LTQ Velos Series - Thermo Fisher Scientific

LTQ Velos Series - Thermo Fisher Scientific
Achieving Peak
Instrument
Performance
For the LTQ Velos, Velos Pro, LTQ Orbitrap Velos,
Orbitrap Velos Pro, and Orbitrap Elite
Reference Manual
97655-97003 Revision A
October 2012
© 2012 Thermo Fisher Scientific Inc. All rights reserved.
Automatic Gain Control, DirectJunction, EASY-Spray, Foundation, Ion Max, LTQ Orbitrap Velos,
LTQ Velos, Nanospray Flex, nanoViper, Orbitrap Elite, Orbitrap Velos Pro, Pierce, Proteome Discoverer, and
Velos Pro are trademarks, and LTQ, Orbitrap, Thermo Scientific, Unity, 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:
Adobe and Reader are registered trademarks of Adobe Systems Incorporated. Hamilton is a registered
trademark of Hamilton Company. Liquinox is a registered trademark of Alconox, Inc. MICRO-MESH is a
registered trademark of Micro-Surface Finishing Products, Inc. Microsoft and Windows are registered
trademarks of Microsoft Corporation.
Mascot is a registered service mark of Matrix Science Ltd. in the United States.
Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
product operation. This document is copyright protected and any reproduction of the whole or any part of this
document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.
The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document supersede
all previous information received by the purchaser.
Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or errorfree and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might
result from any use of this document, even if the information in the document is followed properly.
This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This
document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of
Sale shall govern all conflicting information between the two documents.
Release history: Revision A, October 2012
Software version: Microsoft Windows 7 Professional (32 bit)—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 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 products:
• LTQ Velos Mass Spectrometer (August 2008)
• LTQ Velos/ETD System (November 2008)
• Velos Pro Mass Spectrometer (April 2011)
• Velos Pro/ETD System (April 2011)
Note For the Orbitrap systems, refer to their product documentation for the EC Declarations of Conformity.
LTQ Velos Mass Spectrometer (August 2008)
EMC Directive 2004/108/EEC
EMC compliance has been evaluated by TÜV Rheinland of North America, Inc.
EN 55011: 2007, A2: 2007
EN 61000-4-3: 2006
EN 61000-3-2: 2006
EN 61000-4-4: 2004
EN 61000-3-3: 1995, A1: 2001, A2: 2005
EN 61000-4-5: 2005
EN 61326-1: 2006
EN 61000-4-6: 2007
EN 61000-4-2: 1995, A1: 1999, A2: 2001
EN 61000-4-11: 2004
FCC Class A, CFR 47 Part 15: 2007
Low Voltage Safety Compliance
This device complies with Low Voltage Directive 2006/95/EEC and harmonized standard EN 61010-1:2001.
LTQ Velos/ETD System (November 2008)
EMC Directive 2004/108/EEC
EMC compliance has been evaluated by TÜV Rheinland of North America, Inc.
EN 61326-1: 2006
EN 61000-4-4: 2004
EN 55011: 2007
EN 61000-4-5: 2005
EN 61000-3-2: 2006
EN 61000-4-6: 2007
EN 61000-3-3: 2005
EN 61000-4-11: 2004
EN 61000-4-2: 2001
FCC Part 15: 2007
EN 61000-4-3: 2006
Velos Pro Mass Spectrometer (April 2011)
EMC Directive 2004/108/EEC
EMC compliance has been evaluated by TÜV Rheinland of North America, Inc.
EN 61326-1: 2006
EN 61000-4-3: 2006
EN 55011: 2007, A2: 2007
EN 61000-4-4: 2004
CFR 47, FCC Part 15, Subpart B, Class A: 2009
EN 61000-4-5: 2005
EN 61000-3-2: 2006
EN 61000-4-6: 2007
EN 61000-3-3: 1995, A1: 2001, A2: 2005
EN 61000-4-11: 2004
EN 61000-4-2: 1995, A1: 1999, A2: 2001
Low Voltage Safety Compliance
This device complies with Low Voltage Directive 2006/95/EEC and harmonized standard EN 61010-1:2001.
Velos Pro/ETD System (April 2011)
EMC Directive 2004/108/EEC
EMC compliance has been evaluated by TÜV Rheinland of North America, Inc.
EN 61326-1: 2006
EN 61000-4-3: 2006
EN 55011: 2007, A2: 2007
EN 61000-4-4: 2004
CFR 47, FCC Part 15, Subpart B, Class A: 2009
EN 61000-4-5: 2005
EN 61000-3-2: 2006
EN 61000-4-6: 2007
EN 61000-3-3: 1995, A1: 2001, A2: 2005
EN 61000-4-8: 1993, A1: 2001
EN 61000-4-2: 1995, A1: 1999, A2: 2001
EN 61000-4-11: 2004
Low Voltage Safety Compliance
This device complies with Low Voltage Directive 2006/95/EEC and harmonized standard EN 61010-1:2001.
FCC Compliance Statement
THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES. OPERATION IS SUBJECT TO
THE FOLLOWING TWO CONDITIONS: (1) THIS DEVICE MAY NOT CAUSE HARMFUL
INTERFERENCE, AND (2) THIS DEVICE MUST ACCEPT ANY INTERFERENCE RECEIVED,
INCLUDING INTERFERENCE THAT MAY CAUSE UNDESIRED OPERATION.
CAUTION Read and understand the various precautionary notes, signs, and symbols contained inside
this manual pertaining to the safe use and operation of this product before using the device.
Notice on Lifting and Handling of
Thermo Scientific Instruments
For your safety, and in compliance with international regulations, the physical handling of this Thermo Fisher
Scientific instrument requires a team effort to lift and/or move the instrument. This instrument is too heavy and/or
bulky for one person alone to handle safely.
Notice on the Proper Use of
Thermo Scientific Instruments
In compliance with international regulations: Use of this instrument in a manner not specified by Thermo Fisher
Scientific could impair any protection provided by the instrument.
Notice on the Susceptibility
to Electromagnetic Transmissions
Your instrument is designed to work in a controlled electromagnetic environment. Do not use radio frequency
transmitters, such as mobile phones, in close proximity to the instrument.
For manufacturing location, see the label on the instrument.
WEEE Compliance
This product is required to comply with the European Union’s Waste Electrical & Electronic Equipment (WEEE)
Directive 2002/96/EC. It is marked with the following symbol:
Thermo Fisher Scientific has contracted with one or more recycling or disposal companies in each European Union
(EU) Member State, and these companies should dispose of or recycle this product. See www.thermoscientific.com/
rohsweee 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.thermoscientific.com/rohsweee.
Conformité DEEE
Ce produit doit être conforme à la directive européenne (2002/96/EC) des Déchets d'Equipements Electriques et
Electroniques (DEEE). Il est marqué par le symbole suivant:
Thermo Fisher Scientific s'est associé avec une ou plusieurs compagnies de recyclage dans chaque état membre de
l’union européenne et ce produit devrait être collecté ou recyclé par celles-ci. Davantage d'informations sur la
conformité de Thermo Fisher Scientific à ces directives, les recycleurs dans votre pays et les informations sur les
produits Thermo Fisher Scientific qui peuvent aider la détection des substances sujettes à la directive RoHS sont
disponibles sur www.thermoscientific.com/rohsweee.
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 das Gerät nicht mit
abgenommenem Deckel. Nehmen Sie die
Schutzabdeckung von Leiterplatten nicht
ab.
Choc électrique: L’instrument utilise des
tensions capables d’infliger des blessures
corporelles. 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
enlever 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 chimiques
dangereux peuvent se trouver dans
l’instrument. Portez des gants pour
manipuler tous produits chimiques
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 los
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
Vorsichtsmaßnahmen, 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
manipulation de 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 manipular 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
außerdem 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’une 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.
C
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xv
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xvi
Adobe 3D Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xvi
Safety and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii
Safety Precautions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xviii
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xix
Thermo Scientific
Chapter 1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Pumping Down the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Instrument Control Software. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Daily Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Chapter 2
Stable Ionization Spray . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3
Ion Source Types. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Maintaining Spray Stability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Chapter 3
Mass Spectrometer Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Probe Types for Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Calibration Mixture. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Types of Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Chapter 4
Tuning the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
Tune Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Tuning the Ion Optic Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Multipoles MP00 RF Lens and MP0. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Front Lens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Multipole RF Amplitude . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Achieving Peak Instrument Performance Reference Manual
xi
Contents
Chapter 5
Diagnostics for Signal Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21
Workflow for Resolving Signal Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Evaluating the System Parameters Associated with Signal Intensity . . . . . . . . . . 24
Injection Time. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Spray Stability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Manual TIC Tune. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Electron Multiplier Gain . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Transfer Lenses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
System Evaluation Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Reporting Unresolved Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Chapter 6
Cleaning the Ion Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .53
Preparing the Work Area. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Tools and Supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Ion Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Cleaning the Exit Lens and S-Lens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Cleaning Lens L0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Cleaning the Split Gate Lens, Lens L1, and Multipoles MP0 and MP1. . . . . . . 60
Chapter 7
Orbitrap Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .65
Additional Calibrations for the Orbitrap System . . . . . . . . . . . . . . . . . . . . . . . . 65
pAGC Scaling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Mass Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Advanced Signal Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Calibrating the Orbitrap System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Checking and Improving the Mass Accuracy . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Chemical Background Ions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Scatter Plot in Thermo Proteome Discoverer. . . . . . . . . . . . . . . . . . . . . . . . . 69
Lock Masses and Lock Mass Abundance . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Chapter 8
Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .73
Appendix A Online Resources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .75
Planet Orbitrap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
San Jose Product Support Engineering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Online Product Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .77
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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.
Thermo Scientific
Adobe 3D Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xvi
Version Info window (example) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Syringe Pump dialog box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Diagnostics dialog box showing the System Evaluation page (Velos Pro) . . . . . . . 6
API stability evaluation results (Orbitrap Elite, HESI probe, and SIM
scan type) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
ESI probe (installed) and HESI-II probe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Calibrate dialog box showing the Check page . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Ion Optics dialog box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Front lens tune curve at m/z 1522 with MP0 offset at –8.5 V . . . . . . . . . . . . . . 18
Tune dialog box showing the Semi-Automatic page . . . . . . . . . . . . . . . . . . . . . 19
Diagnostics workflow (Chart 1 of 2) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Diagnostics workflow (Chart 2 of 2) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Location of the spectrum’s injection time (IT) . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Examples of TIC graphs (Velos Pro) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Tune dialog box showing the Manual page . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
New electron multipliers’ voltages over time (LTQ Velos example, fairly
continuous usage) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Calibrate dialog box showing the Check page (Velos Pro). . . . . . . . . . . . . . . . . 29
Diagnostics dialog box showing the System Evaluation page (Velos Pro) . . . . . . 33
Graph: signal intensity versus the front lens voltages . . . . . . . . . . . . . . . . . . . . . 34
Graph: normalized signal intensity versus the MP0–MP00 gradient for a
clean system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Graph: signal intensity versus the MP0–MP00 gradient for a contaminated
system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Ion optics showing the test area for the source optics flight time
evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Example graphs of the MP00/L0/MP0 flight times (Velos Pro) . . . . . . . . . . . . . 38
Graph of the source optics flight time evaluation (Velos Pro, light use) . . . . . . . 39
Graph of the source optics flight time evaluation (Velos Pro, heavy use) . . . . . . 40
Ion optics showing the test area for the multipole MP0 flight time
evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Example graphs of the multipole MP0 flight time (Velos Pro) . . . . . . . . . . . . . . 42
Graph of the multipole MP0 flight time evaluation (Velos Pro, light use). . . . . . 42
Graph of the multipole MP0 flight time evaluation (Velos Pro, heavy use) . . . . . 43
Ion optics showing the test area for the ion optics charging evaluation . . . . . . . . 44
Graphs of the ion optics charging evaluation for a clean system
(Velos Pro) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Achieving Peak Instrument Performance Reference Manual
xiii
Figures
Figure 32.
Figure 33.
Figure 34.
Figure 35.
Figure 36.
Figure 37.
Figure 38.
Figure 39.
Figure 40.
Figure 41.
Figure 42.
Figure 43.
Figure 44.
Figure 45.
Figure 46.
xiv
Graphs of the ion optics charging evaluation showing an example of a
contaminated MP00 rf lens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Graphs of the ion optics charging evaluation showing an example of a
contaminated MP0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Graphs of the ion optics charging evaluation showing an example of a
contaminated exit lens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Graphs of the ejection and multiplier gain ratio evaluation (Velos Pro) . . . . . . . 50
Ion path through the Velos Pro ion optics (illustrated side view) . . . . . . . . . . . . 56
Exit lens and S-lens removed from the ion source interface cage . . . . . . . . . . . . 57
Lens L0 removed from the MP00 rf lens assembly . . . . . . . . . . . . . . . . . . . . . . . 59
MP0 and MP1 ion guides for the Velos Pro . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Common contamination areas on the inner surface areas of MP0
(Velos Pro) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Graph: pAGC scale factor versus lg(target) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Calibrate dialog box showing the Semi-Automatic page (Orbitrap systems) . . . 68
Report Item Distribution chart’s scatter plot (example with lock mass
correction) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Define Scan dialog box (Orbitrap Elite, partial) . . . . . . . . . . . . . . . . . . . . . . . . 71
Lock Masses dialog box. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Diagnostics dialog box showing the Set Device page . . . . . . . . . . . . . . . . . . . . . 72
Achieving Peak Instrument Performance Reference Manual
Thermo Scientific
P
Preface
The Achieving Peak Instrument Performance Reference Manual describes how to maintain a
stable ionization spray; how to use the tune, calibrate, and diagnostic features in the Tune Plus
application to achieve peak instrument performance; and how to clean the ion optic elements.
Use the information in this manual for these Thermo Scientific™ mass spectrometers:
• Stand-alone instruments: LTQ™ Velos™ and Velos Pro™
• Hybrid Orbitrap™ systems: LTQ Orbitrap Velos™, Orbitrap Velos Pro™, and
Orbitrap Elite™
This manual focuses on the linear ion trap optics, with additional information for hybrid
Orbitrap systems in Chapter 7, “Orbitrap Systems.”
Contents
• Related Documentation
• Adobe 3D Toolbar
• Safety and Special Notices
• Safety Precautions
• Contacting Us
 To suggest changes to documentation or to Help
Complete a brief survey about this document by clicking the button below.
Thank you in advance for your help.
Thermo Scientific
Achieving Peak Instrument Performance Reference Manual
xv
Preface
Related Documentation
Thermo Fisher Scientific provides additional documents for these instruments that are
accessible from the data system computer. If you received your instrument before October
2012, contact your local Thermo Fisher Scientific sales representative about receiving the
printed quick reference card, Achieving Peak Performance (P/N 97655-97002), that
complements this reference manual.
 To view document manuals
To access the manuals for the mass spectrometer, from the Microsoft™ Windows™ taskbar,
choose Start > All Programs (or Programs) > Thermo Instruments > Manuals >
model, where model is your specific model, and then click the PDF file to view.
The software also provides Help. To access the Help, choose Help from the menu bar.
Adobe 3D Toolbar
This manual includes 3-D models that you can manipulate by using the Adobe™ 3D Toolbar
(Figure 1). Make sure that the data system computer has the Adobe Reader™ software
installed, version 9 or later.
Figure 1.
Adobe 3D Toolbar
Default View button
 To activate the 3-D image
Click the image.
 To deactivate the 3-D image
Right-click the image, and then choose Disable Content from the shortcut menu.
 To move the image back into the viewing area
Do one of the following:
• In the 3D Toolbar, click the Default View (
) button.
• Right-click the image, and then choose Parts Option > Fit Visible.
For information about the 3D & Multimedia preference settings, refer to the Adobe Reader
Help.
xvi
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Thermo Scientific
Preface
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.
Table 1 lists additional caution-specific symbols that appear in the Achieving Peak Instrument
Performance Reference Manual.
Table 1. Caution-specific symbols and their meanings
Symbol
Meaning
Chemical: Hazardous chemicals might be present in the instrument.
Wear gloves when handling carcinogenic, corrosive, irritant,
mutagenic, or toxic chemicals. Use only approved containers and
procedures for disposing of waste oil.
Eye Hazard: Eye damage could occur from splattered chemicals or
airborne particles. Wear safety glasses when handling chemicals or
servicing the instrument.
Hot Surface: Allow heated components to cool before touching or
servicing the instrument.
Thermo Scientific
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Preface
Safety Precautions
Observe the following safety precautions before you shut down the mass spectrometer and
remove components for cleaning.
CAUTION If you must turn off the mass spectrometer in an emergency, turn off the
main power switch located on the right-side power panel. This switch turns off all power
to the mass spectrometer, 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.
To turn off the LC, autosampler, and data system computer in an emergency, use their
respective on/off switch or button.
CAUTION To avoid an electrical shock, be sure to follow the instructions in “Shutting
Down the Mass Spectrometer Completely” in Chapter 3 of the LTQ Series Hardware
Manual.
CAUTION Do not turn the instrument on if you suspect that it has incurred any kind of
electrical damage. Instead, disconnect the power supply cord and contact Unity™ Lab
Services for a product evaluation. Do not attempt to use the instrument until it has been
evaluated. (Electrical damage might have occurred if the system shows visible signs of
damage, or has been transported under severe stress.)
CAUTION Do not disconnect the power supply cord at the mass spectrometer while the
other end is still plugged into the electrical outlet.
CAUTION Do not place any objects—especially containers with liquids—on top of the
instrument, unless instructed to in the documentation. Leaking liquids might contact the
electronic components and cause an electrical short circuit.
CAUTION Hot surface Allow heated components to cool to room temperature
(approximately 20 minutes) before servicing them.
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Preface
Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need.
Topic
Web site
Use a single source for integrated
lab service, support, and supply
management.
www.unitylabservice.com
Find local contact information for
sales or service.
www.thermoscientific.com/wps/portal/ts/contactus
Copy manuals from the Internet.
mssupport.thermo.com
Unity Lab Services is part of Thermo Fisher
Scientific.
Agree to the Terms and Conditions, and then click
Customer Manuals in the left margin.
Access the Thermo Scientific
Knowledge Base.
Suggest changes to documentation
or to Help.
www.thermokb.com
• Fill out a reader survey online at:
www.surveymonkey.com/s/PQM6P62
• Send an e-mail message to the Technical
Publications Editor at:
[email protected]
Thermo Scientific
Achieving Peak Instrument Performance Reference Manual
xix
1
Introduction
This chapter provides general information for achieving peak performance from the following
Thermo Scientific stand-alone mass spectrometers and hybrid Orbitrap systems:
LTQ Velos, Velos Pro, LTQ Orbitrap Velos, Orbitrap Velos Pro, and Orbitrap Elite.
Contents
• Pumping Down the Mass Spectrometer
• Instrument Control Software
• Daily Operation
Pumping Down the Mass Spectrometer
To help optimize the performance of the mass spectrometers, make sure that you do the
following:
• Stand-alone mass spectrometers: Pump down the vacuum system for at least 15 hours.
For instructions, refer to “Starting the Mass Spectrometer” in Chapter 3 of the LTQ Series
Hardware Manual.
After two hours, you can view the mass spectrum to determine if the system is
functioning correctly. However, the electron multiplier lifetime and gain calibration
might be affected.
• Hybrid Orbitrap instruments: Bake out the system for at least 8 hours. For instructions,
refer to the getting started guide for your Orbitrap model.
IMPORTANT
• Pump-down times of less than 15 hours on new instruments or after venting the mass
spectrometer might cause incorrect calibration of the transfer lenses and might
increase the aging of the electron multipliers.
• If the instrument is new, you must calibrate the instrument after completing the
pump-down time. For instructions, refer to Chapter 3 in the LTQ Series Getting
Started Guide.
Thermo Scientific
Achieving Peak Instrument Performance Reference Manual
1
1
Introduction
Instrument Control Software
Instrument Control Software
If you use old versions of the LTQ instrument control (IC) software, the mass spectrometer
might have reduced functionality or lack optimal tuning or calibration. Always verify that the
instrument control software is up-to-date. After you upgrade the instrument control software,
Thermo Fisher Scientific recommends that you run the automatic calibration.
Note (LTQ 2.7 SP1 and later) The option to Enable Sweep Gas While in Standby on the
instrument configuration window’s Ion Source page is the default selection with a default
flow rate of 5 (arb unit). This option improves robustness by minimizing the amount of
particulate matter that enters the mass spectrometer.
 To identify the version level of the IC software
From the Microsoft Windows taskbar, choose Start > All Programs (or Programs) >
Thermo Foundation x.x > Version Info, where x.x is the installed version of Thermo
Foundation™, to open the Version Info window (Figure 2).
Figure 2.
Version Info window (example)
LTQ instrument control
software version 2.7 SP1
To obtain the latest version of the LTQ instrument control software, contact Unity Lab
Services for assistance.
Daily Operation
To ensure the proper operation of the instrument, Thermo Fisher Scientific recommends that
you perform the daily preventive maintenance described in Chapter 4 of the LTQ Series
Hardware Manual.
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2
Stable Ionization Spray
This chapter identifies the various ion sources designed for the Thermo Scientific LTQ Series
mass spectrometers, and describes how to achieve and maintain a stable ionization spray.
Contents
• Ion Source Types
• Maintaining Spray Stability
Ion Source Types
Table 2 shows the Thermo Scientific atmospheric pressure ionization (API) ion sources that
can attach to the LTQ Series mass spectrometers and defines their applicable ionization
modes. For additional information, refer to the documentation provided with the ion source
and Appendix A, “Online Resources.”
Table 2. Thermo Scientific API ion sources for the LTQ Series mass spectrometers (Sheet 1 of 2)
API source housing
Ionization mode
Ion Max™ (shown) or Ion Max-Sa
Electrospray ionization A type of atmospheric pressure ionization that is
(ESI)
currently the softest ionization technique
available to transform ions in solution into ions
in the gas phase.
Thermo Scientific
Definition
Heated-electrospray
ionization (HESI)
Converts ions in solution into ions in the gas
phase by using ESI in combination with heated
auxiliary gas.
Atmospheric pressure
chemical ionizationb
(APCI)
A soft ionization technique done in an ion source
operating at atmospheric pressure. Electrons
from a corona discharge initiate the process by
ionizing the mobile phase vapor molecules. A
reagent gas forms, which efficiently produces
positive and negative ions of the analyte through
a complex series of chemical reactions.
Achieving Peak Instrument Performance Reference Manual
3
2
Stable Ionization Spray
Ion Source Types
Table 2. Thermo Scientific API ion sources for the LTQ Series mass spectrometers (Sheet 2 of 2)
API source housing
Ionization mode
Definition
EASY-Spray™
Nanoelectrospray
(nanospray) ionization
(nanoESI or NSI)
A type of ESI that accommodates very low flow
rates of sample and solvent at 1–20 nL/min (for
static nanospray) or 100–1000 nL/min (for
dynamic nanospray, which is also called nanoESI
nanoLC gradient separation).
• EASY-Spray ion source—Provides an integrated, temperature
controlled column-emitter solution that requires you to make just a
single nanoViper™ connection between the LC and the MS source to
achieve exceptional nanoflow LC/MS performance.
Nanospray Flex™
• Nanospray Flex ion source—Enables the use of nanoscale flow rates
and maintains excellent spray stability to ensure efficient evaporation
and ionization of liquid samples. The included DirectJunction™
adapter offers total flexibility with respect to column and emitter
choices.
Nanospray (NSI-1 Dynamic Nanospray
Probe with the NSI-1 Basec)
• Nanospray ion source—Enables sensitive nanospray analysis with
minimal dead volume. The Nanospray ion source is a comprehensive
solution with a high-resolution imaging system for direct observation
and optimization of the spray. A consumables kit accompanies each
Nanospray probe.
a
The Ion Max-S is identical to the Ion Max, except that the Ion Max has an adjustable probe mount and a front door with a view window.
b
This manual excludes information for the APCI mode.
c
For use with the Ion Max or Ion Max-S source housing
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2
Stable Ionization Spray
Maintaining Spray Stability
Maintaining Spray Stability
Before you perform any tune, calibration, or diagnostic procedure, make sure that you
establish stable ionization spray conditions.
IMPORTANT Failure to maintain a stable spray might compromise the data quality or
result in a poor tune, calibration, or diagnostic result.
Follow these procedures:
1. To infuse the calibration solution into the ion source, on page 5
2. To adjust the spray stability, on page 6
 To infuse the calibration solution into the ion source
1. Set up the syringe pump to infuse a solution.
You can use the calibration solution, but it is not required for this evaluation. For
instructions, refer to “Setting Up the Syringe Pump for Tuning and Calibration” in
Chapter 3 of the LTQ Series Getting Started Guide.
2. Open the Tune Plus application, and then choose Setup > Syringe Pump to open the
Syringe Pump dialog box (Figure 3).
Figure 3.
Syringe Pump dialog box
3. Under Flow Control, select the On option, and then enter an appropriate value in the
Flow Rate (μL/min) box.
• For ESI and HESI modes, enter 5.00.
• For NSI mode, refer to the product user guide.
Refer to the product documentation.
Thermo Scientific
Achieving Peak Instrument Performance Reference Manual
5
2
Stable Ionization Spray
Maintaining Spray Stability
4. Under Type, do the following:
• Select the Hamilton or Unimetrics option.
Note A 500 μL Unimetrics syringe is supplied with the LTQ Series mass
spectrometer.
• In the Volume (μL) list, select 250 or 500 as appropriate.
5. Click Apply or OK to start the syringe pump.
You can also use the syringe pump on/off button that is located above the syringe pump.
 To adjust the spray stability
1. Run the API Stability Evaluation diagnostic as follows:
a. In the Tune Plus application, choose Diagnostics > Diagnostics, click Tools, and
then select System Evaluation (Figure 4).
Figure 4.
Diagnostics dialog box showing the System Evaluation page (Velos Pro)
Tools button
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Achieving Peak Instrument Performance Reference Manual
API Stability Evaluation
Thermo Scientific
2
Stable Ionization Spray
Maintaining Spray Stability
b. Select the API Stability Evaluation check box, and then click Start.
Note Because the API stability evaluation runs indefinitely, when you are ready
to end the evaluation, click Stop and then click OK, which closes the dialog box.
The API stability evaluation generates a real-time graph showing the relative standard
deviation (RSD) of the total ion current (TIC) for a 10 Da selected ion monitoring
(SIM) scan that is centered around the most abundant mass-to-charge ratio in the
current spectrum. Figure 5 shows an example. When you change the parameters,
such as the spray voltage, the RSD value shown in the graph decreases or increases,
depending on whether the change makes the spray more or less stable. The actual
RSD value and its rating (for example, excellent or good) appear above the graph.
Figure 5.
API stability evaluation results (Orbitrap Elite, HESI probe, and SIM scan type)
Signal stability rating and RSD result
2. In the Tune Plus window, choose Settings > type Source, where type is ESI, Heated ESI,
or NSI, to open the source dialog box.
Thermo Scientific
Achieving Peak Instrument Performance Reference Manual
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2
Stable Ionization Spray
Maintaining Spray Stability
3. While you observe the real-time signal stability graph, adjust the following parameters in
the type Source dialog box so that the value of the %RSD becomes less than 15%.
Although the goal is 15% or less for the RSD of the TIC, you can often reduce the
%RSD much more by adjusting these parameters.
• Electrospray voltage—Use the following values.
ESI or HESI probe
EASY-Spray nanospray
ion source
Nanospray Flex ion source or
NSI-1 dynamic nanospray probe
4.5 kV
1.4–2.4 kV
1.5–2.5 kV
• Sheath, auxiliary, and sweep gas flow rates—Refer to Table 3 in Chapter 1 of the
LTQ Series Getting Started Guide.
• (HESI only) Heater temperature—Use the range from Off to 50 °C. For additional
information, refer to the Tune Plus Help (Heated ESI Source dialog box topic).
4. When you are ready, click OK in each open dialog box.
Note Before you run the calibrations or diagnostic tests that require the use of the
calibration solution, Thermo Fisher Scientific recommends that the %RSD value be less
than 15 percent.
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3
Mass Spectrometer Calibration
This chapter shows the probe types that you can use to calibrate the mass spectrometer,
specifies the appropriate calibration mixtures (calmix), discusses two calibrations that have the
most affect on sensitivity, and recommends the calibration checks that you should run. You
must periodically calibrate the mass spectrometer to maintain peak performance over time.
Before you calibrate the mass spectrometer, ensure that the ionization spray is stable by
following the instructions in Chapter 2, “Stable Ionization Spray.”
Contents
• Probe Types for Calibration
• Calibration Mixture
• Types of Calibration
Probe Types for Calibration
When calibrating the mass spectrometer, use only an ESI or HESI type probe (Figure 6). Do
not attempt to calibrate the mass spectrometer with an NSI probe, which can affect the
calibration results.
Figure 6.
ESI probe (installed) and HESI-II probe
HESI-II probe
ESI probe
Thermo Scientific
Achieving Peak Instrument Performance Reference Manual
9
3
Mass Spectrometer Calibration
Calibration Mixture
Calibration Mixture
Make sure that the calibration mixture (calmix) is fresh and that you have the correct solution
for either the stand-alone mass spectrometer or the hybrid Orbitrap system. Use the calmix
solution provided in the Velos Pro Preinstallation Kit (P/N OPTON-20042) or in the
applicable LTQ Orbitrap Preinstallation Kit. You can also order the appropriate Pierce™
ready-made solution at www.thermo.com/pierce.
To order another preinstallation kit, which includes the positive calmix solution, contact
Unity Lab Services.
• For the LTQ Velos and Velos Pro
stand-alone mass spectrometers and the
hybrid Orbitrap systems:
Pierce LTQ Velos ESI Positive Ion
Calibration Solution (P/N 88323)
Positive
• For the LTQ Orbitrap Velos,
Orbitrap Velos Pro, and Orbitrap Elite
systems:
Pierce ESI Negative Ion Calibration
Solution (P/N 88324)
Negative
Note
• For diagnosing instrument problems, use the positive ion calibration solution—even
if you observe the problem in negative ion mode.
• For negative mode calibration of the hybrid Orbitrap systems, use the negative ion
calibration solution.
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3
Mass Spectrometer Calibration
Types of Calibration
Types of Calibration
IMPORTANT You must pump down the ion trap vacuum system for at least 15 hours
before running the calibrations.
In the Tune Plus application, the Calibrate dialog box has the following calibration categories
(pages) for the mass spectrometer in the normal mass range (m/z 50–2000):
• Automatic—Performs an automatic optimization of all calibration parameters.
• Semi-Automatic—Performs an automatic calibration of all the calibration parameters or
performs calibration of specific parameters.
• Check—Performs an automatic check of all the calibration parameters or performs a
calibration check of specific parameters (Figure 7).
Figure 7.
Calibrate dialog box showing the Check page
Positive ion mode
Negative ion mode
Note After performing a calibration or calibration check, green checks , red X marks
, or both appear in the Result column of the Semi-Automatic or Check page of the
Calibrate dialog box. A green check indicates a successful calibration, and a red X indicates
a failed calibration for the corresponding item. The Status box at the bottom of the
Calibrate dialog box provides additional information.
Thermo Scientific
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11
3
Mass Spectrometer Calibration
Types of Calibration
IMPORTANT To determine if the instrument calibration is within specifications, run all
of the calibration checks once a week or monthly, depending on the instrument’s
condition and its usage.
Run the actual calibration for any calibration check that fails. If an actual calibration
repeatedly fails, contact Unity Lab Services for assistance.
Make sure that you check the calibrations for the Transfer Lenses and the Electron Multiplier
Gain in both positive and negative ion modes (Figure 7) because these calibrations affect
sensitivity and can change more often than other calibration parameters with instrument
usage. (When you select either the Positive Ion Mode or Negative Ion Mode check box, the
Tune Plus application automatically selects both calibrations in that mode.)
For calibration instructions, see “Evaluating the System Parameters Associated with Signal
Intensity” on page 24.
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4
Tuning the Mass Spectrometer
A proper instrument tune not only provides optimal sensitivity, it also provides for longer
periods between cleaning cycles and more stable, long-term performance. Ensure that you
periodically check the tune of the mass spectrometer to maintain peak instrument
performance over time. This chapter describes the operational features of the tune files and
the optimum tune settings for the ion optics.
During normal use of a mass spectrometer, residue can accumulate on the ion optic elements.
Over time, this accumulated residue can alter the performance characteristics of the ion
optics, which can result in reduced signal sensitivity. In some cases, this reduction can be
significant and occur more rapidly depending on the extent of the sample cleanup, the extent
of the instrument use, and most importantly whether you use nonoptimized tune values.
IMPORTANT To obtain high levels of sensitivity over a longer period of time, the ion
optics settings must provide a sufficient voltage gradient that is appropriate for a range of
optical element surface conditions. For details, see “Tuning the Ion Optic Elements” on
page 15.
Note For the instrument control software, ensure that you have LTQ 2.7 SP1 or later
installed on the data system computer. If the installed version is earlier than 2.7 SP1, you
might have to manually set some of the ion optics parameters. To upgrade the instrument
control software, contact Unity Lab Services for assistance.
Contents
• Tune Files
• Tuning the Ion Optic Elements
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Tuning the Mass Spectrometer
Tune Files
Tune Files
The Tune Plus application uses tune files to store and set the values of various parameters that
correspond to the installed ion source and probe.
Note Each type of probe, such as APCI, HESI or NSI, has its own tune file, and each
tune file also has information for the different ion sources.
Note the following about the tune files:
• Before you tune the instrument, make sure that you install the appropriate ion source
probe for your experiment.
• When you switch from one type of probe to another, the Tune Plus application
automatically loads the last saved tune parameters for the newly installed probe and
overwrites the tune values from the previously installed probe.
• If you make changes to the tune parameters and do not save them before switching to
another type of probe, the changes are lost.
• If you make changes to the tune parameters, the title bar for the Tune Plus window
updates only after you save the tune file.
• If you want to use any of the tune parameters determined by using a different probe:
a. Write down the applicable parameters and their values (or save a screen capture of the
dialog box).
b. Install the new probe.
c. Open the default tune file associated with the installed probe and manually enter the
new parameters’ values into the Ion Optics dialog box.
d. Save the tune file with the new settings.
Tip To more easily locate a tune file, you might want to include the probe type in
the file name.
Note the following about tune files and ETD systems:
• For LTQ 2.6 SP3 or earlier, the ETD parameters are saved in the tune file associated with
a specific ion source probe.
• For LTQ 2.7 and later, the Tune Plus application saves the ETD parameters (excluding
the ETD reaction time) in an ETD-dedicated system file. This means, for ETD systems
you can switch to another ion source probe type without losing the current ETD
parameters.
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Tuning the Mass Spectrometer
Tuning the Ion Optic Elements
Tuning the Ion Optic Elements
Tune parameters are instrument parameters whose values can vary with the type of
experiment. To achieve the highest sensitivity or the lowest limits of detection for an analyte
of interest, tune the mass spectrometer with that analyte. In addition, appropriate tuning can
improve long-term performance by ensuring that the voltage gradient on the ion optics is
appropriate for a wide variety of conditions.
For additional information about tuning the ion optics, refer to the LTQ Series Getting Started
Guide. For cleaning instructions, see Chapter 6, “Cleaning the Ion Optics.”
These are the critical ion optic components and parameters to tune:
• Multipoles MP00 RF Lens and MP0
• Front Lens
• Multipole RF Amplitude
Multipoles MP00 RF Lens and MP0
You must tune the multipole MP00 rf lens (more commonly called MP00) and multipole
MP0 offsets appropriately to achieve high sensitivity over long periods of run time. In
particular, the voltage difference between these two optical elements is critical in addition to
the absolute values.
In the Ion Optics dialog box (Figure 8), make sure that you set the voltage difference between
the Multipole 0 Offset and Multipole 00 Offset (also called the MP0–MP00 gradient) to
–5.5 V or greater (positive ion mode). This setting establishes an adequate voltage gradient to
ensure that ions will have sufficient ion kinetic energy to overcome any small potential
barriers caused by normal levels of residue buildup on the optical surfaces. The recommended
MP0–MP00 gradient and the values stored in the default tune files are –7.0 V (positive ion
mode) and 7.0 V (negative ion mode) for LTQ 2.7 SP1 and later.
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Tuning the Mass Spectrometer
Tuning the Ion Optic Elements
Figure 8.
Ion Optics dialog box
MP0 offset – MP00 offset = –7.0
(default for the positive ion mode)
Make sure that this value is 800.
See page 17 for guidelines.
 To set the ion optics parameters
1. Attach the ion source housing to the mass spectrometer, and then install an ESI, HESI, or
NSI probe as appropriate for the experiment.
For ESI and HESI modes, refer to Chapter 2 in the LTQ Series Getting Started Guide. For
NSI mode, refer to the product documentation.
2. Establish a stable spray (see “Maintaining Spray Stability” on page 5).
3. Open the Tune Plus application, click the Open button, and then open the default tune
file associated with the installed probe.
4. Save the tune file to a new name (for example, ESI_mytune_date).
5. Choose Setup > Ion Optics to open the Ion Optics dialog box.
6. Ensure that the ion optic values are as shown in Figure 8 on page 16. If they are not,
manually type the values.
Use negative voltages for positive ion mode and positive voltages for negative ion mode.
IMPORTANT (For LTQ 2.7 SP1 and later only) The default ion optics values
typically provide an optimum tune for both sensitivity and long-term instrument
performance. However, because each system might have slight differences, you should
follow the procedure, “To tune the front lens” on page 18, and use the optimized
value.
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Tuning the Mass Spectrometer
Tuning the Ion Optic Elements
7. Click OK.
8. Click the Save button.
IMPORTANT Save the tune method before you change the type of probe. Because a
tune file is source-type dependent, when you change the source type (for example,
from HESI to NSI), you must repeat this tune procedure and save the tune file to
another name.
Front Lens
Because of the sharpness of its tuning curve, the front lens voltage is the next most critical
setting that can affect the sensitivity and the long-term performance of the ion optics. The
front lens voltage depends on the multipole MP0 offset. For the default MP0 offset range
(–8 to –12 V), the front lens voltage optimizes at a value slightly more positive than the MP0
voltage. A more positive front lens voltage decelerates the ions, which allows more efficient
trapping of the ions as they enter the high-pressure ion trap. The relationship between the
MP0 voltage setting and the front lens varies from instrument to instrument. Therefore, you
must tune the front lens in semi-automatic mode.
Figure 9 shows the result of the semi-automatic tune, indicating the sharpness of the
optimum operating range and the determination of the optimum front lens voltage, which is
positioned at the peak of the tuning curve (approximately –8.5 V for this example). (The red
curve is a smoothed version of the blue curve.)
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Tuning the Mass Spectrometer
Tuning the Ion Optic Elements
Figure 9.
Front lens tune curve at m/z 1522 with MP0 offset at –8.5 V
 To tune the front lens
1. Follow the procedure, “To set the ion optics parameters” on page 16.
2. In the Tune Plus window, click the Tune button to open the Tune dialog box, and then
click the Semi-Automatic tab.
3. In the What to Optimize list, select Front Lens (V) (Figure 10).
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Tuning the Mass Spectrometer
Tuning the Ion Optic Elements
Figure 10. Tune dialog box showing the Semi-Automatic page
4. Under Optimization Range, ensure that the Start, End, and Step values are as shown in
Figure 10.
The optimum front lens voltage is directly dependent on the multipole MP0 offset,
which has a default value of –9 V. Typically, you set the front lens voltage to a value
within a few volts of the MP0 voltage. For an MP0 offset of –9 V, the front lens voltage is
usually in the range of –7.0 to –10.0 V (default value is –8.5 V).
Note Remember that the ion optic voltages are negative for positive ion mode and
positive for negative ion mode.
5. Under What to Optimize On, do one of the following as applicable for the experiment:
• Select the Base Peak option.
–or–
• Select the Mass (m/z) option, and then enter the mass of the analyte.
6. Click Start.
7. When the semi-automatic tune finishes, click the Save button.
Tip Usually, a full automatic tune is unnecessary. However, you can run the automatic
tune to ensure that the default values yield optimum results. If the automatic tune’s
performance results are within ±20 percent of the default values, Thermo Fisher Scientific
recommends that you use the default values to ensure optimized long-term performance.
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Tuning the Mass Spectrometer
Tuning the Ion Optic Elements
Multipole RF Amplitude
To contain and transport the ions effectively requires a multipole rf amplitude higher than
600 Vp-p (Figure 8 on page 16). This is especially true at the higher multipole offset values
used in the new default tune files and the higher mass-to-charge ratio ions.
(LTQ Velos and Velos Pro only) For LTQ 2.7 and later, the default tune files set the multipole
rf amplitude to the optimum value of 800 Vp-p. If you have an older version of the instrument
control software, install LTQ 2.7 SP1 or later; otherwise, you must enter all recommended
values manually.
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5
Diagnostics for Signal Issues
This chapter provides a workflow chart to help you resolve certain signal issues, such as a loss
of sensitivity or signal instability. Make sure to follow the order in which the tests are
presented, and use the appropriate calibration solution (calmix) for your mass spectrometer
(see page 10).
Record any test failures and submit the data to Unity Lab Services, which is part of Thermo
Fisher Scientific, as noted in “Reporting Unresolved Issues” on page 51.
CAUTION For proper performance, operate the mass spectrometer at the proper vacuum
levels. Operating the instrument with poor vacuum levels can cause reduced sensitivity,
tuning problems, and reduced electron multiplier life.
Contents
• Workflow for Resolving Signal Issues
• Evaluating the System Parameters Associated with Signal Intensity
• Reporting Unresolved Issues
Workflow for Resolving Signal Issues
If you suspect that there might be a problem with the signal, follow the diagnostic workflow
charts shown in Figure 11 and Figure 12.
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Diagnostics for Signal Issues
Workflow for Resolving Signal Issues
Figure 11. Diagnostics workflow (Chart 1 of 2)
Signal sensitivity is
not as expected.
A
Yes
Is the
injection time (IT)
stable?
No
Check the
TIC value.
Does the TIC
graph show
oscillation?
No
Yes
Run the
Transfer Lenses
calibration check.
Run the
Transfer Lenses
calibration.
No
Did the
calibration check
pass?
Yes
Repeat the
Transfer Lenses
calibration.
No
Did the
calibration
pass?
Check the
signal stability.
Yes
Did the
calibration
pass?
No
Contact Unity
Lab Services.
Is the
spray stability
(RSD) less than
15%?
No
Adjust the spray
conditions.
Yes
Reevaluate the
signal sensitivity.
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5 Diagnostics for Signal Issues
Workflow for Resolving Signal Issues
Figure 12. Diagnostics workflow (Chart 2 of 2)
A
Is the injection
time (IT) less than
0.2 ms?
No
Run the Electron
Multiplier Gain
calibration check.
Yes
Did the
calibration check
pass?
No
Run the Electron
Multiplier Gain
calibration.
Yes
Run the system
diagnostics tools
(1–5, in order).
Did the
calibration
pass?
No
Repeat the
Electron Multiplier
Gain calibration.
Yes
Resolve the issues
as noted in the
diagnostic results.
Yes
Did the
calibration
pass?
No
Issue is not due to
spray or ion optics.
Thermo Scientific
Reevaluate the
signal sensitivity.
Contact Unity
Lab Services.
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Diagnostics for Signal Issues
Evaluating the System Parameters Associated with Signal Intensity
Evaluating the System Parameters Associated with Signal Intensity
If a spectrum shows a reduction or loss in signal intensity, review the following parameters in
this order:
1. Injection Time
2. Spray Stability
3. Manual TIC Tune, on page 25
4. Electron Multiplier Gain, on page 28
5. Transfer Lenses, on page 31
6. System Evaluation Tools, on page 32 (consists of six diagnostic tests)
Injection Time
Injection time (IT) (also called ion injection time or ion time) is the amount of time, in
milliseconds, that ions are allowed to accumulate in the ion trap mass analyzer. With
Automatic Gain Control™ (AGC) on, the injection time is set automatically for each scan (up
to the set maximum injection time) based on the AGC target value specified in the Injection
Control dialog box. The actual injection time for a scan, which is displayed above the
spectrum (Figure 13), fluctuates with each completed scan.
Figure 13. Location of the spectrum’s injection time (IT)
Injection time (ms)
Typical injection times when you infuse the normal calibration solution are less than 0.2 ms
for an m/z 150–2000 full MS scan with a target value of 3 × 104. If the injection time is
greater than 0.2 ms, try resolving the issue as follows:
• Make sure that the calibration solution is fresh and that you have the correct solution; see
“Calibration Mixture” on page 10.
• Make sure that the spray is stable. (See “Maintaining Spray Stability” on page 5.)
• Make sure that you use the correct tune values for the ion optics.
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Evaluating the System Parameters Associated with Signal Intensity
• See the diagnostics workflow chart in Figure 12 on page 23.
• Clean or change the ion transfer tube.
CAUTION Hot surface The ion transfer tube operates above 250 °C (482 °F). Allow
the ion sweep cone and the ion transfer tube to cool to room temperature
(approximately 20 minutes) before touching them. Be aware that if you remove the
ion transfer tube when it is 200 °C or higher, you might damage the end of the tube.
You do not have to vent the system to remove the ion transfer tube. For instructions, refer
to “Cleaning the API Ion Transfer Tube, Spray Cone, and Ion Sweep Cone” in Chapter 5
of the LTQ Series Hardware Manual. Also, read the precautions in “Safety Precautions” on
page xviii.
Spray Stability
Follow the procedure, “To adjust the spray stability” on page 6, to evaluate and then, if
needed, adjust the spray stability.
Manual TIC Tune
The total ion current (TIC) is the sum of the ion current intensities across the scan range in a
mass spectrum. The TIC tune is a generic tool that generates a real-time graph of the TIC as a
function of the scan number. Use the TIC manual tune to observe the signal stability and the
effects of changes to various parameters.
The TIC tune can also help diagnose a particular issue that causes signal oscillation. TIC
oscillations, as shown in Figure 14 (top, right graph), are direct scan-to-scan changes where
the peak alternates between a high and low level. If you see TIC oscillation, it might indicate
that the transfer lenses are out of calibration or that the ion trap might be contaminated; see
the diagnostics workflow chart in Figure 12 on page 23.
Figure 14 shows TIC graphs with and without oscillation, and an unstable TIC graph
without oscillation.
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Figure 14. Examples of TIC graphs (Velos Pro)
TIC
TIC with oscillation
Unstable TIC without oscillation
Upper and lower oscillation limits
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5 Diagnostics for Signal Issues
Evaluating the System Parameters Associated with Signal Intensity
 To evaluate the TIC graph
1. Set up the syringe pump to infuse a solution.
You can use the calibration solution, but it is not required for this evaluation.
2. In the Tune Plus window, click the Tune button to open the Tune dialog box.
3. Click the Manual tab, and then select the TIC option (Figure 15).
Figure 15. Tune dialog box showing the Manual page
4. Click Start.
A message box appears.
5. Click OK when you are ready to continue.
6. In the Tune Plus window, click the Display Graph View button.
7. Observe the TIC in the Graph view pane.
Figure 14 on page 26 shows examples of TIC graphs.
8. If there is TIC oscillation, do the following:
a. Follow the procedure in “Electron Multiplier Gain” on page 28.
b. Follow the procedure in “Transfer Lenses” on page 31.
c. If the oscillation persists, the ion trap or its lenses might be contaminated. Save screen
captures or save your observations to a RAW file (choose File > Save As).
IMPORTANT Only a qualified engineer from Unity Lab Services can provide
service on the ion trap.
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Diagnostics for Signal Issues
Evaluating the System Parameters Associated with Signal Intensity
Electron Multiplier Gain
The calibration check for the electron multiplier gain determines if the multipliers have
achieved the expected gain setting. The gain of the electron multiplier (EM) is the ratio of the
signal out to the signal in. The EM gain is critical to ensure that the proper number of ions
have accumulated in the ion trap and for proper quantitative performance. As the multipliers
age, you must adjust the operating voltage to maintain a fixed gain. Because the electron
multipliers age more rapidly when they are new, to ensure proper gain, calibrate the new
multipliers every 3 days for the first month or so of operation or until the multipliers’ voltages
begin to flatten out (plateau).
As the multipliers’ voltages start to flatten out, the multiplier gain changes more slowly. The
amount of time to reach the voltage plateau varies with conditions, treatment, and instrument
use. For example, electron multipliers in heavily used instruments plateau faster than
instruments that are used only occasionally.
After the multipliers’ voltages flatten out, you can run the multiplier gain calibration check
less often, for example, every 2–4 weeks. If the results of the calibration check indicate a
failure, run the actual calibrations on the Semi-Automatic page of the Calibrate dialog box.
The graph in Figure 16 shows an example of the rate of voltage change for two new electron
multipliers in an LTQ Velos mass spectrometer. In this example, approximately 28 days
passed before the voltages started to flatten out.
Figure 16. New electron multipliers’ voltages over time (LTQ Velos example, fairly continuous usage)
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Evaluating the System Parameters Associated with Signal Intensity
 To evaluate the electron multiplier gain
Note Run this calibration check, and if needed the actual calibration, once a week.
1. Set up the syringe pump to infuse the calibration solution.
2. Make sure that the tune voltages are correct (see “Tuning the Ion Optic Elements” on
page 15) and that the spray is stable (see “Maintaining Spray Stability” on page 5).
3. In the Tune Plus window, click the Calibrate button to open the Calibrate dialog box.
4. For the Mass Range, select the Normal option.
5. Click the Check tab, and then select the Electron Multiplier Gain check box under
Positive Ion Mode (Figure 17) or Negative Ion Mode, as applicable.
Do not run the electron multiplier gain for both polarities at the same time.
Figure 17. Calibrate dialog box showing the Check page (Velos Pro1)
Electron Multiplier Gain
check box (positive ion mode)
Calibration status area
1
Thermo Scientific
The Trap HCD Activation option appears only when the stand-alone Velos Pro mass spectrometer has an
activated Trap-HCD license.
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Evaluating the System Parameters Associated with Signal Intensity
6. Click Start.
A message box appears.
7. Click OK when you are ready to continue.
The calibration check starts. When it is completed, review the Result column and the
bottom status information. See the note on page 11 for an explanation of the Result
column.
8. If the calibration check fails, do the following:
a. Save a screen capture of the dialog box. (See “Reporting Unresolved Issues” on
page 51.)
b. See the diagnostics workflow chart in Figure 12 on page 23, and follow the next
procedure, To calibrate the electron multiplier gain.
 To calibrate the electron multiplier gain
1. In the Calibrate dialog box, click the Semi-Automatic tab.
2. Select the Electron Multiplier Gain check box under the appropriate polarity mode.
3. Click Start.
A message box appears.
4. Click OK when you are ready to continue.
The calibration starts. When it is completed, review the Result column and the bottom
status information. See the note on page 11 for an explanation of the Result column.
5. If the calibration fails, do the following:
a. Save a screen capture of the dialog box. (See “Reporting Unresolved Issues” on
page 51.)
b. Make sure that the ionization spray is stable. (See “Maintaining Spray Stability” on
page 5.)
c. Repeat this calibration, and then follow the procedure, “To run the ejection and
multiplier gain ratio” on page 51.
If the problem persists, contact Unity Lab Services for assistance.
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Evaluating the System Parameters Associated with Signal Intensity
Transfer Lenses
The transfer lenses calibration check determines if the ion transmission through the transfer
lenses is within tolerance. Run this check once a month (in the applicable polarity mode) or
more often if you suspect that there is charging contamination. After an actual calibration, the
efficiency of the ion transmissions is typically above 90 percent.
Calibration check results that are less than 70 percent indicate a failure of the ion transmission
efficiency. In this case, run the actual calibration on the Semi-Automatic page of the Calibrate
dialog box. If an actual calibration repeatedly fails, there might be some contamination of
components within the ion trap assembly. Contact Unity Lab Services for assistance.
 To evaluate the transfer lenses
Note Run this calibration check, and if needed the actual calibration, once a month.
1. Set up the syringe pump to infuse the calibration solution.
2. In the Tune Plus window, click the Calibrate button to open the Calibrate dialog box.
3. For the Mass Range, select the Normal option.
4. Click the Check tab, and then select the Transfer Lenses check box under the
appropriate ion mode (Figure 17 on page 29).
5. Click Start.
A message box appears.
6. Click OK when you are ready to continue.
The calibration check starts. When it is completed, review the Result column and the
bottom status information. See the note on page 11 for an explanation of the Result
column.
7. If the calibration check fails, do the following:
a. Save a screen capture of the dialog box. (See “Reporting Unresolved Issues” on
page 51.)
b. See the diagnostics workflow chart in Figure 12 on page 23, and follow the next
procedure, To calibrate the transfer lenses.
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Diagnostics for Signal Issues
Evaluating the System Parameters Associated with Signal Intensity
 To calibrate the transfer lenses
1. In the Calibrate dialog box, click the Semi-Automatic tab.
2. Select the Transfer Lenses check box under the appropriate ion mode.
3. Click Start.
A message box appears.
4. Click OK when you are ready to continue.
The calibration starts. When it is completed, review the Result column and the bottom
status information. See the note on page 11 for an explanation of the Result column.
5. If the calibration fails, repeat this calibration procedure.
If the problem persists, contact Unity Lab Services for assistance.
System Evaluation Tools
IMPORTANT If you run more than one diagnostic test at a time, the four below tests are
run in alphabetical order instead of the specified order and the data shown in the graphs is
not saved.
Run all of the following diagnostic tools2 one at a time and in the stated order:
1. Multipole Gradient Evaluation
2. Source Optics Flight Time Evaluation, on page 37
3. Multipole MP0 Flight Time Evaluation, on page 41
4. Ion Optics Charging Evaluation, on page 44
IMPORTANT This diagnostic evaluation can discharge the system. Therefore, run
this evaluation in this stated order and be aware that running this test a second time
might not show the same behavior.
5. Ejection and Multiplier Gain Ratio, on page 49
2
32
This list of system evaluation tools is only available with LTQ 2.7 SP1 and later.
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5 Diagnostics for Signal Issues
Evaluating the System Parameters Associated with Signal Intensity
 To view the list of system evaluation procedures
1. Open the Tune Plus application, and then choose Diagnostics > Diagnostics to open the
Diagnostics dialog box.
2. Click Tools, and then select System Evaluation (Figure 18).
Figure 18. Diagnostics dialog box showing the System Evaluation page (Velos Pro)
Tools button
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Diagnostics for Signal Issues
Evaluating the System Parameters Associated with Signal Intensity
Multipole Gradient Evaluation
The multipole gradient evaluation is a diagnostic tool that provides information about the
sensitivity of the system as a function of the multipole MP0–MP00 voltage gradient (see
page 15), which can help determine the condition (level of contamination) of the ion optic
elements.
This diagnostic evaluation sets the optics to their standard default settings, turns off the AGC,
and changes the MP0 offset to various preset voltages, which then changes the MP0–MP00
gradient. With each new MP0 offset value, the Tune Plus application optimizes the front lens
voltage at various mass-to-charge ratios, as shown in Figure 19.
Figure 19. Graph: signal intensity versus the front lens voltages
To determine the condition of the ion optics, review the generated real-time graph of the
normalized signal intensity versus the MP0–MP00 gradient. Example graphs that show clean
and contaminated systems are shown in Figure 20 and Figure 21 on page 36, respectively.
Loss of signal at the lower gradients (Figure 21) indicates that the optics have some level of
contamination and might possibly need cleaning when the voltage gradients become too high.
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Evaluating the System Parameters Associated with Signal Intensity
Figure 20. Graph: normalized signal intensity versus the MP0–MP00 gradient for a clean system
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Evaluating the System Parameters Associated with Signal Intensity
Figure 21. Graph: signal intensity versus the MP0–MP00 gradient for a contaminated system
Better signals at higher
MP0–MP00 gradients
Shows loss of signal at low
MP0–MP00 gradients
 To run the multipole gradient evaluation
Note If the instrument is in negative ion mode, this diagnostic test automatically sets
the mode to positive before starting.
1. Set up the syringe pump to infuse the positive calibration solution.
2. Open the System Evaluation diagnostics page (see page 33), and then select the
Multipole Gradient Evaluation check box.
3. Click Start.
A message box appears.
4. Click OK when you are ready to continue.
The multipole gradient evaluation generates a real-time graph of the signal intensity
versus the MP0–MP00 gradient (Figure 20 on page 35 and Figure 21 on page 36).
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Evaluating the System Parameters Associated with Signal Intensity
5. (Optional) Save a screen capture of the diagnostic test results and the Tune Plus window.
6. Follow the procedure in the next section.
Source Optics Flight Time Evaluation
The source optics flight time evaluation is a diagnostic tool that measures the flight time of
ions with various mass-to-charge ratios from the exit lens through multipole MP0 (Figure 22).
The flight time can help determine the condition (level of contamination) of the ion optics.
For the LTQ Velos mass spectrometer and LTQ Orbitrap Velos system, this evaluation
includes the flight time through the S-lens.
Figure 22. Ion optics showing the test area for the source optics flight time evaluation
(LTQ Velos only)
Test area
Charging, and other issues, can cause the flight times to be long, especially at low
MP0–MP00 gradients.
The following figures display different graphs for this diagnostic test:
• Figure 23—Show fast flight times to reach the peak heights, which indicate no or low
levels of contamination.
• Figure 24 on page 39—Shows a lightly used instrument.
• Figure 25 on page 40—Shows a heavily used instrument.
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Diagnostics for Signal Issues
Evaluating the System Parameters Associated with Signal Intensity
Figure 23. Example graphs of the MP00/L0/MP0 flight times (Velos Pro)
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Evaluating the System Parameters Associated with Signal Intensity
Figure 24. Graph of the source optics flight time evaluation (Velos Pro, light use)
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Diagnostics for Signal Issues
Evaluating the System Parameters Associated with Signal Intensity
Figure 25. Graph of the source optics flight time evaluation (Velos Pro, heavy use)
 To run the source optics flight time evaluation
Note If the instrument is in negative ion mode, this diagnostic test automatically sets
the mode to positive before starting.
1. Set up the syringe pump to infuse the positive calibration solution.
2. Open the System Evaluation diagnostics page (see page 33), and then select the Source
Optics Flight Time Evaluation check box.
3. Click Start.
A message box appears.
4. Click OK when you are ready to continue.
This evaluation generates a real-time graph of the signal intensity at various
mass-to-charge ratios as a function of time delay (Figure 23 on page 38).
5. (Optional) Save a screen capture of the diagnostic test results and the Tune Plus window.
6. Follow the procedure in the next section.
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5 Diagnostics for Signal Issues
Evaluating the System Parameters Associated with Signal Intensity
Multipole MP0 Flight Time Evaluation
The multipole MP0 flight time evaluation is a diagnostic tool that measures the flight time of
various mass ions from lens L0 through multipole MP0 (Figure 26), which can help
determine the condition (level of contamination) of MP0.
Figure 26. Ion optics showing the test area for the multipole MP0 flight time evaluation
Test area
Charging, and other issues, can cause the flight times to be long, especially at low
MP0–MP00 gradients.
The following figures display different graphs for this diagnostic test:
• Figure 27—Shows fast flight times to reach the peak heights, which indicate no or low
levels of contamination.
• Figure 28—Shows a lightly used instrument.
• Figure 29 on page 43—Shows a heavily used instrument.
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Diagnostics for Signal Issues
Evaluating the System Parameters Associated with Signal Intensity
Figure 27. Example graphs of the multipole MP0 flight time (Velos Pro)
Figure 28. Graph of the multipole MP0 flight time evaluation (Velos Pro, light use)
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5 Diagnostics for Signal Issues
Evaluating the System Parameters Associated with Signal Intensity
Figure 29. Graph of the multipole MP0 flight time evaluation (Velos Pro, heavy use)
 To run the multipole MP0 flight time evaluation
Note If the instrument is in negative ion mode, this diagnostic test automatically sets
the mode to positive before starting. Be aware that changing the polarity can affect
any charging conditions such that the results of subsequent diagnostic tests might be
affected. Therefore, the diagnostic tests that you conduct after this one might not
show the symptoms of charging.
1. Set up the syringe pump to infuse the positive calibration solution.
2. Open the System Evaluation diagnostics page (see page 33), and then select the
Multipole MP0 Flight Time Evaluation check box.
3. Click Start.
A message box appears.
4. Click OK when you are ready to continue.
This evaluation generates a real-time graph of the signal intensity at various
mass-to-charge ratios as a function of the time delay (Figure 27 on page 42).
5. (Optional) Save a screen capture of the diagnostic test results and the Tune Plus window.
6. Follow the procedure in the next section.
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Diagnostics for Signal Issues
Evaluating the System Parameters Associated with Signal Intensity
Ion Optics Charging Evaluation
The ion optics charging evaluation is a diagnostic tool that sequentially tests each of the ion
optic elements, from the exit lens up to and including the center lens (Figure 30 [center lens is
not shown]), to determine if any specific optical elements might be charging and, therefore,
need cleaning.
Figure 30. Ion optics showing the test area for the ion optics charging evaluation
Test area (partial shown)
This diagnostic evaluation uses the Turbo Scan rate to help speed up the evaluation. At the
start of the test, the graph plots the TIC in positive ion mode for 30 seconds, the instrument
changes to negative mode and transmits a negative ion beam (100 ms injection time) for
80 seconds to the optical element being tested, and then the instrument changes back to
positive mode before again plotting the positive TIC for 30 seconds.
If an optical element has a charge, the top graph in the Tune Plus Graph view shows an
intensity spike after the element’s exposure to the negative ions. As you review the graph,
notice any spikes that indicate which elements you might have to clean. The positive
ion-to-negative ion flux ratio is displayed in the graph because this ratio can affect the results
of the evaluation and, therefore, should be taken into account.
A high flux ratio is due to low negative ion flux and a low negative ion flux is due to the
following:
• The multiplier gain and transfer lenses have never been calibrated in negative ion mode.
• The instrument has never been tuned for negative ions.
• The sheath gas is not appropriate for negative ion mode.
The bottom Tune Plus graph shows the ratio of each optical element’s signal before and after
being exposed to the negative ions as a function of the mass-to-charge ratio. Because charging
effects can be very dependent on the mass-to-charge ratio, this graph provides a very sensitive
test of any potential optic issues. Signal ratios above the reference threshold of 2.0 indicate
significant charging effects and further indicate the need to clean the element.
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5 Diagnostics for Signal Issues
Evaluating the System Parameters Associated with Signal Intensity
The following figures display different graphs for this diagnostic test:
• Figure 31—Shows a clean system.
• Figure 32—Shows a contaminated MP00 rf lens.
• Figure 33 on page 47—Shows a contaminated MP0.
• Figure 34 on page 48—Shows a contaminated exit lens.
Figure 31. Graphs of the ion optics charging evaluation for a clean system (Velos Pro)
The x axis represents the cumulative mass
range 0–2000 for each ion optic element.
Thermo Scientific
Threshold
set at 2.0
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Diagnostics for Signal Issues
Evaluating the System Parameters Associated with Signal Intensity
Figure 32. Graphs of the ion optics charging evaluation showing an example of a contaminated MP00 rf lens
Indicates charging
of MP00.
Unstable signals
Pre/post TIC signal ratio for MP00
is above the set threshold.
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5 Diagnostics for Signal Issues
Evaluating the System Parameters Associated with Signal Intensity
Figure 33. Graphs of the ion optics charging evaluation showing an example of a contaminated MP0
Indicates charging
of MP0.
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Diagnostics for Signal Issues
Evaluating the System Parameters Associated with Signal Intensity
Figure 34. Graphs of the ion optics charging evaluation showing an example of a contaminated exit lens
Indicates charging of the exit lens.
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5 Diagnostics for Signal Issues
Evaluating the System Parameters Associated with Signal Intensity
 To run the ion optics charging evaluation
Note If the instrument is in negative ion mode, this diagnostic test automatically sets
the mode to positive before starting.
1. Set up the syringe pump to infuse the positive calibration solution.
2. Open the System Evaluation diagnostics page (see page 33), and then select the
Ion Optics Charging Evaluation check box.
3. Click Start.
A message box appears.
4. Click OK when you are ready to continue.
This evaluation generates two graphs. The top graph is a real-time graph of the total ion
current (TIC) before and after the various ion optical elements are exposed to a negative
ion beam (see the description on page 44). The bottom graph shows the signal intensity
ratio (before and after negative ion exposure) as a function of the mass-to-charge ratio for
each ion optics element (Figure 31 on page 45 through Figure 34 on page 48).
5. (Optional) Save a screen capture of the diagnostic test results and the Tune Plus window.
6. Follow the procedure in the next section.
Ejection and Multiplier Gain Ratio
The ejection and multiplier gain ratio is a diagnostic tool that measures the ratio of the signals
produced by the ions that are ejected out of one side of the ion trap compared to the other
side. This signal ratio can indicate an asymmetry of the ejection slot geometry, a blockage of
the slot by foreign material, or an electron multiplier gain mismatch.
This diagnostic evaluation independently measures the signal intensity for various masses on
the detectors on both sides of the ion trap, calculates the ratio of the signal, and then generates
a real-time graph as a function of the mass-to-charge ratio. The top graph in Figure 35 shows
multiple measurements of the signal (x axis) to each detector, and the bottom graph shows the
signal ratio as a function of the mass-to-charge ratio at nearly 1.0 for all points.
Mismatches in signal are often due to ion trap geometries or contaminated slots, which cause
asymmetric ejection even at an optimum resonance ejection phase. To eliminate a gain
mismatch as the cause of a signal ratio failure, Thermo Fisher Scientific recommends that you
run this diagnostic evaluation after you run the multiplier gain calibration.
Note The ejection and multiplier gain ratio is no longer a part of the multiplier gain
calibration check.
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Diagnostics for Signal Issues
Evaluating the System Parameters Associated with Signal Intensity
Figure 35. Graphs of the ejection and multiplier gain ratio evaluation (Velos Pro)
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Diagnostics for Signal Issues
Reporting Unresolved Issues
 To run the ejection and multiplier gain ratio
Note This diagnostic procedure runs in either positive or negative ion mode.
1. Set up the syringe pump to infuse the calibration solution.
2. Open the System Evaluation diagnostics page (see page 33), and then select the
Ejection and Multiplier Gain Ratio check box.
3. Click Start.
A message box appears.
4. Click OK when you are ready to continue.
This evaluation generates a real-time graph (Figure 35 on page 50, lower graph) of the
signal intensity ratio as a function of the mass-to-charge ratios.
5. (Optional) Save a screen capture of the diagnostic test results and the Tune Plus window.
6. When you are ready, click OK to close the dialog box.
This completes the recommended diagnostic testing. You can now begin to resolve any found
issues, as recommended in this manual, and clean components as necessary.
Reporting Unresolved Issues
Be sure to report any tune, calibration, or diagnostic test failures to Unity Lab Services.
 To report unresolved diagnostic issues
1. Take screen captures of the failing results.
You can use your computer keyboard (PRINT SCREEN for the entire desktop or
ALT+PRINT SCREEN for only the active window) or use the Snipping Tool feature
provided with Microsoft Windows 7 and later.
2. Copy all of the text generated in the Status or Testing area of the applicable dialog box.
3. Open a text editor and paste the Tune Plus images and text into a new document.
4. Fully describe the problem, and then save the document.
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Diagnostics for Signal Issues
Reporting Unresolved Issues
5. Send an e-mail message to Unity Lab Services with the following:
• Attachments:
–
The text document that contains the screen captures, readback text, and
description of the problem. Also state when the problem started and its duration.
–
Any supportive RAW files that demonstrate the problem.
–
The last few LOG files that are stored in the data system computer at:
C:\Thermo\Instruments\LTQ\system\logs
• Instrument information:
–
Model name (for example, Velos Pro or Orbitrap Elite)
–
Serial number (If you have an Orbitrap system, provide the serial numbers for
both the front and back instruments.)
The serial number label is located on the back of each instrument. The front
instrument has a second label located on the inside chassis behind the front door.
• Your contact information
• Your request for service
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6
Cleaning the Ion Optics
This chapter describes how to clean the exit lens and S-lens from the ion source interface;
lens L0 from the MP00 rf lens assembly; and the split gate lens, lens L1, and multipoles MP0
and MP1 from the MP0 and MP1 ion guides.
For optimal results, follow these guidelines when performing the procedures in this chapter:
• Proceed methodically.
• Always wear a new pair of lint- and powder-free gloves when handling internal
components. 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 surface.
• Never overtighten a screw or use excessive force.
IMPORTANT
• Put on a new pair of lint- and powder-free gloves before starting each removal,
cleaning, and reinstallation procedure.
• Make sure that you do not introduce any scratches or surface abrasions while
handling the ion optic components. Even small scratches can affect performance if
they are close to the ion flight path. Avoid using tools, such as pliers, that might
scratch these components.
Contents
• Preparing the Work Area
• Tools and Supplies
• Ion Optics
• Cleaning the Exit Lens and S-Lens
• Cleaning Lens L0
• Cleaning the Split Gate Lens, Lens L1, and Multipoles MP0 and MP1
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Cleaning the Ion Optics
Preparing the Work Area
Preparing the Work Area
 To prepare the work area before removing the mass spectrometer components
Do the following:
• Make sure that the surrounding area is neat and clean.
• Prepare a clean work surface by covering the area with lint-free paper or a large sheet
of clean aluminum foil.
• Have nearby the necessary tools, supplies, and replacement parts (when applicable).
Tools and Supplies
The mass spectrometer requires very few tools to perform routine maintenance procedures.
Table 3 lists the necessary tools, equipment, and chemicals for maintaining the instrument.
(Two of the tools are already in the kits.) In addition, you can use the contents of the
PM Cleaning Kit (P/N 97455-62051).
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). The MSDSs must be freely available to lab personnel to
examine at any time. MSDSs 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 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.
Table 3. Tools, equipment, and chemicals (Sheet 1 of 2)
Description
Part number
Tools
54
Fused-silica cutting tool
–
Hex ball driver, 3 mm
00725-00048a
Hex driver (or ball driver), 1/4 in.
–
Hex ball driver set: 0.050 in., 1/16 in., 5/64 in.,
3/32 in., 7/64 in., 1/8 in., 9/64 in., 5/32 in., and
3/16 in.
00025-03025
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Cleaning the Ion Optics
Tools and Supplies
Table 3. Tools, equipment, and chemicals (Sheet 2 of 2)
Description
Part number
Ion transfer tube removal tool
70111-20258b
Screwdriver, Phillips #2
–
Screwdrivers, slotted: large and small
–
Wrenches, open-end: 5/16 in., 3/8 in., and 1/2 in.
–
Equipment
Aluminum foil, heavy gaugec
Fisher Scientific: 01-213-104
Chamois-tipped swabs
00301-01912
Cotton-tipped applicators
Fisher Scientific: A030102000
Gloves, lint-free and powder-free
Fisher Scientific:
• 19-120-2947A (size small)
• 19-120-2947B (size medium)
• 19-120-2947C (size large)
• 19-120-2947D (size X-large)
Thermo Scientific:
• 23827-0008 (size medium)
• 23827-0009 (size large)
Graduated cylinder or beaker (for use with methanol)
–
Lint-free industrial tissues
–
Magnification device
–
MICRO-MESH™ polishing swab, 6000 grit (light
purple color), 2.25 in. long
00301-01911
Sonicator
–
Chemicals
Clean, dry, nitrogen gas
–
Detergent (for example, Liquinox™)
(Liquinox) Fisher Scientific:
• 50-821-299 (1 quart)
• 50-821-298 (1 gallon)
Thermo Scientific
Methanol, LC/MS-grade
Fisher Scientific: A456-1
Water, LC/MS-grade
Fisher Scientific: W6-1
Water, tap
–
a
Provided in the HESI-II Probe Kit
b
Provided in the MS Accessory Kit
c
Rinse each sheet with acetone before use.
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Cleaning the Ion Optics
Ion Optics
Ion Optics
Use the procedures in this section to clean the S-lens, exit lens, lens L0, lens L1, split gate lens,
and multipoles MP0 and MP1. These components are located from the beginning of the ion
path up until the front lens, as shown in Figure 36. For instructions about how to remove
these components from the LTQ Velos or Velos Pro mass spectrometer, refer to Chapter 5 in
the LTQ Series Hardware Manual.
Note Before you continue, read the precautions in “Safety Precautions” on page xviii.
CAUTION If the diagnostic results indicate problems with the front lens or ion trap,
contact Unity Lab Services. To prevent accidental damage to the ion trap, do not attempt
to service these areas yourself.
Figure 36. Ion path through the Velos Pro ion optics (illustrated side view)
Ion transfer
tube
S-lens
Exit lens
Lens L1
Lens L0
Split gate lens
Front lens
Ion sweep cone
over the spray cone
MP00 rf lens
(also called MP00)
MP0 (Velos Pro shown)
Customer and Thermo Fisher service area
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MP1
High pressure
ion trap (partial)
Thermo Fisher
service area only
Thermo Scientific
6 Cleaning the Ion Optics
Cleaning the Exit Lens and S-Lens
Cleaning the Exit Lens and S-Lens
When directed by the diagnostic results, follow the procedure in this section to clean the exit
lens or S-lens. (To view a 3-D model of the exit lens and S-lens, click Figure 37.)
For instructions about how to remove these components from the ion source interface, refer
to “Cleaning the Exit Lens and S-Lens on the Velos Pro” in Chapter 5 of the LTQ Series
Hardware Manual.
Note Before you continue, read the precautions in “Safety Precautions” on page xviii.
Figure 37. Exit lens and S-lens removed from the ion source interface cage
S-lens
Exit lens
Ion source
interface cage
You need the following tools and supplies to remove and clean these components.
Tools
Supplies
Ion transfer tube removal tool
Chamois-tipped swabs
Magnification device
Detergent (for example, Liquinox)
Slotted screwdriver, small
Gloves, lint- and powder-free
Sonicator
Lint-free industrial tissues
(Optional) Soft toothbrush (or similar tool)
Methanol, LC/MS-grade
(Optional) Tweezers, plastic (or similar tool) Micro-Mesh polishing swab, 6000 grit
Thermo Scientific
(Optional) Wrenches, open-ended, large
Nitrogen gas
–
Water, LC/MS-grade
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Cleaning the Exit Lens and S-Lens
 To clean the exit lens and S-lens
CAUTION Do not clean the exit lens or S-lens with abrasives, acidic or caustic
substances, or detergents not stated in this chapter.
IMPORTANT
Always use LC/MS-grade methanol and LC/MS-grade water.
1. Using a magnification device, inspect the exit lens and S-lens for any lint, particulates,
and sample buildup or coatings.
2. For 10 minutes, sonicate the components in either a 50:50 solution of methanol/water or
a 1% solution of Liquinox in water. If a sonicator is not available, do the following:
a. To clean the exit lens, use a soft toothbrush with a 1% solution of Liquinox in water.
b. To clean the S-lens, use chamois-tipped swabs with a 1% solution of Liquinox in
water. To clean the areas that you cannot reach with the chamois-tipped swab, use the
6000 grit Micro-Mesh polishing swabs.
3. For the exit lens, clean the bore by using the 6000 grit Micro-Mesh polishing swabs.
4. Rinse the components thoroughly with water.
5. Sonicate the components in water for 10 minutes.
6. Sonicate the components in methanol for 10 minutes.
7. Rinse the components with methanol.
8. Dry the components with nitrogen gas to make sure that the solvent evaporates.
9. Using a magnification device, inspect the components for any residual lint or particulates.
Note Inspect the orifices to confirm that no lint or particulates are present in the bore
of the orifices. Use plastic tweezers or a similar tool to remove any lint or particulate.
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Cleaning the Ion Optics
Cleaning Lens L0
Cleaning Lens L0
When directed by the diagnostic results, follow the procedure in this section to clean lens L0.
(To view a 3-D model of lens L0, click Figure 38.)
For instructions about how to remove lens L0 from the outer cage and MP00 rf lens assembly,
refer to “MP00 RF Lens Maintenance” in Chapter 5 of the LTQ Series Hardware Manual.
Note Before you continue, read the precautions in “Safety Precautions” on page xviii.
Figure 38. Lens L0 removed from the MP00 rf lens assembly
Outer cage
Lens L0
MP00 rf lens
You need the following tools and supplies to remove and clean this component.
Thermo Scientific
Tools
Supplies
5/32 in. hex ball driver
Chamois-tipped swabs
Phillips screwdriver
Detergent (for example, Liquinox)
Magnification device
Gloves, lint- and powder-free
Slotted screwdriver
Graduated cylinder (for use with methanol)
Sonicator
Lint-free industrial tissues
–
Methanol, LC/MS-grade
–
Micro-Mesh polishing swab, 6000 grit
–
Nitrogen gas
–
Water, LC/MS-grade and tap
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Cleaning the Split Gate Lens, Lens L1, and Multipoles MP0 and MP1
 To clean lens L0
IMPORTANT
Always use LC/MS-grade methanol and LC/MS-grade water.
1. Using a magnification device, inspect the component for any lint, particulates, and
sample buildup or coatings.
2. For 10 minutes, sonicate the component in either a 50:50 solution of methanol/water or
a 1% solution of Liquinox in water.
3. Using the 6000 grit Micro-Mesh polishing swabs, clean the bore in the lens.
4. Rinse the component thoroughly with water.
5. Sonicate the component in water for 10 minutes.
6. Sonicate the component in methanol for 10 minutes.
7. Rinse the component with methanol.
8. Dry the component with nitrogen gas to make sure that all the solvent evaporates.
9. Using a magnification device, inspect the component for any lint or particulates.
Note Inspect the orifice to confirm that no lint or particulates are present in the bore
of the orifice. Use plastic tweezers or a similar tool to remove the lint or particulate.
Cleaning the Split Gate Lens, Lens L1, and Multipoles MP0 and MP1
When directed by the diagnostic results, follow the procedures in this section to clean the
split gate lens, lens L1, or multipoles MP0 and MP1. (To view a 3-D model of the MP0 and
MP1 ion guides mounted on the vacuum manifold’s top cover plate, click Figure 39.)
For instructions about how to remove these components from the vacuum manifold’s top
cover plate, refer to “MP0 and MP1 Ion Guides Maintenance” in Chapter 5 of the LTQ Series
Hardware Manual.
Note Before you continue, read the precautions in “Safety Precautions” on page xviii.
IMPORTANT After you remove the top cover plate from the vacuum manifold, cover
the opening with a large, lint-free tissue or a large, clean sheet of aluminum foil to keep
the ion trap clean.
Follow these procedures, as applicable:
• To clean multipoles MP0 and MP1, on page 62
• To clean the split gate lens and lens L1, on page 63
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6 Cleaning the Ion Optics
Cleaning the Split Gate Lens, Lens L1, and Multipoles MP0 and MP1
Figure 39. MP0 and MP1 ion guides for the Velos Pro
MP1
Split gate lens
Lens L1
MP0
Vacuum
manifold’s top
cover plate
You need the following tools and supplies to remove and clean these components.
Tools
Supplies
1/4 in. hex driver
Chamois-tipped swabs
5/64 in. hex ball driver
Detergent (for example, Liquinox)
Magnification device
Gloves, lint- and powder-free
Phillips screwdriver
Graduated cylinder (for use with methanol)
Sonicator
Lint-free industrial tissues
(Optional) Tweezers, plastic (or similar tool) Methanol, LC/MS-grade
Thermo Scientific
–
Nitrogen gas
–
Water, LC/MS-grade and tap
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Cleaning the Ion Optics
Cleaning the Split Gate Lens, Lens L1, and Multipoles MP0 and MP1
 To clean multipoles MP0 and MP1
IMPORTANT
Always use LC/MS-grade methanol and LC/MS-grade water.
1. Using a magnification device, inspect the components for any lint, particulates, and
sample buildup or coatings.
2. Sonicate the components in a 1% solution of Liquinox in water for 10 minutes.
3. Soak chamois-tipped swabs in a 1% solution of Liquinox in water, and then clean the
components.
Because multipole MP0 has a bent design, the areas of ion collisions on the inner surface
of the rods are more concentrated after the multipole changes direction. When cleaning
MP0, spend extra time at the areas shown in Figure 40.
Figure 40. Common contamination areas on the inner surface areas of MP0 (Velos Pro)
After the downward bend (top rod)
After the upward bend
(bottom rod)
Ion path
4. Rinse the components thoroughly with water.
5. Sonicate the components in water for 10 minutes.
6. Sonicate the components in methanol for 10 minutes.
7. Soak chamois-tipped swabs in methanol, and then clean the components.
8. Rinse the components with methanol.
9. Dry the components with nitrogen gas to make sure that all the solvent evaporates.
10. Using a magnification device, inspect the components for any residual lint or particulates.
Note Inspect the inside surfaces and edges to confirm that no lint or particulates are
present. Use plastic tweezers or a similar tool to remove the lint or particulate.
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6 Cleaning the Ion Optics
Cleaning the Split Gate Lens, Lens L1, and Multipoles MP0 and MP1
 To clean the split gate lens and lens L1
IMPORTANT
Always use LC/MS-grade methanol and LC/MS-grade water.
1. Using a magnification device, inspect the components for any lint, particulates, and
sample buildup or coatings.
Note After use, the surfaces can be discolored, which is normal and not to be
confused with sample buildup or coatings.
2. Soak lint-free tissues or chamois-tipped swabs in a 50:50 solution of methanol/water, and
then clean the components.
3. Sonicate the components in methanol for 10 minutes.
Note If using buffers or salt solutions in the mass spectrometer, you might need to
use an aqueous solution for cleaning. If using an aqueous solution, flush the items
with LC/MS-grade water and then with LC/MS-grade methanol.
4. Dry the components with nitrogen gas to make sure that all the solvent evaporates.
5. Using a magnification device, inspect the components for any residual lint or particulates.
Note Inspect the inside surfaces and edges to confirm that no lint or particulates are
present. Use plastic tweezers or a similar tool to remove the lint or particulate.
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7
Orbitrap Systems
This chapter provides additional information for achieving peak performance from the hybrid
Orbitrap systems.
Contents
• Additional Calibrations for the Orbitrap System
• Checking and Improving the Mass Accuracy
Additional Calibrations for the Orbitrap System
In addition to running the calibration checks for the Electron Multiplier Gain and Transfer
Lenses, you should run two or three more semi-automatic calibrations, depending on which
Orbitrap model you have (see Table 4 on page 67).
IMPORTANT
Run these calibrations once per week as applicable for your model.
• pAGC Scaling
• Mass Calibration
• Advanced Signal Processing, on page 67
pAGC Scaling
The predictive Automatic Gain Control (pAGC) predicts the injection time for precursor ions
based on its relative signal and the injection time of the previous full MS scan. The pAGC
scaling calibration generates a real-time graph (Figure 41) of the pAGC scaling factor versus
the base 10 logarithm of the target value, written as “lg(target).” The graph starts from a target
of 1 × 104 and ends with a target of 5 × 106, which scales the abundance (ion trap
[IT])/abundance (Fourier transform [FT]). (The red curve in the figure is a smoothed version
of the blue curve.)
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Orbitrap Systems
Additional Calibrations for the Orbitrap System
Note the following about the pAGC scaling calibration:
• It eliminates time spent with a prescan execution.
• The injection time for data-dependent scans is predicted based on the abundance of the
precursor ions in the master scan, which can be an IT or FT full MS scan.
• Before you run LC-MS/MS experiments by using pAGC, you must scale the FT
abundance.
• The scaling value at lg(6) (target is 1 × 106) should be in the range of 60 to 100.
Figure 41. Graph: pAGC scale factor versus lg(target)
Mass Calibration
The mass calibration performs a mass calibration of the Orbitrap mass analyzer.
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7 Orbitrap Systems
Additional Calibrations for the Orbitrap System
Advanced Signal Processing
The Orbitrap Elite system includes Advanced Signal Processing (ASiP). ASiP uses the two
types of information provided by the Fourier transformations: the magnitude and the phase
component. For the LTQ Orbitrap Velos and Orbitrap Velos Pro hybrid systems, the phase
information is not used, only the magnitude information is used. However, for the Orbitrap
Elite with the ASiP calibration, the resolving power increases by a factor of approximately 2.
To use phase information to enhance resolution, all of the ions must have the same phase,
which occurs when the ions are injected into the hybrid Orbitrap. Therefore, the
synchronization of the injection and detection of ions is the critical step. With the Orbitrap
Elite, the injection of the ions from the C-trap into the Orbitrap mass analyzer and the start of
the transient recording is synchronized.
The start time of the transient recording is very close to zero but not exactly. This inaccuracy
is in the range of tens of nanoseconds and comes from, for example, a time-of-flight effect
during injection and delays in the electronics. Because the exact start time is unknown, the
ASiP calibration extrapolates backwards to time zero and then gives you the estimated start
time and initial phase.
Calibrating the Orbitrap System
Note Follow this procedure once a week.
 To calibrate the Orbitrap system
1. Set up the syringe pump to infuse the calibration solution.
2. In the Tune Plus window, click the Calibrate button to open the Calibrate dialog box.
3. For the Mass Range, select the Normal option.
4. Click the Semi-Automatic tab, and then under the appropriate ion mode select the
applicable check boxes for your model as listed in Table 4.
Figure 42 lists the applicable calibrations for the various models. For the Orbitrap Elite
system, when you select the Mass Calibration check box, the Advanced Signal Processing
check box is automatically selected.
Table 4. Semi-automatic calibrations for the hybrid Orbitrap systems
LTQ Orbitrap Velos and
Orbitrap Velos Pro
Orbitrap Elite
pAGC Scaling


Mass Calibration


Semi-automatic calibration
Advanced Signal Processing
Thermo Scientific

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Checking and Improving the Mass Accuracy
Figure 42. Calibrate dialog box showing the Semi-Automatic page (Orbitrap systems)
Select the applicable
calibrations for the system.
5. Click Start.
The following message appears: Please ensure that the syringe pump is full.
6. Click OK.
The calibration starts. When it is completed, review the Result column and the bottom
status information. See the note on page 11 for an explanation of the Result column.
7. If the calibration fails, repeat this calibration procedure.
If the problem persists, contact Unity Lab Services for assistance.
Checking and Improving the Mass Accuracy
This section provides a few tips for checking and improving the mass accuracy of an Orbitrap
spectrum.
• Chemical Background Ions
• Scatter Plot in Thermo Proteome Discoverer
• Lock Masses and Lock Mass Abundance, on page 69
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Checking and Improving the Mass Accuracy
Chemical Background Ions
Check the mass accuracy of the known chemical background ions. If their mass accuracy is
acceptable, the mass accuracy of the analyte ions are also acceptable.
Scatter Plot in Thermo Proteome Discoverer
If you are using the Thermo Proteome Discoverer™ application for peptide and protein mass
spectrometry analyses, open and display the Report Item Distribution chart as a scatter plot.
For instructions, refer to Chapter 6, “Interpreting Search Results,” in the Proteome Discoverer
User Guide.
The average mass accuracy in the example plot shown in Figure 43 is –0.19 ppm with a
standard deviation of 0.81 ppm. In this example, the plot shows both very high accuracy and
precision due to the on-the-fly recalibration by using the lock mass option. In general, if the
scatter plot points are significantly off-center to either side, run an FT mass calibration.
Figure 43. Report Item Distribution chart’s scatter plot1 (example with lock mass correction)
Lock Masses and Lock Mass Abundance
Thermo Fisher Scientific recommends that you use a lock mass to improve mass accuracy and
precision.
• Lock Masses
• FT Lock Mass Abundance, on page 72
1
Thermo Scientific
Generated with the Mascot™ search engine and the Thermo Proteome Discoverer application
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Lock Masses
You can use chemical background ions as lock masses in the spectrum for the mass
spectrometer to use as references for internal mass calibration. When you specify lock masses
in the Lock Masses dialog box, you improve both the mass accuracy and precision of the mass
measurements. If you do not specify any lock masses, the instrument uses the external mass
calibration. Therefore, regardless of whether you specify lock masses, you must also externally
calibrate the instrument.
When there are analytes with high abundant signal intensities, the lock mass ions can be
suppressed and, therefore, not present in the spectrum. If the instrument does not find the
lock mass in one FTMS full scan, it applies the correction from a previous scan where the lock
mass was found. The system then keeps this correction until the lock mass is found again in
the spectrum. Using the correction is advisable because the slow drift of the Orbitrap
electronics causes the drift of the mass accuracy of the Orbitrap mass analyzer. For example, at
the beginning of a liquid chromatography (LC) run, background ions such as m/z 445
(polysiloxane) are present, which the instrument can use as the lock mass.
When you set the lock mass abundance to a value greater than zero percent, the lock mass is
artificially mixed into the spectrum.
• If no lock masses are found in the full spectrum, the instrument tries to improve the
abundance of the lock mass by performing additional SIM injections of the specified lock
mass.
• If the given lock mass cannot be found in the spectrum because the instrument runs in
MSn mode or as a SIM scan type, the instrument adds the lock mass by using SIM
injections.
In either situation, you can use lock masses for all FTMS scan types and varying lock mass
abundances. All that is required is enabling mass locking and specifying the list of reference
mass-to-charge ratios.
 To define a scan with mass locking
1. In the Tune Plus window, click the Define Scan button to open the Define Scan
dialog box.
2. Under Scan Description, in the Analyzer list, select FTMS.
3. Under Locking, select the On check box (Figure 44).
The locking feature is available with the FTMS analyzer only.
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Figure 44. Define Scan dialog box (Orbitrap Elite, partial)
Locking area on the
Define Scan dialog box
4. Press Masses to open the Lock Masses dialog box (Figure 45).
Figure 45. Lock Masses dialog box
5. Enter one or more masses on the Pos or Neg page (as appropriate for the experiment), and
then click OK.
6. In the Define Scan dialog box, set the remaining parameters to define the scan.
For additional information, refer to the getting started guide for your Orbitrap system.
7. Click OK.
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FT Lock Mass Abundance
You can find the setting for the FT Lockmass Abundance on the Set Device page under Tools
in the Diagnostics dialog box (Figure 46). For methods with FTMS selected as the detector of
the fragment ions (Figure 44 on page 71) and with the lock mass abundance set to zero
percent, the system uses the lock mass correction from the full Orbitrap FTMS scan.
When you set the lock mass abundance to greater than zero percent, the instrument performs
additional SIM scans to increase the signal of the lock mass ions. For LTQ 2.7 and later, the
default lock mass abundance value is zero percent.
Tip For best results, Thermo Fisher Scientific recommends that you use the lock mass
abundance value of zero percent.
 To set the FT lock mass abundance
1. In the Tune Plus window, choose Diagnostics > Diagnostics, click Tools, and then select
Set Device.
2. Select FT Lockmass Abundance (%) (Figure 46).
Figure 46. Diagnostics dialog box showing the Set Device page
3. Make sure that the Value box is set to 0, and then click Set.
The default lock mass abundance value is 0%.
4. Click OK.
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Troubleshooting
Table 5 lists some problems that might occur with the mass spectrometer and their possible
solutions.
Table 5. Troubleshooting solutions (Sheet 1 of 2)
Problem
Oscillating signal intensity
Possible solutions
• Make sure that the spray is stable (see “Maintaining Spray Stability” on
page 5).
• If the problem persists, do the following:
Loss of signal intensity
–
Run the Transfer Efficiency Evaluation diagnostic.
–
If the evaluation fails, run the Transfer Lenses calibration for the
appropriate ion mode.
–
If the calibration consistently fails, contact Unity Lab Services for
assistance. See “Reporting Unresolved Issues” on page 51.
• Make sure that you pumped down the instrument under vacuum for at least
15 continuous hours since the last time you vented the instrument. Failure
to do so might cause incorrect calibration.
• Make sure that the ion transfer tube is not restricted; clean or replace it if
needed.
• Check the tune. Make sure that the MP0–MP00 gradient is at least –5.5 V.
• Check the signal by using direct infusion of the calibration solution.
• Check the electron multiplier gain calibration.
• Run the following charging diagnosticsa (see page 32), and then clean the
ion optics as directed by the results:
a. Multipole Gradient Evaluation
b. Source Optics Flight Time Evaluation
c. Multipole MP0 Flight Time Evaluation
d. Ion Optics Charging Evaluation (run last)
• If the problem persists, check the LC system.
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Troubleshooting
Table 5. Troubleshooting solutions (Sheet 2 of 2)
Problem
Complete loss of signal
Possible solutions
• In the Tune Plus application, check the Status View for any faults. If
necessary, run the appropriate diagnostics tests.
• Make sure that the ion transfer tube is not restricted; clean or replace it if
needed.
• Check the source spray conditions by using direct infusion of the calibration
solution.
• Open a different tune file because the current tune file might have become
corrupt (see page 14).
• Press the reset button on the mass spectrometer (refer to Chapter 3 in the
LTQ Series Hardware Manual).
• If the problem persists, check the LC system.
Failure of the electron multiplier
gain calibration—the signal is too
weak
• Make sure that the spray is stable (see “Maintaining Spray Stability” on
page 5).
• Make sure that the calibration mixture (calmix) is fresh and that you have
the correct solution for either the stand-alone or Orbitrap instrument
(www.thermo.com/pierce).
–
Stand-alone: Pierce LTQ Velos ESI Positive Ion Calibration Solution
(P/N 88323)
–
Orbitrap: Pierce ESI Negative Ion Calibration Solution (P/N 88324)
• Manually set the multiplier gain to a higher voltage through the Set Device
page on the Diagnostics dialog box, and then repeat the calibration.
• If the gain is above 2500 V, contact Unity Lab Services to replace the
electron multipliers.
Failure of the transfer lenses
calibration
• Repeat the transfer lenses calibration in the mode that failed.
Failure of the ejection and
multiplier gain evaluation
• Make sure that the spray is stable (see “Maintaining Spray Stability” on
page 5).
• If the problem persists, contact Unity Lab Services for assistance.
• Repeat the electron multiplier gain calibration.
• If the problem persists, contact Unity Lab Services for assistance.
a
Available with LTQ 2.7 SP1 or later
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A
Online Resources
This appendix provides additional online resources.
Contents
• Planet Orbitrap
• San Jose Product Support Engineering
• Online Product Information
Planet Orbitrap
Visit the Thermo Scientific Web site dedicated to Orbitrap systems:
PlanetOrbitrap.com
San Jose Product Support Engineering
The San Jose Product Support Engineering Web site contains factory communications,
documentation, and answers to frequently asked questions (FAQs). You must register and log
in to access some of these areas.
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A
Online Resources
Online Product Information
Online Product Information
Item
Ion sources, various
Consumables
Web site
Ion Max
Thermo Scientific
EASY-Spray
Planet Orbitrap and Thermo Scientific
Nanospray Flex
Thermo Scientific
Nanospray
Thermo Scientific
Fisher Scientific, Chemicals and Bioreagents
Fisher Scientific, Liquid Chromatography/Mass Spectrometry
Unity Lab Services
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I
Index
Numerics
D
3-D models
exit lens and S-lens 57
lens L0 59
MP0 and MP1 ion guides 61
Define Scan dialog box 71
diagnostics
system parameters, evaluating 24
workflow charts 22
documentation survey xix
A
advanced signal processing calibration, Orbitrap systems 67
APCI mode, note 4
automatic calibration 2
automatic tuning 19
C
Calibrate dialog box, Check page 11
calibration checks, description 11
calibration mixtures
calmix 10
infusing 5
part numbers 10
Pierce (ready-made) 10
cleaning procedures
exit lens 58
lens L0 60
lens L1 63
MP0 and MP1 62
S-lens 58
split gate lens 63
compliance
FCC v
regulatory iii
WEEE vii
contacting us xix
Thermo Scientific
E
electromagnetic compatibility v
electrospray
ionization (ESI) 3
voltage 8
EMC compliance iii
emergency shut down xviii
exit lens, cleaning 58
F
FCC compliance v
figures, list of xiii
front lens, cleaning 56
G
gloves, note 53
H
heated-electrospray ionization (HESI) 3
heater temperature (HESI) 8
I
injection time 24
instrument control software
note 13
version 2
ion optics
description 56
dialog box 16
MP0-MP00 voltage gradient, guidelines for 15
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Index: K
ion optics charging evaluation 44
ion path, drawing 56
ion source types
EASY-Spray 4
Ion Max and Ion Max-S 3
Nanospray Flex 4
NSI-1 dynamic nanospray probe with NSI-1 base 4
ion sweep cone, hot surface caution 25
ion transfer tube, hot surface caution 25
ion trap
blockage 49
cleaning 56
contaminated
cleaning by Thermo Fisher 27
signs of 25
nanospray ionization (NSI) 4
negative ion flux 44
negative ion mode 16
O
Orbitrap systems
calibration checks 65
mass accuracy, improving 68
procedures
additional calibrations 67
setting the FT lock mass abundance 72
oscillations, TIC 25
P
K
kits
PM Cleaning 54
Velos Pro Preinstallation 10
knowledge base, Thermo Scientific xix
L
lens L0, cleaning 60
lens L1, cleaning 63
license, Trap-HCD 29
lock mass abundance 72
lock masses
artificially mix 70
description 70
Lock Masses dialog box 71
M
mass calibration, Orbitrap systems 66
mass spectrometers
daily operation 2
emergency shut down xviii
instrument control software 2
pumping down the vacuum system 1
residue buildup 13
shutting down completely xviii
signal sensitivity 13
tune files 14
MP0 and MP1, cleaning 62
MP0, high contamination areas (Velos Pro) 62
MSDS 54
multipole gradient evaluation 34
multipole MP0 flight time evaluation 41
multipole rf amplitude, setting 20
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N
Achieving Peak Instrument Performance Reference Manual
pAGC scaling calibration, Orbitrap systems 65
Pierce calibration solutions 10
Planet Orbitrap, Web site 75
positive ion mode 16
power supply cord xviii
probe types, calibration 9
procedures
calibration checks
electron multiplier gain 29
transfer lenses 31
calibrations
electron multiplier gain 30
transfer lenses 32
cleaning
exit lens 58
lens L0 60
MP0 and MP1 62
S-lens 58
tools and supplies 54
defining a scan, lock masses 70
diagnostics
API stability evaluation 6
ejection and multiplier gain ratio 51
ion optics charging evaluation 49
multipole gradient evaluation 36
multipole MP0 flight time evaluation 43
source optics flight time evaluation 40
evaluating the TIC graph 27
setting the ion optics parameters 16
tuning the front lens 18
product information, online 76
Product Support Engineering, Web site 75
Thermo Scientific
Index: R
R
regulatory compliance iii
relative standard deviation 7
resources, additional 75
robustness feature 2
S
safety standards iii
scatter plot, Orbitrap systems 69
semi-automatic tuning 18
S-lens, cleaning 58
split gate lens, cleaning 63
spray stability
adjusting 6
maintaining 5
survey link xix
Syringe Pump dialog box 5
system evaluation tools, list of 32
T
tools and supplies 54
total ion current 7
transfer lenses 31
transfer lenses, out of calibration 25
Tune dialog box
Manual page 27
Semi-Automatic page 19
tune files
ETD systems 14
mass spectrometers 14
tuning
automatic 19
default ion optics values 16
front lens 17
manual, results 25
MP00 rf lens and MP0 15
saving the tune file 17
semi-automatic 18
V
vacuum manifold opening 60
voltage gradient 13
W
WEEE compliance vii
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