Thermo Scientific LCQ Fleet User manual

LTQ Series
Getting Connected Guide
97055-97071 Revision A January 2008

© 2007 Thermo Fisher Scientific Inc. All rights reserved.
Xcalibur, Surveyor, SpectraSYSTEM, and Accela are registered trademarks of Thermo Fisher Scientific Inc. in
the United States.
LCQ, LXQ, Fleet, LTQ, and IonMax are trademarks of Thermo Fisher Scientific Inc.
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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.
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Sale shall govern all conflicting information between the two documents.
Release history: Revision A released January 2008.
Software Version: Xcalibur 2.0.7 or higher, MALDI Source 2.5.0, LTQ Series 2.5
For Research Use Only. Not regulated for medical or veterinary diagnostic use by U.S. Federal Drug
Administration or other competent authorities.

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.
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 Fisher Scientific. To ensure continued compliance with EMC and safety
standards, replacement parts and additional components, options, and peripherals must be ordered from
Thermo Fisher Scientific or one of its authorized representatives.
This document contains the testing and evaluation results for these Thermo Scientific products:
•LCQ Fleet (March 2007)
•LXQ (February 2005)
•LTQ XL (September 2006)
•LTQ XL with the ETD module (January 2007)
•MALDI LTQ XL (August 2007)
LCQ Fleet (March 2007)
EMC Directive 89/336/EEC as amended by 92/31/EEC and 93/68/EEC
EMC compliance has been evaluated by TUV Rheinland of North America.
Low Voltage Safety Compliance
Compliance with safety issues is declared under Thermo Fisher Scientific sole responsibility. This device complies with
Low Voltage Directive 73/23/EEC and harmonized standard EN 61010-1:2001.
EN 55011:1998, A1: 1999, A2: 2002 EN 61000-4-3: 2002
EN 61000-3-2: 2000 EN 61000-4-4: 1995, A1: 2000, A2: 2001
EN 61000-3-3: 1995, A1: 2001 EN 61000-4-5: 1995, A1: 2001
EN 61326-1: 1997, A1: 1998, A2: 2001, A3: 2003 EN 61000-4-6: 2003
EN 61000-4-2: 2001 EN 61000-4-11: 1994, A1: 2001
FCC Class A, CFR 47 Part 15: 2005 CISPR 11: 1998, A1: 1999, A2: 2002

LXQ (February 2005)
EMC - Directive 89/336/EEC as amended by 92/31/EEC and 93/68/EEC
EMC compliance has been evaluated by U.L. Underwriter’s Laboratory Inc.
Low Voltage Safety Compliance
Compliance with safety issues is declared under Thermo Fisher Scientific sole responsibility. This device complies with
Low Voltage Directive 73/23/EEC and harmonized standard EN 61010-1:2001.
LTQ XL (September 2006)
EMC Directive 89/336/EEC
EMC compliance has been evaluated by TUV Rheinland of North America, Inc.
Low Voltage Safety Compliance
Compliance with safety issues is declared under Thermo Fisher Scientific sole responsibility. This device complies with
Low Voltage Directive 73/23/EEC and harmonized standard EN 61010-1:2001.
EN 55011: 1998 EN 61000-4-3: 2002, A1: 2002
EN 61000-3-2: 1995, A1: 1998, A2: 1998, A14: 2000 EN 61000-4-4: 1995, A1: 2001, A2: 2001
EN 61000-3-3: 1995 EN 61000-4-5: 1995, A1: 2001
EN 61326-1: 1997 EN 61000-4-6: 1996, A1: 2001
EN 61000-4-2: 1995, A1: 1998, A2: 2001 EN 61000-4-11: 1994, A1: 2001
FCC Class A, CFR 47 Part 15, Subpart B: 2004 CISPR 11: 1999, A1: 1999, A2: 2002
EN 55011: 1998, A1: 1999, A2: 2002 EN 61000-4-3: 2002
EN 61000-3-2: 1995, A1: 1998, A2: 1998, A14: 2000 EN 61000-4-4: 1995, A1: 2001, A2: 2001
EN 61000-3-3: 1995, A1:2001 EN 61000-4-5:1995, A1: 2001
EN 61326-1: 1997, A1: 1998, A2: 2001, A3: 2003 EN 61000-4-6: 2003
IEC 61000-4-2: 2001 EN 61000-4-11: 2001
FCC Class A, CFR 47 Part 15: 2005 CISPR 11: 1999, A1: 1999, A2: 2002

LTQ XL with the ETD module (January 2007)
EMC Directive 89/336/EEC
EMC compliance has been evaluated by TUV Rheinland of North America, Inc.
Low Voltage Safety Compliance
Compliance with safety issues is declared under Thermo Fisher Scientific sole responsibility. This device complies with
Low Voltage Directive 73/23/EEC and harmonized standard EN 61010-1:2001.
MALDI LTQ XL (August 2007)
EMC Directive 204/108/EC
EMC compliance has been evaluated by TUV Rheinland of North America.
Low Voltage Safety Compliance
Compliance with safety issues is declared under Thermo Fisher Scientific sole responsibility. This device complies with
Low Voltage Directive 2006/95/EC and harmonized standard EN 61010-1:2001.
Safety of Laser Products
Compliance with safety of laser products is declared under Thermo Fisher Scientific sole responsibility. This device
complies with the harmonized standard IEC/EN 60825-1/A2: 2001.
EN 61000-3-2: 1995, A1: 1998, A2: 1998, A14: 2000 EN 61000-4-4:1995, A1: 2000, A2:2001
EN 61000-3-3: 1995, A1:2001 EN 61000-4-5: 1995, A1: 2001
EN 61326-1: 1997, A1:1998, A2:2001, A3:2003 EN 61000-4-6: 2003
EN 61000-4-2: 2001 EN 61000-4-11: 1994, A1: 2001
EN 61000-4-3: 2002 CISPR 11: 1999, A1: 1999, A2: 2002
FCC Class A, CFR 47 Part 15: 2005
EN 55011: 1998, A1: 1999, A2: 2002 EN 61000-4-3: 2002
EN 61000-3-2: 2000 EN 61000-4-4: 1995, A1: 2000, A2: 2001
EN 61000-3-3: 1995, A1: 2001 EN 61000-4-5: 2001
EN 61326-1: 1998, A2: 2001, A3: 2003 EN 61000-4-6: 2003
EN 61000-4-2: 2001 EN 61000-4-11: 2001
FCC Class A, CFR 47 Part 15: 2005 CISPR 11: 1998, A1:1999, A2: 2002

FCC Compliance Statement
Notice on Lifting and Handling of
Thermo Scientific Instruments
For your safety, and in compliance with international regulations, the physical handling of this Thermo Fisher
Scientific instrument requires a team effort to lift and/or move the instrument. This instrument is too heavy and/or
bulky for one person alone to handle safely.
Notice on the Proper Use of
Thermo Scientific Instruments
In compliance with international regulations: Use of this instrument in a manner not specified by Thermo Fisher
Scientific could impair any protection provided by the instrument.
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.
For manufacturing location, see the label on the instrument.
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.

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 Fisher Scientific qui peuvent aider la détection des
substances sujettes à la directive RoHS sont disponibles sur www.thermo.com/WEEERoHS.

Thermo Scientific LTQ Series Getting Connected Guide ix
C
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi
About This Guide. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi
Safety and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xii
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii
Chapter 1 Line Power, Vacuum System, Gases, and Ethernet Communication. . . . . . . . . . .1
Connecting the MS Detector to Line Power . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Connecting the Forepump to the LCQ Fleet or LXQ MS Detector . . . . . . . . . . 2
Connecting the Vacuum Hose. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Connecting the Forepump to the Laboratory Exhaust System . . . . . . . . . . . . . 4
Connecting the Forepump to Line Power . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Connecting the Forepumps to the LTQ XL MS Detector. . . . . . . . . . . . . . . . . . 6
Connecting the Gases to the MS Detector. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Connecting the Nitrogen Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Connecting the Helium Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Connecting the MS Detector to the Data System Computer. . . . . . . . . . . . . . . . 9
Chapter 2 Connecting Probes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11
Connecting the ESI Probe to the MS Detector . . . . . . . . . . . . . . . . . . . . . . . . . 11
Connecting the APCI Probe to the MS Detector. . . . . . . . . . . . . . . . . . . . . . . . 12
Chapter 3 Connecting the MALDI LTQ XL System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
Connecting the MALDI LTQ XL System Forepumps to Line Power . . . . . . . . 14
Connecting the MALDI LTQ XL Vacuum System. . . . . . . . . . . . . . . . . . . . . . 15
Connecting the MALDI Control Module to the MALDI LTQ XL System. . . . 17
Connecting the MALDI CCD Camera to the Data System Computer . . . . . . . 20
Chapter 4 Connecting External Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
External Devices Controlled by the Xcalibur Data System. . . . . . . . . . . . . . . . . 24
Making Contact Closure with Devices Controlled by Xcalibur . . . . . . . . . . . 24
Selecting the Appropriate Start Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . 25
External Devices Not Controlled by the Xcalibur Data System . . . . . . . . . . . . . 27
Making Contact Closure with Devices Not Controlled by Xcalibur . . . . . . . 27
Starting a Sequence Run from Xcalibur . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Contents

Contents
xLTQ Series Getting Connected Guide Thermo Scientific
Chapter 5 Connecting a Thermo Scientific LC System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
Contact Closure Cables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Making Contact Closure with a Surveyor Plus LC System . . . . . . . . . . . . . . . . 35
Making Contact Closure with an Accela LC System . . . . . . . . . . . . . . . . . . . . . 37
Chapter 6 Connecting the Inlet Plumbing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .39
Sample Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Fittings, Tubing, Unions, and Sample Loops . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Setting Up the Inlet for Direct Infusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Setting Up the Syringe. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Connecting an Infusion Line to the Grounding Union . . . . . . . . . . . . . . . . . 44
Setting Up the Inlet for High-Flow Infusion . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Connecting the Syringe to the Union Tee . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Connecting the Union Tee to the Divert/Inject Valve. . . . . . . . . . . . . . . . . . 47
Connecting the LC Pump to the Divert/Inject Valve . . . . . . . . . . . . . . . . . . 48
Connecting the Divert/Inject Valve to a Waste Container. . . . . . . . . . . . . . . 48
Connecting the Union Tee to the Ion Source . . . . . . . . . . . . . . . . . . . . . . . . 49
Setting Up the Inlet for Loop Injections (Flow Injection Analyses) . . . . . . . . . . 51
Setting Up the Inlet for an LC/MS System with an Autosampler . . . . . . . . . . . 53
Connecting the Grounding Union to the ESI Probe Sample Inlet. . . . . . . . . . . 55
Chapter 7 Connecting the 4-Port Serial PCB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .57
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .59