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