 6 L/min

API 4000 Site Planning Guide System Requirements
13
Suggested Gas Configurations
Gas connection schematic using dewar and separate air
Gas connection schematic using cylinders or separate air and house air
CAUTION! Operation of the API 4000 instrument requires that, if house gases are
being supplied, each supply be separately regulated at the instrument.
The preferred gas line connections are compression fittings. Liquid pipe sealant is not
acceptable for gas line connections. If threaded fittings must be used, only Teflon tape is
acceptable for sealing the threads. Soldered fittings are not acceptable unless the tubing is
thoroughly cleaned afterward.

System Requirements API 4000 Site Planning Guide
14
Gas Cylinder Considerations
• Fasten all gas cylinders securely to an immovable bulkhead or to a permanent wall.
NOTE: It is the user’s responsibility to permanently install gas supplies that conform
to local safety and building codes.
• Ensure that, when gas cylinders are stored in confined areas, such as a room,
ventilation is adequate to prevent accumulations that could displace sufficient oxygen
to suffocate the user. Move or store gas cylinders only in a vertical position with the
valve cap in place.
• Locate gas cylinders away from heat or ignition sources, including heat lamps.
Cylinders have a pressure-relief device that releases the contents of the cylinder if the
temperature exceeds 52°C (125°F).
• When storing cylinders outside of a building, the cylinders should be stored so that
they are protected against temperature extremes (including direct sunlight) and should
be stored above the ground on a suitable floor.
• Mark gas cylinders clearly to identify the contents and status (full, empty, etc.).
• Do not attempt to refill gas cylinders.
• Use only approved regulators and hose connectors. Left-hand thread fittings are used
for fuel gas tank connections, whereas right-hand fittings are used for oxidant and
support gas connections.
• Arrange gas hoses where they cannot be damaged or stepped on and where things
cannot be dropped on them.
• Perform periodic gas leak tests by applying a soap solution to all joints and seals.

API 4000 Site Planning Guide System Requirements
15
Exhaust Requirements
Exhaust from the API 4000 instrument originates from the source exhaust and roughing
pump(s).
Source Exhaust Pump
During operation, solvent vapors and effluent are exhausted from the vent chamber under
the ion source housing by the source exhaust pump (venturi pump) to a 1.27 cm (0.50 in.)
barbed fitting. This effluent must be drained to a drain vessel and vented to a fume hood or
an outside port. It is the responsibility of the customer to provide the proper plumbing
from the drain vessel to the ventilation point.
Roughing Pump Exhaust
The customer will be provided with the installation kit that includes a smoke eliminator
(mist filter) for the roughing pump(s). The system includes fittings and tubing to connect
the roughing pump(s) to the fume hood or other vents.
Venting System Recommendations
The following are recommendations for a customer-supplied vent system that may be used
to vent the roughing pump(s) and the ion source exhaust.
The exhaust flow rate at the instrument (the ability to vent the system) is dependent on the
blower provided by the customer, the duct length, the material and the number of elbows
(or bends) used. If an excessively long duct system or a system with many bends is used, a
stronger blower may be necessary to provide sufficient exhaust volume at the instrument.
Smooth stainless steel tubing should be used instead of flexible stainless steel tubing
where flexibility is not required to reduce system friction loss or drag. A length of smooth
stainless steel ducting has 20 to 30% less friction loss than a comparable length of flexible
ducting. When smooth stainless steel tubing is used, elbows must be used to turn corners.
These elbows should turn at an angle of 45 degrees to reduce friction losses, and a
minimum number of elbows should be used.
Additional recommendations for the venting system include the following items:
• The duct casing and venting system should be made of materials suitable for
temperatures as high as 70 °C (158 °F) and should meet local building standards.
• The vent system should produce a static vacuum of approximately 2 cm (0.75 in) of
water.
• The blower should be located as close to the discharge outlet as possible. All joints on
the discharge side should be airtight.
• The outlet end of the system should be equipped with a backdraft damper and the
necessary precautions should be taken to keep the exhaust outlet away from open
windows or inlet vents. The exhaust outlet should extend above the roof for proper
dispersal.
• The exhaust end of the system should be equipped with an exhaust stack to improve
the overall efficiency of the system.

System Requirements API 4000 Site Planning Guide
16
• The length of the duct that enters the blower must be a straight length and at least ten
times the duct’s diameter. An elbow entrance into the blower inlet causes a loss in
efficiency.
• Make-up air must be in the same quantity as the air exhausted by the system. An
airtight lab causes an efficiency loss in the exhaust system.
• The system should be checked to ensure it is drawing properly by placing a piece of
tissue near the mouth of the vent.
• The blower must be equipped with a power indicator light located near the instrument
to indicate to the operator when the blower is on.
Drain Vessel Considerations
A 10 L (3 gallon) drain vessel is supplied with the instrument. The vessel is made of
HDPE and is used to gather the effluent from the ion source housing. The drain vessel can
be placed under a fume hood, or a positive flow vent can be loosely coupled with the short
vent hose on the vessel to remove the exhaust gases from the laboratory. For loose
coupling, the small-diameter vent hose attached to the vessel may be inserted into a large-
diameter house exhaust pipe so that air is drawn along with the exhaust waste.
CAUTION! Do not connect the vent fitting on the drain vessel directly to a positive
flow vent. The additional vacuum could trip the source exhaust pump pressure
switch, indicating that the source exhaust pump is working when it is not, and
enable the instrument electronics.
WARNING! The drain vessel should NOT be stored in an enclosed storage area.
The drain system should be checked regularly and replaced when necessary.
NOTE: Should it become necessary to replace the drain vessel, the replacement should
be made from a material not likely to be attacked by samples being analyzed. Glass or
other brittle materials must not be used.