Thermo Scientific MS/ETD User manual

MS/ETD System
Getting Connected Guide
98000-97005Rev A April 2007

© 2007 Thermo Fisher Scientific Inc. All rights reserved.
Xcalibur™ and LTQ™ are trademarks of Thermo Fisher Scientific Inc.
All other trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries.
Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use
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Fisher Scientific Inc.
The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document
supersede all previous information received by the purchaser.
Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or error-
free and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might
result from any use of this document, even if the information in the document is followed properly.
This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a
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Terms and Conditions of Sale shall govern all conflicting information between the two documents.
Printing History: Revision A released in April 2007
Software Version: Xcalibur 2.0, LTQ 2.3

Regulatory Compliance
Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with
applicable domestic and international regulations. When the system is delivered to you, it meets all pertinent
electromagnetic compatibility (EMC) and safety standards as described below.
EMC Directive 89/336/EEC
EMC compliance has been evaluated by TUV Rheinland of North America, Inc.
Low Voltage Safety Compliance
This device complies with Low Voltage Directive 73/23/EEC and harmonized standard EN 61010-1:2001.
Changes that you make to your system may void compliance with one or more of these EMC and safety standards.
Changes to your system include replacing a part or adding components, options, or peripherals not specifically
authorized and qualified by Thermo Electron. To ensure continued compliance with EMC and safety standards,
replacement parts and additional components, options, and peripherals must be ordered from Thermo Electron or one
of its authorized representatives.
FCC Compliance Statement
EN 61000-3-2 1995, A1; 1998, A2; 1998, A14; 2000 IEC 61000-4-4 A2; 2001; A2-1995
EN 61000-3-3 1998 EN 61000-4-5 1995, A1; 2001
EN 61326-1 1998, A3 IEC 61000-4-5 2005
EN 61000-4-2 2000 EN 61000-4-6 1996, A1; 2001
IEC 61000-4-2 2001 IEC 61000-4-6 2004
EN 61000-4-4 1995, A1; 2001 EN 61000-4-11 1994, A1; 2001
IEC 61000-4-11 2001-03
FCC Class A, CFR 47 Part 15, 2005 CISPR 11 1999, A1; 1999, A2; 2002
THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES. OPERATION IS SUBJECT TO
THE FOLLOWING TWO CONDITIONS: (1) THIS DEVICE MAY NOT CAUSE HARMFUL
INTERFERENCE, AND (2) THIS DEVICE MUST ACCEPT ANY INTERFERENCE RECEIVED,
INCLUDING INTERFERENCE THAT MAY CAUSE UNDESIRED OPERATION.
CAUTION: Read and understand the various precautionary notes, signs, and symbols
contained inside this manual pertaining to the safe use and operation of this product before
using the device.

Notice on Lifting and Handling of
Thermo Electron San Jose Instruments
For your safety, and in compliance with international regulations, the physical handling of this
Thermo Electron San Jose instrument requires a team effort for lifting and/or moving the instrument. This
instrument is too heavy and/or bulky for one person alone to handle safely.
Notice on the Proper Use of
Thermo Electron San Jose Instruments
In compliance with international regulations: If this instrument is used in a manner not specified by
Thermo Electron San Jose, the protection provided by the instrument could be impaired.
Notice on the Susceptibility
to Electromagnetic Transmissions
Your instrument is designed to work in a controlled electromagnetic environment. Do not use radio frequency
transmitters, such as mobile phones, in close proximity to the instrument.

WEEE Compliance
This product is required to comply with the European Union’s Waste Electrical & Electronic
Equipment (WEEE) Directive 2002/96/EC. It is marked with the following symbol:
Thermo Fisher Scientific has contracted with one or more recycling or disposal companies in each
European Union (EU) Member State, and these companies should dispose of or recycle this product.
See www.thermo.com/WEEERoHS for further information on Thermo Fisher Scientific’s compliance
with these Directives and the recyclers in your country.
WEEE Konformität
Dieses Produkt muss die EU Waste Electrical & Electronic Equipment (WEEE) Richtlinie 2002/96/EC
erfüllen. Das Produkt ist durch folgendes Symbol gekennzeichnet:
Thermo Fisher Scientific hat Vereinbarungen mit Verwertungs-/Entsorgungsfirmen in allen EU-
Mitgliedsstaaten getroffen, damit dieses Produkt durch diese Firmen wiederverwertet oder entsorgt
werden kann. Mehr Information über die Einhaltung dieser Anweisungen durch Thermo Fisher
Scientific, über die Verwerter, und weitere Hinweise, die nützlich sind, um die Produkte zu
identifizieren, die unter diese RoHS Anweisung fallen, finden sie unter www.thermo.com/
WEEERoHS.

Conformité DEEE
Ce produit doit être conforme à la directive européenne (2002/96/EC) des Déchets d'Equipements
Electriques et Electroniques (DEEE). Il est marqué par le symbole suivant:
Thermo Fisher Scientific s'est associé avec une ou plusieurs compagnies de recyclage dans chaque état
membre de l’union européenne et ce produit devrait être collecté ou recyclé par celles-ci. Davantage
d'informations sur la conformité de Thermo Fisher Scientific à ces directives, les recycleurs dans votre
pays et les informations sur les produits Thermo Electron qui peuvent aider la détection des substances
sujettes à la directive RoHS sont disponibles sur www.thermo.com/WEEERoHS.

Thermo Electron Corporation MS/ETD Getting Connected Guide vii
Preface............................................................................................... ix
About This Guide............................................................................... ix
Related Documentation...................................................................... ix
Safety and Special Notices................................................................... ix
Contacting Us...................................................................................... x
Assistance ......................................................................................... x
Changes to the Manual and Online Help ......................................... x
Chapter 1 Making the External Connections..............................................................1
Vacuum and Gas Connections............................................................. 2
Electrical Connections ......................................................................... 6
Chapter 2 Powering Up ...................................................................................................9
Chapter 3 Upgrading the Software and Configuring the System ..........................11
Index...............................................................................................................15
Contents

Thermo Electron Corporation MS/ETD Getting Connected Guide ix
Preface
About This Guide Welcome to the Thermo Electron MS/ETD System. The MS/ETD System is a
member of Thermo Electron family of mass spectrometer (MS) detectors.
This manual describes how to upgrade an LTQ mass spectrometer to an LTQ XL
mass spectrometer, how to connect the ETD Module to the mass spectrometer, and
how to connect the MS/ETD System (consisting of the ETD Module and the LTQ
XL MS detector) to hook-ups in your laboratory.
This manual is intended to be used by Thermo Electron Service Engineers only.
Related
Documentation
In addition to this guide, Thermo Electron provides the following documents for
the MS/ETD System as PDF files:
• MS/ETD System Preinstallation Guide
• MS/ETD System Getting Started
•MS/ETD Module Hardware Manual
• LTQ XL manual set
Help is also available from within the software.
Safety and Special
Notices
Make sure you follow the precautionary statements presented in this guide. The
safety and other special notices appear in boxes.
Safety and special notices include the following:
CAUTION Highlights laser-related hazards to human beings. It includes
information specific to the class of laser involved. Each DANGER notice is
accompanied by the international laser radiation symbol.
CAUTION Highlights hazards to humans. Each CAUTION notice is
accompanied by an appropriate CAUTION symbol.

Preface
xMS/ETD Getting Connected Guide Thermo Electron Corporation
Contacting Us There are several ways to contact Thermo Electron.
Assistance For new product updates, technical support, and ordering information, contact us
in one of the following ways:
Visit Us on the Web
www.thermo.com/finnigan
Contact Technical Support
Phone: [phone]
Fax: [phone]
[email protected]
Contact Customer Service
In the US and Canada for ordering information:
Phone: [phone]
Fax: [phone]
International contacts for ordering information:
Visit www.thermo.com/finnigan for the current listing,
CAUTION Highlights electric shock related hazards to human beings. Each
electric shock notice is accompanied by the international High Voltage symbol.
CAUTION Highlights heat-related hazards to human beings. Each Heat notice is
accompanied by the international Heat symbol.
IMPORTANT Highlights information necessary to avoid damage to software, loss
of data, invalid test results, or information critical for optimal performance of the
system.
Note Highlights information of general interest.
Note Helpful information that can make a task easier.

Preface
Thermo Electron Corporation MS/ETD Getting Connected Guide xi
Changes to the Manual
and Online Help
To suggest changes to this guide or to the online Help, use either of the following
methods:
• Fill out a reader survey online at www.thermo.com/lcms-techpubs
• Send an e-mail message to the Technical Publications Editor at
[email protected]

Thermo Electron Corporation MS/ETD Getting Connected Guide 1
Chapter 1 Making the External
Connections
This chapter explains the external connections that are made to the MS/ETD
system. External connections consist of connections to vacuum pumps, gases and
sources of electricity.
This chapter contains the following sections:
•Vacuum and Gas Connections
•Electrical Connections

1Making the External Connections
Vacuum and Gas Connections
2MS/ETD Getting Connected Guide Thermo Electron Corporation
Vacuum and Gas
Connections
This section describes how to make the vacuum and gas connections to the
MS/ETD system.
To connect the vacuum hoses and gas lines to the MS/ETD system
1. To connect the vacuum hose to the forepump port for the MS detector
a. Attach the forepump O-ring to the MS forepump port on the back of the
ETD module as shown in Figure 1.
Figure 2 shows the forepump ports on the back of the ETD module.
Figure 1. Attaching the O-ring to the forepump port for the MS detector
Figure 2. Forepump ports
MS Detector
Forepump Port
ETD Module
Forepump Port

1 Making the External Connections
Vacuum and Gas Connections
Thermo Electron Corporation MS/ETD Getting Connected Guide 3
b. Place the forepump hose clamp on the end of the vacuum hose, and then
attach the hose to the forepump port for the MS detector.
c. Tighten the hose clamp around the vacuum hose and port as shown in
Figure 3.
Figure 3. Tightening the forepump hose clamp to the forepump port of the MS
detector
2. Attach the ETD helium line to the helium port on the back of the ETD
module as shown in Figure 4.
.
Figure 4. ETD helium line attached to the helium port
Helium Line

1Making the External Connections
Vacuum and Gas Connections
4MS/ETD Getting Connected Guide Thermo Electron Corporation
3. To connect the vacuum hose to the forepump port for the ETD module
a. Attach the O-ring to the forepump port for the ETD module as shown in
Figure 5.
Figure 5. Attaching the O-ring to the forepump port for the ETD module
b. Place the forepump hose clamp for the ETD module on the end of the
hose that will attach to the port and then attach the hose to the forepump
port of the ETD module.
c. Tighten the forepump hose clamp for the ETD module around the hose
and port as shown in Figure 6.

1 Making the External Connections
Vacuum and Gas Connections
Thermo Electron Corporation MS/ETD Getting Connected Guide 5
Figure 6. Tightening the forepump hose clamp to the forepump port for the ETD
module
4. Insert the MS/ETD system nitrogen line (friction fit) into its fitting as shown
in Figure 7.
Figure 7. Insert the nitrogen line into its fitting
Nitrogen Line

1Making the External Connections
Electrical Connections
6MS/ETD Getting Connected Guide Thermo Electron Corporation
Electrical
Connections
This section describes how to make the electrical connections to the MS/ETD
system. Do not plug the electrical cords into their wall outlets until you read the
instructions in Chapter 2, “Powering Up.”
To make electrical connections to the MS/ETD System
1. Ensure that the power cords for the ETD module and MS detector are not
connected to line power.
2. Connect the forepump for the ETD module to its electrical cord as shown in
Figure 8.
Figure 8. ETD forepump electrical connection
3. Plug the forepump electrical cord into the Forepump receptacle on the ETD
module power panel as shown in Figure 9. The Main Power and Service Mode
switches for the MS detector must be in the Off position. The ETD module
power and service switches can be in the On and Operating Mode positions
respectively.
CAUTION Be sure that the forepump electrical switch is in the Off position
before you plug it in.
CAUTION Power to the ETD module is controlled by the Main Power switch
on the Power Entry Module of the MS detector. Be sure that the Main Power
and Service Mode switches on the MS detector are in the Off position before
connecting power cords to the ETD module and the MS detector. See
Figure 10.

1 Making the External Connections
Electrical Connections
Thermo Electron Corporation MS/ETD Getting Connected Guide 7
Figure 9. ETD power cords plugged in to the ETD module Power Panel
4. Plug the power cord into the Power In receptacle on the Power Entry Module
of the ETD module (see Figure 9).
Service Switch
Power Switch
Forepump
Receptacle Power
Receptacle
CAUTION Be sure that the MS Main Power and Service Mode switches are in
their Off positions before connecting power cords to the MS detector.

1Making the External Connections
Electrical Connections
8MS/ETD Getting Connected Guide Thermo Electron Corporation
5. Ensure that the Main Power and Service Mode switches for the MS detector
are in the Off position, and then plug the power cords from the two forepumps
into the Mechanical Pumps/Accessory receptacles on the Power Entry Module
of the MS detector (see Figure 10 and Figure 11).
Figure 10. Main Power switch of the MS detector in the Off position and the power
cords are plugged in to their receptacles on the Power Entry Module
Figure 11. Service Mode switch for the MS detector in the Off position
The system is ready to be powered up as discussed in Chapter 2, “Powering Up.”