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
in the product operation. This document is copyright protected and any reproduction of the whole or
any part of this document is strictly prohibited, except with the written authorization of Thermo
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
purchaser. This document shall in no way govern or modify any Terms and Conditions of Sale, which
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.