Thermo Scientific TSQ Series User manual

For Research Use Only
Not for use in Diagnostic
Procedures
TSQ Series
Hardware Manual
70111-97163 Revision CJune 2014

© 2014 Thermo Fisher Scientific Inc. All rights reserved.
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All other trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries.
Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
product operation. This document is copyright protected and any reproduction of the whole or any part of this
document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.
The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document supersede
all previous information received by the purchaser.
Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or error-
free and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might
result from any use of this document, even if the information in the document is followed properly.
This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This
document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of
Sale shall govern all conflicting information between the two documents.
Release history: Revision A, February 2008; Revision B, June 2008; Revision C, June 2014.
Software Version: (Thermo) Foundation 2.0 and later; TSQ 2.5 and later
For Research Use Only. Not regulated for medical or veterinary diagnostic use by U.S. Federal Drug
Administration or other competent authorities.

Regulatory Compliance
Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with
applicable domestic and international regulations. When the system is delivered to you, it meets all pertinent
electromagnetic compatibility (EMC) and safety standards as described below.
Changes that you make to your system may void compliance with one or more of these EMC and safety standards.
Changes to your system include replacing a part or adding components, options, or peripherals not specifically
authorized and qualified by Thermo Fisher Scientific. To ensure continued compliance with EMC and safety
standards, replacement parts and additional components, options, and peripherals must be ordered from
Thermo Fisher Scientific or one of its authorized representatives.
TSQ Quantum Access
EMC Directive 89/336/EEC, 92/31/EEC, 93/68/EEC
EMC compliance has been evaluated by TUV Rheinland of North America, Inc.
Low Voltage Safety Compliance
This device complies with the Low Voltage Directive EN 61010-1:2001.
•TSQ Quantum Access
•TSQ Quantum Ultra
•TSQ Vantage
EN 61326 A1, A2, A3 (1997, 1998, 2001, 2003) EN 61000-4-6 (2003)
EN 61000-4-2 (2001) EN 61000-4-11 (2001)
EN 61000-4-3 (2002) EN 61000-3-2 (2000)
EN 61000-4-4, A1, A2 (1995, 2000, 2001) EN 61000-3-3, A1 (1995, 2001)
EN 61000-4-5 (2001) CFR 47 - Part 15 - Subpart B: 2005 - Class A
EN 61000-4-8 (2001)

TSQ Quantum Ultra
EMC Directive 89/336/EEC as amended by 92/31/EEC and 93/68/EEC
EMC compliance has been evaluated by U.L. Underwriter’s Laboratory Inc.
Low Voltage Safety Compliance
This device complies with Low Voltage Directive 73/23/EEC and harmonized standard EN 61010-1: 2001.
TSQ Vantage
EMC Directive 2004/108/EC
EMC compliance has been evaluated by TUV Rheinland of North America, Inc.
Low Voltage Safety Compliance
This device complies with the Low Voltage Directive 2006/95/EC and harmonized standard EN 61010-1.
EN 55011 1998 EN 61000-4-3 2002
EN 61000-3-2 1995, A1; 1998, A2;
1998, A14; 2000
EN 61000-4-4 1995, A1; 2001, A2; 2001
EN 61000-3-3 1998 EN 61000-4-5 1995, A1; 2001
EN 61326-1 1998 EN 61000-4-6 1996, A1; 2001
EN 61000-4-2 2000 EN 61000-4-11 1994, A1; 2001
FCC Class A, CFR 47 Part 15
and Part 18
2005 CISPR 11 1999, A1; 1999, A2; 2002
EN 61326-1 (2006) EN 61000-4-2 (2001)
CisPR11 (1998) EN 61000-4-3 (2006)
EN 55011; A1; A2 (1998, 1999, 2002) EN 61000-4-4 (2004)
CFR 47 (2007) EN 61000-4-5 (2006)
EN 61000-3-2 (2006) EN 61000-4-8 (2001)
EN 61000-3-3; A1; A2 (1995, 2001, 2005) EN 61000-4-11 (2004)

FCC Compliance Statement
Notice on Lifting and Handling of
Thermo Scientific Instruments
For your safety, and in compliance with international regulations, the physical handling of this Thermo Fisher
Scientific instrument requires a team effort to lift and/or move the instrument. This instrument is too heavy and/
or bulky for one person alone to handle safely.
Notice on the Proper Use of
Thermo Scientific Instruments
In compliance with international regulations: Use of this instrument in a manner not specified by Thermo Fisher
Scientific could impair any protection provided by the instrument.
Notice on the Susceptibility
to Electromagnetic Transmissions
Your instrument is designed to work in a controlled electromagnetic environment. Do not use radio frequency
transmitters, such as mobile phones, in close proximity to the instrument.
For manufacturing location, see the label on the instrument.
THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES. OPERATION IS SUBJECT TO
THE FOLLOWING TWO CONDITIONS: (1) THIS DEVICE MAY NOT CAUSE HARMFUL
INTERFERENCE, AND (2) THIS DEVICE MUST ACCEPT ANY INTERFERENCE RECEIVED,
INCLUDING INTERFERENCE THAT MAY CAUSE UNDESIRED OPERATION.
CAUTION Read and understand the various precautionary notes, signs, and symbols contained
inside this manual pertaining to the safe use and operation of this product before using the device.

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

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

CAUTION
Symbol
CAUTION VORSICHT ATTENTION PRECAUCION AVVERTENZA
Electric Shock: This instrument uses high
voltages that can cause personal injury.
Before servicing, shut down the instrument
and disconnect the instrument from line
power. Keep the top cover on while operating
the instrument. Do not remove protective
covers from PCBs.
Elektroschock: In diesem Gerät werden
Hochspannungen verwendet, die
Verletzungen verursachen können.
Vor Wartungsarbeiten muß das Gerät
abgeschaltet und vom Netz getrennt werden.
Betreiben Sie Wartungsarbeiten nicht mit
abgenommenem Deckel. Nehmen Sie die
Schutzabdeckung von Leiterplatten nicht ab.
Choc électrique : l’instrument utilise des
tensions capables d’infliger des blessures
corprelles. L’instrument doit être arrêté
et débranché de la source de courant
avant tout intervention. Ne pas utiliser
l’instrument sans son couvercle. Ne pas
elensver les étuis protecteurs des cartes de
circuits imprimés.
Descarga eléctrica: Este instrumento utiliza
altas tensiones, capaces de producir lesiones
personales. Antes de dar servicio de
mantenimiento al instrumento, éste debera
apagarse y desconectarse de la línea de
alimentacion eléctrica. No opere el
instrumento sin sus cubiertas exteriores
quitadas. No remueva las cubiertas
protectoras de las tarjetas de circuito impreso.
Shock da folgorazione. L’apparecchio
è alimentato da corrente ad alta tensione che
puo provocare lesioni fisiche.
Prima di effettuare qualsiasi intervento
di manutenzione occorre spegnere ed isolare
l’apparecchio dalla linea elettrica.
Non attivare lo strumento senza lo schermo
superiore. Non togliere i coperchi a protezione
dalle schede di circuito stampato (PCB).
Chemical: This instrument might contain
hazardous chemicals. Wear gloves when
handling toxic, carcinogenic, mutagenic, or
corrosive or irritant chemicals. Use approved
containers and proper procedures to dispose
waste oil.
Chemikalien: Dieses Gerät kann gefährliche
Chemikalien enthalten. Tragen Sie
Schutzhandschuhe beim Umgang mit
toxischen, karzinogenen, mutagenen oder
ätzenden/reizenden Chemikalien. Entsorgen
Sie verbrauchtes Öl entsprechend den
Vorschriften in den vorgeschriebenen
Behältern.
Chimique : des produits chemiques
dangereux peuven se trouver dans
l’instrument. Proted dos gants pour manipuler
tous produits chemiques toxiques,
cancérigènes, mutagènes, ou
corrosifs/irritants. Utiliser des récipients et
des procédures homologuées pour se
débarrasser des déchets d’huile.
Química: El instrumento puede contener
productos quimicos peligrosos. Utilice guantes
al manejar productos quimicos tóxicos,
carcinogenos, mutagenos o
corrosivos/irritantes. Utilice recipientes y
procedimientos aprobados para deshacerse
del aceite usado.
Prodotti chimici. Possibile presenza di
sostanze chimiche pericolose
nell’apparecchio. Indossare dei guanti per
maneggiare prodotti chimici tossici,
cancerogeni, mutageni, o corrosivi/irritanti.
Utilizzare contenitori aprovo e seguire la
procedura indicata per lo smaltimento dei
residui di olio.
Heat: Before servicing the instrument, allow
any heated components to cool.
Hitze: Warten Sie erhitzte Komponenten erst
nachdem diese sich abgekühlt haben.
Haute Temperature : permettre aux
composants chauffés de refroidir avant tout
intervention.
Altas temperaturas: Permita que lop
componentes se enfríen, ante de efectuar
servicio de mantenimiento.
Calore. Attendere che i componenti riscaldati
si raffreddino prima di effetturare l’intervento
di manutenzione.
Fire: Use care when operating the system in
the presence of flammable gases.
Feuer: Beachten Sie die einschlägigen
VorsichtsmaBnahmen, wenn Sie das System
in Gegenwart von entzündbaren Gasen
betreiben.
Incendie : agir avec précaution lors de
l’utilisation du système en présence de gaz
inflammables.
Fuego: Tenga cuidado al operar el sistema en
presencia de gases inflamables.
Incendio. Adottare le dovute precauzioni
quando si usa il sistema in presenza di gas
infiammabili.
Eye Hazard: Eye damage could occur from
splattered chemicals or flying particles. Wear
safety glasses when handling chemicals or
servicing the instrument.
Verletzungsgefahr der Augen: Verspritzte
Chemikalien oder kleine Partikel können
Augenverletzungen verursachen. Tragen Sie
beim Umgang mit Chemikalien oder bei der
Wartung des Gerätes eine Schutzbrille.
Danger pour les yeux : des projections
chimiques, liquides, ou solides peuvent être
dangereuses pour les yeux. Porter des
lunettes de protection lors de toute
manipulationde produit chimique ou pour
toute intervention sur l’instrument.
Peligro par los ojos: Las salicaduras de
productos químicos o particulas que salten
bruscamente pueden causar lesiones en los
ojos. Utilice anteojos protectores al mnipular
productos químicos o al darle servicio de
mantenimiento al instrumento.
Pericolo per la vista. Gli schizzi di prodotti
chimici o delle particelle presenti nell’aria
potrebbero causare danni alla vista. Indossare
occhiali protettivi quando si maneggiano
prodotti chimici o si effettuano interventi di
manutenzione sull’apparecchio.
General Hazard: A hazard is present that is
not included in the above categories. Also,
this symbol appears on the instrument to
refer the user to instructions in this manual.
Allgemeine Gefahr: Es besteht eine
weitere Gefahr, die nicht in den vorstehenden
Kategorien beschrieben ist. Dieses Symbol
wird im Handbuch auBerdem dazu
verwendet, um den Benutzer auf
Anweisungen hinzuweisen.
Danger général : indique la présence d’un
risque n’appartenant pas aux catégories
citées plus haut. Ce symbole figure
également sur l’instrument pour renvoyer
l’utilisateur aux instructions du présent
manuel.
Peligro general: Significa que existe un
peligro no incluido en las categorias
anteriores. Este simbolo también se utiliza en
el instrumento par referir al usuario a las
instrucciones contenidas en este manual.
Pericolo generico. Pericolo non compreso
tra le precedenti categorie. Questo simbolo è
utilizzato inoltre sull’apparecchio per
segnalare all’utente di consultare le istruzioni
descritte nel presente manuale.
When the safety of a procedure is
questionable, contact your local Technical
Support organization for Thermo Fisher
Scientific San Jose Products.
Wenn Sie sich über die Sicherheit
eines Verfahrens im unklaren sind,
setzen Sie sich, bevor Sie fortfahren,
mit Ihrer lokalen technischen
Unterstützungsorganisation für Thermo
Fisher Scientific San Jose Produkte in
Verbindung.
Si la sûreté d’un procédure est incertaine,
avant de continuer, contacter le plus proche
Service Clientèle pour les produits de Thermo
Fisher Scientific San Jose.
Cuando la certidumbre acerca de un
procedimiento sea dudosa, antes de proseguir,
pongase en contacto con la Oficina de
Asistencia Tecnica local para los productos
de Thermo Fisher Scientific San Jose.
Quando e in dubbio la misura di sicurezza per
una procedura, prima di continuare, si prega di
mettersi in contatto con il Servizio di
Assistenza Tecnica locale per i prodotti di
Thermo Fisher Scientific San Jose.

CAUTION
Symbol
CAUTION
Electric Shock: This instrument uses high voltages that
can cause personal injury. Before servicing, shut down the
instrument and disconnect the instrument from line power.
Keep the top cover on while operating the instrument. Do
not remove protective covers from PCBs.
Chemical: This instrument might contain hazardous
chemicals. Wear gloves when handling toxic, carcinogenic,
mutagenic, or corrosive or irritant chemicals. Use approved
containers and proper procedures to dispose waste oil.
Heat: Before servicing the instrument, allow any heated
components to cool.
Fire: Use care when operating the system in the presence of
flammable gases.
Eye Hazard: Eye damage could occur from splattered
chemicals or flying particles. Wear safety glasses when
handling chemicals or servicing the instrument.
General Hazard: A hazard is present that is not included in
the above categories. Also, this symbol appears on the
instrument to refer the user to instructions in this manual.
When the safety of a procedure is questionable, contact
your local Technical Support organization for Thermo Fisher
Scientific San Jose Products.

Thermo Scientific TSQ Series Hardware Manual xi
C
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xv
About This Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
Related Documentation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
Safety and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
Safety Precautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvi
Solvent and Gas Purity Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xvii
Service Philosophy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii
Level of Repair. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xviii
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xviii
Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Ionization Modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3
Ion Polarity Modes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3
Scan Modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3
Q1MS and Q3MS Scan Modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4
Product Scan Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
Parent Scan Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6
Neutral Loss Scan Modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
Data Dependent Scan Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8
Scan Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Full Scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Selected Ion Monitoring. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Selected Reaction Monitoring. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10
AutoSIM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10
Data Types. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10
Profile Data Type. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10
Centroid Data Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10
Mass/Charge Range . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11
Chapter 2 Functional Description. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14
Liquid Chromatograph. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
Syringe Pump. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
Divert/Inject Valve. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .16
Contents

Contents
xii TSQ Series Hardware Manual Thermo Scientific
Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .18
Controls and Indicators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .18
API Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21
Ion Source Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .22
Ion Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
Mass Analyzer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27
Ion Detection System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
Vacuum System and Inlet Gases Hardware. . . . . . . . . . . . . . . . . . . . . . . . . . .35
Electronic Assemblies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .40
Data System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .41
Computer Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .41
Data System / Mass Spectrometer / LC Interface . . . . . . . . . . . . . . . . . . . . . .42
Data System / Local Area Network Interface . . . . . . . . . . . . . . . . . . . . . . . . .42
Printer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .42
Chapter 3 System Shutdown, Startup, and Reset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Shutting Down the System in an Emergency . . . . . . . . . . . . . . . . . . . . . . . . . . .45
Placing the System in Standby Condition. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .47
Shutting Down the System Completely . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .48
Starting Up the System after a Complete Shutdown. . . . . . . . . . . . . . . . . . . . . .49
Starting Up the LC. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .49
Starting Up the Data System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .49
Starting Up the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .50
Starting Up the Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .51
Setting Up Conditions for Operation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .51
Resetting the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .52
Resetting the Data System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .52
Resetting the Data System by Using the Windows Shutdown and Restart
Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .52
Resetting the Data System by Turning the Personal Computer Off Then On 53
Turning Off Selected Mass Spectrometer Components . . . . . . . . . . . . . . . . . . .53
Chapter 4 Daily Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Things to Do Before Operating the TSQ System . . . . . . . . . . . . . . . . . . . . . . . .57
Checking the Argon and Nitrogen Supplies . . . . . . . . . . . . . . . . . . . . . . . . . .58
Checking the ESI Fused-Silica Sample Tube for Elongation. . . . . . . . . . . . . .58
Checking the System Vacuum Levels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .58
Things to Do After Operating the TSQ System . . . . . . . . . . . . . . . . . . . . . . . . .59
Flushing the Sample Transfer Line, Sample Tube, and API Probe . . . . . . . . .60
Placing the System in Standby Condition. . . . . . . . . . . . . . . . . . . . . . . . . . . .61
Cleaning the Ion Sweep Cone and Ion Transfer Tube . . . . . . . . . . . . . . . . . .61
Emptying the Solvent Waste Bottle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .62
Chapter 5 Removing and Reinstalling the Ion Source Housing . . . . . . . . . . . . . . . . . . . . . . . 63
Removing the Ion MAX or Ion MAX-S Ion Source Housing. . . . . . . . . . . . . . .63
Installing the Ion MAX or Ion MAX-S Ion Source Housing . . . . . . . . . . . . . . .65
Ion MAX and Ion MAX-S Housing Maintenance . . . . . . . . . . . . . . . . . . . . . . .66

Contents
Thermo Scientific TSQ Series Hardware Manual xiii
Chapter 6 Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Frequency of Cleaning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .69
Maintaining the Ion Sweep Cone and Ion Transfer Tube. . . . . . . . . . . . . . . . . .70
Removing and Cleaning the Ion Transfer Tube . . . . . . . . . . . . . . . . . . . . . . .70
Maintaining the Ion Source Interface Assembly . . . . . . . . . . . . . . . . . . . . . . . . .72
Shutting Down and Venting the System. . . . . . . . . . . . . . . . . . . . . . . . . . . . .73
Removing the Ion MAX or Ion MAX-S Ion Source Housing . . . . . . . . . . . . .73
Removing the Ion Source Interface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .73
Removing the S-Lens and Exit Lens (TSQ Vantage) . . . . . . . . . . . . . . . . . . .74
Cleaning the S-Lens and Exit Lens (TSQ Vantage) . . . . . . . . . . . . . . . . . . . .75
Removing the Tube Lens and Skimmer (TSQ Quantum Access and
TSQ Quantum Ultra). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .76
Cleaning the Tube Lens and Skimmer (TSQ Quantum Access and
TSQ Quantum Ultra). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .77
Reinstalling the S-Lens and Exit Lens (TSQ Vantage) . . . . . . . . . . . . . . . . . .77
Reinstalling the Tube Lens and Skimmer (TSQ Quantum Access and
TSQ Quantum Ultra): . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .78
Reinstalling the Ion Source Interface Assembly. . . . . . . . . . . . . . . . . . . . . . . .79
Reinstalling the Ion MAX or Ion MAX-S Ion Source Housing. . . . . . . . . . . .79
Starting Up the System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .79
Cleaning the Q00 Ion Optics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .79
Shutting Down and Venting the System. . . . . . . . . . . . . . . . . . . . . . . . . . . . .80
Removing the Ion MAX-S Ion Source Housing . . . . . . . . . . . . . . . . . . . . . . .80
Removing the Ion Source Interface Assembly . . . . . . . . . . . . . . . . . . . . . . . . .80
Removing the Ion Optics Cage Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . .80
Disassembling the Ion Optics Cage Assembly. . . . . . . . . . . . . . . . . . . . . . . . .84
Cleaning Q00 and L0. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .85
Reassembling the Ion Optics Cage Assembly . . . . . . . . . . . . . . . . . . . . . . . . .86
Reinstalling the Ion Optics Cage Assembly. . . . . . . . . . . . . . . . . . . . . . . . . . .87
Reinstalling the Ion Source Interface Assembly. . . . . . . . . . . . . . . . . . . . . . . .88
Reinstalling the Ion MAX-S Ion Source Housing . . . . . . . . . . . . . . . . . . . . . .88
Starting Up the System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .88
Maintaining the Forepump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .89
Cleaning the Fan Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .89
Chapter 7 Diagnostics and PCB and Assembly Replacement . . . . . . . . . . . . . . . . . . . . . . . . 91
Running the TSQ System Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .91
Replacing a Fuse. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .93
Replacing PCBs and Power Supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .93
Chapter 8 Replaceable Parts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
MS Accessory Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .95
TSQ Vantage Instrument Specific Accessory Kit . . . . . . . . . . . . . . . . . . . . . . . .96
TSQ Quantum Ultra, Ultra AM, and Ultra EMR Instrument Specific Accessory Kit
96
TSQ Quantum Access Instrument Specific Accessory Kit. . . . . . . . . . . . . . . . . .96
Fittings, Ferrules, and Sample Loops . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .97
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99

Thermo Scientific TSQ Series Hardware Manual xv
P
Preface
About This Guide
This TSQ Series Hardware Manual contains a description of the modes of operation and principle
hardware components of your TSQ system. In addition, this manual provides step-by-step
instructions for cleaning and maintaining your mass spectrometer.
Related Documentation
In addition to this manual, Thermo Fisher Scientific provides the following for TSQ Series mass
spectrometers:
•Preinstallation Requirements Guide
•Getting Connected Guide
•Getting Started Guide
• Help available from within the software
Safety and Special Notices
Make sure you follow the precautionary statements presented in this guide. The safety and other
special notices appear in boxes.
Safety and special notices include the following:
CAUTION Highlights 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.

Preface
xvi TSQ Series Hardware Manual Thermo Scientific
Safety Precautions
Observe the following safety precautions when you operate or perform service on the mass
spectrometer.
CAUTION Do Not Perform Any Servicing Other Than That Contained in the TSQ Series
Hardware Manual. To avoid personal injury or damage to the instrument, do not perform any
servicing other than that contained in the TSQ Series Hardware Manual or related manuals
unless you are qualified to do so.
CAUTION Shut Down the Mass Spectrometer and Disconnect It From Line Power Before
You Service It. High voltages capable of causing personal injury are used in the instrument.
Some maintenance procedures require that the mass spectrometer be shut down and
disconnected from line power before service is performed. Do not operate the mass
spectrometer with the top or side covers off. Do not remove protective covers from PCBs.
CAUTION Respect Heated Zones. Treat heated zones with respect. The ion transfer capillary
and the APCI vaporizer might be very hot and might cause severe burns if they are touched.
Allow heated components to cool before you service them.
CAUTION Place the Mass Spectrometer in Standby (or Off) Before You Open the
Atmospheric Pressure Ionization (API) Source. The presence of atmospheric oxygen in the
API source when the mass spectrometer is On could be unsafe. (The TSQ automatically turns
the mass spectrometer Off when you open the API source; however, it is best to take this added
precaution.)
CAUTION Provide and Adequate Fume Exhaust System. It is your responsibility to provide
an adequate fume exhaust system. Samples and solvents that are introduced into the TSQ mass
spectrometer will eventually be exhausted from the forepump. Therefore, the forepump should
be connected to a fume exhaust system. Consult local regulations for the proper method of
exhausting the fumes from your system.
CAUTION Use Care When Changing Vacuum Pump Oil. Treat drained vacuum pump oil
and pump oil reservoirs with care. Hazardous compounds introduced into the system might
have become 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, the pump must be
decontaminated by the user and certified to be free of contamination before repairs or
adjustments are made by a Thermo Fisher Scientific San Jose Customer Support Engineer or
before it is sent back to the factory for service.

Preface
Thermo Scientific TSQ Series Hardware Manual xvii
Solvent and Gas Purity Requirements
Use the highest purity solvents available. The TSQ mass spectrometer is extremely sensitive to
solvent impurities. Some solvent impurities are transparent to UV/Visible detectors, but are easily
detected by the TSQ mass spectrometer. Liquid chromatography grade is the minimum acceptable
purity. Higher grade solvents are preferred. Distilled water is recommended. Deionized water
contains chemicals and is not recommended.
The following is a list of international sources that can supply high quality solvents:
The TSQ mass spectrometer uses argon as a collision gas. The argon must be high purity
(99.995%). The required gas pressure is 135 ± 70 kPa (20 ± 10 psig). Thermo Fisher Scientific has
found that particulate filters are often contaminated and are therefore not recommended.
Service Philosophy
Servicing the TSQ system consists of performing procedures required to maintain system
performance standards, prevent system failure, restore the system to an operating condition, or all
of the above. Routine and preventive maintenance procedures are documented in this manual.
The user is responsible for routine and preventive maintenance during and after the warranty
period. Regular maintenance increases the life of the system, maximizes the up-time of your
system, and allows you to achieve optimum system performance.
Only a Thermo Fisher Scientific customer support engineer can perform services not described in
this manual.
Level of Repair
Thermo Fisher Scientific’s service philosophy for the TSQ system calls for troubleshooting to the
lowest part, assembly, or module listed in Chapter 8, “Replaceable Parts.”
For mechanical failures: A mechanical assembly typically is to be repaired to the level of the
smallest item listed in Chapter 8, “Replaceable Parts.”
Solvent source Telephone number
Fisher Global Chemicals Tel: [phone]
Mallinckrodt/Baker, Inc. Tel: [phone]
Fax: [phone]
Burdick & Jackson, Inc. Tel: [phone]
Fax: [phone]

Preface
xviii TSQ Series Hardware Manual Thermo Scientific
Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need.
YTo contact Technical Support
Find software updates and utilities to download at www.mssupport.thermo.com.
YTo contact Customer Service for ordering information
YTo copy manuals from the Internet
Go to mssupport.thermo.com and click Customer Manuals in the left margin of the window.
YTo suggest changes to documentation or to Help
• Fill out a reader survey online at www.thermo.com/lcms-techpubs.
• Send an e-mail message to the Technical Publications Editor at
[e-mail].
Phone [phone]
Fax [phone]
E-mail [e-mail]
Knowledge base www.thermokb.com
Phone [phone]
Fax [phone]
E-mail [e-mail]
Web site www.thermo.com/ms

Thermo Scientific TSQ Series Hardware Manual 1
1
Introduction
TSQ™ Series mass spectrometers are members of the Thermo Scientific family of mass
spectrometers. The TSQ Series mass spectrometer is an advanced analytical instrument that
includes a syringe pump, a divert/inject valve, a mass spectrometer, and the Xcalibur™ data system.
In a typical analysis, a sample can be introduced in the following ways:
• Using the syringe pump (direct infusion)
• Using the divert/inject valve fitted with a sample loop and LC (flow injection analysis)
• Using the divert/inject valve and HPLC fitted with a column (LC/MS)
In a typical analysis, a liquid chromatograph (LC) introduces a sample. The LC separates the
sample into its various components. The components elute from the LC and pass into the mass
spectrometer where they are analyzed.
Analysis by direct infusion or flow injection provides no chromatographic separation of
components in the sample before they pass into the mass spectrometer. The data from the mass
spectrometer is then stored and processed by the data system.
The TSQ mass spectrometer consists of an atmospheric pressure ionization (API) source, ion
optics, triple-stage mass analyzer, and ion detection system. A vacuum manifold encloses the ion
optics, mass analyzer, ion detection system, and part of the API source. Ionization of the sample
takes place in the API source. The specific process used to ionize the sample is known as the
ionization mode. The ion optics transmit the ions produced in the ion source into the mass
analyzer, where they are separated according to their mass-to-charge ratio. The polarity of the
potentials applied to the lenses in the ion source and ion optics determines whether they transmit
positively charged ions or negatively charged ions to the mass analyzer. You can configure the TSQ
mass spectrometer to analyze positively or negatively charged ions (called the positive or negative
ion polarity mode).
Contents
•Ionization Modes
•Ion Polarity Modes
•Scan Modes
•Scan Types
•Data Types
•Mass/Charge Range

1Introduction
2TSQ Series Hardware Manual Thermo Scientific
The TSQ instrument’s triple-stage mass analyzer performs either one or two stages of mass analysis:
• The TSQ system is operated as a conventional mass spectrometer with one stage of mass
analysis. The ion source ionizes the sample and the ion products are subjected to mass analysis
in the first rod assembly. The second and third rod assemblies transmit the resulting
mass-selected ions to the ion detection system.1
• The TSQ system is operated as a tandem mass spectrometer with two stages of mass analysis.
The ion source ionizes the sample and the ion products are mass analyzed by the first rod
assembly. In this case, however, mass-selected ions exiting the first rod assembly collide with an
inert gas in the second rod assembly and fragment to produce a set of ions known as product
ions. (A chamber called the collision cell surrounds the second rod assembly. The collision cell
can be pressurized with an inert gas.) The product ions undergo further mass analysis in the
third rod assembly to detect selected ions. Two stages of mass analysis yield far greater chemical
specificity than a single stage can achieve, because of the system’s ability to select and
determine two discrete but directly related sets of masses.
In a first stage of mass analysis the TSQ systems can be used to elucidate the structures of pure
organic compounds and the structures of the components within mixtures. Furthermore, in a
second stage of mass analysis, the mass spectrometer can fragment and separate each ionic fragment
of a molecule formed in the ion source to build up an entire structure for the molecule, piece by
piece. Thus, TSQ systems make investigating all pathways for the formation and fragmentation of
each ion in the mass spectrum possible.
The two stages of mass analysis, with resultant reduction of chemical noise in the final mass
spectrum, allow for very selective and sensitive analysis.
Each sequence of single- or triple-stage mass analysis of the ions is called a scan. The TSQ mass
spectrometer uses several different scan modes and different scan types to filter, fragment, or
transmit ions in the mass analyzer. Along with the ionization and ion polarity modes, the ability to
vary the scan mode and scan type affords the user great flexibility in the instrumentation for
solving complex analytical problems.
1 The instrument can also be used as a single-stage mass spectrometer by transmitting the ions through the first and
second rod assemblies followed by mass analysis in the third rod assembly.