6500 and 6500+ Series of Instruments

Site Planning Guide

RUO-IDV-01-1150-C | D5032387 E February 2016

This document is provided to customers who have purchased SCIEX equipment to use in the operation of such SCIEX
equipment. This document is copyright protected and any reproduction of this document or any part of this document is
strictly prohibited, except as SCIEX may authorize in writing.
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. Warranties
are as stated therein.
Portions of this document may make reference to other manufacturers and/or their products, which may contain parts whose
names are registered as trademarks and/or function as trademarks of their respective owners. Any such use is intended only
to designate those manufacturers' products as supplied by SCIEX for incorporation into its equipment and does not imply
any right and/or license to use or permit others to use such manufacturers' and/or their product names as trademarks.
SCIEX warranties are limited to those express warranties provided at the time of sale or license of its products and are SCIEX’s
sole and exclusive representations, warranties, and obligations. SCIEX makes no other warranty of any kind whatsoever,
expressed or implied, including without limitation, warranties of merchantability or fitness for a particular purpose, whether
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and assumes no responsibility or contingent liability, including indirect or consequential damages, for any use by the purchaser
or for any adverse circumstances arising therefrom.
For research use only. Not for use in diagnostic procedures.
AB Sciex is doing business as SCIEX.
The trademarks mentioned herein are the property of AB Sciex Pte. Ltd. or their respective owners.
AB SCIEX™ is being used under license.
© 2016 AB Sciex

AB Sciex Pte. Ltd.

Blk 33, #04-06
Marsiling Ind Estate Road 3
Woodlands Central Indus. Estate.
SINGAPORE 739256

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Contents

Chapter 1 Introduction...............................................................................................................................5
Customer Site Planner Responsibilities..............................................................................................................................5
FSE Responsibilities............................................................................................................................................................6
During Installation.......................................................................................................................................................6
Operator Familiarization..............................................................................................................................................7
Technical Support..............................................................................................................................................................7
Chapter 2 Site Planning Checklist..............................................................................................................8
Customer Information........................................................................................................................................................8
Requirements.....................................................................................................................................................................8
Site Layout Requirements............................................................................................................................................8
Electrical Requirements................................................................................................................................................9
Gas Supply Requirements..........................................................................................................................................11
Ventilation and Waste-Collection Requirements........................................................................................................12
Computer and Network Requirements.......................................................................................................................12
Environmental Requirements.....................................................................................................................................13
Mass Spectrometer Bench Requirements...................................................................................................................14
Solutions and Equipment Requirements....................................................................................................................14
Product Familiarization..............................................................................................................................................14
Additional Site Planning............................................................................................................................................15
Comments and Exceptions...............................................................................................................................................15
Signoff.............................................................................................................................................................................15
Appendix A Site Requirements................................................................................................................16
Site Layout Requirements................................................................................................................................................16
Laboratory Layout and Site Clearances......................................................................................................................16
Weights and Dimension.............................................................................................................................................17
Electrical Requirements....................................................................................................................................................18
Mains Supply Connections.........................................................................................................................................18
Mains Supply Fluctuations.........................................................................................................................................21
Protective Earth Conductor........................................................................................................................................21
Uninterruptible Power Supply or Power Conditioner..................................................................................................21
System Electrical Specifications..................................................................................................................................21
Gas Supply Requirements................................................................................................................................................24
Optional Gas Generators...........................................................................................................................................26
Ventilation and Waste Collection Requirements..............................................................................................................26
Computer and Network Requirements.............................................................................................................................29
Acquisition Computer Requirements..........................................................................................................................29
Printer Requirements.................................................................................................................................................29
LAN Connection (Optional)........................................................................................................................................29
Environmental Requirements...........................................................................................................................................30

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Contents

BioSafety Requirements.............................................................................................................................................30
Sound Pressure Level.................................................................................................................................................31
Vibration....................................................................................................................................................................31
Customer-Supplied Solutions and Equipment..................................................................................................................31
Appendix B Equipment Safety Categories..............................................................................................33
Revision History........................................................................................................................................34

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Introduction 1
This guide is for the site planner, the individual responsible for preparing the facility for the installation of the
® +
QTRAP 6500 or 6500 system.
For safety and regulatory information, refer to the System User Guide, available at sciex.com.

Note: If the site preparation tasks are not complete when the SCIEX Field Service Employee (FSE) arrives, then
the scheduled installation will be postponed.

Customer Site Planner Responsibilities

Complete the Site Planning Checklist on page 8, in consultation with facilities services personnel (gas, electrical,
ventilation, and information technology [IT]), and return it to the FSE before the completion date. Refer to Signoff
on page 15.

Note: The FSE will follow up if the checklist is not received prior to the scheduled installation date.

• Verify that adequate space and the required shipping or receiving facilities are available. Refer to Site Layout
Requirements on page 16.
• Provide all required electrical receptacles. Refer to Electrical Requirements on page 18.
• Provide all required gas supplies, including shut off valves and regulators at the installation point. Refer to Gas
Supply Requirements on page 24.
• Provide and install all required vents and ventilation devices. Refer to Ventilation and Waste Collection
Requirements on page 26.
• Verify that the requirements for the computer and network are met. Refer to Computer and Network
Requirements on page 29.
• Provide a printer and (optional) active, tested LAN connection. Refer to Computer and Network Requirements
on page 29.
• Verify that the requirements for the operating environment are met. Refer to Environmental Requirements on
page 30.

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Introduction

• Provide all required solutions and laboratory equipment, including all fittings, and sample tubing for the liquid
chromatography (LC) equipment, unless purchased from SCIEX. Refer to Customer-Supplied Solutions and
Equipment on page 31.

CAUTION: Potential System Damage. Do not unpack the mass spectrometer crate or
computer boxes. The FSE will unpack and help move the mass spectrometer at the time
of the installation.

• When the shipment arrives, inspect the packaging for damage and inspect the shock and tip sensors, noting
any issues on the delivery receipt. Then, contact SCIEX Customer Service or the local FSE to schedule the
installation.
• If available, identify a qualified maintenance person (QMP) who is suitably aware of the electrical and chemical
risks associated with servicing laboratory equipment. The FSE will review the Qualified Maintenance
Person Guide with this person during the installation.
• Provide five staff members to assist in moving the system during installation.

FSE Responsibilities
• Review the checklist and discuss outstanding issues with the site planner.
• Supply all fittings, plugs, and cables required to connect the mass spectrometer to the electrical receptacles
and regulators. Electrical receptacles must be within the maximum distances described in this document.
• Assemble and set up any optional SCIEX benches ordered with the mass spectrometer.
• Unpack and set up the mass spectrometer, with the assistance of customer staff.
• Unpack and set up the acquisition computer.
• Unpack and set up optional LC equipment sold and supported by SCIEX. Integrate other supported LC equipment.
• Unpack and set up optional gas generator equipment sold by SCIEX.
• Test and qualify the system to the specifications in the Installation Checklist and Data Log.

During Installation

WARNING! Lifting Hazard. Make sure that at least six people are available to lift
the mass spectrometer. Follow established safe lifting procedures. Refer to Weights
and Dimension on page 17 for the weights of system components.

The FSE unpacks the system (with the assistance of customer staff), sets up the system, and then confirms its
operation. When the system reaches proper vacuum, the FSE conducts system performance tests.

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 Introduction

Note: It takes several days for the FSE to set up the system and confirm operation.

Operator Familiarization
During installation, the FSE provides a system and software overview, reviews data, and provides some basic
operator familiarization. Training for auxiliary equipment supplied by other manufacturers is not provided by the
FSE.

Note: Online training is available at sciex.com/education .

Technical Support
SCIEX and its representatives maintain a staff of fully-trained service and technical specialists located throughout
the world. They can answer questions about the system or any technical issues that might arise. For more
information, visit the SCIEX Web site at sciex.com.

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Site Planning Checklist 2

Customer Information
Organization
Address

City
Country
Telephone Zip/Postal code
Site planner contact Fax
name
E-mail address

Requirements
Site Layout Requirements
Refer to Site Layout Requirements on page 16.

Requirement Complete
The measured building clearances can accommodate the equipment and crate dimensions.  
If the requirements cannot be met, then contact the FSE.

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 Site Planning Checklist

Electrical Requirements
Refer to Electrical Requirements on page 18.

Requirement Complete N/A

Installation of electrical supplies and fixtures complies with local regulations and  
safety standards.
One branch circuit is provided for the mass spectrometer. The mains supply outlet  
is less than 1.6 m (63 inches) from the mass spectrometer. One outlet is required.
The outlet is accessible so that the mass spectrometer can be disconnected in an
emergency.
One branch circuit is provided for the roughing pumps. The mains supply outlet  
for the roughing pumps is less than 1.6 m (63 inches) from the roughing pumps.
Two outlets are required.
One branch circuit is provided for the acquisition computer, monitor, printer ,  
and options. At least two outlets are required, for the acquisition computer and
monitor.
For LC equipment and other options, contact the manufacturer for more
information.
(Optional) One branch circuit is provided for a standalone gas generator with an
   
air compressor. Contact the manufacturer of the gas generator for more
information.
The mains supply voltage does not fluctuate more than ±10% from the nominal  
voltage.

Note: Peripheral devices might have different mains supply fluctuation limits.
Confirm the mains supply fluctuation limit with the vendor of each peripheral
device that will be used with the mass spectrometer.

The mains supply includes a correctly installed protective earth conductor.  

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Site Planning Checklist

Requirement Complete N/A

(Optional) A customer-supplied UPS or power conditioner is provided for the
   
system. The UPS or power conditioner must deliver 230 VAC, 50 Hz or 60 Hz,
5000 VA (minimum). Refer to Uninterruptible Power Supply or Power Conditioner
on page 21.

Note: SCIEX sells and supports several UPS power protection units for mass
spectrometer systems that are custom configured to provide a total backup
power solution. Contact a SCIEX sales representative for more information.

A qualified electrician has determined the appropriate AC mains supply  

configuration based on the system electrical specifications found in System
Electrical Specifications on page 21.

Electrical Requirements (International)

Refer to Electrical Requirements on page 18.

Requirement Complete N/A

Electrical installations use locally approved standard connections and cables.
   

Electrical Requirements (North America)

Refer to Electrical Requirements on page 18.

Requirement Complete N/A

Branch circuits for the mass spectrometer and roughing pump are 15 A, 200 VAC
   
to 240 VAC (220 VAC typical), 50 Hz or 60 Hz. Receptacles for these branch
circuits are equipped with CSA/NEMA 6-15R straight-blade receptacles.
The branch circuit for the computer, monitor, and options is 15 A, 100 VAC to
   
240 VAC (120 VAC typical), 50 Hz or 60 Hz.
For requirements for LC equipment, contact the manufacturer.

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 Site Planning Checklist

Gas Supply Requirements

Refer to Gas Supply Requirements on page 24.

Requirement Complete N/A

Installation of gas supplies and connections complies with local regulations and  
safety standards.
Gas 1/Gas 2/bath gas is available:  
• Zero-grade air or a SCIEX-recommended gas generator
• Delivery pressure of 100 psi (6.89 bar) to 105 psi (7.25 bar) maximum with
® ®+
flows up to 22 L/min (or 26 L/min when the SelexION or SelexION
differential mobility separation technology device is installed)

Source exhaust gas is available:  

• Clean, dry, and oil-free air or ultra-high purity (UHP) nitrogen (99.999%) or
a SCIEX-recommended gas generator
• Delivery pressure of 55 psi (3.79 bar) minimum with flows up to 25 L/min
TM
Curtain Gas supply/bath gas/CAD gas is available:  
• UHP nitrogen or a SCIEX-recommended gas generator
• Delivery pressure of 55 psi (3.79 bar) to 60 psi (4.14 bar) with flows up to
18 L/min

(Optional) If a SCIEX mass spectrometer bench with a built-in gas generator or

   
if a SCIEX-recommended wall-mounted gas generator without a compressor is
used, then a supply of compressed oil-free air is provided. Contact the
manufacturer for more information.

TM
Note: Under normal conditions, bath gas is taken from the same supply as the Curtain Gas and CAD gas
flows.

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Site Planning Checklist

Ventilation and Waste-Collection Requirements

Refer to Ventilation and Waste Collection Requirements on page 26.

Requirement Complete
Installation of plumbing and ventilation fixtures complies with local regulations and safety  
standards.
Ventilation of the laboratory environment in which the mass spectrometer will be used complies  
with local regulations and the air exchange rate is appropriate for the work performed.
A minimum of 10 air exchanges/hour is required.
A negative flow vent is provided with a total flow rate capacity of 283 L/min (10 cfm), as  
measured at the inlet to the laboratory ventilation system.
A smooth fitting is provided for the roughing pump, with an outside diameter (o.d.) of 3.2 cm  
(1.25 inches). The vent is within 1.5 m (60 inches) of the exhaust port on the roughing pump
and at least 1 m (40 inches) above the floor.
A fitting is provided for the source exhaust drain bottle with an o.d. of 2.5 cm (1.0 inch). The  
vent is within 1.5 m (60 inches) of the source exhaust drain bottle.

Computer and Network Requirements

Refer to Computer and Network Requirements on page 29.

Requirement Complete N/A

A table is provided for the data acquisition workstation, located within 3 m (120  
inches) of the mass spectrometer.
A computer name and password are available.  
(Optional) A network or IT specialist is available to install the security software
   
while the FSE is present.
A network printer or a dedicated printer and necessary print drivers are available.  
(Optional) An active, tested LAN connection is available.
   
(Optional) The computer name and password supplied are a network computer
   
name and domain password.
(Optional) A network or IT specialist is available to connect the computer to the
   
company LAN while the FSE is present.
Internet access is available or software installation DVDs are available.  

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 Site Planning Checklist

Environmental Requirements
Refer to Environmental Requirements on page 30.

Requirement Complete N/A

The size of the laboratory is at least 31.7 cubic meters (1120 cubic feet).  
An ambient temperature of 15 °C to 30 °C (59 °F to 86 °F) is maintained.  
Over time, the temperature remains within a range of 4 °C (7.2 °F), with the rate
of the change in temperature not exceeding 2 °C (3.6 °F) per hour. Ambient
temperature fluctuations exceeding the limits might result in mass shifts in spectra.

Note: Peripheral devices might have different operating environment

requirements. Confirm the operating environment requirements with the vendor
of each peripheral device that will be used with the system.

Relative humidity is 20% to 80%, non-condensing.  

Air conditioning provides a minimum of 8700 Btu/hr (mass spectrometer and  
roughing pump only).
(Optional) A customer-supplied soft wall is installed behind the mass spectrometer
   
to reduce noise.

BioSafety Requirements
Refer to BioSafety Requirements on page 30.
Requirement Complete
The site is not designated as BioSafety Level 3 (BSL-3) or BioSafety Level 4 (BSL-4).  

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Site Planning Checklist

Mass Spectrometer Bench Requirements

Refer to Site Layout Requirements on page 16.

Requirement Complete
A moveable or fixed bench that meets the physical requirements (dimensions and mass) of  
the system as listed in Weights and Dimension on page 17 is provided for the mass
spectrometer with 1 m (40 inches) of clearance on all sides for service access.

Note: If the bench is moveable, then make sure that it is fixed during normal use.

Solutions and Equipment Requirements

Refer to Customer-Supplied Solutions and Equipment on page 31.

Requirement Complete
All of the required solutions and bottles are available.  
All of the required LC equipment and supplies are available.  

Product Familiarization
Requirement Complete N/A
An account has been obtained on the SCIEX Learning Portal, and the online  
learning modules have been completed.
Go to training.sciex.com and then click the link to request an account. When the
account information is received, complete the online learning modules.
(English-language proficiency) The Documentation Overview e-Learning module
   
has been completed, if required.
System documentation has been obtained and reviewed.  
Go to sciex.com/products.
(Optional) A qualified maintenance person (QMP) who is suitably aware of the
   
electrical and chemical risks associated with servicing laboratory equipment is
available for review of the service procedures with the FSE.

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Additional Site Planning

Requirement Complete N/A
Site planning for optional peripheral devices and software is completed, as
   
required.

Comments and Exceptions

Signoff
Site planner contact name Completion date
(yyyy-mm-dd)
I acknowledge that all of the installation requirements, as specified in this document, have  
been met.
FSE name Return date
(yyyy-mm-dd)
FSE e-mail

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Site Requirements A

Site Layout Requirements

Return to checklist.

Laboratory Layout and Site Clearances

Make sure that the site meets the required building clearances for installation and service access. Refer to Figure
A-1.

Figure A-1 Laboratory Layout

Item Description
1 Distance to wall, minimum 1 m (40 inches)
2 Acquisition computer

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Item Description
3 Distance to computer, up to approx 3 m (120 inches)
4 Optional LC system
5 Mass spectrometer (front), 79 cm × 79 cm (32 inches × 32 inches)

Weights and Dimension

Refer to the following tables for weights and dimensions and make sure that the system can be moved to the
installation site. Make sure that the installation site can accommodate the equipment dimensions, weight, and
associated clearance.
The mass spectrometer has been designed to support 77.5 kg (170 lbs). The optional SCIEX bench is designed to
support the weight of the mass spectrometer plus its associated load, roughing pumps, and an additional 77.5 kg
(170 lbs).

Table A-1 Mass Spectrometer and Bench

Equipment Height Width Length Weight

Crate 85 cm (34 inches) 112 cm (44 inches) 100 cm (39 inches) 88 kg (194 lbs)
Mass spectrometer 59 cm (24 inches) 79 cm (32 inches) 79 cm (32 inches) 130 kg (285 lbs)
Roughing pump 22 cm (9 inches) 30 cm (12 inches) 42 cm (17 inches) 34 kg (75 lbs)
(each)
Mass spectrometer 78 cm (31 inches) 100 cm (40 inches) 84 cm (34 inches) 136 kg (302 lbs)
bench (optional)
Mass spectrometer 78 cm (31 inches) 100 cm (40 inches) 84 cm (34 inches) 158 kg (348 lbs)
bench with gas
generator (optional)

Table A-2 Acquisition Computer

Equipment Height Width Length Weight

Dell OptiPlex XE2 36.0 cm (14.2 17.5 cm (6.9 inches) 41.7 cm (16.4 inches) 9.4 kg (20.68 lbs)
inches)
Monitor 35.42 cm (13.9 51.2 cm (20.1 inches) 18.0 cm (7.0 inches) 5.58 kg (12.28 lbs)
inches)
Shipping weight The acquisition computer and monitor are included in the Accessories box.

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Site Requirements

Electrical Requirements
Return to checklist.

WARNING! Electrical Shock Hazard. Use only qualified personnel for the installation
of all of the electrical supplies and fixtures, and make sure that all of the installations
adhere to local regulations and safety standards.

The total combined system (mass spectrometer and roughing pump) power consumption is 3400 VA (50 Hz or 60
Hz) at 230 VAC.
If the voltage changes more than 10% in 24 hours, use a power conditioner. High or low voltages can adversely
affect the electronic components of the equipment.

Mains Supply Connections

WARNING! Electrical Shock Hazard. Make sure that the system can be disconnected
from the AC mains supply outlet in an emergency. Do not block the AC mains supply
outlet.

Provide a minimum of three branch circuits. Refer to Figure A-2.

• One branch circuit for the mass spectrometer.
• One branch circuit for the roughing pumps.
• One branch circuit for the acquisition computer, monitor, and printer. This branch circuit can also be used for
®
options such as the NanoSpray ion source, and the mass spectrometer bench.
• (Optional) One branch circuit for a standalone gas generator with a compressor. Contact the manufacturer of
the gas generator for more information. The optional mass spectrometer bench can also be connected to this
branch circuit.

For electrical requirements for SCIEX-supplied components, refer to System Electrical Specifications on page 21.
For requirements for other components, such as the optional LC system, contact the manufacturer.

Note: Use receptacles that comply with local standards. Receptacles shown in Figure A-2 are representations
only.

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Figure A-2 Branch Circuit Configuration

Item Description
1 Branch circuit for the mass spectrometer. One outlet is required. It must be within 1.6 m (63
inches) of the mass spectrometer.
2 Branch circuit for the roughing pump. Two outlets are required. Outlets must be within 1.6 m
(63 inches) of the roughing pump.
3 Additional branch circuit for the acquisition computer, monitor, and printer, as well as any
options. The optional mass spectrometer bench can be connected to this branch circuit.
4 (Optional) One branch circuit with one or more outlets for a standalone gas generator with a
compressor. Contact the manufacturer of the gas generator for more information. The optional
mass spectrometer bench can be connected to this branch circuit.

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Site Requirements

International Requirements
• For installations outside of North America, use locally approved standard connections and cables.

Table A-3 Socket Types

Region Mains Power Socket Type

Central Europe CEE 7/7
Italy CEI 23-50 or CEE 7/7
Switzerland SEV1011
United Kingdom/Ireland BS13
Australia/New Zealand AS/NZS 3112
China GB-2009
Japan L6/20P
South Korea KSC8305
North America CSA/NEMA 6-15

North American Requirements

• Branch circuits for the mass spectrometer and roughing pump (branch circuits 1 and 2 in Figure A-2 on page
19) must be 15 A 200 VAC to 240 VAC (typical 220 V), 50 Hz or 60 Hz. Receptacles are equipped with CSA/NEMA
6-15R straight blade receptacles. Refer to Figure A-3.
• The branch circuit for the acquisition computer and monitor (branch circuit 4 in Figure A-2 on page 19) can
be 15 A 120 VAC.
• (Optional) Branch circuits and receptacles for the gas generator must meet the requirements in the documentation
supplied by the manufacturer.

Figure A-3 Duplex Receptacle and Plug

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Mains Supply Fluctuations

In areas where the mains supply is subject to voltage fluctuations exceeding ±10% of the nominal value (200 VAC
to 240 VAC), a power conditioner is required. High or low voltages can adversely affect the electronic components
of the mass spectrometer. Refer to Uninterruptible Power Supply or Power Conditioner on page 21.

Note: Peripheral devices might have different mains supply fluctuation limits. Confirm the mains supply fluctuation
limit with the vendor of each peripheral device that will be used with the mass spectrometer.

Protective Earth Conductor

WARNING! Electrical Shock Hazard. Do not intentionally interrupt the protective

earth conductor. Any interruption of the protective earth conductor creates an
electrical shock hazard.

The mains supply must include a correctly installed protective earth conductor that must be installed or checked
by a qualified electrician before the system is connected.

Uninterruptible Power Supply or Power Conditioner

Use a pure sine-wave uninterruptible power supply (UPS) or power conditioner to maintain the system supply
(mass spectrometer, computer, monitor, and roughing pump) during power outages.

Table A-4 UPS and Power Conditioner Requirements

Specification Requirement
Output voltage 200 VAC to 240 VAC True on line (double conversion)
Frequency 50 Hz or 60 Hz
Waveform Pure sine-wave
Minimum peak current 3 × nominal current
Output voltage distortion < 3%
Output protection Circuit breaker
Minimum power requirement 5000 VA

System Electrical Specifications

These tables contain the electrical specifications for the mass spectrometer, roughing pump, computer, and monitor.

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Site Requirements

Note: Specifications are subject to change without notice.

Table A-5 Mass Spectrometer Electrical Specifications

Specification Value
Nominal input voltage 200 VAC to 240 VAC
Frequency 50 Hz or 60 Hz
Maximum input current 10 A
Maximum input power 1000 VA

Table A-6 Roughing Pump Electrical Specifications

Specification Value
Nominal input voltage 200 VAC to 240 VAC
Frequency 50 Hz or 60 Hz
Maximum input current 6A
(each)
Maximum input power 1200 VA
(each)

Table A-7 Computer Electrical Specifications

Specification Value
Computer (Dell OptiPlex XE2)
Nominal input voltage 90 VAC to 264 VAC
Frequency 47 Hz or 63 Hz
Maximum input current 5 A (at 90 VAC) or 2.5 A (at 264 VAC)
Maximum input power 365 W
Monitor (Dell UltraSharp P2214H 21.5" Widescreen Flat Panel)
Nominal input voltage 100 VAC to 240 VAC
Frequency 50 Hz or 60 Hz
Maximum input current 2.5 A

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Table A-8 System Bench Electrical Specifications

Specification Value
Nominal input voltage 200 VAC to 240 VAC
Frequency 50 Hz or 60 Hz
Maximum input current 2A
Maximum input power 240 VA

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Site Requirements

Gas Supply Requirements

Return to checklist.

WARNING! Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Use only

qualified personnel for the installation of all gas supplies and connections,
and make sure that all installations adhere to local regulations and safety
standards.

CAUTION: Potential System Damage. Regulate each supply separately at the mass
spectrometer to prevent over pressure damage to the mass spectrometer.

CAUTION: Potential System Contamination. Use compression fittings for gas line connections.
Do not use liquid pipe sealant. If threaded fittings must be used, then Teflon tape can be
used to seal the threads. Do not use soldered fittings unless the tubing is thoroughly
cleaned afterwards.

Figure A-4 Recommended Gas Connections

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Item Gas Description Pressure Flow Rate Tubing

(max)
TM
1 Curtain Gas UHP N2 only 55 psi (3.79 bar) 18 L/min 1/4 inch (0.64 cm)
supply /bath minimum to 60 psi
gas/CAD gas (4.14 bar)
maximum
2 Gas 1/Gas 2/bath Zero grade air or 100 psi (6.89 bar) 22 L/min (or 26 1/4 inch (0.64 cm)
gas ultra-high purity to 105 psi (7.25 L/min with the
®
(UHP) N2 bar) SelexION or
®+
(99.999%) SelexION
technology option)
3 Source exhaust Clean, dry, oil-free 55 psi (3.79 bar) 25 L/min 1/4 inch (0.64 cm)
air or UHP N2 minimum to 60 psi
(4.14 bar)
maximum

Note: Gas quality, flows, and pressures must meet the requirements in Figure A-4, or a SCIEX-approved gas
generator must be used.

TM
Note: Under normal conditions, bath gas is taken from the same supply as Curtain Gas and CAD gas.

Note: Under some conditions, using air instead of nitrogen for Gas 1/Gas 2 might improve sensitivity and
signal-to-noise.

®
Note: When using the NanoSpray ion source, do not use UHP nitrogen for Gas 1/Gas 2, as there is an increased
risk of corona discharge, which can damage the emitter tip.

Note: The air input fitting on the back panel is a quick connect, shown in Figure A-5. The nitrogen input fitting
is a 1/4-inch Swagelok connection, shown in Figure A-6. All connections to the laboratory supply are Swagelok
connections, shown in Figure A-6.

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Figure A-5 Quick-connect Fitting

Figure A-6 Swagelok Connection and Tubing

Optional Gas Generators

Gas generators are available from SCIEX. Refer to the documentation supplied by the manufacturer for specifications
and for the number and type of outlets required.

Ventilation and Waste Collection Requirements

Return to checklist.

WARNING! Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Make

sure that the source exhaust system is connected and functioning and that
good general laboratory ventilation is provided. Adequate laboratory
ventilation is required to control solvent and sample emissions and to provide
for safe operation of the mass spectrometer.

WARNING! Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Use only

qualified personnel for the installation of plumbing and ventilation fixtures,
and make sure that all installations follow local bylaws and regulations.

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CAUTION: Potential System Damage. Do not connect the source exhaust hose to the vent.
The connection must be made by a qualified FSE.

• Provide a ventilation system with a total negative flow rate capacity of 283 L/min (10 cfm) at item 1 in Figure
A-7 and a minimum of 10 air exchanges per hour.
• Provide a smooth fitting for the roughing pump, with an outside diameter (o.d.) of 3.2 cm (1.25 inches). The
vent must be within 1.5 m (60 inches) of the exhaust port on the roughing pump, and at least 1 m (40 inches)
above the floor. Refer to Figure A-7.
• Provide a fitting for the source exhaust drain bottle with an o.d. of 2.5 cm (1.0 inch). The vent must be within
1.5 m (60 inches) of the source exhaust drain bottle. Refer to Figure A-7.

Figure A-7 Vent Connections

Item Description
1 Vent
2 Source exhaust hose: 2.5 cm (1 inch) inside diameter (i.d.)
3 Roughing pump exhaust hose: 3.2 cm (1.25 inches) i.d.

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Item Description
4 Source exhaust drain bottle. Make sure that the bottle is secured at all times to prevent spills.
5 Source exhaust drain tubing: 1.6 cm (0.625 inch) i.d.

Note: Source exhaust hose connections at the drain bottle, mass spectrometer, and the lab vent are secured
with hose clamps.

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Computer and Network Requirements

Return to checklist.

Acquisition Computer Requirements

The acquisition computer and monitor are provided with the mass spectrometer. The acquisition computer controls
the mass spectrometer. It should be used exclusively for data acquisition.
• Provide a table for the acquisition computer and monitor, within 3 m (120 inches) of the mass spectrometer.
• Provide a computer name and password that comply with these guidelines:
• The computer name does not have any spaces.
• The password for the computer is not blank.

Note: If the acquisition computer will be connected to the LAN, then this must be a network computer name
and password. Refer to LAN Connection (Optional) on page 29.

CAUTION: Potential System Damage. Other than security software, do not install
additional software on the acquisition computer. Changes to the configured software
could void the system warranty and cause the system to stop operating.

• If security software is required, then make sure that an IT specialist is available to install the security software
(anti-virus, anti-malware, or backup software) while the FSE is present.

Printer Requirements
The system can be connected to a network or dedicated printer.

Note: To use a network printer, connect the acquisition computer to the company network.

• Make sure that a printer and its associated print drivers are available before the scheduled installation.

LAN Connection (Optional)

To connect the acquisition computer to the network:
• Make sure that an active, tested LAN connection is in place before the scheduled installation date.
• Provide network credentials for the acquisition computer that comply with the guidelines provided for the
computer name and password, as specified previously.

Note: Do not change the network computer name after the software has been installed.

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• Make sure that an IT specialist is available to connect the computers to the LAN while the FSE is present.

Note: Internet access is required to download the necessary software from sciex.com/software-downloads-x2110.
We recommend that all of the software be downloaded in advance of the scheduled installation to expedite the
installation. If Internet access is not available, then the required software DVDs must be purchased in advance
and be available during the hardware installation. For more information, contact your sales representative.

Environmental Requirements
Return to checklist.

DANGER! Explosion Hazard. Do not operate the system in an environment containing

explosive gases. The system is not designed for operation in an explosive
environment.

• Minimum room size of 31.7 cubic meters (1120 cubic feet)

• An ambient temperature of 15 °C to 30 °C (59 °F to 86 °F)
Over time, the temperature must remain within a range of 4 °C (7.2 °F), with the rate of the change in
temperature not exceeding 2°C (3.6°F) per hour. Ambient temperature fluctuations exceeding the limits might
result in mass shifts in spectra.
• Relative humidity from 20% to 80%, non-condensing
• Cooling and venting for the mass spectrometer and roughing pump: 8700 Btu/hr

CAUTION: Potential System Damage. Do not place the roughing pump in an enclosed
unventilated area. Otherwise, the roughing pump will fail prematurely or shut down from
overheating and might cause severe damage to the mass spectrometer.

Note: Operation of the mass spectrometer at altitudes higher than 2000 m (6400 feet) above sea level might
impact mass spectrometer operation.

Note: Optional devices might have different operating environment requirements. Confirm the operating
environment requirements with the manufacturer of each peripheral device that will be used with the system.

BioSafety Requirements
The site must not be designated BioSafety Level 3 (BSL-3) or BioSafety Level 4 (BSL-4). SCIEX does not install,
service, or repair SCIEX systems in areas designated BSL-3 or BSL-4.

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Sound Pressure Level

Sound Pressure Value
Average sound pressure level for the mass spectrometer 6500: 70 dBa
+
6500 : 68 dBa

A sound pressure level of 85 dBA above a reference sound pressure of 20 μPa is at present regarded by many
authorities as the threshold at which a hazard might be caused. Special means, such as the use of protective ear
pieces, can make a higher sound pressure level non-hazardous to the operator.
SCIEX recommends that the sound pressure level be measured or calculated by the user both at the operator's
position in normal use and at whatever point 1 m from the enclosure of the equipment has the highest sound
pressure level. Refer to Laboratory Layout and Site Clearances on page 16 to minimize sound pressure levels to
the operator. Other methods such as the introduction of acoustic barriers or the fitting of noise-reducing baffles
or hoods might be used to minimize sound pressure levels.

Vibration
• The packaged mass spectrometer was tested to confirm that the effects of transportation do not affect mass
spectrometer performance upon arrival at the customer destination.
• The mass spectrometer is designed to operate in any laboratory environment that accommodates precision
analytical instrumentation.

Customer-Supplied Solutions and Equipment

Return to checklist.

WARNING! Toxic Chemical Hazard. Refer to the chemical product Safety Data Sheets
and follow all of the safety guidelines when handling, storing, and disposing of
chemicals. For health and safety precautions, refer to the System User Guide.

• Appropriate personal protective equipment, including powder-free gloves (nitrile or neoprene are recommended)
and safety glasses
• MS-grade ammonium acetate (100 mg)
• MS-grade acetonitrile (2 L)
• MS-grade methanol (2 L)
• MS-grade isopropanol (2 L)
• HPLC-grade deionized (DI) water (2 L)
• Formic acid, 99% or higher (50 mL)

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• Pipettors (20 µL, 100 µL or 200 µL, 1 mL) and tips

• LC system, including waste bottles and required tubing and cutter, unless ordered through SCIEX.
For requirements and specifications for the LC system, contact the manufacturer.
• Mass spectrometer bench, unless ordered through SCIEX. Refer to Weights and Dimension on page 17 .
• Table for the computer and monitor
• Printer
• Refrigeration for the MS PPG Chemical Kit provided by SCIEX
• (Recommended) A secondary containment tray to be installed under the roughing pumps, to capture potential
chemical spills

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Equipment Safety Categories B
Description Category
Equipment pollution degree Pollution Degree 2
Mains supply transient overvoltage Overvoltage Category II

Note: Environments with a Pollution Degree 2 rating include laboratories and sales and commercial areas.

For more information, refer to the International Electrotechnical Commission standards IEC 61010-1 and IEC 60364.

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Revision History

Document Number Reason for Change Date

D5032387 A First release of document. September 2012
D5032387 B Corrected source exhaust gas pressure value to 55 psi. December 2012
Revises system mains supply configuration. Added
laboratory layout diagram. Other minor revisions to align
content with other site planning guides.
RUO-IDV-01-0557-A Applied new template. Clarified gas generator mains June 2014
supply configuration. Updated source exhaust
information. Other minor revisions to align content with
other site planning guides.
+
RUO-IDV-01-0557-B Updated for 6500 series of instruments. June 2015
RUO-IDV-01-0557-C Updated "Computer and Network Requirements" and February 2016
"LAN Connection (Optional)" sections with the internet
access requirement when downloading the optional
software. Deleted note specifying not to use
polyethylene vials or bottles in the section
"Customer-Supplied Solutions and Equipment."

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