ETD Module Hardware Manual Revision C

ETD Module Hardware Manual Revision C
ETD Module
Hardware Manual
For Velos Pro and LTQ XL Mass Spectrometers
(compatible with Orbitrap Velos Pro, LTQ Orbitrap Velos,
Orbitrap Elite, and LTQ Orbitrap XL)
98000-97004 Revision D
September 2015
© 2015 Thermo Fisher Scientific Inc. All rights reserved.
Automatic Gain Control, Foundation, Ion Max-S, LTQ XL, Velos, and Velos Pro are trademarks; Unity is a
registered service mark; and Ion Max, LTQ, Orbitrap, Thermo Scientific, and Xcalibur are registered
trademarks of Thermo Fisher Scientific Inc. in the United States.
The following are registered trademarks in the United States and other countries: Microsoft and Windows are
registered trademarks of Microsoft Corporation.
The following are registered trademarks in the United States and possibly other countries: Alconox and
Liquinox are registered trademarks of Alconox, Inc. Convectron is a registered trademark of Granville-Phillips
Company. Dremel is a registered trademark of Robert Bosch Tool Corporation. Micro-90 is a registered
trademark of International Products Corporation. Sigma-Aldrich and Supelco are registered trademarks of
Sigma-Aldrich Co. Swagelok is a registered trademark of Swagelok Company. Torx is a registered trademark of
Acument Intellectual Properties LLC. Vespel and Viton are registered trademarks of E. I. du Pont de Nemours
& Company.
PEEKsil is a trademark of SGE International Pty Ltd Corp.
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.
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: Rev A, March 2008; Rev B, April 2009; Rev C, June 2012; Rev D, Sept 2015
Software version: Microsoft Windows 7 Professional (32-bit and 64-bit) SP1—Thermo Foundation 2.0 and
later, and Thermo Xcalibur 2.2 and later; Windows XP Workstation SP3—Foundation 1.0.2 SP2 or earlier,
and Xcalibur 2.1 SP1 or earlier; Thermo LTQ Tune Plus 2.7.0 and later
For Research Use Only. Not for use in diagnostic procedures.
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 in the next section or sections by product name.
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.
Regulatory compliance results for the following Thermo Scientific MS/ETD systems (MSs):
• Velos Pro/ETD System
• LTQ XL/ETD System
Note Thermo Fisher Scientific no longer ships the LTQ Velos mass spectrometer. Previously installed
MS/ETD systems were tested in accordance with applicable standards at that time (for example,
EN 61326-0-1: 2006 (EMC) and EN/UL 61010-1 Second Edition (product safety).
Velos Pro/ETD System
EMC Directive 2004/108/EC
EMC compliance has been evaluated by TUV Rheinland of North America, Inc.
CFR 47, FCC Part 15, Subpart B, Class A: 2015
EN 61000-3-2: 2006 + A1+ A2
CISPR 11: 2009 + A1
EN 61000-3-3: 2013
CISPR 22: 2008
EN 61000-4-2: 2009
ICES-003: 2014
EN 61000-4-3: 2006 + A1+ A2
BSMI CNS 13438: 2006
EN 61000-4-4: 2004 + A1
EN 55011: 2009 + A1
EN 61000-4-5: 2006
EN 55022: 2010
EN 61000-4-6: 2009
EN 61326-1: 2013
EN 61000-4-11: 2004
Low Voltage Safety Compliance
This device complies with Low Voltage Directive 2006/95/EC and harmonized standard IEC/EN/CSA/UL 61010-1,
Third Edition.
LTQ XL/ETD System
EMC Directive 2004/108/EC
EMC compliance has been evaluated by TUV Rheinland of North America, Inc.
CFR 47, FCC Part 15, Subpart B, Class A: 2013
EN 61000-3-2: 2006 + A1+ A2
CISPR 11: 2009 + A1
EN 61000-3-3: 2008
CISPR 24: 2010
EN 61000-4-2: 2009
AS/NZS CISPR 22: 2009
EN 61000-4-3: 2006 + A1+ A2
ICES-003: 2012
EN 61000-4-4: 2004 + A1
EN 55011: 2009 + A1
EN 61000-4-5: 2006
EN 55024: 2010
EN 61000-4-6: 2009
EN 61326-1: 2013
EN 61000-4-11: 2004
Low Voltage Safety Compliance
This device complies with Low Voltage Directive 2006/95/EC and harmonized standard IEC/EN/CSA/UL 61010-1,
Second Edition.
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: This instrument must be used in the manner specified by Thermo Fisher
Scientific to ensure protections provided by the instrument are not impaired. Deviations from specified instructions on
the proper use of the instrument include changes to the system and part replacement. Accordingly, order replacement
parts from Thermo Fisher Scientific or one of its authorized representatives.
WEEE Directive
2012/19/EU
Thermo Fisher Scientific is registered with B2B Compliance (B2Bcompliance.org.uk) in the UK and with the
European Recycling Platform (ERP-recycling.org) in all other countries of the European Union and in Norway.
If this product is located in Europe and you want to participate in the Thermo Fisher Scientific Business-to-Business
(B2B) Recycling Program, send an email request to [email protected] with the following information:
• WEEE product class
• Name of the manufacturer or distributor (where you purchased the product)
• Number of product pieces, and the estimated total weight and volume
• Pick-up address and contact person (include contact information)
• Appropriate pick-up time
• Declaration of decontamination, stating that all hazardous fluids or material have been removed from the product
For additional information about the Restriction on Hazardous Substances (RoHS) Directive for the European Union,
search for RoHS on the Thermo Fisher Scientific European language websites.
IMPORTANT This recycling program is not for biological hazard products or for products that have been medically
contaminated. You must treat these types of products as biohazard waste and dispose of them in accordance with
your local regulations.
Directive DEEE
2012/19/EU
Thermo Fisher Scientific s'est associé avec une ou plusieurs sociétés de recyclage dans chaque état membre de l’Union
Européenne et ce produit devrait être collecté ou recyclé par celle(s)-ci. Pour davantage d'informations, rendez-vous sur
la page www.thermoscientific.fr/rohs.
WEEE Direktive
2012/19/EU
Thermo Fisher Scientific hat Vereinbarungen mit Verwertungs-/Entsorgungsfirmen in allen EU-Mitgliedsstaaten
getroffen, damit dieses Produkt durch diese Firmen wiederverwertet oder entsorgt werden kann. Weitere Informationen
finden Sie unter www.thermoscientific.de/rohs.
C
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiv
Cautions and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
Safety Precautions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xvi
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xviii
Thermo Scientific
Chapter 1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Chapter 2
Functional Description. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3
Power Panel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Interface PCB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
ETD Control PCB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Heater Control PCB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
LEDs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Flow Control. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Reagent Heaters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Ion Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Chapter 3
Shutdown and Startup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11
Shutting Down the ETD Module in an Emergency . . . . . . . . . . . . . . . . . . . . . 12
Opening the Tune Plus Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Placing the ETD Module in Standby Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Shutting Down the MS/ETD System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Starting Up the MS/ETD System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Chapter 4
Daily Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19
Before Operating the MS/ETD System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Checking the System Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Checking the Vacuum Pressure Levels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Checking the Gas Supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Turning On the Reagent Ion Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
After Operating the MS/ETD System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Placing the MS/ETD System in Standby Mode. . . . . . . . . . . . . . . . . . . . . . . 27
Purging the Oil in the Forepump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
ETD Module Hardware Manual
ix
Contents
Chapter 5
Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .29
Maintenance Schedule. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Work Area Preparations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Guidelines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Tools and Supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Cleaning Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Cleaning Stainless Steel Parts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Cleaning Nonstainless Steel Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Ion Volume Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Inlet Valve Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Removing the Access Panels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Ion Source Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Inspecting or Replacing the Ion Source Filament. . . . . . . . . . . . . . . . . . . . . . 53
Cleaning the Ion Source Lenses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Cleaning the Ion Source Block . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Reagent Vials Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Shutting Down the MS/ETD System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Replacing the Reagent Vials. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Starting Up the MS/ETD System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Forepump Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Fan Filter Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Chapter 6
Diagnostics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .75
Running the ETD Module Diagnostics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Replacing a Fuse in the ETD Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Replacing Power Supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Replacing PCBs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Chapter 7
Reagent Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .79
Chapter 8
Replaceable Parts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .81
ETD Ship Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
ETD Accessory Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
ETD Reagent Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
ETD Nitrogen Scrubber (Gas Filter) Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
Inlet Valve Seal Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Reagent Inlet Module Installation Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Miscellaneous Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Forepump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Ion Volume Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Ion Source Filament Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .85
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ETD Module Hardware Manual
Thermo Scientific
F
Figures
Figure 1.
Figure 2.
Figure 3.
Figure 4.
Figure 5.
Figure 6.
Figure 7.
Figure 8.
Figure 9.
Figure 10.
Figure 11.
Figure 12.
Figure 13.
Figure 14.
Figure 15.
Figure 16.
Figure 17.
Figure 18.
Figure 19.
Figure 20.
Figure 21.
Figure 22.
Figure 23.
Figure 24.
Figure 25.
Figure 26.
Figure 27.
Figure 28.
Figure 29.
Figure 30.
Figure 31.
Figure 32.
Figure 33.
Figure 34.
Figure 35.
Thermo Scientific
LTQ XL MS with the ETD module and NSI source . . . . . . . . . . . . . . . . . . . . . . 1
Internal back view of the ETD module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
ETD module power panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
ETD module status LEDs for the Velos Pro/ETD and LTQ XL/ETD systems . . 7
Power panel for the Velos Pro and LTQ XL mass spectrometers . . . . . . . . . . . . 12
Tune Plus window for the Velos Pro/ETD system . . . . . . . . . . . . . . . . . . . . . . 13
Reagent Ion Source dialog box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Reagent Ion Source dialog box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Vacuum dialog box. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Reagent page of the Vacuum dialog box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Reagent Ion Source dialog box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Mass spectrum for the reagent ion displayed in Tune Plus for the Velos Pro/
ETD system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Inlet valve components (back of the ETD module). . . . . . . . . . . . . . . . . . . . . . 38
Ion volume insertion and removal tool components . . . . . . . . . . . . . . . . . . . . . 39
Guide bar positioned for insertion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Guide bar insertion complete . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
First stop of the ion volume tool guide bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Reagent Ion Source dialog box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Inlet valve lever in the open position . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Ion volume tool handle in the unlock position . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Ion volume tool fully inserted into the inlet valve showing the guide ball just
past the first mark . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Ion volume tool handle in the locked position . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Ion volume assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Placement of the ion volume on the ion volume tool . . . . . . . . . . . . . . . . . . . . . 45
Inlet valve components (back of the ETD module). . . . . . . . . . . . . . . . . . . . . . 47
Inlet valve seal tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Inlet valve seal tool inserted into the inlet valve . . . . . . . . . . . . . . . . . . . . . . . . . 48
Inlet valve seal on the inlet valve seal tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Inlet valve seal disengaged from the tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
ETD module (back view) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Interior of vacuum manifold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Ion source assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Ion source assembly (exploded view) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Removing the magnet yoke from the assembly . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Removing the feedthrough cable connectors . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
ETD Module Hardware Manual
xi
Figures
Figure 36.
Figure 37.
Figure 38.
Figure 39.
Figure 40.
Figure 41.
Figure 42.
Figure 43.
Figure 44.
Figure 45.
Figure 46.
Figure 47.
Figure 48.
Figure 49.
Figure 50.
Figure 51.
Figure 52.
Figure 53.
Figure 54.
Figure 55.
Figure 56.
Figure 57.
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ETD Module Hardware Manual
Removing the alignment studs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Retainer clip thumbscrew . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Detaching the ion source PCB from the assembly . . . . . . . . . . . . . . . . . . . . . . . 58
Removing the filament assembly retainer clip . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Removing the filament assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Filament wire visible through the bottom electron lens hole . . . . . . . . . . . . . . . 59
Filament assembly ready to be installed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Filament assembly retainer clip ready to be installed . . . . . . . . . . . . . . . . . . . . . 60
Cartridge heaters aligned with the ion source block . . . . . . . . . . . . . . . . . . . . . . 61
Retainer clip thumbscrew . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Reinstalling the alignment studs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Reattaching the feedthrough cable connectors . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Ion source assembly repositioned in the magnet yoke . . . . . . . . . . . . . . . . . . . . 63
Ion source lens assembly (exploded view) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Location of retainer clip thumbscrew . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Block heater ring, lens holder, and thermal spacer . . . . . . . . . . . . . . . . . . . . . . . 65
Ion source components (exploded view) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Ion source block . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Reagent inlet source heating unit (EMI cover not shown). . . . . . . . . . . . . . . . . 71
Reagent inlet source heating unit with the vial heater cover removed . . . . . . . . . 72
Diagnostics dialog box showing the System Evaluation page (Velos Pro/ETD). . 76
ETD reagent (fluoranthene radical anion) generation from fluoranthene . . . . . . 80
Thermo Scientific
P
Preface
The ETD Module Hardware Manual describes the modes of operation and hardware
components for the Thermo Scientific™ Velos Pro™/ETD, LTQ™ Velos™/ETD, and
LTQ XL™/ETD systems. It also provides the systems’ cleaning and maintenance procedures.
For hardware information about the mass spectrometers, refer to the LTQ Series Hardware
Manual. For information about the required gases, refer to the LTQ Series Getting Connected
Guide.
Note For the LTQ Velos/ETD system, follow the Velos Pro/ETD system information,
unless otherwise noted.
Contents
• Related Documentation
• Cautions and Special Notices
• Safety Precautions
• Contacting Us
 To suggest changes to the documentation or to the Help
Complete a brief survey about this document by clicking the button below.
Thank you in advance for your help.
Thermo Scientific
ETD Module Hardware Manual
xiii
Preface
Related Documentation
The Velos Pro and LTQ XL mass spectrometers (MSs) include complete documentation. In
addition to this guide, you can also access the following documents as PDF files from the data
system computer:
• LTQ Series Preinstallation Requirements Guide
• LTQ Series Getting Connected Guide
• LTQ Series Getting Started Guide
• LTQ Series Hardware Manual
• ETD Module Getting Started Guide
• Safety and Regulatory Guide
The ETD module also ships with a printed copy of the Safety and Regulatory Guide. This
guide contains important safety information about Thermo Scientific liquid
chromatography (LC) and mass spectrometry (MS) systems. Make sure that all lab
personnel have read and have access to this document.
 To view the product manuals
From the Microsoft™ Windows™ taskbar, choose Start > All Programs > Thermo
Instruments > Manuals > model, where model is your specific LTQ Series model, and
then open the PDF file to view it.
Note For Thermo Xcalibur™ version 2.0.7 or earlier (Microsoft Windows XP
operating system), choose Start > All Programs > Xcalibur > Manuals > LTQ >
model.
 To view the data system Help
• From the application window, choose Help from the menu bar.
• If information about setting parameters is available for a specific view, page, or dialog
box, click Help or press the F1 key for information about setting parameters.
 To download user documentation from the Thermo Scientific website
1. Go to www.thermoscientific.com.
2. In the Search box, type the product name and press ENTER.
3. In the left pane, select Documents & Videos, and then under Refine By Category, click
Operations and Maintenance.
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Preface
4. (Optional) Narrow the search results or modify the display as applicable:
• For all related user manuals and quick references, click Operator Manuals.
• For installation and preinstallation requirements guides, click Installation
Instructions.
• For documents translated into a specific language, use the Refine By Language
feature.
• Use the Sort By options or the Refine Your Search box (above the search results
display).
5. Download the document as follows:
a. Click the document title or click Download to open the file.
b. Save the file.
Cautions and Special Notices
Make sure you follow the cautions and special notices presented in this guide. Cautions and
special notices appear in boxes; those concerning safety or possible system damage also have
corresponding caution symbols.
This guide uses the following types of cautions and special notices.
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.
Note Highlights information of general interest.
Tip Highlights helpful information that can make a task easier.
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Preface
The ETD Module Hardware Manual contains the following caution-specific symbols
(Table 1).
Table 1. Caution-specific symbols and their meanings
Symbol
Meaning
Chemical hazard: Observe Good Laboratory Practices (GLP) when
handling chemicals. Only work with volatile chemicals under a fume
or exhaust hood.Wear gloves and other protective equipment, as
appropriate, when handling toxic, carcinogenic, mutagenic, corrosive,
or irritant chemicals. Use approved containers and proper procedures
to dispose of waste oil and when handling wetted parts of the
instrument.
Hot surface: Allow heated components to cool before touching or
servicing the instrument.
Risk of electric shock: This instrument uses voltages that can cause
electric shock and/or personal injury. Before servicing, shut down the
instrument and disconnect it from line power. While operating the
instrument, keep covers on.
Risk of eye injury: Eye injury could occur from splattered chemicals or
airborne particles. Wear safety glasses when handling chemicals or
servicing the instrument.
Safety Precautions
Observe the following safety precautions when you operate or perform service on the mass
spectrometer.
CAUTION Make sure you have sufficient nitrogen for the API source and reagent
inlet. Before beginning normal operation each day, make sure that you have sufficient
nitrogen for your API source and reagent inlet. The presence of atmospheric oxygen in the
API source and reagent inlet could be unsafe when the mass spectrometer and ETD
module are turned on. (The MS/ETD system automatically turns the mass spectrometer
off when you run out of nitrogen; however, it is best to take this added precaution.)
CAUTION Place the MS/ETD system in Standby (or Off) mode before you open the
atmospheric pressure ionization (API) source. The presence of atmospheric oxygen in
the API source when the mass spectrometer and ETD module are turned on could be
unsafe. (The MS/ETD system automatically turns the mass spectrometer and ETD
module off when you open the API source; however, it is best to take this added
precaution.)
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CAUTION Shut down the mass spectrometer and ETD module and disconnect them
from line power before servicing. High voltages capable of causing personal injury are
used in the instrument. Some maintenance procedures require that the mass spectrometer
and ETD module be shut down and disconnected from line power before service is
performed. Do not operate the mass spectrometer and ETD module with the top or side
covers off. Do not remove protective covers from printed circuit boards (PCBs).
CAUTION Do not perform any servicing other than that contained in the ETD Module
Hardware Manual. To avoid personal injury or damage to the instrument, do not
perform any servicing other than that contained in this manual or related manuals unless
you are qualified to do so.
CAUTION Respect heated zones. Treat heated zones with respect. The ion transfer tube,
the atmospheric pressure chemical ionization (APCI) vaporizer, and reagent ion source
might be very hot and might cause severe burns if touched. Allow heated components to
cool to room temperature before you service them.
CAUTION Use care when changing the vacuum pump oil. Treat drained vacuum pump
oil and pump oil reservoirs with care. Hazardous compounds introduced into the system
might have dissolved in the pump oil. Always use approved containers and procedures for
disposing of waste oil. Whenever a pump has been operating on a system used for the
analysis of toxic, carcinogenic, mutagenic, or corrosive/irritant chemicals, you must
decontaminate the pump and certify that it is free of contamination before repairs or
adjustments are made by a Thermo Fisher Scientific field service engineer or before it is
sent back to the factory for service.
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CAUTION Provide an adequate fume exhaust system and contain waste streams.
The API source can accommodate high flow rates. Therefore, you must make provisions
to collect the waste solvent. Connect the API source housing drain to the solvent waste
container provided with the instrument, and vent the waste container to a fume exhaust
system. For more information, refer to Chapter 3, “Ion Max and Ion Max-S Ion Sources,”
in the LTQ Series Getting Connected Guide.
You must provide an adequate fume exhaust system. Samples and solvents that are
introduced into the ETD module are eventually exhausted from the forepump. Therefore,
connect the forepump to a fume exhaust system. Consult local regulations for the proper
method of exhausting the fumes from your system.
Equip your lab with at least two fume exhaust systems:
• The analyzer optics can become contaminated if the API source drain tube and the
exhaust tubing from the forepumps connect to the same fume exhaust system. Route
the exhaust tubing from the forepumps to a dedicated fume exhaust system.
• Do not vent the PVC drain tube (or any vent tubing connected to the waste
container) to the same fume exhaust system that the forepumps connect to. Vent the
waste container to a dedicated fume exhaust system. The exhaust system for the
Ion Max™ or Ion Max-S™ API source must accommodate a flow rate of up to
30 L/min (64 ft3/h).
Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need. You
can use your smartphone to scan a QR code, which opens your email application or browser.
Contact us
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ETD Module Hardware Manual
Customer Service and Sales
Technical Support
(U.S.) 1 (800) 532-4752
(U.S.) 1 (800) 532-4752
(U.S.) 1 (561) 688-8731
(U.S.) 1 (561) 688-8736
us.customer-support.analyze
@thermofisher.com
us.techsupport.analyze
@thermofisher.com
Thermo Scientific
Preface
Contact us
Customer Service and Sales
Technical Support
 To find global contact information or customize your request
1. Go to www.thermoscientific.com.
2. Click Contact Us, select the Using/Servicing a Product option, and then
type the product name.
3. Use the phone number, email address, or online form.
 To find product support, knowledge bases, and resources
Go to www.thermoscientific.com/support.
 To find product information
Go to www.thermoscientific.com/lc-ms.
Note To provide feedback for this document:
• Send an email message to Technical Publications ([email protected]).
• Complete a survey at www.surveymonkey.com/s/PQM6P62.
Thermo Scientific
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Preface
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1
Introduction
The Velos Pro/ETD and LTQ XL/ETD (see Figure 1) systems are members of the Thermo
Scientific family of mass spectrometers (MSs). The Velos Pro/ETD and LTQ XL/ETD
systems are advanced analytical instruments that include a syringe pump, a divert/inject valve,
a mass spectrometer, the ETD module, and the Xcalibur data system.
Figure 1.
LTQ XL MS with the ETD module and NSI source
In liquid chromatography/mass spectroscopy (LC/MS) analysis, you first inject a sample into
an LC column. In the LC column, the sample separates into its components. These
components elute from the LC column and pass sequentially into the mass spectrometer for
analysis.
In the case of direct infusion or flow injection, no LC is performed. The sample enters the
mass spectrometer without being separated into its components.
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1
Introduction
With the ETD module, you can analyze the sample (direct infusion/flow injection) or its
components (LC/MS) by electron transfer dissociation (ETD). The data system stores and
processes the data from the mass spectrometer.
The Velos Pro/ETD and LTQ XL/ETD systems consist of an API source, ion optics, a mass
analyzer, an ion detection system, and a reagent ion source (ETD module). A vacuum
manifold encloses the ion optics, mass analyzer, ion detection system, reagent ion source, and
part of the API source. Ionization of the analyte occurs in the API source. The specific
method used to ionize the analyte is called the ionization technique. The ion optics transmit
the analyte ions produced in the API source into the mass analyzer, where they are trapped in
stable orbits by a time-varying electric field. The polarity of the potentials applied to the API
source and ion optics determines whether positively charged analyte ions or negatively
charged analyte ions transmit to the mass analyzer. You can configure the MS/ETD system to
analyze positively or negatively charged ions (called the positive or negative ion polarity
mode).
Negatively charged reagent ions (fluoranthene radical anions) from the reagent ion source
(ETD module) can also fragment protein or peptide analyte ions in the mass analyzer. These
negatively charged ions transfer electrons to protein or peptide analyte cations and cause them
to dissociate and produce C and Z type product ions (versus the Y and B type product ions
produced by collision-induced dissociation [CID]). The resulting analyte product ions
provide another way of analyzing these molecules as compared to CID and pulsed Q
collision-induced dissociation (PQD).
The lenses in the API source and ion optics act as a gate to start and stop the transmission of
ions from the API source to the mass analyzer. The Automatic Gain Control™ (AGC) feature
controls the function of these lenses by setting them to transmit the optimum number of ions
to the mass analyzer.
The mass analyzer measures the mass-to-charge ratios (m/z) of the ions produced in the API
source. Selected ions, ejected from the mass analyzer, reach the ion detection system where
they produce a signal. The signal produced is then amplified by the detection system
electronics.
The Xcalibur data system analyzes the ion detection system signal and serves as the user
interface to the mass spectrometer, autosampler, and LC. For information about the data
system processing and instrument control application, refer to the Xcalibur application Help.
Each sequence of injecting the mass analyzer with ions followed by mass analysis of the ions is
called a scan. The MS/ETD system can use several different scan modes, scan types, and
dissociation techniques to inject, dissociate, and eject ions from the mass analyzer. The ability
of this instrumentation to vary the scan mode, scan type, and dissociation technique, as well
as the ionization and ion polarity modes, provides exceptional flexibility to solve complex
analytical problems.
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2
Functional Description
This chapter describes the principal components of the ETD module and their functions.
Note For the LTQ Velos/ETD system, follow the Velos Pro/ETD system information,
unless otherwise noted.
Contents
• Power Panel
• Interface PCB
• ETD Control PCB
• Heater Control PCB
• LEDs
• Flow Control
• Reagent Heaters
• Ion Source
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Functional Description
Figure 2 shows the inside of the ETD module, and the following sections describe the ETD
module’s major components.
Figure 2.
Internal back view of the ETD module
DC high voltage
(HV) supply PCB
Display PCB
Heater control PCB
Vacuum manifold
(contains the ion source
and ion volume)
Ion gauge
Inlet valve solenoid
Cover over the vial heaters
in the reagent inlet
Inlet valve lever in the
closed (down) position
Control PCB
Power module
Turbo pump
Connector to the interface PCB
(behind the control PCB)
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Functional Description
Power Panel
Power Panel
Figure 3 shows the ETD module’s right-side power panel.
Figure 3.
ETD module power panel
Electronics service switch
ETD module
power switch
Forepump receptacle
ETD module power
The power panel for the ETD module contains a power switch (circuit breaker) and an
electronics service switch. During normal operation, the ETD Power switch is in the On (up)
position and the electronics service switch is in the Operating Mode (up) position. As a safety
feature, both components of the MS/ETD system (the mass spectrometer and the ETD
module) shut down with one set of switches—the mass spectrometer switches. Before
performing maintenance on the ETD module as described in Chapter 5, “Maintenance,” you
set the mass spectrometer’s electronics service switch to the Service Mode (down) position.
The electronics service switch turns the power on or off to all ETD module components,
except the turbo pump and forepump.
The ETD module power panel also contains a Power In receptacle that connects the module
to line power and a Forepump receptacle to power the ETD module’s forepump. For more
information about connecting the MS/ETD system, refer to the LTQ Series Getting Connected
Guide.
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2
Functional Description
Interface PCB
Interface PCB
The interface printed circuit board (PCB) provides an electronic connection between the
ETD module and the mass spectrometer. This board also gives the mass spectrometer panel
switches control over the mass spectrometer and ETD module.
• The mass spectrometer’s power switch turns power on and off to all components in both
the mass spectrometer and the ETD module.
• The mass spectrometer’s electronics service switch turns power on and off to all mass
spectrometer and ETD module components, except to the vacuum pumps connected to
the mass spectrometer and the ETD module.
Note The ability to control the power from one location—the mass spectrometer’s power
panel switches—to all components of the MS/ETD system is a safety feature.
ETD Control PCB
The ETD control PCB controls most of the ETD module functions:
• ETD module operating logic
• Heater temperature and readback logic (for the reagent heaters, transfer line heater, and
restrictor oven heater)
• Ion gauge
• Ion source (filament, ion source heater, and lenses)
• Oven cooling gas control
• Convectron™ gauge
• Reagent gas flow
The DC HV supply PCB connects to the ETD control PCB.
Heater Control PCB
The heater control PCB contains the power source and temperature sensing circuitry for the
four heaters in the reagent inlet, which are the transfer line heater, restrictor oven heater, and
two vial heaters. The heater control PCB sends temperature information to the heater
temperature and readback logic on the ETD control PCB. The heater temperature and
readback logic control how the heater control PCB applies power to the ETD module heaters.
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2
Functional Description
LEDs
LEDs
Figure 4 shows the ETD module status LEDs, which are described in Table 2. (The status
LEDs are not provided for the Orbitrap™/ETD systems.)
Figure 4.
Power
ETD module status LEDs for the Velos Pro/ETD and LTQ XL/ETD systems
Vacuum
Filament
System
Ion/Ion Reaction
Table 2. ETD module status LED descriptions (Sheet 1 of 2)
LED
State
Description
Power
Green
The ETD module is receiving power.
Off
The ETD module is not receiving power.
Green
The vacuum pressure is within the allowable
operating range.
Yellow
A vacuum sensor detects a fault and the ETD
module has gone into standby mode.
Off
High voltage is not being applied to the ETD
module.
Green
The filament is on.
Yellow
There is a filament fault, such as a burnt out
filament.
Off
The filament is off.
Flashing yellow
All of the electronics are on and the restrictor,
transfer line, and ion source heaters are on but
not at their target temperatures. The vial heaters
are off.
Solid yellow
The restrictor, transfer line, and ion source
heaters have reached their target temperatures.
The vial heaters remain off.
Flashing green
The vial heaters are on but not at their target
temperatures. The restrictor, transfer line, and
ion source heaters are at their target
temperatures.
Solid green
The five heaters (restrictor, transfer line, ion
source, and both vial heaters) are at their target
temperatures.
Off
Power is not being supplied to the ETD module.
Vacuum
Filament
System
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2
Functional Description
Flow Control
Table 2. ETD module status LED descriptions (Sheet 2 of 2)
LED
State
Description
Ion/Ion Reaction
Blue, sequentially
lighting up
An ETD activation (or ion/ion reaction) is being
used during a scan.
On
A scan has stopped. This is not a fault.
Off
No scan is occurring.
For information about the mass spectrometer LEDs, refer to Chapter 2, “Functional
Description,” in the LTQ Series Hardware Manual.
Flow Control
The ETD module contains an electronic pressure regulator for flow control of the chemical
ionization (CI) gas/reagent carrier gas. The ETD control PCB provides the control signal.
This gas serves several functions in the ETD module:
• As a carrier gas, the nitrogen sweeps the reagent (fluoranthene) from the vial to the ion
source where the reagent radical anions form.
• As a CI vehicle, the nitrogen undergoes collisions with 70 eV electrons from the filament
in the ion volume. These 70 eV electrons knock electrons off of the nitrogen molecules
(creating nitrogen ions). The secondary electrons resulting from these collisions have near
thermal-kinetic energies. The fluoranthene captures these thermal electrons to form
reagent radical anions that react with the analyte.
Reagent Heaters
The reagent inlet contains the reagent heaters that heat the reagent (fluoranthene) to obtain a
sufficient amount of reagent vapor in the carrier gas. The heater control PCB powers the
reagent heaters. The ETD control PCB, in turn, controls the heater control PCB.
When the reagent ion source goes into standby mode, the two reagent heaters and the
filament turn off. An audible rush (hissing noise) from the reagent ion source area in the back
of the ETD module confirms the flow of the nitrogen cooling gas (if enabled).
Note When the reagent ion source is off or in standby mode, cooling gas (nitrogen) turns
on. This is normal operation. For information about the cooling gas, refer to “Specifying
the Reagent Ion Source for the Mass Spectrometer” in Chapter 2 of the ETD Module
Getting Started Guide.
CAUTION Hot surface. When the reagent ion source is off, the restrictor oven, transfer
line, and ion source remain at 160 °C (320 °F).
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Functional Description
Ion Source
If enabled in Thermo Foundation™ Instrument Configuration, the cooling gas (nitrogen)
turns off when the reagent heaters reach 70 °C (158 °F). To replace the reagent vials, follow
the procedure “Reagent Vials Maintenance.”
Note The rushing or hissing noise of the nitrogen coming from the back of the ETD
module stops when the cooling gas (nitrogen) turns off.
CAUTION Hot surface. Do not attempt to handle the vials or vial holders when the
cooling nitrogen turns off at 70 °C (158 °F). They are still too hot to handle. To replace
the reagent vials, follow the procedure “Reagent Vials Maintenance.”
When starting at room temperature, the reagent heaters and vials take at least 20 minutes to
stabilize at the configured vial operating temperature (Thermo Fisher Scientific recommends
the 90 °C setting). The ion source receives the reagent only after the temperatures stabilize.
For information about setting the vial temperature, refer to Chapter 2, “Setting Up the
Xcalibur Instrument Configuration,” in the ETD Module Getting Started Guide.
Ion Source
The reagent molecules are converted to reagent ions in the ion source. Figure 32 and
Figure 33 show the ion source assembly, which contains the filament, reagent ion volume, ion
source heater, and so on. The filament is the source of 70 eV electrons that collide with the
nitrogen molecules to form nitrogen cations and near-thermal-energy electrons, which the
reagent molecules capture to yield reagent anions. The reagent ion volume is the space where
this reaction takes place. The ETD Control PCB controls the ion source heater.
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Functional Description
Ion Source
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3
Shutdown and Startup
As a safety feature, both components of the MS/ETD system (the mass spectrometer and the
ETD module) shut down with one set of switches—the mass spectrometer switches. This
safety feature is one of the functions of the ETD module interface board (see page 6).
For a description of the ETD module’s power panel, see page 5. For information about the
cooling gas, refer to step 3 on page 11 of the ETD Module Getting Started Guide.
Note
• If you are not going to use the system or ETD module for a short period of time, such
as overnight or through the weekend, place the system in standby mode as described
in “Placing the ETD Module in Standby Mode.”
• If you are not going to use the system for an extended period of time or if it must be
shut down for maintenance or service, follow the procedure “Shutting Down the
MS/ETD System.”
Refer to Chapter 3 in the LTQ Series Hardware Manual for the following:
• The mass spectrometer’s shutdown and startup procedures
• A table showing the On/Off status of mass spectrometer components when the mass
spectrometer is in standby or off mode
Contents
• Shutting Down the ETD Module in an Emergency
• Opening the Tune Plus Window
• Placing the ETD Module in Standby Mode
• Shutting Down the MS/ETD System
• Starting Up the MS/ETD System
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Shutdown and Startup
Shutting Down the ETD Module in an Emergency
Shutting Down the ETD Module in an Emergency
CAUTION If you must turn off the ETD module in an emergency, turn off the mass
spectrometer’s Main Power switch located on its right-side power panel (Figure 5). This
switch turns off all power to the mass spectrometer and the ETD module, including the
forepumps, without harming components within the system. However, do not use this
method as part of the standard shutdown procedure. Instead, refer to “Shutting Down the
Mass Spectrometer Completely” in Chapter 3 of the LTQ Series Hardware Manual.
If you turn off the mass spectrometer’s Main Power switch and the ETD module remains
on, turn off the ETD module’s main ETD Power switch located on its right-side power
panel. Contact your local Thermo Fisher Scientific field service engineer regarding the
connection malfunction.
To turn off the LC, autosampler, and data system computer in an emergency, use their
respective on/off switch or button.
Figure 5.
Power panel for the Velos Pro and LTQ XL mass spectrometers
Reset button
Electronics service switch
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Main Power switch
Thermo Scientific
3 Shutdown and Startup
Opening the Tune Plus Window
Opening the Tune Plus Window
There are several ways to open the Tune Plus window (Figure 6).
 To open the Tune Plus window
Do one of the following:
• On the Windows taskbar, choose Start > All Programs > Thermo Instruments >
LTQ > model Tune, where model is your specific MS/ETD system.
Note For LTQ Series version 2.5.0 or earlier, choose Start > All Programs >
Xcalibur > model Tune.
• In the Xcalibur application, click the Roadmap View icon (under the menu bar), the
Instrument Setup icon, the model MS icon, and then Tune Plus.
–or–
• In the Xcalibur application, click the Roadmap View icon (under the menu bar), the
Instrument Setup icon, and the model MS icon. Then, from the main toolbar
choose model > Start Tune Plus.
Figure 6.
Thermo Scientific
Tune Plus window for the Velos Pro/ETD system
ETD Module Hardware Manual
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3
Shutdown and Startup
Placing the ETD Module in Standby Mode
Placing the ETD Module in Standby Mode
If you are not going to use the ETD module for a short period of time (see page 11), place the
ETD module in standby mode.
 To place the ETD module in Standby mode
1. Complete all data acquisition, if any.
2. Open the Tune Plus window (see page 13).
3. Choose Setup > Reagent Ion Source to open the Reagent Ion Source dialog box
(Figure 7).
Figure 7.
Reagent Ion Source dialog box
4. Clear the Filament On check box.
When you clear this check box, the filament turns off and the ETD module’s Filament
LED turns off. The System LED switches from either solid green or flashing green to
solid yellow. This change signifies that the vial heaters are off and that the restrictor,
transfer line, and ion source heaters are on and at their target temperatures.
5. (Optional) If you are not going to use the ETD module for several days or more, clear the
Reagent Ion Source On check box.
When you clear this check box, the reagent vial heaters turn off. If you selected the
Use Cooling Gas check box for the reagent ion source configuration, the cooling gas turns
on and stays on until the reagent vial heaters reach 70 °C. For information about the
cooling gas option, refer to “Specifying the Reagent Ion Source for the Mass
Spectrometer,” in Chapter 2 of the ETD Module Getting Started Guide.
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3 Shutdown and Startup
Shutting Down the MS/ETD System
Tip If you place the MS/ETD system in standby mode, instead of only the ETD
module, the reagent vial heaters turn off followed by a 1 hour delay until the cooling
gas turns on (if enabled).
CAUTION Hot surface.
• Install or exchange the reagent vials by following the procedure “Reagent Vials
Maintenance.” Note that the reagent vials are too hot to touch when the cooling
nitrogen turns off at 70 °C (158 °F). Verify that the reagent vials are cool to the touch
before handling them.
• The restrictor, transfer line, and ion source heaters operate at 160 °C (320 °F). Do not
attempt to touch them unless you have shut down the MS/ETD system (Shutting
Down the MS/ETD System) and these heaters have cooled to room temperature.
For more information about the ETD module LEDs, see “LEDs.” For information about the
Filament On check box, refer to the Tune Plus application Help. For more information about
turning the reagent heaters on and off, see “Reagent Heaters.”
Shutting Down the MS/ETD System
The mass spectrometer’s power switches control the power to the MS/ETD system (ETD
module and mass spectrometer). The ETD module’s power switches control only the ETD
module. When the system is fully operational (all systems on), the mass spectrometer’s Main
Power switch is in the On position and its electronics service switch is in the Electronics
Normal position.
Normally the ETD module’s power and electronics service switches are not used and remain
on. To place the MS/ETD system in service mode, use the mass spectrometer’s electronics
service switch. Turn the MS/ETD system on and off with the mass spectrometer‘s power
switch.
IMPORTANT If you accidentally turn off the ETD module’s electronics service switch,
turn the ETD module switch back on, and then turn off and on the mass spectrometer’s
electronics service switch (not the power switch).
CAUTION Hot surface. When the MS/ETD system is on, the flow restrictor, transfer line,
and ion source heaters can reach 160 °C (320 °F). The vial heaters can be at 108 or 90 °C,
depending on the reagent ion source configuration. (Thermo Fisher Scientific
recommends the 90 °C setting.) Do not attempt to replace the reagent vials or service
heated components until they have cooled to room temperature, which can take an hour
or more.
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3
Shutdown and Startup
Shutting Down the MS/ETD System
 To shut down the MS/ETD system
1. Complete all data acquisition, if any.
2. Turn off the flow of sample solution from the LC (or other sample introduction device).
Note For instructions about operating the LC from the front panel, refer to the LC
manual.
3. Open the Tune Plus window (see page 13).
4. Choose Setup > Reagent Ion Source to open the Reagent Ion Source dialog box
(Figure 8).
Figure 8.
Reagent Ion Source dialog box
Actual vial temperature
5. Clear the Reagent Ion Source On check box.
6. Observe the vial temperature in the Actual column on the right.
If enabled, nitrogen cooling gas flows until the vial cools to 70 °C.
7. Click OK.
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3 Shutdown and Startup
Starting Up the MS/ETD System
8. Choose Control > Off to turn off the MS/ETD system.
CAUTION
• Turning off the mass spectrometer also turns off the ion source sheath gas,
auxiliary gas, high voltage, and all of the ETD module heaters. You must choose
Control > Off to turn off all of the ETD module heaters.
• The ability to control the service mode for both the mass spectrometer and the
ETD module at one location (at the mass spectrometer’s electronics service
switch) is a safety feature. Therefore, do not toggle the ETD module electronics
service switch to the Service Mode position while the mass spectrometer switches
are in their On (up) positions. This could cause communication problems
between the mass spectrometer and the ETD module.
You can determine the status of the ETD module from its status LEDs on the front panel;
see “LEDs.”
9. Turn off the mass spectrometer’s Main Power switch.
Starting Up the MS/ETD System
If you followed the procedures in the LTQ Series Hardware Manual to shut down the system
completely, you must turn the LC and data systems back on before turning on the MS/ETD
system, which does not operate until it receives instructions from the data system.
 To start the MS/ETD system
1. Turn on the flows for the helium and nitrogen gases at their tanks, if they are off.
2. Turn on the mass spectrometer’s Main Power switch.
3. Wait at least 1 hour to allow the mass spectrometer to pump down.
4. Make sure that the mass spectrometer’s electronics service switch is in the Electronics
Normal position.
The system starts up and goes into standby mode. The ion source heater, flow restrictor,
and transfer line heaters start heating.
The ETD module’s status LEDs indicate the MS/ETD system states as it powers up:
• The MS/ETD system’s Power LED is solid green when the MS/ETD system power
is on.
• The Vacuum LED is solid green when the MS/ETD system vacuum pressure is in the
proper range as measured by both the ion and Convectron gauges.
• The Filament LED is off when the filament is off.
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Shutdown and Startup
Starting Up the MS/ETD System
The ETD module’s system LED changes to solid yellow when the restrictor, transfer line,
and ion source heaters reach their target temperatures and the vial heaters are off.
The carrier/CI gas turns on.
The mass spectrometer LED flashes yellow when all of the following occur:
• The MS/ETD system electronics are on.
• The restrictor, transfer line, and ion source heaters are on but not at their target
temperatures.
• The vial heaters are off.
For more information about the ETD module’s status LEDs, see “LEDs.”
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4
Daily Operation
To ensure the proper operation of the ETD module, Thermo Fisher Scientific recommends
that you perform daily preventive maintenance. This chapter specifies the items to check
before operating the system and the cleaning procedures to perform after completing the
analyses.
Note You do not need to tune and calibrate the ETD module as part of your daily
routine. However, ensure that you perform ETD-related calibration at least every three
months (on the Semi-Automatic page of the Calibrate dialog box, Electron Multiplier
Gain for the negative ion mode and Reagent Ion Selection). For information about tuning
and calibrating the ETD module, refer to the ETD Module Getting Started Guide.
IMPORTANT For LTQ version 2.7 or later, the Tune Plus application saves the ETD
parameters (excluding the ETD reaction time) in an ETD-dedicated system file. This
means you can switch to another ion source probe type without losing the current ETD
parameters. In LTQ version 2.6 SP3 or earlier, the ETD parameters were saved in the tune
file associated with a specific ion source probe.
Contents
• Before Operating the MS/ETD System
• Turning On the Reagent Ion Source
• After Operating the MS/ETD System
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4
Daily Operation
Before Operating the MS/ETD System
Before Operating the MS/ETD System
Follow these preventive maintenance procedures every day before beginning the first analysis.
Note Before performing these procedures for the MS/ETD system, perform the
corresponding procedures for the mass spectrometer as described in Chapter 4, “Daily
Operation,” in the LTQ Series Hardware Manual.
• Checking the System Mode
• Checking the Vacuum Pressure Levels
• Checking the Gas Supplies
Checking the System Mode
Before beginning your daily work, turn on the mass spectrometer.
 To turn on the mass spectrometer
1. Open the Tune Plus window (see page 13).
2. Click the On/Standby button to select the On mode.
On
20
Standby
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4 Daily Operation
Before Operating the MS/ETD System
Note
When on, the System LED on the mass spectrometer’s front panel turns green and the
high voltage to the electron multipliers turns on. (The status LEDs are not provided
for the Orbitrap/ETD systems.)
The following conditions can cause the MS/ETD system to remain in standby mode
even though you try to turn it on:
• Attempting to turn on the reagent ion source when the restrictor, source, and
transfer line heaters are not at their target temperatures.
• When either the mass spectrometer or the ETD module goes into standby mode.
If enabled, the reagent vial nitrogen cooling turns on if the vials are at an elevated
temperature.
Exception: If you place the MS/ETD system in standby mode, the cooling
nitrogen turns on after a 1-hour delay.
• Whenever the pressure in the mass spectrometer or the ETD module exceeds its
protection limit. If enabled, the reagent vial nitrogen cooling turns on if the vials
are at an elevated temperature.
• Whenever the flow of reagent ions becomes insufficient as determined by the
AGC setting. When this occurs, the MS/ETD system completes the current
Xcalibur sequence step before entering standby mode. This prevents the loss of
analysis results that might be affected by the reduced reagent ion production.
Checking the Vacuum Pressure Levels
Before beginning daily operation of the MS/ETD system, check the system’s vacuum pressure
levels and check for major air leaks. If there is a major air leak, the system does not pump
down to sufficient levels to turn on the system.
CAUTION For proper performance, operate the MS/ETD system at the proper vacuum
levels. Operating the system with poor vacuum levels can cause reduced sensitivity, tuning
problems, and reduced filament life.
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4
Daily Operation
Before Operating the MS/ETD System
 To check the vacuum pressure
1. In the Tune Plus window, choose Setup > Vacuum to open the Vacuum dialog box
(Figure 9).
Figure 9.
Vacuum dialog box
2. Click the Reagent tab (Figure 10).
Figure 10. Reagent page of the Vacuum dialog box
3. Compare the current values of the pressures in the vacuum manifold with the following
gauge values.
Condition
Ion gauge reading
(reagent source region)
Convectron gauge
reading (reagent foreline)
CI gas pressure set to 20 psi
15–35 × 10–5 Torr
0.01–0.05 Torr
Note
• If the current pressure values are higher than normal, there might be an air leak.
• If the pressure is above 40 × 10–5 Torr in the reagent source region and the system
restarted within the last 30 to 60 minutes, wait another 30 minutes and recheck
the pressure. If the pressure decreases with time, check the pressure periodically
until it is within the typical range for the ETD module.
• If the pressure remains high, the system might have an air leak.
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4 Daily Operation
Before Operating the MS/ETD System
 To check the system for major air leaks
Listen for a rush of air or a hissing sound coming from the instrument.
Possible causes of a major leak might be a loose or disconnected fitting, an improperly
positioned O-ring, or an open valve.
 To fix an air leak
1. Shut down the system. See “Shutting Down the MS/ETD System.”
2. Make a visual inspection of the vacuum system and vacuum lines for leaks.
3. Check each fitting and flange on the system for tightness, and tighten the fittings or
flanges that are loose.
Do not tighten fittings indiscriminately. Pay particular attention to fittings that have
changed recently or to fittings subjected to heating and cooling.
4. Make sure that the cover plate for the vacuum manifold (Figure 2) is properly positioned.
Note If the air leak persists, contact your local Thermo Fisher Scientific field service
engineer for assistance.
Checking the Gas Supplies
Before beginning daily operation of the MS/ETD system, check the gas supplies. The mass
spectrometer uses helium as a damping gas and collision activation partner in the mass
analyzer, and nitrogen as the API sheath gas, auxiliary gas, and sweep gas. The ETD module
requires an additional ultra-high-purity reagent carrier gas mixture.
 To check the gas supplies
1. Check that the gas lines connect properly to the back of the ETD module.
2. Check that gases are flowing and that the pressure for each gas is as follows:
• Helium: 275 ±70 kPa (40 ±10 psi)
• Nitrogen: 689 ±138 kPa (100 ±20 psi)
• Reagent carrier gas: 689 ±138 kPa (100 ±20 psi)
3. Make sure that you have sufficient gas to complete your analysis. If necessary, replace the
helium, nitrogen, or reagent carrier gas tank.
Note Typical daily nitrogen gas consumption (when nitrogen is on 24 hours per day) is
2832 L (100 ft3).
For more information about the gas requirements, refer to the LTQ Series Preinstallation
Requirements Guide.
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4
Daily Operation
Turning On the Reagent Ion Source
Turning On the Reagent Ion Source
Even when the ETD module is on, the reagent ion source within it stays off until you turn
it on.
 To turn on the reagent ion source
1. Open the Tune Plus window (see page 13).
2. Set the reagent ion source as follows:
a. Choose Setup > Reagent Ion Source to open the Reagent Ion Source dialog box
(Figure 11).
Figure 11. Reagent Ion Source dialog box
b. Select the following check boxes:
• Reagent Ion Source On
• Filament On
• View Reagent Ion Spectra
For tuning, you must manually select the Filament On check box.
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4 Daily Operation
Turning On the Reagent Ion Source
c. Click OK.
The reagent ion peaks appear in the Tune Plus spectrum view (Figure 12).
Note
If the reagent vials are not at their target temperature, a message appears:
Reagent Vial NOT At Temperature! Please wait …
The System LED on the ETD module flashes green to indicate that the reagent
vial heaters are turned on but not at their target temperatures (the other heaters
are at their target temperatures).
When the reagent vial heaters reach their target temperatures, which can take
20 minutes or more, the System LED illuminates solid green.
When the reagent vials reach their target temperature, voltage is applied to the
ETD module ion optics, and when the check box is selected, the filament turns
on and the Filament LED illuminates solid green.
(The status LEDs are not provided for the Orbitrap/ETD systems.)
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4
Daily Operation
Turning On the Reagent Ion Source
Figure 12. Mass spectrum for the reagent ion displayed in Tune Plus for the Velos Pro/ETD system
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4 Daily Operation
After Operating the MS/ETD System
3. Check the mass spectrum and do one of the following:
• If m/z 202 has satisfactory abundance and the reagent ion isolation is suppressing the
background anions (for example, m/z 216, and so on), proceed to step 4.
• If the intensity is not satisfactory, do the following:
–
Make sure that you have a recent calibration of the Electron Multiplier Gain for
the negative ion mode, which is on the Semi-Automatic page of the Calibrate
dialog box. If the calibration is old, check the calibration status on the Check
page, and then recalibrate if necessary. For information, refer to the LTQ Series
Getting Started Guide.
–
Tune the reagent ion optics as described in Chapter 3, “Tuning,” in the ETD
Module Getting Started Guide.
• If the reagent ion isolation is not suppressing the background anions, perform the
Reagent Ion Selection calibration on the Semi-Automatic page of the Calibrate dialog
box, Electron Multiplier Gain for the negative ion mode.
4. In the Reagent Ion Source dialog box, clear the View Reagent Ion Spectra check box.
This action clears the Tune Plus spectrum view from the ETD module.
After Operating the MS/ETD System
Follow these preventive maintenance procedures every day after completing your daily work:
• Placing the MS/ETD System in Standby Mode
• Purging the Oil in the Forepump
Placing the MS/ETD System in Standby Mode
 To place the MS/ETD system in standby mode
1. Follow the procedure “Placing the ETD Module in Standby Mode.”
2. In the Tune Plus window, click the On/Standby button to select the Standby mode.
On
Thermo Scientific
Standby
If the reagent ion source is on when you place the mass spectrometer in standby mode,
the filament turns off immediately but the vial heaters stay on for 60 minutes before they
turn off and the cooling gas begins. Therefore, you can perform quick, minor
maintenance procedures on the MS/ETD system without cooling the reagent vials.
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4
Daily Operation
After Operating the MS/ETD System
Purging the Oil in the Forepump
Purge (decontaminate) the oil in the forepump daily to remove water and other dissolved
chemicals, which can cause corrosion and decrease the lifetime of the forepump. The best
time to purge the oil is at the end of the working day.
For instructions, refer to the forepump’s documentation. Remember to close the purge valve
before continuing normal operation.
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5
Maintenance
Perform maintenance on the ETD module on an as-needed basis or when the ion signal
deteriorates.
Contents
• Maintenance Schedule
• Work Area Preparations
• Guidelines
• Tools and Supplies
• Cleaning Parts
• Ion Volume Maintenance
• Inlet Valve Maintenance
• Removing the Access Panels
• Ion Source Maintenance
• Reagent Vials Maintenance
• Forepump Maintenance
• Fan Filter Maintenance
Maintenance Schedule
Over time, the ion signal from the ETD module decreases as the internal components become
dirty and therefore need to be cleaned. Before performing any procedure in this chapter, run
the diagnostics as described in Chapter 6, “Diagnostics,” to determine if there are any
problems with the major electronic circuit boards.
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5
Maintenance
Maintenance Schedule
The first and easiest procedure to perform is to clean or replace the ion volume as described in
“Ion Volume Maintenance.” You can perform this procedure without shutting down and
venting the system. If the performance of the ETD module does not improve, you must shut
down and vent the system to perform the procedures on the ion source components and
reagent vials.
How often you clean the reagent ion source depends on the amount of time that the source is
operating. In general, the closer a component is to where the reagent ions are generated, the
more quickly it becomes dirty. For example, you must clean the ion volume and ion volume
holder more often than the lenses. Therefore, you typically need to clean the ion source block
with every third (or less) lens cleaning.
Table 3 lists the maintenance procedures and their recommended frequency.
Table 3. ETD module maintenance procedures and frequency
Component
Procedure
Recommended frequency
Location
Cooling fans
Clean the fan filter.
Every 4 months
page 74
Forepump
Purge (decontaminate) the oil and
check for leaks.
Daily
page 73
Change the oil.
Every 3 months, or if the oil is
cloudy or discolored
Add oil.
As needed, based on the oil level
Inlet valve components
Replace the inlet valve
components.
As the components wear out,
which could be after several years
page 47
Ion source block
Clean the ion source block.
Every 6 months, depending on the
usage
page 66
Ion source filament
Inspect or replace the filament.
As needed, depending on
analytical conditions, source usage,
and reagent ion abundance
page 53
Ion source lenses
Clean the ion source lenses.
As needed, depending on usage
page 64
Ion volume
Clean or replace the ion volume.
As needed, depending on usage
page 37
Reagent vials
Replace the reagent vials.
Annually to eliminate the
possibility that the septum on the
vials might start to leak with age
page 68
See also the
manufacturer’s
documentation.
For instructions about maintaining the mass spectrometer, refer to the LTQ Series Hardware
Manual. For instructions about maintaining the LC modules, refer to that instrument’s
manual.
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5 Maintenance
Work Area Preparations
Work Area Preparations
 To prepare the work area
Do the following:
• Cover the area with clean, lint-free paper or a large sheet of clean aluminum foil.
• Have nearby the necessary tools, supplies, and replacement parts (when applicable).
Guidelines
For optimal results, follow these guidelines when performing the procedures in this chapter.
• Proceed methodically.
• Always wear protective eye wear when cleaning parts or changing the reagent vials.
• Always wear a new pair of lint- and powder-free gloves when handling the internal source
components or clean parts, or when changing the reagent vials. Never reuse gloves after
you remove them because the surface contaminants on them recontaminate clean parts.
• Always place the components on a clean, lint-free work surface.
• Never overtighten a screw or use excessive force.
Tools and Supplies
You can remove and disassemble many parts by hand. Make sure you have all the necessary
tools before starting a procedure. Table 4 lists the tools, equipment, and chemicals you need
to provide for maintenance of the reagent ion source. Have a set of tools to use exclusively for
maintaining the reagent ion source and that are free of grease and other residues.
CAUTION Make sure to maintain the cleanliness of the parts when you handle them. If
you are not returning the parts directly to the instrument after cleaning, place them on
clean, unused aluminum foil.
Table 4. Tools, equipment, and chemicals (Sheet 1 of 3)
Description
Part number
Tools
Thermo Scientific
Forcepsa
76360-0400
Hex or hex ball drivers: 2 mm, 2.5 mm, 3 mm, 4 mm,
1/16 in., 5/64 in., 7/64 in., 9/64 in., and 5/32 in.
–
Ion volume insertion and removal toolb
98000-60028
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5
Maintenance
Tools and Supplies
Table 4. Tools, equipment, and chemicals (Sheet 2 of 3)
Description
Part number
Pliers
–
Screwdriver, Phillips, #2
–
Screwdriver, slotted, small
–
Tweezers, large
–
Wrench, adjustable
–
Wrench, socket, 1/2 in.
–
Wrenches, open-ended: 1/4 in., 5/16 in., 7/16 in.,
1/2 in., and 9/16 in.
–
(Optional, recommended) Dremel™ rotary tool or
equivalent, cordless
–
Equipment
Aluminum foil, heavy gaugec
Aluminum oxide abrasive, number 600
Fisher Scientific 01-213-104
a
32000-60340
Beakers, glass: 100 mL and 500 mL
–
Cotton-tipped applicators
Fisher Scientific A030102000
Gloves, lint-free and powder-free
Fisher Scientific 19-120-2947d
Unity Lab Services:
• 23827-0008 (size medium)
• 23827-0009 (size large)
Lamp, small, high-intensity
–
Protective eye wear
–
Sonicator
–
(Optional) Oven
–
Chemicals
Acetone (or other suitable polar solvent)
32
HPLC grade
Fisher Scientific A949
GC Resolv
Fisher Scientific A928-4
(amber glass, 4L)
Clean, dry gas (air or nitrogen)
–
Detergent (Alconox™, Liquinox™, Micro-90™, or
equivalent)
–
Glycerol, reagent grade
–
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5
Maintenance
Cleaning Parts
Table 4. Tools, equipment, and chemicals (Sheet 3 of 3)
Description
Part number
Water, deionized
–
Water, tap
–
a
Provided in the ETD Accessory Kit.
b
Provided with your ETD module order.
c
Rinse each sheet with acetone before use.
d
Multiple sizes are available.
CAUTION Avoid exposure to potentially harmful materials.
By law, producers and suppliers of chemical compounds are required to provide their
customers with the most current health and safety information in the form of Material
Safety Data Sheets (MSDSs) or Safety Data Sheets (SDSs). The MSDSs and SDSs must
be freely available to lab personnel to examine at any time. These data sheets describe the
chemicals and summarize information on the hazard and toxicity of specific chemical
compounds. They also provide information on the proper handling of compounds, first
aid for accidental exposure, and procedures to remedy spills or leaks.
Read the MSDS or SDS for each chemical you use. Store and handle all chemicals in
accordance with standard safety procedures. Always wear protective gloves and safety
glasses when you use solvents or corrosives. Also, contain waste streams, use proper
ventilation, and dispose of all laboratory reagents according to the directions in the MSDS
or SDS.
Cleaning Parts
To clean parts, follow one of these procedures:
• Cleaning Stainless Steel Parts
• Cleaning Nonstainless Steel Parts
IMPORTANT
• Prepare a clean work surface by covering the area with aluminum foil, dull side up.
• Put on a new pair of lint- and powder-free gloves before starting each of these cleaning
procedures.
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Maintenance
Cleaning Parts
Cleaning Stainless Steel Parts
The reagent ion source, ion volume assembly, ion source block, and lenses are made from
stainless steel. To clean these parts, follow the procedure in this section.
CAUTION Use caution, because exposure to liquids can damage some components.
You need the following tools and supplies (see also Table 4).
Tools
Supplies
Forceps
Acetone, reagent grade (or other suitable
polar solvent)
Sonicator
Aluminum foil
(Optional) Dremel rotary tool or equivalent, Aluminum oxide abrasive, number 600
cordless
(Optional) Oven
Clean, dry gas (air or nitrogen)
–
Cotton-tipped applicators
–
Detergent (Alconox, Micro-90, or
equivalent)
–
Glass beakers: 100 mL and 500 mL
–
Glycerol, reagent grade
–
Water, deionized
–
Water, tap
CAUTION Do not use this procedure to clean ceramic, aluminum, or gold-plated parts.
For those types of parts, see “Cleaning Nonstainless Steel Parts.”
 To clean stainless steel parts
1. Clean the parts with an aluminum oxide slurry as follows:
a. In a 100 mL glass beaker, make a slurry of number 600 aluminum oxide and glycerol.
b. Dip a clean, cotton-tipped applicator into the slurry and clean the parts thoroughly.
Contamination often appears as dark or discolored areas, but might not be visible.
The heaviest contamination is usually found around apertures, such as the electron
entrance hole on the reagent ion source.
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5
Maintenance
Cleaning Parts
Note To speed up the cleaning process and make it more efficient, you can use a
Dremel tool—be sure to wear protective eye wear when using this tool. Cut the
wood handle of a cotton-tipped applicator to 5 cm (2 in.) long and secure it in
the chuck of a Dremel tool. Dip the cotton tip into the slurry. Set the Dremel
tool to its lowest speed and clean the parts.
CAUTION To prevent personal injury, use a cordless Dremel tool or, if you use a
corded tool, be sure to keep the tool away from possible hazards, such as standing
water or flammable solvents.
c. Cut the wooden end of a cotton-tipped applicator at an angle to clean the inside
corners.
d. Rinse the parts with clean tap water.
e. Remove any remaining slurry by using a clean, cotton-tipped applicator.
Tip Do not let the slurry dry on the metal because dried aluminum oxide is
difficult to remove.
2. Clean the parts in a detergent solution as follows:
a. In a 500 mL glass beaker, make a solution of detergent and warm tap water.
b. Use forceps to place the parts in the beaker containing the warm detergent solution.
c. Place the beaker and its contents in the sonicator for 5 min.
d. Rinse the parts with clean tap water.
3. Clean the parts in deionized water as follows:
a. Use forceps to place the parts in a 500 mL glass beaker containing deionized water.
b. Place the beaker and its contents in the sonicator for 5 min.
c. If the water is cloudy after sonicating, pour off the water, add fresh water, and place
the beaker and its contents in the sonicator again for 5 min. Repeat until the water is
clear.
4. Clean the parts in fresh acetone as follows:
a. Use forceps to place the parts in a 500 mL glass beaker containing fresh acetone.
b. Place the beaker and its contents in the sonicator for 5 min.
5. Blow-dry the parts immediately by using clean, dry gas (air or nitrogen).
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Maintenance
Cleaning Parts
6. Complete the drying process, as follows:
• Use forceps to place the parts in a 500 mL glass beaker, cover it with aluminum foil,
and then put it in an oven set at 100 °C (212 °F) for 30 min.
–or–
• Lay the parts on clean aluminum foil (dull side facing up) and let them dry for
30 min.
7. Wait until the parts are cool before reassembling them.
Cleaning Nonstainless Steel Parts
The reagent ion source’s block heater ring, filament spacer, lens holder, and spacers are
nonstainless steel parts made from aluminum or ceramic. To clean these parts, follow the
procedure in this section.
You need the following tools and supplies (see also Table 4):
•
•
•
•
•
•
•
•
Acetone, reagent grade (or other suitable polar solvent)
Clean, dry gas (air or nitrogen)
Cotton-tipped applicators
Detergent (Alconox, Micro-90, or equivalent)
Forceps
Glass beakers, 500 mL
Water, deionized
Water, tap
CAUTION Do not use this procedure to clean stainless steel parts—instead, see “To clean
stainless steel parts.” Do not allow the aluminum oxide slurry to contact the aluminum,
ceramic, or gold-plated portions of nonstainless steel parts.
 To clean nonstainless steel parts
1. Clean the parts in a detergent solution as follows:
a. In a 500 mL glass beaker, make a solution of detergent and warm tap water.
b. Dip a clean, cotton-tipped applicator in the detergent mixture and scrub the parts.
Note Do not soak or sonicate the parts in detergent.
2. Using forceps, rinse the parts thoroughly with tap water.
CAUTION Do not leave aluminum parts, such as the block heater ring, in the
detergent. Basic solutions, such as detergent, discolor aluminum.
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5 Maintenance
Ion Volume Maintenance
3. Using forceps, rinse the parts in a 500 mL glass beaker containing deionized water.
Change the water if it becomes cloudy.
Note Do not soak or sonicate the parts in water.
4. Using forceps, rinse the parts in a 500 mL glass beaker containing acetone.
Change the acetone if it becomes cloudy.
Note Do not soak or sonicate the parts in acetone.
5. Blow-dry the parts immediately using clean, dry gas (air or nitrogen).
Ion Volume Maintenance
The reagent ion source consists of an ion volume, a filament, and ion source lenses. To restore
system performance, always clean the ion volume first as described in the following procedure.
Reagent molecules interact with energetic electrons to form ions in the ion volume. In
general, the closer a component is to where the reagent ions are generated, the more quickly it
becomes dirty. For example, the ion volume needs to be cleaned more often than other parts.
With the ion volume tool, you can access the ion volume by entering the probe interlock
through the inlet valve without shutting down and venting the system.
If cleaning or replacing the ion volume does not improve performance, clean the ion source
lenses (see Cleaning the Ion Source Lenses). If cleaning either of these components does not
restore system performance, clean the ion source block (see Cleaning the Ion Source Block).
To maintain the ion volume, follow these procedures:
1. To insert the ion volume tool into the inlet valve
2. To open the probe interlock
3. To remove the ion volume
4. To reinstall the ion volume
In addition to the appropriate cleaning tools and supplies, you need the following items (see
also Table 4):
•
•
•
•
Thermo Scientific
Aluminum foil
Gloves, lint- and power-free
Ion volume insertion and removal tool
Protective eye wear
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Maintenance
Ion Volume Maintenance
IMPORTANT
• Prepare a clean work surface by covering the area with aluminum foil, dull side up.
• Put on a new pair of lint- and powder-free gloves before starting each of these
removal, cleaning, and reinstallation procedures.
For field service use only
Part number
Ion volume
98000-20052
Ion volume holder
70001-20532
 To insert the ion volume tool into the inlet valve
1. Put on a pair of new, lint- and powder-free gloves and protective eye wear.
Before proceeding, familiarize yourself with the location of the inlet valve components on
the back of the ETD module (Figure 13).
Figure 13. Inlet valve components (back of the ETD module)
Inlet valve knob
Inlet valve plug
Inlet valve lever
Guide bar opening
2. Make sure the inlet valve lever is in the down (closed) position (Figure 13).
Also, note the components of the ion volume insertion and removal tool (Figure 14). The
guide bar has first and second stops and first and second marks (Figure 21 shows a
close-up view).
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Ion Volume Maintenance
Figure 14. Ion volume insertion and removal tool components
Alignment line
Lock position
Ion volume tool
Unlock position
Ion volume tool
handle
Bayonet lock
Second stop
First stop
Guide ball
Guide ball track
Guide bar
Guide ball hole
Guide bar handle
3. Hold the guide bar with the handle horizontal, pointing toward the right (Figure 15).
Figure 15. Guide bar positioned for insertion
Inlet valve lever in the
down (closed) position
Guide bar opening
Guide bar handle
4. Insert the guide bar into the guide bar opening in the back of the ETD module, and push
it in as far as it will go.
IMPORTANT The use of the guide bar is required. It has a solenoid actuated stop
position that prevents you from moving the ion volume tool too far, which could
cause catastrophic venting of the system. Therefore, by using the guide bar you
prevent damage to the system, including the turbo pump.
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Ion Volume Maintenance
5. Rotate the guide bar 90-degrees clockwise to lock it in position (Figure 16).
The guide bar handle now points down.
Figure 16. Guide bar insertion complete
6. Rotate the inlet valve knob (Figure 13) counterclockwise and remove the inlet valve plug.
The inlet valve knob has a stainless steel ferrule inside. Keep the inlet valve knob and
ferrule together.
Note The inlet valve plug prevents air from entering the vacuum manifold in case the
inlet valve is inadvertently opened.
7. Insert the ion volume tool’s guide ball into the guide bar’s guide ball hole (Figure 17).
Figure 17. First stop of the ion volume tool guide bar
Inlet valve knob
Ion volume tool
Guide bar
First stop
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Ion Volume Maintenance
8. Slide the ion volume tool forward in the guide bar track until it is at the first stop on the
guide bar (Figure 17).
This location prevents the probe from being pulled forward when the inlet valve is
evacuated.
9. Use your fingers to tighten the inlet valve knob to ensure a leak-tight seal (Figure 17).
 To open the probe interlock
1. Open the Tune Plus window (see page 13).
2. Click the On/Standby button to select the Standby mode.
3. Choose Setup > Reagent Ion Source to open the Reagent Ion Source dialog box
(Figure 18).
Figure 18. Reagent Ion Source dialog box
4. Click Open Probe Interlock.
When the probe interlock has pumped down to less than 0.1 mTorr, a message appears:
The Ball Valve can now be opened.
If a pressure of 0.1 mTorr or less is not reached, check to ensure that the inlet valve knob
is tight. If the inlet valve knob is tight but the pressure remains high, replace the inlet
valve seal as described in “Inlet Valve Maintenance.”
Do not close the Reagent Ion Source dialog box.
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Maintenance
Ion Volume Maintenance
 To remove the ion volume
1. Attach the ion volume tool to the ion volume inside the ion source as follows:
a. Push the inlet valve lever up to open the inlet valve (Figure 19).
Figure 19. Inlet valve lever in the open position
Inlet valve lever in the
open (up) position
b. Turn the ion volume tool handle to the unlock position (Figure 20), which indicates
that the ion volume tool is in position to accept the ion volume.
Figure 20. Ion volume tool handle in the unlock position
Unlock position
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c. Slide the ion volume tool into the inlet valve opening until the guide ball is located
just past the first mark on the guide bar (Figure 21).
Figure 21. Ion volume tool fully inserted into the inlet valve showing the guide ball just
past the first mark
Second mark
First mark
Second stop
d. Turn the ion volume tool handle to the locked position (Figure 22).
Listen for a click, indicating that the handle is fully engaged in the locked position
and is holding the ion volume.
Figure 22. Ion volume tool handle in the locked position
Locked position
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Ion Volume Maintenance
2. Remove the ion volume from the ion source as follows:
a. Withdraw the ion volume tool (the ion volume is attached) until the guide ball
reaches the first stop (see Figure 17 for the first stop position).
CAUTION Do not withdraw the ion volume tool beyond the point where the
guide ball reaches the first stop in the guide bar. Close the inlet valve before
withdrawing the ion volume tool past the first stop. Otherwise, the system vents
to the atmosphere, which might require cleaning the components that are under
vacuum.
b. Close the inlet valve by pushing the inlet valve lever down.
The probe interlock dialog box displays a message indicating that the valve is closed.
c. Loosen the inlet valve knob.
d. Withdraw the ion volume tool completely from the inlet valve by pulling the ion
volume tool in the guide bar to the guide ball hole.
e. Remove the ion volume tool from the guide bar.
CAUTION Hot surface. The ion volume might be too hot to touch. Let it cool to
room temperature before handling it.
3. Remove the ion volume from the ion volume tool as follows:
a. Turn the ion volume tool handle to the unlock position (Figure 20).
b. After the part has cooled, press the ion volume into the tip of the ion volume tool and
rotate it to disconnect the bayonet pin on the ion volume holder from the bayonet
pin lock on the ion volume tool (Figure 23).
Figure 23. Ion volume assembly
Bayonet pin
lock
Bayonet pin
Ion volume tool
Ion volume holder
Spring washer
Ion volume
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Ion Volume Maintenance
4. Press the ion volume into the ion volume holder, and then rotate and remove it from the
ion volume holder.
Rotate the ion volume holder and ion volume in opposite directions to separate the two
components.
5. Clean the ion volume and ion volume holder, as described in “Cleaning Stainless Steel
Parts.” Make sure you remove the ion burn from the inside of the holes in the ion
volume.
 To reinstall the ion volume
1. Attach the ion volume to the ion volume tool as follows:
a. Press the ion volume into the ion volume holder and rotate the ion volume to secure
it to the ion volume holder.
b. Align the arrow on the ion volume holder with the arrow on the ion volume tool
(Figure 24).
Figure 24. Placement of the ion volume on the ion volume tool
Ion volume
tool
Ion volume
CAUTION To avoid damage to the ion source, make sure that the arrows on the
ion volume tool and ion volume are aligned.
c. Press the ion volume holder into the tip of the ion volume tool and rotate it
counterclockwise to lock the bayonet pin.
d. Turn the ion volume tool handle to the lock position (Figure 22).
2. Insert the ion volume into the ion source as follows:
a. Insert the guide ball on the ion volume tool into the guide ball hole and slide it
forward until the guide ball is at the first stop (Figure 17).
b. Tighten the inlet valve knob to ensure a leak-tight seal.
c. Follow the procedure “To open the probe interlock.”
d. After evacuation is complete, push the inlet valve lever up to open the inlet valve
(Figure 19).
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e. Slide the ion volume tool into the inlet valve opening (Figure 21).
f.
Listen for a click indicating a connection between the ion volume and the ion source
block.
g. The guide ball is now slightly beyond the second stop (and first mark) on the guide
bar (Figure 21).
h. Turn the ion volume tool handle to the unlock position (Figure 20).
i.
Pull the ion volume tool away from the ion volume to the first stop position, and
then turn the ion volume tool handle to the locked position (Figure 22).
CAUTION Do not withdraw the ion volume tool beyond the point where the
guide ball reaches the first stop in the guide bar. Close the inlet valve before
withdrawing the ion volume tool past the first stop. Otherwise, the system vents
to the atmosphere, which might require cleaning the components that are under
vacuum.
3. Remove the ion volume tool as follows:
a. Close the inlet valve by pushing down on the inlet valve lever (Figure 17).
b. Loosen the inlet valve knob.
c. Continue withdrawing the ion volume tool completely from the inlet valve by sliding
the ion volume tool through the guide ball track in the guide bar to the guide ball
hole.
d. Lift the ion volume tool out of the ion volume guide bar.
4. (Optional) Remove the guide bar by rotating it 90-degrees counterclockwise and sliding it
out of the guide bar opening.
5. Replace the inlet valve plug and tighten the inlet valve knob (Figure 13).
A Tune Plus message box opens.
6. Click Close to close the message box.
7. Retune the mass spectrometer.
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Inlet Valve Maintenance
Inlet Valve Maintenance
This section describes how to replace the worn out inlet valve components (inlet valve seal or
inlet valve). In addition to the appropriate cleaning tools and supplies, you need the inlet valve
seal and lint- and power-free gloves (see also Table 4).
For field service use only
Part number
Inlet Valve Seal Kit
119265-0003
Inlet valve seal removal tool
119283-0001
0.530 in. ID O-rings (2)
3814-6530
 To replace the inlet valve components
1. Make sure the inlet valve lever in the down (closed) position (Figure 25).
Figure 25. Inlet valve components (back of the ETD module)
Inlet valve knob
Inlet valve plug
Inlet valve lever
Guide bar opening
2. Rotate the inlet valve knob counterclockwise and remove the inlet valve plug.
The inlet valve knob has a stainless steel ferrule inside. Keep the inlet valve knob and
ferrule together.
Note The inlet valve plug prevents air from entering the vacuum manifold in case the
inlet valve is inadvertently opened.
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Maintenance
Inlet Valve Maintenance
3. Remove the inlet valve seal as follows:
a. Pull out the knob on the inlet valve seal tool (Figure 26).
Figure 26. Inlet valve seal tool
Knob
b. Insert the tool straight into the inlet valve.
Figure 27. Inlet valve seal tool inserted into the inlet valve
Inlet valve
seal tool
c. Press the knob on the tool until it stops.
d. Remove the tool.
The inlet valve seal should be on the tool (Figure 28).
Figure 28. Inlet valve seal on the inlet valve seal tool
\
Inlet valve seal
Note Use only the inlet valve seal tool to remove or install the inlet valve seal.
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Inlet Valve Maintenance
4. Loosen the knob to disengage the seal (Figure 29).
Figure 29. Inlet valve seal disengaged from the tool
Inlet valve seal with O-rings
Inlet valve seal tool
5. Discard the seal and its O-rings.
6. Place the two new O-rings into the slots on the new inlet valve seal (Figure 29).
7. Insert the new inlet valve seal as follows:
a. Place the new inlet valve seal onto the inlet valve seal tool.
b. Insert the inlet valve seal tool into the inlet valve until it stops.
c. Remove the tool.
The O-rings secure the inlet valve seal in the opening.
8. Reinstall the ferrule, knob, and plug into the inlet valve opening.
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Maintenance
Removing the Access Panels
Removing the Access Panels
Some of the ETD module maintenance procedures require that you remove the ETD main
access panel, the side access panel, or both panels (Figure 30). To remove these panels, follow
the procedures in this section.
Figure 30. ETD module (back view)
Panel fasteners
Main access panel
Inlet valve knob
Inlet valve plug
Inlet valve lever
Guide bar opening
Side access panel
Panel fasteners
Fan filter
In addition to the appropriate cleaning tools and supplies, you need a 7/64 in. hex or hex ball
driver and a Phillips #2 screwdriver (see also Table 4).
IMPORTANT
• Prepare a clean work surface by covering the area with aluminum foil, dull side up.
• Put on a new pair of lint- and powder-free gloves before starting each of these
removal, cleaning, and reinstallation procedures.
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Removing the Access Panels
 To remove the ETD main access panel
1. Place the mass spectrometer’s electronics service switch in the Service Mode position.
CAUTION In Service mode all power to the MS/ETD system electronics turns off.
There are no user accessible components that carry a voltage in this mode. However,
the vacuum pumps continue to operate.
CAUTION Hot surface. When the MS/ETD system is on, the flow restrictor, transfer
line, and ion source heaters can reach 160 °C (320 °F). The vial heaters can be at
108 or 90 °C, depending on the reagent ion source configuration. (Thermo Fisher
Scientific recommends the 90 °C vial setting.) Do not attempt to replace the reagent
vials or service heated components until they have cooled to room temperature, which
can take an hour or more.
2. Remove the inlet valve lever (Figure 30) by pulling it down and away from the back
panel. Do not rotate the lever up. It must remain in its down (closed) position to avoid
catastrophic venting of the system.
CAUTION To prevent a catastrophic venting of the system, the inlet valve lever must
be in place and in the down position.
3. Use your fingers to unscrew the inlet valve knob and remove the inlet valve plug, inlet
valve knob, and internal ferrule.
4. Using the Phillips #2 screwdriver, loosen the captive screws on the back panel.
5. Tilt the top of the panel toward you and lift it up and away from the ETD module.
 To remove the ETD side access panel
1. Place the mass spectrometer’s electronics service switch in the Service Mode position.
CAUTION In Service mode all power to the MS/ETD system electronics turns off.
There are no user accessible components that carry a voltage in this mode. However,
the vacuum pumps continue to operate.
CAUTION Hot surface. When the MS/ETD system is on, the flow restrictor, transfer
line, and ion source heaters can reach 160 °C (320 °F). The vial heaters can be at
108 or 90 °C, depending on the reagent ion source configuration. Do not attempt to
replace the reagent vials or service heated components until they have cooled to room
temperature, which can take an hour or more.
2. Using the 7/64 in. hex driver, loosen the captive hex socket-head screws securing the
external side panel, and then remove the panel.
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Ion Source Maintenance
3. Using the #2 Phillips screwdriver, loosen the captive screws securing the internal metal
side panel, and the remove the panel.
CAUTION Hot surface. The reagent vial heaters, ion source heater, flow restrictor,
and transfer lines are heated components that are accessible under the side access
panel. Verify that they are safe to touch before handling them.
To replace the panels, follow the above steps in reverse order and reverse the instructions in
each step.
Ion Source Maintenance
Maintaining the ion source requires that you shut down and vent the MS/ETD system. The
procedures in this section are arranged in order according to how likely the maintenance
would need to be done to restore the system to complete functionality. However, Thermo
Fisher Scientific recommends that you clean all the elements of the ion source while you have
it disassembled.
To maintain the ion source, follow these procedures:
• Inspecting or Replacing the Ion Source Filament
• Cleaning the Ion Source Lenses
• Cleaning the Ion Source Block
In addition to the appropriate cleaning tools and supplies, you need the following items (see
also Table 4):
•
•
•
•
•
•
•
•
•
52
Aluminum foil
Gloves, lint-free and powder-free
Hex or hex ball driver, 9/64 in.
Lamp, small, high-intensity
Magnification device
Pliers
Protective eye wear
Screwdriver, Phillips, #2
Tweezers, large
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5 Maintenance
Ion Source Maintenance
IMPORTANT
• Prepare a clean work surface by covering the area with aluminum foil, dull side up.
• Put on a new pair of lint- and powder-free gloves before starting each of these
removal, cleaning, and reinstallation procedures.
For field service use only
Part number
Filament Assembly DSQ II
120320-0030
Inspecting or Replacing the Ion Source Filament
The number of ions produced in the ion source is approximately proportional to the filament
emission current. Low ion production, for example, can indicate filament problems. If the
instrument indicates a filament fault or a failure to regulate, or if the reagent ion signal
intensity decreases over time, the filament might have sagged, failed, or is failing and must be
replaced.
 To inspect or replace the ion source filament
1. Prepare a clean work space by covering the area with aluminum foil, dull side up.
2. Shut down and vent the MS/ETD system. See “Shutting Down the MS/ETD System.”
3. Unplug the mass spectrometer and ETD module power supply cords.
CAUTION The ion source might be too hot to touch even if the cooling nitrogen has
completed its cycle. Make sure that the ion source has cooled to room temperature (at
least 1 hour after venting) before handling it.
4. Remove the ETD module’s main (back) access panel (see page 50).
CAUTION Keep the inlet valve lever in the down (closed) position whenever it is not
explicitly required to be in the up position (open), even if the vacuum manifold is at
atmospheric pressure. This is consistent with maintenance procedures that rely on the
inlet valve lever being closed at the appropriate step to prevent the accidental loss of
vacuum. If the vacuum is accidentally lost, the system might be damaged. At a
minimum, the components that were under vacuum may need cleaning.
5. Put on a pair of new, lint- and powder-free gloves.
6. Using the 9/64 in. hex driver, remove the four hex socket-head screws that secure both the
EMI cover and the probe plate to the vacuum manifold (Figure 2).
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Ion Source Maintenance
7. Remove the ion source assembly as follows:
a. Unplug the 12-pin feedthrough cable (Figure 31).
Figure 31. Interior of vacuum manifold
Transfer line bellows
Ion source assembly
Unplugged 12-pin
feedthrough cable
Thumbscrews
b. Loosen the thumbscrews (Figure 31).
c. Remove the ion source assembly from the vacuum manifold.
CAUTION To prevent unsecured components inside the lens holder from falling
out, keep the tips of your gloved fingers on both the front edge of the lens holder
and the back of the magnet yoke when handling the ion source assembly. See
Figure 32.
A clip holds the ion source assembly together. As you remove the assembly, gently
shift it to the left before and while pulling it out. This allows the assembly to
disengage from the transfer line bellows (Figure 31) as you remove it.
Or, gently depress the transfer line bellows to disengage it from the ion source
assembly.
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Figure 32. Ion source assembly1
12-pin feedthrough
cable connector
Magnet yoke
Magnet
Ion source block PCB
Ceramic lens holder
Block heater ring
Retainer clip
Retainer clip thumbscrew
Magnet
Thumbscrew
1
Ion source block
Your block heater ring might look different from that shown in these drawings and photographs.
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Ion Source Maintenance
Figure 33 shows an exploded view of the ion source assembly.
Figure 33. Ion source assembly (exploded view)
Filament assembly
retainer clip
Ion
source
block
Filament assembly
Filament insulator
Ion source
PCB
Magnet
yoke
Prefilter lens
retainer
Alignment
studs (3x)
Prefilter lens
Thermal spacer
Lens assembly
Block heater ring
Ion volume holder
Ion volume
Retainer clip thumbscrew
Index screw
Magnets (2x)
Retainer clip
Set screw
Ball plunger
Thumbscrews (2x)
8. Remove the filament assembly as follows:
a. Remove the magnet yoke from the rest of the assembly (Figure 34).
Figure 34. Removing the magnet yoke from the assembly
Magnet
yoke
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b. Disconnect the 12-pin feedthrough cable connectors from the ion source PCB, block
heater ring, and lens assembly (Figure 35).
Figure 35. Removing the feedthrough cable connectors
c. Remove the three alignment studs (Figure 36).
Figure 36. Removing the alignment studs
d. Loosen the retainer clip thumbscrew (Figure 37).
Figure 37. Retainer clip thumbscrew
Retainer
clip
thumbscrew
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Ion Source Maintenance
e. Gently pull the ion source PCB away from the assembly, disconnecting the filament
connectors, RTD temperature sensor, and three cartridge heaters (Figure 38).
CAUTION Do not bend or twist the cartridge heaters or RTD temperature sensor.
Figure 38. Detaching the ion source PCB from the assembly
Filament
connectors
RTD temperature sensor
f.
Cartridge heaters
Slide off the filament assembly retainer clip (Figure 39).
Figure 39. Removing the filament assembly retainer clip
Filament
assembly
retainer clip
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g. Remove the filament assembly (Figure 40).
Figure 40. Removing the filament assembly
Tip Now is a good time to clean the ion source lenses. See “Cleaning the Ion
Source Lenses.”
9. Turn the filament assembly over and, using a strong light and a magnification device,
verify that the filament wire is centered in the electron lens hole.
Figure 41 shows the centered filament wire as seen from the bottom of the filament
through the electron lens hole. If the filament wire is sagging, not centered, or otherwise
damaged, you must replace the filament assembly.
Figure 41. Filament wire visible through the bottom electron lens hole
Direction of
light source
Thermo Scientific
Centered wire
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Ion Source Maintenance
10. Install the filament assembly as follows:
a. Put the existing or new filament assembly into the ion source block, aligning the
filament leads as shown in Figure 42.
Figure 42. Filament assembly ready to be installed
Filament leads
b. Slide the filament assembly retainer clip back over the filament assembly (Figure 43).
Figure 43. Filament assembly retainer clip ready to be installed
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c. Align the cartridge heaters on the ion source PCB with the holes in the ion source
block, and the filament leads with the ion source PCB connectors (Figure 44).
Figure 44. Cartridge heaters aligned with the ion source block
Filament
connectors
RTD temperature sensor
Cartridge heaters
d. Gently press the ion source PCB onto the ion source block, positioning the RTD
temperature sensor under the retainer clip (Figure 44), and make sure that the PCB
fits snugly against the ion source block.
e. Tighten the retainer clip thumbscrew (Figure 45).
Figure 45. Retainer clip thumbscrew
Retainer
clip
thumbscrew
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f.
Reinstall the three alignment studs (Figure 46) and hand-tighten only.
Figure 46. Reinstalling the alignment studs
g. Reattach the leads for the 12-pin feedthrough cable to the ion source PCB, block
heater ring, and lens assembly (Figure 47).
To ensure the correct installation of the triple-lead connector to the lenses, position
the beveled edge of the connector against the thermal spacer.
Tip The lens lead only makes contact with the top of the pins. It does not go
down into the slot.
Figure 47. Reattaching the feedthrough cable connectors
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Ion Source Maintenance
h. Reposition the magnet yoke around the ion source assembly (Figure 48).
Figure 48. Ion source assembly repositioned in the magnet yoke
Magnet yoke
11. Reinstall the ion source assembly as follows:
a. Place the ion source assembly in the vacuum manifold and hand-tighten the
thumbscrews all the way in.
b. Reconnect the feedthrough connector (notch at the top) to the vacuum manifold.
12. Using the 7/64 in. hex driver and hex socket-head screws, reinstall the vacuum manifold
probe plate and EMI cover.
13. If you do not need to clean any parts, reinstall the main access panel, inlet valve knob, and
inlet valve plug.
14. Plug in the mass spectrometer and ETD module power supply cords.
15. Restore the MS/ETD system to operational status. See Chapter 3, “Shutdown and
Startup.”
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Ion Source Maintenance
Cleaning the Ion Source Lenses
If you cleaned the ion volume and did not find any problems with the filament, try cleaning
the ion source lenses. The ion source lenses are in direct contact with reagent ions introduced
into the ETD module and must be cleaned periodically, though not as often as the ion
volume.
 To clean the ion source lenses
1. Remove and disassemble the ion source lens assembly as follows:
a. See step 3 through step 8g in “Inspecting or Replacing the Ion Source Filament.”
Figure 49 shows an exploded view of the ion source lens assembly.
Figure 49. Ion source lens assembly (exploded view)
Prefilter
lens
Prefilter lens
retainer
Thermal spacer
Lens
holder
Lens
spacer
Lens 1
Lens
spacer
Split gate lens
Lens 2
Lens
clip
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b. Loosen the retainer clip thumbscrew, and then remove the retainer clip (Figure 50).
Figure 50. Location of retainer clip thumbscrew
Retainer clip thumbscrew
c. Separate the block heater ring, lens holder, and thermal spacer (Figure 51).
Figure 51. Block heater ring, lens holder, and thermal spacer
Block heater ring
Thermal spacer
Lens holder
d. Using the clean tweezers, remove the lens clip, lenses, and spacers from the lens
holder (Figure 49) and place them on the aluminum foil.
CAUTION Do not chip the lens holder.
e. Pinch the prefilter lens retainer with your fingers or the pliers, and then remove the
prefilter lens from the thermal spacer (Figure 49).
2. Clean the lenses as described in Cleaning Stainless Steel Parts and the lens spacers and lens
holder as described in Cleaning Nonstainless Steel Parts.
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Ion Source Maintenance
3. Reassemble the ion source assembly as follows:
a. Insert the components of the lens assembly into the lens holder (Figure 50).
b. Using the clean tweezers, reinstall the lens clip.
c. Place the prefilter lens in the thermal spacer.
d. Pinch the prefilter lens retainer with your fingers or the pliers and reinstall it to secure
the prefilter lens.
4. Reassemble the ion source assembly and reinstall it into the vacuum manifold as described
in step 10a through step 12 in “Inspecting or Replacing the Ion Source Filament.”
5. Using the 9/64 in. hex driver, reinstall the probe plate and the EMI cover to the vacuum
manifold (Figure 2).
6. Plug in the mass spectrometer and ETD module power supply cord.
7. Restore the MS/ETD system to operational status. See Chapter 3, “Shutdown and
Startup.”
Cleaning the Ion Source Block
If you change or check the filament and you observe significant ion burn or carbon buildup
around the electron entrance hole of the ion source block, Thermo Fisher Scientific
recommends that you clean the ion source block. Generally, you must clean the ion source
block once every six months, depending on the usage.
 To clean the ion source block
1. Remove the ion source lens assembly (Figure 49). See step 3 through step 8g in
“Inspecting or Replacing the Ion Source Filament.”
2. Remove the lenses and spacers. See step 1b through step 1e in “Cleaning the Ion Source
Lenses.”
See Figure 52 to locate the following components that must be removed from the ion
source block before cleaning: ion source block, ion volume, and ion volume holder.
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5 Maintenance
Ion Source Maintenance
Figure 52. Ion source components (exploded view)
Filament assembly
retainer clip
Filament assembly
Filament insulator
Ion source block
Ion
volume
Alignment
studs
Ion source PCB
(heater assembly)
Block heater ring
Ion volume
holder
Retainer clip
Index
screw
Set
screw
Retainer clip thumbscrew
Ball plunger
3. Remove the filament insulator (ring) from the ion source block.
4. Remove the retainer clip thumbscrew and retainer clip.
5. Clean the ion source block (Figure 53) as described in “Cleaning Stainless Steel Parts.”
Note For the ion source block, ion burn accumulates in the hole that is opposite from
the filament. Spend extra time cleaning this area.
IMPORTANT Because it is difficult to properly adjust the retention of the ion volume,
Thermo Fisher Scientific recommends that you do NOT remove the set screw and
ball plunger from the ion source block.
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Maintenance
Reagent Vials Maintenance
Figure 53. Ion source block
Areas to clean
thoroughly
6. Clean the ion volume and ion volume holder as described in “Cleaning Nonstainless Steel
Parts.”
7. Reassemble the ion source block, and then the ion source assembly.
8. Reinstall the ion source assembly into the vacuum manifold by following in reverse order
the procedure in “Cleaning the Ion Source Lenses.”
9. Restore the MS/ETD system to operational status. See Chapter 3, “Shutdown and
Startup.”
Reagent Vials Maintenance
Replacing the reagent vials requires that the MS/ETD system be placed in Service mode after
the vials have cooled, which can take at least 1 hour.
To change the reagent vials, follow these procedures:
1. Shutting Down the MS/ETD System
2. Replacing the Reagent Vials
3. Starting Up the MS/ETD System
In addition to the appropriate cleaning tools and supplies, you need the following items (see
also Table 4):
• Gloves, lint-free and powder-free
• Protective eye wear
• Screwdriver, Phillips, #2
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5 Maintenance
Reagent Vials Maintenance
IMPORTANT
• Prepare a clean work surface by covering the area with aluminum foil, dull side up.
• Put on a new pair of lint- and powder-free gloves before starting each of these
removal, cleaning, and reinstallation procedures.
For field service use only
Part number
ETD Reagent Kit
98000-62008
CAUTION Ensure that the crimping cap and membrane (septum) for both vials in the
ETD Reagent Kit are dark blue. The septum prevents the reagent from escaping into the
lab environment. To preserve the integrity of the reagent vial septums, remove and replace
the reagent vials annually or only when they are empty. Never reinstall used vials because
the multiple, unfilled needle openings in a septum could potentially cause leaks.
CAUTION Avoid exposure to potentially harmful materials.
By law, producers and suppliers of chemical compounds are required to provide their
customers with the most current health and safety information in the form of Material
Safety Data Sheets (MSDSs) or Safety Data Sheets (SDSs). The MSDSs and SDSs must
be freely available to lab personnel to examine at any time. These data sheets describe the
chemicals and summarize information on the hazard and toxicity of specific chemical
compounds. They also provide information on the proper handling of compounds, first
aid for accidental exposure, and procedures to remedy spills or leaks.
Read the MSDS or SDS for each chemical you use. Store and handle all chemicals in
accordance with standard safety procedures. Always wear protective gloves and safety
glasses when you use solvents or corrosives. Also, contain waste streams, use proper
ventilation, and dispose of all laboratory reagents according to the directions in the MSDS
or SDS.
For safety information about fluoranthene, see Chapter 7, “Reagent Kit.”
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Maintenance
Reagent Vials Maintenance
Shutting Down the MS/ETD System
 To shut down the system to replace the reagent vials
1. Follow step 1 through step 4 in “Shutting Down the MS/ETD System.”
Note If the vial temperature does not decrease after 5 minutes, check that the reagent
ion source configuration has the Use Cooling Gas option selected. For information
about this option, refer to “Specifying the Reagent Ion Source for the Mass
Spectrometer,” in Chapter 2 of the ETD Module Getting Started Guide. The vials
eventually cool down without the nitrogen but much more slowly.
Tip If your system does not use cooling gas, when in standby mode choose from Tune
Plus Diagnostics > Diagnostics, select Set Device from the Tools list, and then set
the values for the Capillary Heater and Source Heater to 0 °C.
2. When the vial reaches a temperature that is safe for handling (about 30 °C [86 °F]), place
the mass spectrometer’s electronics service switch in the Service Mode position.
Service mode turns off all components except the turbo pump and all forepumps.
CAUTION Hot surface. Do not place the system in Service mode until the vials reach
a safe temperature (about 30 °C [86 °F]). System temperature monitoring stops when
the system is in Service mode. Do not attempt to handle the any components until
they reach a safe temperature.
CAUTION Do not toggle the ETD module’s electronics service switch to the Service
Mode position while the mass spectrometer’s switches are in their On positions. This
could cause communication problems between the mass spectrometer and ETD
module. The ability to control the Service mode for both the mass spectrometer and
the ETD module at one location (the mass spectrometer’s electronics service switch) is
a safety feature.
The MS/ETD system is now in Service mode and the vials are at a safe temperature for
handling. You can now install or replace the reagent vials.
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5 Maintenance
Reagent Vials Maintenance
Replacing the Reagent Vials
After the reagent vial heaters have cooled to room temperature, the reagent vials are ready to
be replaced.
CAUTION Hot surface. Before removing the ETD module’s back panel, follow the
preceding procedure “Shutting Down the MS/ETD System.” Removing the main access
panel before the system is in Service mode triggers the panel’s safety interlock switches and
stops all system activity including temperature monitoring. In the absence of temperature
monitoring, you might attempt to handle the vials before it is safe to do so.
 To replace the reagent vials
1. Remove the ETD module’s main access (back) panel. See “Removing the Access Panels.”
This exposes the reagent inlet source heating unit and the vial heater cover (Figure 54).
Figure 54. Reagent inlet source heating unit (EMI cover not shown)
Reagent inlet
source heating
unit
Vial heater cover
2. Make sure that the vial heater cover is cool to the touch.
CAUTION Hot surface. Verify that the vial heater cover is cool to the touch before
removing it. Allow sufficient time for the vials to cool (up to 90 minutes) and then
place the system in Service mode. Verify that the vial heater cover is safe to handle
before attempting to remove the vial holders and reagent vials.
3. Using the 7/64 in. hex driver, remove the hex socket-head screws in the vial heater cover.
4. Replace the reagent vial as follows:
a. Remove the reagent vial holder, which is typically the Vial 1 holder, by gently pulling
it out of the vial heater.
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Maintenance
Reagent Vials Maintenance
The vial holder is a cylindrical tube with a handling knob at one end and ribs along
its length. These ribs prevent the vial holder from rotating after you place it into the
vial heater (Figure 55).
Figure 55. Reagent inlet source heating unit with the vial heater cover removed
Vial heater
ribs
Vial 1 heater
Vial 2 heater
Vial holder
knob
b. Remove the empty reagent vial.
c. Dispose of the empty fluoranthene vial in accordance with its MSDS.
See the cautionary statement on page 69.
d. Take the vial containing the ETD reagent (fluoranthene) from its box and remove the
aluminum tab from the top of the vial’s crimp seal.
e. Place the reagent vial into the vial holder.
f.
Reinstall the Vial 1 holder into the Vial 1 heater (top vial heater).
Note If you place the reagent vial in the Vial 2 heater, remember to change the
location on the Reagent Ion Source page of the Instrument Configuration
window.
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5 Maintenance
Forepump Maintenance
5. If an empty vial is not already installed, follow this step:
a. Take the empty vial from its box and remove the aluminum tab from the top of the
vial’s crimp seal.
b. Install the vial into the Vial 2 heater (bottom vial heater).
CAUTION The empty vial installed in one of the heaters is an integral part of the
carrier/CI gas system. You must install both vials (reagent and empty) to keep the
carrier/CI gas system closed off from the laboratory. If you do not install the
empty vial, the following occurs:
• The carrier/CI gas containing the reagent might escape to the laboratory
causing a safety problem.
• The ETD module does not operate correctly and the filament burns out.
6. Reinstall the vial heater cover.
7. Reinstall the ETD module’s main access panel. See “Removing the Access Panels.”
Starting Up the MS/ETD System
 To start up the MS/ETD system
Place the mass spectrometer’s electronics service switch in the Normal Service position.
The system starts up and goes into standby mode. The ion source heater, flow restrictor,
and transfer line heaters start heating.
Forepump Maintenance
Maintaining the ETD module forepump requires inspecting, adding, purging, and changing
the pump oil.
Check the forepump oil often. It is a translucent light amber color. During normal operation,
oil must always be visible in the oil level sight glass between the MIN and MAX marks. If the
oil level is below the MIN mark, add oil. If the oil is cloudy or discolored, purge the oil to
decontaminate dissolved solvents. If the pump oil is still discolored, change it. Plan to change
the pump oil after every 3000 hours (or about every 4 months) of operation.
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Maintenance
Fan Filter Maintenance
Because the optional oil mist filter connects to the ballast port, be aware that opening the
valve also drains the oil mist filter. While Thermo Fisher Scientific recommends that you
periodically open the gas ballast valve (on the top of the pump) to purge the accumulated
solvents, opening the valve might allow a large volume of volatile solvent waste to enter the
fume exhaust system. Make sure that your exhaust system can accommodate the periodic
purging of these solvents. The frequency of the purging depends on the throughput of the
system—never operate a pump continuously with the gas ballast valve open.
Refer to the manufacturer’s documentation for procedures to purge, add, and change the
forepump oil.
Fan Filter Maintenance
Clean the fan filter every 4 months, or sooner if it is dirty. The fan filter is located on the back
on the ETD module.
 To clean the fan filter
1. Remove the fan filter from the back of the ETD module by pulling it out of the bracket.
2. Wash the filter in a solution of soap and water.
3. Rinse the filter with tap water.
4. Squeeze the water from the filter and allow it to air dry.
5. Reinstall the filter in the bracket.
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6
Diagnostics
The diagnostics test many of the mass spectrometer and ETD module components. If the
diagnostics indicate that PCBs or other electrical components within the ETD module need
replacement, contact Thermo Fisher Scientific Technical Support or your local Thermo Fisher
Scientific field service engineer.
Contents
• Running the ETD Module Diagnostics
• Replacing a Fuse in the ETD Module
• Replacing Power Supplies
• Replacing PCBs
Running the ETD Module Diagnostics
Use the ETD module diagnostics, which are completely integrated into the mass spectrometer
diagnostics, to test the major electronic circuits within the instrument. Refer to the Tune Plus
application Help and Chapter 6, “Diagnostics,” in the LTQ Series Hardware Manual.
IMPORTANT Thermo Fisher Scientific recommends that you optimize the reagent CI gas
pressure once a week.
 To optimize the reagent CI gas pressure
1. Open the Tune Plus window (see page 13).
2. Choose Setup > Reagent Ion Source to open the Reagent Ion Source dialog box.
3. Select the View Reagent Ion Spectra check box, and then click Apply.
4. Choose Diagnostics > Diagnostics to open the Diagnostics dialog box.
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Diagnostics
Running the ETD Module Diagnostics
5. In the Tools list, click System Evaluation to open the System Evaluation page
(Figure 56).
Figure 56. Diagnostics dialog box showing the System Evaluation page (Velos Pro/ETD)
6. Select the Reagent CI Gas Pressure Evaluation check box.
7. Click Start.
This diagnostic evaluation takes approximately 15 minutes. After the evaluation finishes,
the following message appears in the Testing area:
Est. required CI Gas Pressure for Max Reagent Ion Signal (psi): number
8. In the Reagent Ion Source dialog box, in the CI Gas Pressure (psi) box, enter the
estimated gas pressure number determined from the reagent CI gas pressure evaluation,
and then click OK.
You must manually enter the new reagent CI gas pressure.
9. In the Diagnostics dialog box, click OK.
10. Click File > Save.
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6 Diagnostics
Replacing a Fuse in the ETD Module
Replacing a Fuse in the ETD Module
Fuses protect various electrical circuits whenever an overcurrent condition occurs. The ETD
module’s replaceable fuses are located on the ETD heater control PCB and the 150 Vac power
supply PCB.
Check fuses when power is lost to a fused subsystem.
CAUTION Always shut down the system and disconnect the power cord before you
replace fuses.
Table 5.
Fuses for the ETD heater control PCB (P/N 98000-61031R)
Location
Circuit
Description
Part number
F1, F2
220 Vac
6.3 A, 250 Vac, slow blow, 5 × 20 mm
00006-11450
F3–F10
220 Vac Heater
2.5 A, 250 Vac, fast blow, 5 × 20 mm
00006-11202
Table 6. Fuses for the ±150 Vac power supply PCB (P/N 98000-61040)
Location
Circuit
Description
Part number
F1
24V input
2 A, 250 Vac, fast blow, 5 × 20 mm
00006-02-00006
CAUTION Use only the fuses specified in Table 5 and Table 6. Never replace a fuse with a
fuse of a different type, voltage, or current rating.
Replacing Power Supplies
Due to the complexity of removing and reinstalling the ETD module power supplies, a
Thermo Fisher Scientific field service engineer must replace these components.
Replacing PCBs
Due to the complexity of removing and reinstalling many of the ETD module PCBs, a
Thermo Fisher Scientific field service engineer must replace these boards.
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Diagnostics
Replacing PCBs
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7
Reagent Kit
Table 7 lists the items in the Reagent Kit (P/N 98000-62008) for the Velos Pro/ETD and
LTQ XL/ETD systems.
Table 7. Reagent Kit contents
Description
Part number
Angiotensin I, 1 mg
00301-15517
Fluoranthene, 0.15 g
HAZMAT-00013
CAUTION Avoid exposure to potentially harmful materials.
By law, producers and suppliers of chemical compounds are required to provide their
customers with the most current health and safety information in the form of Material
Safety Data Sheets (MSDSs) or Safety Data Sheets (SDSs). The MSDSs and SDSs must
be freely available to lab personnel to examine at any time. These data sheets describe the
chemicals and summarize information on the hazard and toxicity of specific chemical
compounds. They also provide information on the proper handling of compounds, first
aid for accidental exposure, and procedures to remedy spills or leaks.
Read the MSDS or SDS for each chemical you use. Store and handle all chemicals in
accordance with standard safety procedures. Always wear protective gloves and safety
glasses when you use solvents or corrosives. Also, contain waste streams, use proper
ventilation, and dispose of all laboratory reagents according to the directions in the MSDS
or SDS.
Fluoranthene is used as the ETD reagent in the ETD module. Fluoranthene is potentially
hazardous. Use it in accordance with its MSDS.
The fluoranthene radical anion is generated according to the reaction shown in Figure 57.
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Reagent Kit
Figure 57. ETD reagent (fluoranthene radical anion) generation from fluoranthene
+e→
-•
Fluoranthene
Thermo Fisher Scientific supplies fluoranthene as a two-vial kit. One vial contains 0.15 g of
fluoranthene and the other is the required empty vial. The fluoranthene vial in the
Velos Pro/ETD or LTQ XL/ETD system Reagent Kit is Sigma-Aldrich™ Supelco™ #48535.
To obtain another fluoranthene vial, click the MSDS link from the Sigma-Aldrich website:
www.sigmaaldrich.com/catalog/search/ProductDetail/SUPELCO/48535
Angiotensin I (human acetate hydrate) is potentially hazardous. Use it in accordance with its
MSDS.
The angiotensin I vial in the Velos Pro/ETD or LTQ XL/ETD system Reagent Kit is
Sigma-Aldrich Sigma #A9650. To obtain another angiotensin I vial, click the MSDS link:
www.sigmaaldrich.com/catalog/search/ProductDetail/SIGMA/A9650
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8
Replaceable Parts
This chapter provides the part numbers for the chemical and accessory kits that come with the
ETD module as part of the Velos Pro/ETD or LTQ XL/ETD system. It also lists the
replaceable and consumable parts and their corresponding part numbers.
Note Accessory kits for the Velos Pro and LTQ XL mass spectrometers are listed in the
LTQ Series Hardware Manual.
Contents
• ETD Ship Kit
• ETD Accessory Kit
• ETD Reagent Kit
• ETD Nitrogen Scrubber (Gas Filter) Kit
• Inlet Valve Seal Kit
• Reagent Inlet Module Installation Kit
• Miscellaneous Parts
ETD Ship Kit
ETD Ship Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98000-62004
Exhaust hose, blue, 1.0 in. ID, 1.8 m (6 ft) long . . . . . . . . . . . . . . . . . . . 00301-08301
Fitting, barbed tee, 1.0 in. OD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 00102-10120
Power supply cord, international, 230 Vac, 10 A . . . . . . . . . . . . . . . . . . . 00302-03069
Power supply cord, international, 230 Vac, 15 A . . . . . . . . . . . . . . . . . . . 96000-98036
Power supply cord, North American, 230 Vac, 16 A . . . . . . . . . . . . . . . . 96000-98035
ETD Accessory Kit
ETD Accessory Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98000-62002
Aluminum oxide sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32000-60340
Centering ring, aluminum/neoprene, DN 16 ISO-KF . . . . . . . . . . . . .00108-02-00014
Centering ring with O-ring, nitrile/aluminum, NW40 . . . . . . . . . . . 00108-02-00005
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Replaceable Parts
ETD Reagent Kit
Centering ring with O-ring, Viton™/aluminum, NW25 . . . . . . . . . . . . . 00108-02011
Clamp, swing, aluminum, DN 10-16 ISO-KF . . . . . . . . . . . . . . . . . 00108-02-00015
Clamp, swing, aluminum, NW10/25 . . . . . . . . . . . . . . . . . . . . . . . . 00108-02-00018
Clamp, swing, aluminum, NW40 . . . . . . . . . . . . . . . . . . . . . . . . . . . 00108-02-00004
Clip, hose, stainless steel, 21.8–27 mm (0.85–1.06 in.) ID . . . . . . . . 00201-99-00109
Ferrule, two-piece set, brass, back, 1/8 in. ID . . . . . . . . . . . . . . . . . . . . . 00101-02500
Ferrule, two-piece set, brass, front, 1/8 in. ID . . . . . . . . . . . . . . . . . . . . . 00101-08500
Ferrule, column, graphite/Vespel™, 0.4 mm ID, 1/16 in. OD . . . . . . . . . 00101-18100
Filament assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120320-0030
Fitting, straight tube, 10-32 thread, 1/8 in. l . . . . . . . . . . . . . . . . . . . . . . 00103-10990
Fitting, tube, bulkhead union, 1/4 in. OD . . . . . . . . . . . . . . . . . . . . .00103-01-00001
Fitting, tube, bulkhead union, 1/8 in. OD . . . . . . . . . . . . . . . . . . . . 00101-04-00002
Forceps, specimen, stainless steel, 10 in. . . . . . . . . . . . . . . . . . . . . . . . . . . . 76360-0400
Fuse, fast-blow, 2 A, 250 Vac, 5 × 20 mm . . . . . . . . . . . . . . . . . . . . . 00006-02-00006
Fuse, fast-blow, 2.5 A, 250 Vac, 5 × 20 mm . . . . . . . . . . . . . . . . . . . . . . . 00006-11202
Fuse, slow-blow, 6.3 A, 250 Vac, 5 × 20 mm . . . . . . . . . . . . . . . . . . . . . . 00006-11450
O-ring, Viton, 2-005, 0.101 in. ID, 0.70 in. w . . . . . . . . . . . . . . . . . . . . 00107-02456
O-ring, Viton, 2-116, 0.737 in. ID, 3/32 in. w . . . . . . . . . . . . . . . . . . . . 00107-10056
O-ring, Viton, 2-254, 5.484 in. ID, 0.139 in. w . . . . . . . . . . . . . . . . 00107-01-00054
O-ring, Viton, 2-258, 5.984 in. ID, 0.139 in. w . . . . . . . . . . . . . . . . 00107-01-00055
O-ring, Viton, 1.237 in. ID, 0.103 in. w . . . . . . . . . . . . . . . . . . . . . . . . . 00107-10404
Screw, thumb, knurled, 8-32 thread, 3/8 in. l . . . . . . . . . . . . . . . . . . 00430-01-00004
Swagelok™-type nut, brass, 1/8 in. ID . . . . . . . . . . . . . . . . . . . . . . . . . . . 00101-15500
Tool, lens alignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120271-0001
Tool, Torx™ star-bit driver, T-10 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 00725-01-00022
Tool, Torx star-bit driver, T-27 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 00725-01-00006
Kit, ETD Nitrogen Scrubber . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98000-62011
Kit, Inlet Valve Seal Replacement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119265-0003
Kit, Reagent Inlet Module Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . 98000-62006
ETD Reagent Kit
ETD Reagent Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98000-62008
Chemical, angiotensin I, 1 mg vial . . . . . . . . . . . . . . . . . . . . . . . . . . . HAZMAT-15517
Chemical, fluoranthene, 0.15 g vial . . . . . . . . . . . . . . . . . . . . . . . . . . HAZMAT-00013
ETD Nitrogen Scrubber (Gas Filter) Kit
ETD Nitrogen Scrubber Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98000-62011
Ferrule, two-piece set, brass, back, 1/8 in. ID . . . . . . . . . . . . . . . . . . . . . 00101-02500
Ferrule, two-piece set, brass, front, 1/8 in. ID . . . . . . . . . . . . . . . . . . . . . 00101-08500
Ferrule, two-piece set, stainless steel, 1/8 in. ID . . . . . . . . . . . . . . . . . 00101-08-00009
Hydrocarbon trap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A0950-01600
Swagelok-type nut, brass, 1/8 in. ID . . . . . . . . . . . . . . . . . . . . . . . . . . . . 00101-15500
Swagelok-type nut, stainless steel, 1/8 in. ID . . . . . . . . . . . . . . . . . . . . . . 00101-12900
Tubing, copper, precleaned, 1/8 in. OD, 3 m (10 ft) long . . . . . . . . . . . . 00301-22701
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Replaceable Parts
Inlet Valve Seal Kit
Inlet Valve Seal Kit
Inlet Valve Seal Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119265-0003
O-ring, Viton, 0.530 in. ID, 0.082 in. w . . . . . . . . . . . . . . . . . . . . . . . . . . . 3814-6530
Spool, inlet valve seal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119683-0100
Tool, inlet valve seal removal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119283-0001
Reagent Inlet Module Installation Kit
Reagent Inlet Module Installation Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98000-62006
Ferrule, back, PTFE, for Swagelok 1/16 in. tube . . . . . . . . . . . . . . . . .00101-08-00008
Ferrule, front, PTFE, for Swagelok 1/16 in. tube . . . . . . . . . . . . . . . . .00101-08-00007
Ferrule, Vespel/graphite, 1-hole, 1/16 in. OD, 0.4 mm ID . . . . . . . . . .00101-08-00005
Ferrule, Vespel/graphite, 2-holes, 1/16 in. OD, 0.4 mm ID . . . . . . . . 00101-08-00006
Tubing, fused silica, 0.363 in. OD, 0.1 mm ID, 100 mm long . . . . . . . . 98000-20060
Tubing, PEEKsil™, 1/16 in. OD, 0.05 mm ID, 100 mm long . . . . . . .00109-02-00021
Miscellaneous Parts
Forepump
Forepump oil, 1 L . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 00301-15101
Ion Volume Parts
Ion volume . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98000-20052
Ion volume holder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70001-20532
Ion volume insertion and removal tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98000-60028
Ion Source Filament Parts
Filament Assembly DSQ II . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120320-0030
Thermo Scientific
ETD Module Hardware Manual
83
8
Replaceable Parts
Miscellaneous Parts
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ETD Module Hardware Manual
Thermo Scientific
I
Index
A
air leaks, checking 23
C
cleaning
nonstainless steel parts 36
required supplies and tools 31
stainless steel parts 34
compliance
FCC iv
regulatory iii
contacting us xviii
cooling gas, nitrogen 8–9, 11, 21
figures, list of xi
filament
See ion source, filament
flow control 8
fluoranthene 72, 79
forepump
maintaining 73
oil, purging 28
fuses, replacing 77
G
gloves, part numbers 32
I
D
diagnostics
ETD module 75
reagent CI gas pressure, optimizing 75
directive, WEEE vii
documentation
accessing xiv
additional xiv
downloading documents xiv
E
electromagnetic compatibility iii
emergency shutdown 12
ETD module
LEDs 17
power panel 5
standby mode 14
ETD reagent carrier gas, requirements 23
F
fan filters, cleaning 74
FCC compliance iv
Thermo Scientific
ion source
block, cleaning 66
description 9
filament, replacing 53
lens assembly, cleaning 64
ion volume insertion and removal tool 39
Ion/Ion Reaction LED 8
K
kits
ETD Accessory 81
ETD Nitrogen Scrubber 82
ETD Reagent 82
ETD Ship 81
Inlet Valve Seal 83
Reagent Inlet Module Installation 83
L
LEDs
Filament 7
Ion/Ion reaction 8
Power 7
ETD Module Hardware Manual
85
Index: M
System 7
Vacuum 7
M
main access panel, removing 50
maintenance
fan filters, cleaning 74
forepump oil, purging 28
frequency 30
inlet valve 47
ion volume 37
overview 29
reagent vials 68
supplies and tools 31
MS/ETD system, powering on 17
S
safety precautions xvi
safety standards iii
side access panel, removing 50
stainless steel parts, cleaning 34
standby mode, troubleshooting 21
system shutdown 16
T
Thermo Scientific website, user documents xiv
tuning
reagent ion source setting 24
tuning, ETD settings 19
V
N
nitrogen
cooling 8–9, 11, 21
description, ETD process 8
rate of consumption 23
nonstainless steel parts, cleaning 36
vacuum pressure levels, checking 22
vials
See reagent vials
W
WEEE directive vii
O
oil mist filter, ETD forepump 74
P
power panel
ETD module 5
mass spectrometer 12
printed circuit boards (PCBs)
ETD control 6
heater control 6
interface 6
probe interlock, opening 41
pump
See forepump
R
reagent carrier gas for ETD, requirements 23
reagent inlet 8
reagent ion source, turning on 24
reagent vials
operating temperature 9, 16
replacing 71
regulatory compliance iii
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ETD Module Hardware Manual
Thermo Scientific
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