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.
The following are registered trademarks in the United States and other countries. Microsoft and Windows are
registered trademarks of Microsoft Corporation. Teflon is a registered trademark of E.I. du Pont de Nemours
& Co. Kel-F is a registered trademark of 3M Company, Inc. Swagelok is a registered trademark of Crawford
Fitting Company. Upchurch Scientific is a registered trademark of Upchurch Scientific. Hewlett-Packard and
JetDirect are registered trademarks of Hewlett-Packard. Agilent is a registered trademark of Agilent
Technologies, Inc. Alliance is a registered trademark of Waters Corporation. Tygon is a registered trademark of
the division of Saint-Gobain Performance Plastics Corp. Viton is a registered trademark of DuPont
Performance Elastomers.
PEEK is a trademark of Victrex plc. Super Flangeless is a trademark of Upchurch Scientific.
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 errorfree 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.
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.
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
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.
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.
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
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.
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
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 with the ETD module (January 2007)
EMC Directive 89/336/EEC
EMC compliance has been evaluated by TUV Rheinland of North America, Inc.
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
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.
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
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.
FCC Compliance Statement
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 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.
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 EUMitgliedsstaaten 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.
Contents
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
Thermo Scientific LTQ Series Getting Connected Guide ix
Contents
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
x LTQ Series Getting Connected Guide Thermo Scientific
Preface
About This Guide
This guide provides information on how to connect your LTQ Series mass spectrometer to
line power, the data system computer, the external vacuum system, and the waste exhaust
system. In addition, this guide provides information on how to connect external devices, both
those controlled from or independent of the Xcalibur data system.
The LTQ Series includes the following Thermo Scientific mass spectrometers:
• The LCQ™ Fleet™, a 3D ion trap mass spectrometer.
P
• The LXQ™, a 2D linear ion trap mass spectrometer.
• The LTQ™ XL, a 2D linear ion trap mass spectrometer. You can upgrade the LTQ XL
mass spectrometer to an LTQ XL/ETD system. The ETD module is physically coupled
to the back-end of the 2D ion trap. ETD enables peptide dissociation by transferring
electrons to positively charged peptides, leading to a rich ladder of sequence ions derived
from cleavage at the amide groups along the peptide backbone. Amino acid side chains
and important modifications such as phosphorylation are left intact.
• The LTQ XL MALDI system, an LTQ XL mass spectrometer pre-configured for
compatibility with the MALDI source. The optional API kit allows you to switch the
system to the ESI mode.
Related Documentation
In addition to this guide, Thermo Fisher Scientific provides the following documentation for
the LTQ Series ion trap mass spectrometers:
• A printed copy of the Safety and Regulatory Guide
• PDF files of the documents listed in Ta bl e 1 that you can access from the data system
computer
The Safety and Regulatory Guide contains important safety information about Thermo
Scientific mass spectrometry and liquid chromatography systems. This document is shipped
with every Thermo Scientific mass spectrometer and liquid chromatography device.
Thermo Scientific LTQ Series Getting Connected Guide xi
Preface
Table 1. LTQ Series MS documentation
Model Related Documents
LCQ Fleet LCQ Fleet Getting Started Guide
LCQ Fleet Hardware Guide
LTQ X L LTQ XL Getting Started Guide
LTQ XL Hardware Guide
LTQ X L/E TD MS/ETD System Getting Started Guide
MS/ETD System Getting Connected Guide
MS/ETD System Hardware Guide
LXQ LXQ Getting Started Guide
LXQ Hardware Guide
MALDI Source MALDI Source Hardware Manual
API Source Ion Max and Ion Max-S API Source Hardware Manual
To access the manuals for the mass spectrometer, from the Windows™ XP taskbar, choose
Start > All Programs > Xcalibur > Manuals > Brand name of mass spectrometer and then click
the listing for the PDF that you want to view. The software also provides Help. To access the
Help, choose Help from the menu bar or click the button on the toolbar.
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 hazards to humans, property, or the environment. Each
CAUTION notice is accompanied by an appropriate CAUTION symbol.
IMPORTANT Highlights information necessary to prevent damage to software, loss of
data, or invalid test results; or might contain information that is critical for optimal
performance of the system.
MALDI Source Getting Started Guide
Note Highlights information of general interest.
Tip Highlights helpful information that can make a task easier.
xii LTQ Series Getting Connected Guide Thermo Scientific
Contacting Us
Preface
There are several ways to contact Thermo Fisher Scientific.
Y To contact Technical Support
Phone 800-685-9535
Fax 561-688-8736
E-mail TechSupport.C+MS@thermofisher.com
Knowledge base www.thermokb.com
Find software updates and utilities to download at www.mssupport.thermo.com.
Y To contact Customer Service for ordering information
Phone 800-532-4752
Fax 561-688-8731
Web si te www.thermo.com/finnigan
Y To suggest changes to documentation or to Help
• Fill out a reader survey online at www.thermo.com/lcms-techpubs.
• Send an e-mail message to the Technical Publications Editor at
techpubs.finnigan-lcms@thermofisher.com.
Thermo Scientific LTQ Series Getting Connected Guide xiii
Line Power, Vacuum System, Gases, and Ethernet Communication
This chapter describes how to connect the LTQ Series MS detector to line power, the
forepump, necessary gases, and the data system computer.
Contents
• Connecting the MS Detector to Line Power
• Connecting the Forepump to the LCQ Fleet or LXQ MS Detector
1
• Connecting the Forepumps to the LTQ XL MS Detector
• Connecting the Gases to the MS Detector
• Connecting the MS Detector to the Data System Computer
Connecting the MS Detector to Line Power
Y To connect the LTQ Series MS detector to line power
1. Turn the Main Power circuit breaker to the Off (O) position.
2. Make sure that the Electronics switch is in the Service Mode position.
3. Connect the female plug of the power cord to the POWER IN receptacle of the power
panel.
4. Connect the male plug of the power cord to the 230 Vac power source in your
laboratory.
CAUTION If your local area is subject to power fluctuations or power interruptions, you
must install a power conditioning device or an uninterruptible power supply (UPS) in
your laboratory. For more information, refer to the LTQ S er ie s Preinstallation Requirements
Guide. The UPS must be certified by both North American (UL, CSA) and European
Agencies (TUV, UDE, SEMKO, DEMKO, and so on).
Thermo Scientific LTQ Series Getting Connected Guide 1
1
Line Power, Vacuum System, Gases, and Ethernet Communication
Connecting the Forepump to the LCQ Fleet or LXQ MS Detector
Connecting the Forepump to the LCQ Fleet or LXQ MS Detector
To connect the forepump (also known as a mechanical pump or rotary-vane pump) to the MS
detector and the laboratory exhaust system, follow these procedures:
• Connecting the Vacuum Hose
• Connecting the Forepump to the Laboratory Exhaust System
• Connecting the Forepump to Line Power
Connecting the Vacuum Hose
The vacuum hose accessory kit (P/N 97055-60135) contains the parts required to connect the
forepump to the MS detector. Ta bl e 1 lists the components and Figure 1 shows the
components of the vacuum hose assembly. The adapters at the two ends of the vacuum hose
assembly are connected at the factory.
Table 1. Vacuum hose accessory kit (P/N 97055-60135)
Description Part Number
Vacuum hose, 1.5-in.-ID, 8-ft length 00301-24163
Parts required to connect the vacuum port of the forepump
Centering ring with O-ring, NW25, 26 mm ID, aluminum and
Viton™
Swing clamp, KF 20/25 00102-10020
Hose clamp, high-torque, 1.25 in. to 2.125 in., stainless steel 00201-99-00056
Adapter, 1.5-in. OD for the end that is inserted into the vacuum hose,
1.5-in. OD for the end that connects to the forepump
Parts required to connect the vacuum hose to the vacuum port of the MS detector
Centering ring with O-ring, NW40, 41-mm ID, aluminum and
nitrile
Swing clamp, NW32/40, aluminum 00108-02-00004
Hose clamp, high-torque, 1.25 in. to 2.125 in., stainless steel 00201-99-00056
Adapter, 1.5-in. OD for the end that is inserted into the vacuum hose,
2.16-in. OD for the end that connects to the detector
00108-02011
70111-20210
00108-02-00005
97055-20714
2 LTQ Series Getting Connected Guide Thermo Scientific
Figure 1. Vacuum hose assembly
1
Line Power, Vacuum System, Gases, and Ethernet Communication
Connecting the Forepump to the LCQ Fleet or LXQ MS Detector
Fittings for exhaust port
of forepump
KF20/25
clamp
Fitting adapter for
forepump
Centering ring
Fittings for vacuum port
of MS detector
Hose
clamp
Y To connect the forepump to the LCQ Fleet or LXQ MS detector
Vacuum hose
(1.5-in. ID)
vacuum port of MS detector
Hose
clamp
Fitting adapter for
Centering ring
NW 32/40
1. To connect the vacuum hose to the MS detector:
a. Place the 41-mm (1.6-in.) ID centering ring (P/N 00108-02-00005) on the flange of
the vacuum port located on the rear panel of the MS detector.
b. Using the NW 32/40 swing clamp (00108-02-00004), secure the end the vacuum
hose that has the adapter for the MS detector to the vacuum port on the back of the
MS detector.
clamp
2. To connect the other end of the vacuum hose to the forepump:
a. Place the 26-mm (1.0-in.) ID centering ring (P/N 00108-02011) on the flange of the
inlet port of the forepump.
b. Using the KF20/25 vacuum clamp (P/N 00102-10020), secure the vacuum hose
assembly to the forepump.
Figure 2 on page 4 shows the connection between the vacuum port of the MS detector
and the exhaust port of the forepump.
Thermo Scientific LTQ Series Getting Connected Guide 3
1
Line Power, Vacuum System, Gases, and Ethernet Communication
Connecting the Forepump to the LCQ Fleet or LXQ MS Detector
Connecting the Forepump to the Laboratory Exhaust System
The proper operation of your forepump requires an efficient fume exhaust system. Most
atmospheric pressure ionization (API) applications contribute to the accumulation of solvents
in the forepump. While Thermo Fisher Scientific recommends that you periodically open the
ballast valves (on the top of the pumps) to purge the accumulated solvents, opening the valves
might allow a large volume of volatile solvent waste to enter the fume exhaust system. Choose
an exhaust system that can accommodate the periodic purging of these solvents. The
frequency of the purging depends on the throughput of your system.
Y To connect the exhaust port of the forepump to the laboratory exhaust system
1. Use hose clamps (P/N 00108-09001) to secure the 2.5-cm (1-in.) ID blue exhaust hose to
the forepump exhaust port.
2. Vent the free end of the blue exhaust hose to an external exhaust system in your
laboratory.
The exhaust hose should travel at floor level for a minimum of two meters (78.5 in.)
before it reaches the external exhaust system. This tubing acts as a trap for exhaust fumes
that would otherwise recondense in the forepump oil.
Figure 2 shows the blue exhaust hose connected to the optional oil mist filter, which is
connected to the exhaust port of the forepump.
Figure 2. Connection between the vacuum port and the forepump
MS detector
(rear panel)
EDWARDS
30
EDWARDS
Oil Mist Filter EMF 20
Vacuum port
Blue hose
(connect to external
exhaust system)
Optional oil mist
filter
Edwards forepump
4 LTQ Series Getting Connected Guide Thermo Scientific
Connecting the Forepump to Line Power
The forepump gets its line power from the MS detector. The power outlet for the forepump is
located on the power panel of the MS detector. As Figure 3 shows, the power panel is located
on the lower-right side of the MS detector.
Y To connect the forepump to line power (the forepump outlet of the MS detector)
1. On the power panel, switch the Main Power circuit breaker to the Off position.
2. Connect the power cord plug of the forepump to the Mech. Pumps power receptacle on
the MS detector.
3. Turn on the power switch of the forepump.
Figure 3. View of the line power connection for the forepump (mechanical pump)
1
Line Power, Vacuum System, Gases, and Ethernet Communication
Connecting the Forepump to the LCQ Fleet or LXQ MS Detector
I
0
Electronic Normal
Reset
Ethernet
100 Base T
Service Mode
Power switch
Main power
circuit breaker
Peripheral Control
Start
In
-
+
Analog Input
Main Power
On
Off
Mechanical pump
power receptacle
Power In
V 230 V
Hz 50/60
10A
Mech. Pumps
A 5.5 MAX
MS detector
(right side panel)
Forepump
Thermo Scientific LTQ Series Getting Connected Guide 5
1
Line Power, Vacuum System, Gases, and Ethernet Communication
Connecting the Forepumps to the LTQ XL MS Detector
Connecting the Forepumps to the LTQ XL MS Detector
Because the LTQ XL MS detector has a larger ion transfer tube than the LXQ MS detector, it
draws more ions into its ion trap and requires a second forepump to evacuate its skimmer
region.
Y To connect the forepumps to the LTQ XL MS detector
1. Using a hose clamp (P/N 00108-09001), connect the 3.8-cm (1.5-in.) ID reinforced
vacuum hose to the LTQ XL MS detector vacuum inlet. (The vacuum hose inlet is
located on the lower right side of the back panel of the LTQ XL MS detector.)
2. Connect the Tee (P/N 97055-20222) to the free end of the vacuum hose with a hose
clamp (P/N 00108-09001).
The ID of the TEE arms is 3.5 cm (1.375 inches). The OD of the TEE arms is 3.8 cm
(1.5 inches).
3. Using hose clamps (P/N 00108-09001), connect the 3.8-cm (1.5-in.) ID reinforced
vacuum hoses to the other branches of the Tee connector.
4. Connect a pump fitting adapter (P/N 00108-09005) to the free end of the vacuum hoses
with a hose clamp (P/N 00108-09001).
5. Place a centering ring (P/N 00108-02011) on the flange of each forepump vacuum inlet.
6. Connect the vacuum hose (with the attached fitting adapter) to the pump vacuum inlet.
Secure the hose to the pump using the KF20/25 vacuum hardware clamp
(P/N 00102-10020).
IMPORTANT For proper operation, the forepumps require an efficient fume exhaust
system. Most API applications contribute to the accumulation of solvents in the
forepumps. These solvents must be purged from the forepump oil periodically by
opening the ballast valve located on the top of the pump. Because opening the ballast
valve can release a large volume of volatile solvent waste, the fume exhaust system
must be able to accommodate the effluent resulting from periodic purging.
7. Use hose clamps (P/N 00108-09001) to connect the 2.5-cm (1-in.) ID blue exhaust hoses
from the forepump exhaust ports to the pump exhaust system in your laboratory.
Because the exhaust hose acts as a trap for exhaust fumes that would otherwise recondense
in the forepump oil, it should travel at floor level for a minimum of two meters (78.5 in.)
before it reaches the external exhaust system.
8. Connect the forepumps to line power:
a. Locate the Main Power circuit breaker switch on the power panel and switch the
circuit breaker to the Off position.
b. Connect the power cords attached to the forepumps to the forepump outlets located
on the power panel.
6 LTQ Series Getting Connected Guide Thermo Scientific
1
Line Power, Vacuum System, Gases, and Ethernet Communication
Connecting the Gases to the MS Detector
This section describes how to connect the required gases to the LTQ Series MS detector set up
for the API mode. The LTQ Series MS detector uses nitrogen for the API sheath gas, auxiliary
gas, and sweep gas, and helium for the collision gas. The gas line connections for the LTQ
Series MS detector are located on its back panel as shown in Figure 4.
Figure 4. Back panel of the LTQ Series MS detector
Connecting the Gases to the MS Detector
Nitrogen In
650 ± 140 kPa
(100±20psi)
Helium In
275 ± 75 kPa
(40 ± 10 psi)
(connects to forepump)
To connect the gas lines, follow these procedures:
• Connecting the Nitrogen Source
• Connecting the Helium Source
Connecting the Nitrogen Source
The LTQ Series MS detector requires high purity (99%) nitrogen for the API sheath gas,
auxiliary gas, and sweep gas. Because nitrogen gas usage can be quite high, Thermo Fisher
Scientific recommends one of three nitrogen sources: a large, sealed, thermally insulated
cylinder containing liquid nitrogen from which the nitrogen gas is boiled off; the largest
nitrogen cylinder that can be practically used; or a nitrogen generator. The required gas
pressure is 690 ± 140 kPa (100 ± 20 psi).
For information on modifying the nitrogen line connections inside the MALDI LTQ XL
system, contact your Thermo Fisher Scientific field service engineer. The MALDI LTQ XL
system uses nitrogen to maintain the pressure in the upper sample compartment of the
MALDI sample module.
Vacuum manifold
Thermo Scientific LTQ Series Getting Connected Guide 7
1
Line Power, Vacuum System, Gases, and Ethernet Communication
Connecting the Gases to the MS Detector
Y To connect the nitrogen source to the LTQ Series mass spectrometer
1. Connect an appropriate length of 1/4-in. ID Teflon™ tubing with a brass Swagelok™-type
1/4-in. nut (P/N 00101-12500) and a 2-piece brass 1/4-in. ferrule [P/N 00101-10000
(front), P/N 00101-04000 (back)] to the nitrogen source.
See Figure 5 for the proper orientation of the fitting and ferrule.
2. Connect the opposite end of the Teflon tubing to the press-in fitting labeled
NITROGEN IN and located on the back panel of the LTQ Series MS detector. To
connect the tubing, align the Teflon tubing with the opening in the fitting and firmly
push the tubing into the fitting until the tubing is secure.
Connecting the Helium Source
The helium for the LTQ Series MS detector collision gas must be ultra-high purity (99.999%)
with less than 1.0 ppm each of water, oxygen, and total hydrocarbons. The required gas
pressure is 275 ± 70 kPa (40 ±10 psi). Because particulate filters can be a source of
contamination, Thermo Fisher Scientific does not recommend their use.
You can dispense helium from a tank containing 245 ft
3
of gas, using a Matheson 3120 Series1
regulator or equivalent tank and regulator.
Whether you choose copper or stainless steel gas lines for the helium, use gas lines that are free
of oil and preferably flame dried. Run the gas lines to the back of the LTQ Series MS detector.
Terminate the helium gas supply lines with 1/8-in., female, Swagelok-type connectors.
Y To connect the helium source to the LTQ Series mass spectrometer
1. Connect an appropriate length of 1/8-in. ID copper or stainless steel tubing with a brass
Swagelok-type 1/8-in. nut (P/N 00101-15500) and a 2-piece brass 1/8-in. ID ferrule
[P/N 00101-08500 (front), P/N 00101-2500 (back)] to the HELIUM IN gas inlet
located on the back panel. See Figure 5 for the proper orientation of the fitting and
ferrule.
2. Connect the opposite end of the tubing to the helium gas source, using an appropriate
fitting.
Figure 5. Proper orientation of the Swagelok-type nut and two-piece ferrule
Gas hose Front ferrule
Swagelok-type nut
1
For more information, visit: http://www.matheson-trigas.com
8 LTQ Series Getting Connected Guide Thermo Scientific
Back ferrule
1
Line Power, Vacuum System, Gases, and Ethernet Communication
Connecting the MS Detector to the Data System Computer
Connecting the MS Detector to the Data System Computer
The data system for the LTQ Series MS detector consists of a computer, a monitor, and an
optional printer. The LTQ Series MS detector communicates with the data system computer
through an Ethernet cable.
Y To connect the MS detector to the data system computer
1. Connect a category five network (Ethernet) cable (P/N 00302-01838) to the
ETHERNET 100 BASE-T connector located on the MS detector power panel.
2. Connect the opposite end of the Ethernet cable to the 10/100 Base-T Ethernet switch
(P/N 00825-01015) provided with the MS detector.
3. Connect a second Ethernet cable (P/N 00302-01838) from the Ethernet switch to the
Ethernet card on the data system computer labeled Surveyor MS.
4. Connect the Ethernet switch to line power.
Thermo Scientific LTQ Series Getting Connected Guide 9
Loading...