TSQ Endura and TSQ Quantiva Getting Started Guide Revision B

TSQ Endura and TSQ Quantiva Getting Started Guide Revision B
TSQ Series
TSQ Endura and
TSQ Quantiva
Getting Started Guide
80100-97025 Revision A
July 2015
© 2015 Thermo Fisher Scientific Inc. All rights reserved.
EASY-Max NG and Ion Max NG are trademarks; Unity is a registered service mark; and Hypersil GOLD AQ,
TSQ Endura, TSQ Quantiva, Thermo Scientific, and Xcalibur are registered trademarks of Thermo Fisher
Scientific Inc. in the United States.
The following are registered trademarks in the United States and other countries: Excel, Microsoft, and
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de Nemours & Co.
The following are registered trademarks in the United States and possibly other countries: APPI, PhotoMate,
and Syagen are registered trademarks of Morpho Detection, Inc. Rheodyne is a registered trademark of IDEX
Health & Science, LLC. Tygon is a registered trademark of the division of Saint-Gobain Performance Plastics
Corporation.
Chemyx is a trademark of Chemyx Inc. MX Series II is a trademark of IDEX Health & Science, LLC.
All other trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries.
Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
product operation. This document is copyright protected and any reproduction of the whole or any part of this
document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.
The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document supersede
all previous information received by the purchaser.
This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This
document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of
Sale shall govern all conflicting information between the two documents.
Release history: Rev. A, July 2015
Software version: (Thermo) Foundation 3.0 and later, Xcalibur 3.0 and later, Tune 2.0 and later
For Research Use Only. Not for use in diagnostic procedures.
Regulatory Compliance
Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with
applicable domestic and international regulations. When the system is delivered to you, it meets all pertinent
electromagnetic compatibility (EMC) and safety standards as described in the next section or sections by product name.
Changes that you make to your system may void compliance with one or more of these EMC and safety standards.
Changes to your system include replacing a part or adding components, options, or peripherals not specifically
authorized and qualified by Thermo Fisher Scientific. To ensure continued compliance with EMC and safety standards,
replacement parts and additional components, options, and peripherals must be ordered from Thermo Fisher Scientific
or one of its authorized representatives.
EMC Directive 2004/108/EC
EMC compliance has been evaluated by TÜV Rheinland of North America.
EN 55011: 2009, A1: 2010
EN 61000-4-6: 2009
EN 61000-3-2: 2006, A2: 2009
EN 61000-4-11: 2004
EN 61000-3-3: 2008
EN 61326-1: 2013
EN 61000-4-2: 2009
CISPR 11: 2009, A1: 2010
EN 61000-4-3: 2006, A2: 2010
ICES-003 Issue 5: 2012
EN 61000-4-4: 2004, A1: 2010
CFR 47, FCC Part 15, Subpart B, Class A: 2012
EN 61000-4-5: 2006
Low Voltage Safety Compliance
This device complies with Low Voltage Directive 2006/95/EC and harmonized standard EN/UL/CAN 61010-1.
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.
FCC Compliance Statement
THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES. OPERATION IS SUBJECT TO
THE FOLLOWING TWO CONDITIONS: (1) THIS DEVICE MAY NOT CAUSE HARMFUL
INTERFERENCE, AND (2) THIS DEVICE MUST ACCEPT ANY INTERFERENCE RECEIVED,
INCLUDING INTERFERENCE THAT MAY CAUSE UNDESIRED OPERATION.
CAUTION Read and understand the various precautionary notes, signs, and symbols contained inside
this manual pertaining to the safe use and operation of this product before using the device.
Notice on Lifting and Handling of
Thermo Scientific Instruments
For your safety, and in compliance with international regulations, the physical handling of this Thermo Fisher Scientific
instrument requires a team effort to lift and/or move the instrument. This instrument is too heavy and/or bulky for one
person alone to handle safely.
Notice on the Proper Use of
Thermo Scientific Instruments
In compliance with international regulations: This instrument must be used in the manner specified by Thermo Fisher
Scientific to ensure protections provided by the instrument are not impaired. Deviations from specified instructions on
the proper use of the instrument include changes to the system and part replacement. Accordingly, order replacement
parts from Thermo Fisher Scientific or one of its authorized representatives.
WEEE Directive
2012/19/EU
Thermo Fisher Scientific is registered with B2B Compliance (B2Bcompliance.org.uk) in the UK and with the
European Recycling Platform (ERP-recycling.org) in all other countries of the European Union and in Norway.
If this product is located in Europe and you want to participate in the Thermo Fisher Scientific Business-to-Business
(B2B) Recycling Program, send an email request to [email protected] with the following information:
• WEEE product class
• Name of the manufacturer or distributor (where you purchased the product)
• Number of product pieces, and the estimated total weight and volume
• Pick-up address and contact person (include contact information)
• Appropriate pick-up time
• Declaration of decontamination, stating that all hazardous fluids or material have been removed from the product
For additional information about the Restriction on Hazardous Substances (RoHS) Directive for the European Union,
search for RoHS on the Thermo Fisher Scientific European language websites.
IMPORTANT This recycling program is not for biological hazard products or for products that have been medically
contaminated. You must treat these types of products as biohazard waste and dispose of them in accordance with
your local regulations.
Directive DEEE
2012/19/EU
Thermo Fisher Scientific s'est associé avec une ou plusieurs sociétés de recyclage dans chaque état membre de l’Union
Européenne et ce produit devrait être collecté ou recyclé par celle(s)-ci. Pour davantage d'informations, rendez-vous sur
la page www.thermoscientific.fr/rohs.
WEEE Direktive
2012/19/EU
Thermo Fisher Scientific hat Vereinbarungen mit Verwertungs-/Entsorgungsfirmen in allen EU-Mitgliedsstaaten
getroffen, damit dieses Produkt durch diese Firmen wiederverwertet oder entsorgt werden kann. Weitere Informationen
finden Sie unter www.thermoscientific.de/rohs.
C
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii
Mass Spectrometer Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiv
Installation Kits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
MS Calibration Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
Performance Specification Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xvi
Chemical Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii
Cautions and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xviii
Thermo Scientific
Chapter 1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Ionization Techniques . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Using H-ESI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Using APCI. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Using APPI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Using NSI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
LC Flow Rates Ranges. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Types of Buffers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Method Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Chapter 2
Setting Up the API Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Preparing the Mass Spectrometer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Installing or Removing the API Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Installing the API Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Removing the API Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Preparing the Spray Insert for the API Source . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Installing the Spray Insert . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Adjusting the Spray Direction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Chapter 3
Connecting the Inlet Plumbing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19
Sample Introduction Techniques. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Direct Infusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
High-Flow Infusion. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Loop Injection (Flow-Injection Analysis). . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
High-Performance Liquid Chromatography (HPLC) with an Autosampler. . 21
TSQ Endura and TSQ Quantiva Getting Started Guide
vii
Contents
Plumbing Connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Setting Up the Syringe Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Setting Up the Inlet Plumbing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Setting Up the Inlet for Direct Infusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Setting Up the Inlet for High-Flow Infusion . . . . . . . . . . . . . . . . . . . . . . . . . 26
Setting Up the Inlet for Manual or Auto-Loop Injections . . . . . . . . . . . . . . . 29
Setting Up the Inlet for an LC/MS System with an Autosampler . . . . . . . . . . . 31
Connecting the Grounding Union to the H-ESI Spray Insert . . . . . . . . . . . . . . 32
viii
Chapter 4
Using the Syringe Pump and Divert/Inject Valve . . . . . . . . . . . . . . . . . . . . . . . . . .33
Syringe Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Divert/Inject Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Configurations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Controlling the Divert/Inject Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Chapter 5
Preparing the System for Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .37
Pumping Down the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Setting Up the Syringe Pump for Direct Infusion . . . . . . . . . . . . . . . . . . . . . . . 40
Setting Up the Mass Spectrometer for Calibration. . . . . . . . . . . . . . . . . . . . . . . 41
Chapter 6
Establishing a Stable Ionization Spray . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .43
Evaluating the Spray Stability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Optimizing the API Source Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Chapter 7
Performing the Tune, Calibration, or Calibration Check . . . . . . . . . . . . . . . . . . . .49
Performing System Tune and Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Spray Stability Evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
System Tune and Check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Check Mass Position and Resolution. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Calibrate Mass Position and Resolution. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Detector Gain Calibration. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Chapter 8
Optimizing the API Source Parameters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .55
Setting Up the Plumbing for Compound Optimization . . . . . . . . . . . . . . . . . . 55
Determining the Initial API Source Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Optimizing the RF Lens Voltage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Optimizing the Collision Energy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Chapter 9
Acquiring Sample Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .63
Using the Tune Application to Acquire Sample Data . . . . . . . . . . . . . . . . . . . . 63
Using the Xcalibur Data System to Acquire Sample Data . . . . . . . . . . . . . . . . . 65
TSQ Endura and TSQ Quantiva Getting Started Guide
Thermo Scientific
Contents
Appendix A Using Basic Tune Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .67
Opening the Tune Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Setting the Instrument Power Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Checking the Instrument Readback Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Controlling the Syringe Pump. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Setting the Data Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Setting the Ion Polarity Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Setting the Tune Preferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Using the Mass List Table in the Define Scan Pane . . . . . . . . . . . . . . . . . . . . . . 73
Using the History Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Using the Favorites Pane to Save System Settings . . . . . . . . . . . . . . . . . . . . . . . 76
Appendix B Flushing the Inlet Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .79
Supplies. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Flushing the Inlet Components after Calibration . . . . . . . . . . . . . . . . . . . . . . . 81
Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .83
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .87
Thermo Scientific
TSQ Endura and TSQ Quantiva Getting Started Guide
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Contents
x
TSQ Endura and TSQ Quantiva Getting Started Guide
Thermo Scientific
F
Figures
Figure 1.
Figure 2.
Figure 3.
Figure 4.
Figure 5.
Figure 6.
Figure 7.
Figure 8.
Figure 9.
Figure 10.
Figure 11.
Figure 12.
Figure 13.
Figure 14.
Figure 15.
Figure 16.
Figure 17.
Figure 18.
Figure 19.
Figure 20.
Figure 21.
Figure 22.
Figure 23.
Figure 24.
Figure 25.
Figure 26.
Figure 27.
Figure 28.
Figure 29.
Figure 30.
Figure 31.
Figure 32.
Figure 33.
Figure 34.
Thermo Scientific
Thermo Xcalibur Instrument Setup window showing the scan types . . . . . . . . . . 7
MS API source mount assembly and ion sweep cone . . . . . . . . . . . . . . . . . . . . 11
EASY-Max NG API source with H-ESI spray insert (top, front view). . . . . . . . 13
API source connection to the MS mount assembly (installed ion sweep cone) . . 14
Front-to-back adjustment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Rotational adjustment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Schematics of the sample introduction techniques (examples) . . . . . . . . . . . . . . 22
Proper connection for the PEEK tubing and fitting (syringe adapter assembly). . 23
Plumbing connection for the syringe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Plumbing connections for direct infusion (H-ESI mode) . . . . . . . . . . . . . . . . . . 25
Plumbing connection between the LC union and the union Tee . . . . . . . . . . . 27
Plumbing connection between the union Tee and the divert/inject valve . . . . . 27
Plumbing connection between the union Tee and the grounding union . . . . . . 28
Divert/inject valve setup for manual loop injection . . . . . . . . . . . . . . . . . . . . . . 30
Plumbing connections for manual loop injection (APCI mode) . . . . . . . . . . . . . 31
Plumbing connections for the grounding union (H-ESI mode) . . . . . . . . . . . . . 32
Syringe pump setup (top view) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Divert/inject valve positions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Divert/inject valve plumbed as a loop injector and as a divert valve . . . . . . . . . . 36
Divert/inject valve (front view) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Power entry module (right side of the instrument) . . . . . . . . . . . . . . . . . . . . . . 38
By Board page in the Status pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Plot Chromatogram dialog box with the TIC option selected . . . . . . . . . . . . . . 44
Optimization page of the Ion Source pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Report Generation Options dialog box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Calibration – Options page. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Normalized intensity as a function of the M00 multipole offset voltage . . . . . . . 52
Isotopic peaks of the polytyrosine trimer at a peak width of m/z 0.4 . . . . . . . . . 53
Error range of the polytyrosine 1-3-6 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
LC flow rate of 200 μL/min on the Ion Source – Ion Source page . . . . . . . . . . 56
Define Scan – Optimization page showing the rf lens voltage optimization
settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
RF optimization for the polytyrosine trimer ion . . . . . . . . . . . . . . . . . . . . . . . . 59
Define Scan – Optimization page showing the collision energy optimization
settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Collision energy optimization curve and MS/MS spectrum of the polytyrosine
trimer ion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
TSQ Endura and TSQ Quantiva Getting Started Guide
xi
Figures
Figure 35.
Figure 36.
Figure 37.
Figure 38.
Figure 39.
Figure 40.
Figure 41.
Figure 42.
Figure 43.
Figure 44.
Figure 45.
Figure 46.
Figure 47.
Figure 48.
xii
Data Acquisition pane in the Tune window . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Run Sequence dialog box (partial) showing the selected start instrument . . . . . 65
Change Instruments In Use dialog box showing the MS as the start
instrument. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Tune window showing the Define Scan – Scan page . . . . . . . . . . . . . . . . . . . . . 68
Power mode icons showing the selected icon (mode) . . . . . . . . . . . . . . . . . . . . 69
Toggle button for the syringe modes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Syringe parameter box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Toggle button for the data types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Toggle button for the instrument polarity modes . . . . . . . . . . . . . . . . . . . . . . . 71
Tune Preferences dialog box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Q3 Resolution selected and added to the SRM Table . . . . . . . . . . . . . . . . . . . . 74
History pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Favorites pane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
State name box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
TSQ Endura and TSQ Quantiva Getting Started Guide
Thermo Scientific
P
Preface
The TSQ Endura and TSQ Quantiva Getting Started Guide describes how to set up and
calibrate the Thermo Scientific™ TSQ Endura™ and TSQ Quantiva™ mass spectrometers
(MSs), and acquire MS data.
Contents
• Mass Spectrometer Models
• Related Documentation
• Installation Kits
• Cautions and Special Notices
• Contacting Us
 To suggest changes to the documentation or to the Help
Complete a brief survey about this document by clicking the button below.
Thank you in advance for your help.
Mass Spectrometer Models
This guide is intended for the following mass spectrometer models:
• TSQ Endura—Requires one forepump.
• TSQ Quantiva—Requires two forepumps.
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TSQ Endura and TSQ Quantiva Getting Started Guide
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Preface
Related Documentation
The TSQ Endura and TSQ Quantiva mass spectrometers include complete documentation.
In addition to this guide, you can also access the following documents as PDF files from the
data system computer:
• TSQ Endura and TSQ Quantiva Preinstallation Requirements Guide
• TSQ Endura and TSQ Quantiva Getting Connected Guide
• TSQ Endura and TSQ Quantiva Hardware Manual
• Ion Max NG and EASY-Max NG Ion Sources User Guide
• Safety and Regulatory Guide
The TSQ Endura and TSQ Quantiva also ship with a printed copy of the Safety and
Regulatory Guide. This guide contains important safety information about Thermo
Scientific liquid chromatography (LC) and mass spectrometry (MS) systems. Make sure
that all lab personnel have read and have access to this document.
 To view the product manuals
From the Microsoft™ Windows™ taskbar, do the following:
• For the Thermo Scientific mass spectrometer, choose Start > All Programs >
Thermo Instruments > model x.x, and then open the applicable PDF file.
• For an LC instrument controlled by a Thermo Scientific application, choose Start >
All Programs > Thermo Instruments > Manuals > LC Devices and so on.
The TSQ Endura and TSQ Quantiva application also provides Help.
 To view the Help
Do the following as applicable:
• To access the Tune application Help, click the Options icon,
Tune Help.
, and then choose
• To access the Thermo Xcalibur™ Method Editor Help, choose the appropriate option
from the Help menu.
 To download user documentation from the Thermo Scientific website
1. Go to www.thermoscientific.com.
2. In the Search box, type the product name and press Enter.
3. In the left pane, select Documents & Videos, and then under Refine By Category, click
Operations and Maintenance.
xiv
TSQ Endura and TSQ Quantiva Getting Started Guide
Thermo Scientific
Preface
4. (Optional) Narrow the search results or modify the display as applicable:
• For all related user manuals and quick references, click Operator Manuals.
• For installation and preinstallation requirements guides, click Installation
Instructions.
• For documents translated into a specific language, use the Refine By Language
feature.
• Use the Sort By options or the Refine Your Search box (above the search results
display).
5. Download the document as follows:
a. Click the document title or click Download to open the file.
b. Save the file.
Installation Kits
The TSQ Endura or TSQ Quantiva MS ships with several kits. However for the procedures
in this guide, the following kits provide the necessary components:
• MS Calibration Kit
• Performance Specification Kit
• Chemical Kit
For a full list of the mass spectrometer kits and their contents, refer to the TSQ Endura and
TSQ Quantiva Hardware Manual.
MS Calibration Kit
Table 1. MS Calibration Kit (P/N 80000-62013) (Sheet 1 of 2)
Image
Thermo Scientific
Item
Quantity
Part number
Ferrule, fingertight, natural PEEK
2
00101-18196
Fitting, fingertight, one-piece natural PEEK, 10-32
1
00109-99-00016
Fitting, fingertight, two-piece natural PEEK, two wings,
10-32
2
00101-18081
Fitting, fingertight, two-piece, one wing, 10-32
2
00101-18195
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Table 1. MS Calibration Kit (P/N 80000-62013) (Sheet 2 of 2)
Image
Item
Quantity
Part number
Grounding union, zero-dead-volume (ZDV), stainless
steel, 1/16 in. orifice, 0.010 in. (0.25 mm) thru-hole,
10-32
1
00101-18182
HPLC union, black PEEK, 10-32, 0.01 in. thru-hole
1
00101-18202
—
Syringe, GC, gas tight, 500 μL, 51 mm long
1
00301-01-00040
—
Tubing, natural PEEK, 1/16 in. OD, 0.0025 in. ID,
28 cm (11 in.) long
2
80000-22032
Note Use this tubing with the calibration solutions and for flow rates less than
50 μL/min.
—
Tubing, red PEEK, 1/16 in. OD, 0.005 in. ID, 0.6 m
(2 ft) long
1
00301-22912
—
Tubing, red PEEK, 1/16 in. OD, 0.005 in. ID, 18 cm
(7.1 in.) long
2
80000-22053
Note Use this tubing for flow rates equal to or greater than 50 μL/min.
—
Tubing, Teflon™ FEP, 1/16 in. OD, 0.03 in. ID, 3 cm
(1.2 in.) long
1
00301-22915
Performance Specification Kit
Table 2. Performance Specification Kit (P/N 80100-62008) (Sheet 1 of 2)
Image
Item
—
Column, HPLC, 20 × 2.1 mm ID,
Hypersil GOLD AQ™ C18, 1.9 μm particles
1
00109-01-00013
Fitting, fingertight, one-piece natural PEEK, 10-32
10
00109-99-00016
Needle port, PEEK
1
00110-22030
Sample loop, 2 μL, PEEK
1
00110-16012
Syringe, gas tight, 500 μL
1
00301-19016
—
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Part number
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Preface
Table 2. Performance Specification Kit (P/N 80100-62008) (Sheet 2 of 2)
Image
Item
Quantity
Part number
—
Tubing, red PEEK, 1/16 in. OD, 0.005 in. ID, 3 m
(10 ft) long
1
00301-22912
Union Tee, HPLC, PEEK, 1/16 in. orifice, 0.020 in.
(0.5 mm) thru-hole, 10-32 (provided with fingertight
fittings)
1
00101-18204
Chemical Kit
IMPORTANT Be aware of the following storage precautions for the calibration and
reserpine solutions: Refrigerate the containers after opening. For long-term storage, keep
refrigerated at 2–8 °C (36–46 °F).
Table 3. Chemical Kit (P/N 80100-62006)
Item
Quantity
Part number
Calibration solution, polytyrosine 1-3-6, 10 mL
1
00301-22924
TSQ Reserpine Solution Kit
(contains reserpine standard, 100 pg/μL, 5 × 1 mL, P/N HAZMAT-01-00081)
1
80100-62033
LCMS Functionality Test Kit (for field service use only)
1
HAZMAT-01-00044
Cautions and Special Notices
Make sure that you follow the cautions and special notices presented in this guide. Cautions
and special notices appear in boxes; those concerning safety or possible damage also have
corresponding caution symbols.
This guide uses the following types of cautions and special notices.
CAUTION Highlights hazards to humans, property, or the environment. Each CAUTION
notice is accompanied by an appropriate CAUTION symbol.
IMPORTANT Highlights information necessary to prevent damage to software, loss of
data, or invalid test results; or might contain information that is critical for optimal
performance of the system.
Note Highlights information of general interest.
Tip Highlights helpful information that can make a task easier.
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The TSQ Endura and TSQ Quantiva Getting Started Guide contains the following cautionspecific symbols (Table 4).
Table 4. Caution-specific symbols and their meanings
Symbol
Meaning
Chemical hazard: Wear gloves and other protective equipment, as
appropriate, when handling toxic, carcinogenic, mutagenic, corrosive,
or irritant chemicals. Use approved containers and proper procedures
to dispose of waste oil and when handling wetted parts of the
instrument.
Hot surface: Before touching the API source assembly, allow heated
components to cool.
Risk of electric shock: This instrument uses voltages that can cause
electric shock and/or personal injury. Before servicing, shut down the
instrument and disconnect it from line power. While operating the
instrument, keep covers on.
Risk of eye injury: Eye injury could occur from splattered chemicals or
airborne particles. Wear safety glasses when handling chemicals or
servicing the instrument.
Sharp object: Avoid handling the tip of the syringe needle.
Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need. You
can use your smartphone to scan a QR code, which opens your email application or browser.
Contact us
xviii
Customer Service and Sales
Technical Support
(U.S.) 1 (800) 532-4752
(U.S.) 1 (800) 532-4752
(U.S.) 1 (561) 688-8731
(U.S.) 1 (561) 688-8736
TSQ Endura and TSQ Quantiva Getting Started Guide
Thermo Scientific
Preface
Contact us
Customer Service and Sales
Technical Support
us.customer-support.analyze
@thermofisher.com
us.techsupport.analyze
@thermofisher.com
 To find global contact information or customize your request
1. Go to www.thermoscientific.com.
2. Click Contact Us, select the Using/Servicing a Product option, and then
type the product name.
3. Use the phone number, email address, or online form.
 To find product support, knowledge bases, and resources
Go to www.thermoscientific.com/support.
 To find product information
Go to www.thermoscientific.com/lc-ms.
Note To provide feedback for this document:
• Send an email message to Technical Publications ([email protected]).
• Complete a survey at www.surveymonkey.com/s/PQM6P62.
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1
Introduction
This chapter provides general information about the TSQ Endura and TSQ Quantiva MSs.
For information about using the Thermo Tune application, see Appendix A, “Using Basic
Tune Functions.” For information about daily operation, maintenance, and system startup
and shutdown, refer to the TSQ Endura and TSQ Quantiva Hardware Manual.
Note
• The Glossary defines some of the terms used in this guide.
• To ensure the proper operation of the mass spectrometer, Thermo Fisher Scientific
recommends that you perform the daily preventive maintenance described in the
TSQ Endura and TSQ Quantiva Hardware Manual.
Contents
• Ionization Techniques
• LC Flow Rates Ranges
• Types of Buffers
• Method Editor
Ionization Techniques
This section briefly describes the following ionization modes: heated-electrospray (H-ESI),
atmospheric pressure chemical ionization (APCI), atmospheric pressure photoionization
(APPI), and nanoelectrospray ionization (nanoESI or NSI). For additional information, refer
to the API source’s manual.
• Using H-ESI (Typically preferred for polar compounds)
• Using APCI (Typically preferred for medium polar compounds)
• Using APPI (Typically preferred for certain polar and nonpolar compounds)
• Using NSI (Typically preferred for peptides and proteins)
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Introduction
Ionization Techniques
Using H-ESI
H-ESI is a soft gas phase ionization technique. The H-ESI source transfers ions in solution to
the gas phase. H-ESI can analyze many samples that previously were not suitable for mass
analysis (for example, heat-labile compounds or high molecular mass compounds). You can
use H-ESI to analyze any polar compound that is an ion in solution, including adduct ions.
Included in this class of compounds are biological polymers (such as proteins, peptides,
glycoproteins, and nucleotides), pharmaceuticals and their metabolites, and industrial
polymers. For example, you might analyze polyethylene glycols from a solution containing
ammonium acetate because of adduct formation between NH4+ ions in the solution and
oxygen atoms in the polymer. With H-ESI, the range of molecular masses that the mass
spectrometer can analyze can exceed 50 000 Da if there is multiple charging.
The H-ESI source can produce multiply-charged ions, depending on the structure of the
analyte and the solvent. For example, the mass spectrum of a protein or peptide typically
consists of a distribution of multiply-charged analyte ions. You can mathematically
manipulate this mass spectrum to determine the molecular mass of the sample.
Use H-ESI in either positive or negative ion polarity mode. The polarity of the ions in
solution determines the ion polarity mode: acidic molecules form negative ions in high pH
solution and basic molecules form positive ions in low pH solution. The installed H-ESI
spray insert can be either positively or negatively charged. When it is positively charged, it
generates positive ions. When it is negatively charged, it generates negative ions.
Vary the flow rate into the mass spectrometer over a range of 1–1000 μL/min. See Table 5 for
guidelines.
In H-ESI, because both the buffer type and buffer concentration have a noticeable effect on
sensitivity, you must choose these variables correctly.
Large droplets with high surface tension, low volatility, low surface charge, strong ion
solvation, and high conductivity negatively affect the H-ESI process. Conversely, H-ESI
favors small droplets with low surface tension, high volatility, high surface charge, weak ion
solvation, and low conductivity.
Mixed organic-aqueous solvent systems that include organic solvents, such as methanol,
acetonitrile, and isopropyl alcohol, are superior to water alone for H-ESI. Volatile acids and
bases are good, but for best results do not use salts above 10 mM. Be aware that strong
mineral acids and bases are extremely detrimental to the instrument.
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1 Introduction
Ionization Techniques
IMPORTANT To obtain good H-ESI results, follow these guidelines:
• Keep nonvolatile salts and buffers out of the solvent system. For example, avoid the
use of phosphates and salts that contain potassium or sodium. Use acetate or
ammonium salts instead. Do not use strong mineral acids and bases—they can
damage the instrument.
• Use organic/aqueous solvent systems and volatile acids and bases. Try to avoid the use
of 100 percent aqueous solvents.
• If possible, optimize the pH of the solvent system for the analyte. For example, if the
analyte contains a primary or secondary amine, the mobile phase should be slightly
acidic (pH 2–5). The acidic pH tends to keep positive ions in solution.
Using APCI
Like H-ESI, APCI is a soft gas phase ionization technique. Therefore, the gas phase acidities
and basicities of the analyte and solvent vapor play an important role in the APCI process.
APCI provides molecular mass information for compounds of medium polarity that have
some volatility. APCI is typically used to analyze small molecules with molecular masses up to
about 1000 Da.
Use APCI in either positive or negative ion polarity mode. For most molecules, the positive
ion mode produces a stronger ion current. This is especially true for molecules with one or
more basic nitrogen (or other basic) atoms. Molecules that generally produce strong negative
ions with acidic sites, such as carboxylic acids and acid alcohols, are an exception to this
general rule.
In general, APCI produces fewer negative ions than positive ions. However, the negative ion
polarity mode can be more specific because it generates less chemical noise than does the
positive mode. Consequently, the signal-to-noise ratio (S/N) might be better in the negative
ion mode.
The rate of solvent flowing from the LC into the mass spectrometer in APCI mode is typically
high (200–2000 μL/min). See Table 6 for guidelines.
APCI is a very robust ionization technique. It is not affected by minor changes in most
variables, such as changes in buffer type or buffer strength.
Using APPI
APPI is also a soft ionization technique. In APPI an ion is generated from a molecule when it
interacts with a photon from a light source, such as the Syagen Technology PhotoMate™
APPI™ light source. APPI generates molecular ions for molecules that have an ionization
potential below the photon energy of the light being emitted by the light source.
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Introduction
LC Flow Rates Ranges
Molecules that include steroids, basic-drug entities, and pesticides have ionization potentials
below the threshold. APPI reduces fragmentation because only a small amount of energy is
deposited in the molecule. Molecules, such as the nitrogen sheath and auxiliary gas and the
simple solvents used for LC/MS, are not ionized because their ionization potentials are greater
than the photon energy. The result is selective ionization of an analyte versus the background.
Using NSI
Conventional electrospray (ESI) employs flow rates from 1 μL/min to 1 mL/min. Due to the
high volume of liquid exiting the emitter, a drying gas, thermal heating, or both are often
required to expedite desolvation and droplet shrinkage. NSI (or nanoESI) is a form of ESI
that employs low flow rates of 10–1000 nL/min. NSI generally does not require a drying gas
or thermal heating. Compared with ESI or H-ESI, NSI tolerates a wider range of liquid
compositions including pure water.
As you lower the flow rate, a lower volume of mobile phase passes through the emitter,
producing smaller aerosol droplets. This makes NSI more effective than conventional ESI or
H-ESI at concentrating the analyte at the emitter tip, producing significant increases in
sensitivity demonstrated by the signal response of the mass spectrometer. See Table 7 for
guidelines.
LC Flow Rates Ranges
The H-ESI spray insert can volatilize ions from liquid flows1 of 1–1000 μL/min. This flow
rate range provides for a wide range of separation techniques: CE, CEC, analytical LC,
capillary LC, and microbore LC.
The APCI spray insert can volatilize ions from liquid flows2 of 200–2000 μL/min. This flow
range provides for the use of separation techniques: analytical LC, microbore LC, and
semi-preparative LC.
While changing the flow rate of solvents entering the mass spectrometer, adjust the following
parameters:
• For H-ESI mode, adjust the spray voltage, the ion transfer tube and vaporizer
temperatures, and the flow rates for the sheath, auxiliary, and sweep gases.
• For APCI mode, adjust the corona discharge current, ion transfer tube and vaporizer
temperatures, and the flow rates for the sheath, auxiliary, and sweep gases.
• For NSI mode, adjust the spray voltage and the ion transfer tube temperature.
1
The H-ESI spray insert can generate ions from liquid flows as low as 1 μL/min. However, flows below 5 μL/min
require more care.
2 For the APCI spray insert, flows below 200 μL/min require more care to maintain a stable spray.
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LC Flow Rates Ranges
The following tables list the guidelines (default parameter values for the API source) for
system operation using H-ESI (Table 5), APCI (Table 6), and NSI (Table 7) for a range of LC
solvent flow rates.
Table 5. Guidelines for setting operating parameters for LC/H-ESI/MS
LC flow
rate
(μL/min)
Spray
voltage (V)a
Sheath gas
(arbb units)
Auxiliary gas
(arb units)
Sweep gas
(arb units)
Ion transfer
tube
temperature
(°C)
Vaporizer
temperature
(°C)
Typical
nitrogen gas
consumption
(L/min)
5
Pos: 3500
Neg: –2500
5
5
0
275
20
Less than 1
200
Pos: 3500
Neg: –2500
35
10
0
325
275
8
500
Pos: 3500
Neg: –2500
50
15
2
350
400
13
1000
Pos: 3500
Neg: –2500
60
20
2
380
500
17
a
Positive and negative polarity modes
b
Arbitrary
Table 6. Guidelines for setting operating parameters for LC/APCI/MS
LC flow rate
(μL/min)
Sheath gas
(arba units)
Auxiliary gas
(arb units)
Sweep gas
(arb units)
Ion transfer tube
temperature (°C)
Vaporizer
temperature (°C)
Corona
discharge
current (μA)b
200
25
5
0
250
325
Pos: 4
Neg: –10
1000
45
5
2
275
500
Pos: 4
Neg: –10
a
Arbitrary
b
Positive and negative polarity modes
Table 7. Guidelines for setting operating parameters for LC/NSI/MS
Spray voltage (V)
Sweep gas (arbitrary units)
Ion transfer tube temperature (°C)
Positive mode: 1200
Negative mode: –600
0
325
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Introduction
Types of Buffers
Note
Use the Ion Source page of the Ion Source pane to determine the initial spray voltage,
sheath gas pressure, auxiliary gas pressure, sweep gas pressure, ion transfer tube
temperature, and vaporizer temperature for the LC flow rate of your experiment. See
“Determining the Initial API Source Settings” on page 55.
Use the Ion Source – Optimization page to optimize the spray voltage, sheath gas pressure,
auxiliary gas pressure, and sweep gas pressure for your experiment. See “Determining the
Initial API Source Settings” on page 55.
Types of Buffers
Many LC applications use nonvolatile buffers such as phosphate and borate. Avoid using
nonvolatile buffers because they can cause salt buildup in parts of the API source, such as the
ion transfer tube and nozzle of the spray insert. Using nonvolatile buffers without also
cleaning the API source to remove salt deposits might compromise the integrity of the spray.
For LC/MS experiments, replace nonvolatile buffers with the following volatile buffers:
• Acetic acid
• Ammonium acetate
• Ammonium formate
• Ammonium hydroxide
• Formic acid
• Triethylamine (TEA)
For a list of recommended solvents, refer to the TSQ Endura and TSQ Quantiva
Preinstallation Requirements Guide.
CAUTION Avoid exposure to potentially harmful materials.
By law, producers and suppliers of chemical compounds are required to provide their
customers with the most current health and safety information in the form of Material
Safety Data Sheets (MSDSs) or Safety Data Sheets (SDSs). The MSDSs and SDSs must
be freely available to lab personnel to examine at any time. These data sheets describe the
chemicals and summarize information on the hazard and toxicity of specific chemical
compounds. They also provide information on the proper handling of compounds, first
aid for accidental exposure, and procedures to remedy spills or leaks.
Read the MSDS or SDS for each chemical you use. Store and handle all chemicals in
accordance with standard safety procedures. Always wear protective gloves and safety
glasses when you use solvents or corrosives. Also, contain waste streams, use proper
ventilation, and dispose of all laboratory reagents according to the directions in the MSDS
or SDS.
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Method Editor
For LC applications that require nonvolatile buffers, follow these guidelines for best
performance:
• Optimize the spray insert position.
• Install the mass spectrometer’s optional ion sweep cone.
• Reduce the concentration of buffers to an absolute minimum.
Note You might need to increase the frequency of API source maintenance when you use
nonvolatile buffers.
Method Editor
Use the Method Editor (Figure 1) that opens in the Xcalibur Instrument Setup window to
create an instrument method for your experiment. To save time entering the parameters for an
instrument method, open the system template designed for the experiment type that you want
to perform, enter the parameters specific to the experiment, and then save the entries as part
of an Xcalibur instrument method (.meth file name extension). For additional information,
refer to the Xcalibur Instrument Setup Help.
Figure 1.
Thermo Xcalibur Instrument Setup window showing the scan types
Scan Types icon bar
Thermo Scientific
Mass table
Properties pane
TSQ Endura and TSQ Quantiva Getting Started Guide
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Introduction
Method Editor
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2
Setting Up the API Source
This chapter provides information about setting up the API source for H-ESI, APCI, and
APPI experiments. The API source ships with the mass spectrometer and consists of the
source housing, a heater assembly, and the H-ESI spray insert. For APCI experiments, order
the APCI Installation Kit (P/N OPTON-30159), which includes the APCI spray insert. For
APPI experiments, order the APPI Interface Kit (P/N OPTON-30185).
IMPORTANT
For H-ESI, APCI, and APPI experiments, install the correct API source as follows:
• TSQ Endura MS—Use the Thermo Scientific EASY-Max NG™ API source.
• TSQ Quantiva MS—Use the Thermo Scientific Ion Max NG™ API source.
For NSI experiments, use one of the compatible Thermo Scientific nanospray sources.
Contents
• Preparing the Mass Spectrometer
• Installing or Removing the API Source
• Preparing the Spray Insert for the API Source
Preparing the Mass Spectrometer
Before you install the API source, install or remove the ion sweep cone as specified in the
following procedure.
IMPORTANT For best results, wear clean gloves before you handle the API source’s spray
insert or the mass spectrometer’s ion sweep cone.
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Setting Up the API Source
Preparing the Mass Spectrometer
 To prepare the mass spectrometer
1. Complete all data acquisition, if any.
2. Open the Tune window (see page 68).
3. Place the mass spectrometer in Off mode (see page 69).
The LC/MS system is now in off mode. After the API source housing, spray insert, or
both have cooled to room temperature, you can safely remove these components.
Note Always place the system in off mode before removing the spray insert or the API
source housing. When the system is in off mode, the API gases, high voltage, and
syringe pump are off.
4. If you want to change the installed API source, wait until it has cooled to room
temperature.
For instructions on how to remove the API source, refer to the Ion Max NG and
EASY-Max NG Ion Sources User Guide.
CAUTION Hot surface. Avoid touching the API source housing when the mass
spectrometer is in operation. The external surface of the EASY-Max NG API source
housing can become hot enough to burn your skin.
5. Depending on the ionization mode, do the following (Figure 2):
• For H-ESI, APCI, or APPI mode, install the ion sweep cone over the mass
spectrometer’s spray cone (Figure 2).
• For NSI mode, remove the ion sweep cone from the mass spectrometer by grasping
its outer ridges and pulling it off.
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2 Setting Up the API Source
Installing or Removing the API Source
Figure 2.
MS API source mount assembly and ion sweep cone
Sheath gas line to the
API source
Auxiliary gas line to the
API source
Spray cone (do not remove)
Ion sweep cone
(remove for NSI mode only)
Source drain routes to the back of
the mass spectrometer.
Installing or Removing the API Source
The EASY-Max NG source holds the H-ESI or APCI spray insert. All the wiring and gas
plumbing for this API source are internal. This means you can install or remove the API
source or change the spray insert—all without the use of tools.
Note For instructions on how to configure the EASY-Max NG source for H-ESI, APCI,
or APPI mode, refer to Chapter 3 in the Ion Max NG and EASY-Max NG Ion Sources User
Guide.
The TSQ Endura and TSQ Quantiva MS internally routes the solvent waste from the bottom
of the API source to the back Drain/Waste port.
This section provides the following procedures:
• Installing the API Source
• Removing the API Source
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Setting Up the API Source
Installing or Removing the API Source
Installing the API Source
Complete the appropriate procedure:
• To install the EASY-Max NG API source (instrument calibration and experiments)
• To install the NSI source (experiments)
CAUTION
Use these guidelines for the API source drain:
• Use the Tygon™ tubing provided with the solvent waste container to connect the
solvent waste container to a fume exhaust system.
• To prevent solvent waste from backing up into the mass spectrometer, make sure that
all Tygon tubing is above the level of liquid in the waste container as follows:
–
From the mass spectrometer to the solvent waste container
–
From the waste container to the exhaust system
Equip your lab with at least two fume exhaust systems:
• The analyzer optics become contaminated if the drain/waste tubing and the exhaust
tubing from the forepump connect to the same fume exhaust system. Route the
exhaust tubing from the forepump to a dedicated fume exhaust system.
–
12
Do not vent the Tygon drain tube (or any vent tubing connected to the waste
container) to the same fume exhaust system that connects to the forepump. Vent
the waste container to a dedicated fume exhaust system. The exhaust system for
the API source must accommodate a flow rate of up to 30 L/min (64 ft3/h).
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2 Setting Up the API Source
Installing or Removing the API Source
 To install the EASY-Max NG API source
1. Follow the procedure To prepare the mass spectrometer.
2. For APCI mode, check that the corona discharge needle assembly is installed in the API
source housing.
For instructions, refer to the Ion Max NG and EASY-Max NG Ion Sources User Guide.
3. Unlock the source’s locking levers (down position, Figure 3).
Figure 3.
EASY-Max NG API source with H-ESI spray insert (top, front view)
H-ESI spray insert
Locking lever
(down unlocked position)
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2
Setting Up the API Source
Installing or Removing the API Source
4. Align the two guide pin holes on the back of the source with the guide pins on the front
of the mass spectrometer (Figure 4), and then carefully press the source onto the mass
spectrometer.
Figure 4.
API source connection to the MS mount assembly (installed ion sweep cone)
High voltage (HV)
connection
Guide pins on the MS API source mount assembly (left)
and guide pin holes on the back of the source (right)
5. Lock the source’s locking levers (up position).
6. To switch between ionization modes, refer to the Ion Max NG and EASY-Max NG Ion
Sources User Guide.
7. Verify that the solvent waste system connects to the back Drain/Waste port.
During the initial installation of the mass spectrometer, a Thermo Fisher Scientific
service engineer installs the solvent waste system. For instructions, refer to the
TSQ Endura and TSQ Quantiva Getting Connected Guide.
 To install the NSI source
1. Follow the procedure To prepare the mass spectrometer.
2. For additional instructions, refer to the NSI source manual.
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2 Setting Up the API Source
Preparing the Spray Insert for the API Source
Removing the API Source
To access the ion sweep cone, API source interface, ion transfer tube, internal APCI corona
needle (APCI-configured source), or internal APPI lamp (APPI-configured source), you must
remove the API source from the mass spectrometer.
 To remove the API source
1. Complete all data acquisition, if any.
2. Turn off the liquid flow from the LC (or other sample introduction device) to the API
source.
3. In the Tune window, place the mass spectrometer in Off mode (see page 69).
CAUTION Hot surface. The maximum safety limit for heated surfaces is 70 °C
(158 °F). Although the source falls below this maximum, it can still severely burn you.
Allow the source to cool to room temperature (approximately 20 minutes) before you
touch it.
4. Disconnect the sample line from the grounding union or spray insert, as applicable.
5. Unlock the source’s locking levers.
For the EASY-Max NG API source, see Figure 3.
6. Pull the source straight off of the mass spectrometer.
7. Place the source in a safe location for temporary storage.
Preparing the Spray Insert for the API Source
For detailed instructions, refer to the Ion Max NG and EASY-Max NG Ion Sources User Guide.
• Installing the Spray Insert
• Adjusting the Spray Direction
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Setting Up the API Source
Preparing the Spray Insert for the API Source
Installing the Spray Insert
For H-ESI mode, install the H-ESI spray insert and turn on the source heater. For APCI
mode, install the APCI spray insert. For APPI mode, you can use either of the spray inserts;
refer to “Spray Insert Selection” in Chapter 1 of the Ion Max NG and EASY-Max NG Ion
Sources User Guide.
IMPORTANT For the calibration procedures and experiments with flow rates that are less
than 50 μL/min, make sure that the H-ESI spray insert contains the low-flow metal
needle insert (P/N 80000-60152).
 To install the spray insert
1. Follow the procedure “Installing the API Source.”
2. To switch between ionization modes or change the needle insert, refer to the Ion Max NG
and EASY-Max NG Ion Sources User Guide.
Adjusting the Spray Direction
To maximize sensitivity or robustness, you can adjust the spray direction by a few millimeters.
Typically, you adjust the spray direction while optimizing the API source parameters for the
analytes. Make the adjustment according to the guidelines in Table 8.
Note The depth and angle of the spray insert and heater assembly are not adjustable.
Table 8. Guidelines for adjusting the heater and spray insert position
Adjustment control
Description
Front-to-back position
1
For H-ESI mode, use position 1 for calibrating the mass
spectrometer and for low liquid flow rates (less than
50 μL/min). In position 1, the spray is closest to the entrance
of the mass spectrometer.
2
Use position 2 (default) for liquid flow rates greater than
50 μL/min.
3
Use position 3 for enhanced robustness, for example, when
you use a biological matrix. In position 3, the spray is farthest
from the entrance of the mass spectrometer.
Rotational position
Left, center, right (marks)
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Use the center mark to position the spray closest to the
entrance of the mass spectrometer.
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2 Setting Up the API Source
Preparing the Spray Insert for the API Source
 To adjust the spray direction
CAUTION Hot surface. Avoid touching the API source housing when the mass
spectrometer is in operation. The external surface of the housing can become hot
enough to burn your skin. Allow the housing to cool before you touch it.
1. Loosen the top two retainer knobs that secure the heater assembly.
2. Do any of the following (see Table 8):
• Move the heater forward or backward to the desired position (Figure 5).
Figure 5.
Front-to-back adjustment
Retainer knob for
the spray insert and
the heater
Front-to-back
position indicator
Front-to-back
• Turn the side rotational adjustment knob to rotate the heater (Figure 6).
Figure 6.
Rotational adjustment
Rotational position indicator
Rotational adjustment knob
3. Using your fingers, tighten the top two retainer knobs to secure the heater assembly in its
new position.
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Setting Up the API Source
Preparing the Spray Insert for the API Source
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3
Connecting the Inlet Plumbing
This chapter provides information about the sample introduction techniques and how to set
up the inlet plumbing for these techniques. For operational information about the syringe
pump and divert/inject valve, see Chapter 4, “Using the Syringe Pump and Divert/Inject
Valve.”
The MS Calibration Kit (see Table 1) and Performance Specification Kit (see Table 2) contain
the required components for the inlet plumbing connections.
Contents
• Sample Introduction Techniques
• Plumbing Connections
• Setting Up the Syringe Pump
• Setting Up the Inlet Plumbing
• Setting Up the Inlet for an LC/MS System with an Autosampler
• Connecting the Grounding Union to the H-ESI Spray Insert
Sample Introduction Techniques
The TSQ Endura and TSQ Quantiva MSs have an external syringe pump and divert/inject
valve. The following techniques are available to introduce samples into the API source:
• Direct Infusion
• High-Flow Infusion
• Loop Injection (Flow-Injection Analysis)
• High-Performance Liquid Chromatography (HPLC) with an Autosampler
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Connecting the Inlet Plumbing
Sample Introduction Techniques
Figure 7 shows schematic drawings of these sample introduction techniques.
IMPORTANT Compound optimization solutions, such as the reserpine sample solution,
can contaminate your system at high concentrations. For best results, use the LC flow
technique of automatic-loop injection to introduce optimization solutions into the mass
spectrometer.
Direct Infusion
The direct infusion technique uses the syringe pump to infuse sample directly into the API
source. Use this technique to introduce the calibration solution for calibrating in H-ESI
mode. You can also use this technique to introduce a solution of pure analyte at a steady rate
for qualitative analyses and perform experiments at a low flow rate with the syringe pump.
For plumbing instructions, see “Setting Up the Inlet for Direct Infusion.”
High-Flow Infusion
The high-flow infusion technique uses an LC union Tee to direct the solvent flow from the
syringe pump into the solvent flow produced by an LC pump. The combined solvent flow
goes through the divert/inject valve into the API source. Use this infusion method to perform
experiments at a higher flow rate with an LC system. The high-flow infusion method puts a
comparatively large amount of solvent into the mass spectrometer, which means you might
need to clean the ion spray cone more frequently.
When the divert/inject valve is in the Load position, solvent flow from the LC pump enters
the valve through port 6 and exits the valve through port 5, which connects to the API source.
When the divert/inject valve is in the Inject position, solvent flow from the LC pump enters
the valve through port 6 and exits the valve through port 1 to waste.
For plumbing instructions, see “Setting Up the Inlet for High-Flow Infusion.” For
information about the valve configurations, see “Configurations.”
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Connecting the Inlet Plumbing
Sample Introduction Techniques
Loop Injection (Flow-Injection Analysis)
Use the loop injection technique when there is a limited amount of sample. To use this
technique, attach a sample loop, an injection port fitting, and an LC pump to the
divert/inject valve, and then connect the divert/inject valve to the API source. With the valve
in the Load position, use a syringe to load sample through the injection port fitting into the
sample loop, and then switch the position of the inject valve to the Inject position. Switching
the valve to the Inject position allows the solvent flow from the LC pump to backflush the
sample out of the loop and into the API source.
Additionally, follow these guidelines:
• Use a manual loop injection without chromatographic separation for qualitative or
quantitative analysis when there is a limited amount of a pure sample.
• Use a manual loop injection with chromatographic separation for qualitative or
quantitative analysis when there is a limited amount of a sample mixture. Requires an LC
column between the injection valve and the API source.
• Use an automatic loop injection to optimize the mass spectrometer’s sensitivity to a
compound for an MS/MS experiment.
For plumbing instructions, see “Setting Up the Inlet for Manual or Auto-Loop Injections.”
High-Performance Liquid Chromatography (HPLC) with an Autosampler
To perform loop injection by using the liquid chromatography (LC) technique, install an LC
column between the sample inlet of the API source and port 6 of the divert/inject valve, or
connect an LC system with an autosampler to the mass spectrometer.
To automatically inject a set of samples, connect an LC system with an autosampler to the
divert/inject valve and connect the divert/inject valve to the API source. Use the autosampler
to inject sample solution into the flow from an LC pump. In a typical LC/MS experiment,
direct the solvent flow through an LC column to separate the compounds of a mixture before
they are directed into the API source.
For plumbing instructions, see “Setting Up the Inlet for an LC/MS System with an
Autosampler.”
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Connecting the Inlet Plumbing
Sample Introduction Techniques
Figure 7.
Schematics of the sample introduction techniques (examples)
Legend
Red PEEK tubing
Teflon FEP tubing
Direct infusion
Syringe pump
High-flow infusion
(divert valve)
API source
LC pump
Waste
2
1
6
3
4
Syringe pump
5
API source
Manual loop injection
(loop injector)
LC pump
2
1
6
3
Waste
4
5
API source
Automatic loop injection
(loop injector)
Syringe pump
LC pump
2
1
6
3
Waste
4
5
API source
HPLC with autosampler
(divert valve)
2
1
6
3
4
Waste
5
Column
Autosampler
LC pump
API source
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Connecting the Inlet Plumbing
Plumbing Connections
Plumbing Connections
The modular divert/inject valve shipped with your order is a six-port, two-position,
Rheodyne™ injection valve. The ports use standard 10-32 fittings for high-pressure and
1/16 in. OD tubing. To connect the high-pressure tubing to the valve, use the one-piece
fingertight fittings provided in the MS Calibration Kit (see Table 1 in the Preface).
IMPORTANT To help ensure spray stability, make sure that all PEEK tubing is not
crimped, kinked, or otherwise damaged.
Ensure the following when you make the plumbing connections:
• The ends of the PEEK tubing are squarely cut (Figure 8). For best results, use a polymeric
tubing cutter to ensure square cuts. Poorly cut tubing can cause flow restrictions.
• The PEEK tubing makes contact with the bottom of the receiving port. Tubing that is
not properly seated can add dead volume to a chromatographic system.
• The fittings are not overtightened. Tighten the PEEK fittings by using your fingers only,
not a wrench. Overtightening the PEEK fittings can cause leaks.
Figure 8.
Proper connection for the PEEK tubing and fitting (syringe adapter assembly)
Fingertight
PEEK fitting
Red PEEK tubing
Union with 10-32, coned-bottom,
receiving port
Properly seated, square-cut end
Setting Up the Syringe Pump
Use the syringe pump to directly infuse sample into the API source, to infuse sample into the
solvent stream that is produced by an LC pump, or to automatically load sample into the
divert/inject valve.
IMPORTANT To minimize the possibility of cross-contamination, do the following:
• Use a different syringe and length of PEEK tubing for each type of solution.
• Wipe off the needle tip with a clean, lint-free tissue before reinserting the syringe into
the syringe adapter assembly.
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Connecting the Inlet Plumbing
Setting Up the Inlet Plumbing
 To set up the syringe for infusion or high-flow infusion experiments
1. Load a clean, 500 μL syringe with the sample solution.
CAUTION Sharp object. The syringe needle can puncture your skin. Handle it with
care.
2. Using one of the two-piece, fingertight fittings, connect a 4 cm (1.5 in.) length of Teflon
tubing to the (black) LC union (Figure 9).
The LC union has a 10-32, coned-bottom receiving port.
Figure 9.
Plumbing connection for the syringe
LC union
Fingertight fitting
Fingertight
ferrule
Syringe
Teflon tube
3. Hold the plunger of the syringe in place and carefully insert the tip of the syringe needle
into the free end of the tubing.
Note If necessary, use the syringe needle tip to enlarge the opening slightly in the end
of the tubing.
4. Place the syringe into the syringe holder of the syringe pump.
5. Squeeze the release button on the syringe pump’s pusher block and slowly move the
pusher block until it contacts the syringe plunger.
Setting Up the Inlet Plumbing
This section describes how to set up the inlet plumbing for the following techniques:
• Setting Up the Inlet for Direct Infusion
• Setting Up the Inlet for High-Flow Infusion
• Setting Up the Inlet for Manual or Auto-Loop Injections
IMPORTANT To help ensure spray stability, make sure that all PEEK tubing is not
crimped, kinked, or otherwise damaged.
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Connecting the Inlet Plumbing
Setting Up the Inlet Plumbing
Setting Up the Inlet for Direct Infusion
Figure 10 shows the inlet plumbing connections to introduce sample into the API source by
using direct infusion. For instrument calibration, remember to use the natural PEEK tubing.
 To connect an infusion line between the LC union and the grounding union
1. Set up the syringe pump; see “Setting Up the Syringe Pump.”
2. Use red PEEK tubing (infusion line) to connect the LC union to the grounding union as
follows (Figure 10):
• Using a two-piece fingertight fitting, connect one end of the tubing to the free end of
the LC union that connects to the syringe.
• Using a two-piece fingertight fitting, connect the other end to the grounding union.
3. Follow the procedure in “Connecting the Grounding Union to the H-ESI Spray Insert.”
This completes the inlet setup for the direct infusion technique.
Figure 10. Plumbing connections for direct infusion (H-ESI mode)
Two-piece, two-wing
fingertight fitting
Syringe
LC union and
fingertight fitting
Red PEEK tubings
Two-piece
fingertight fitting
Sample inlet
(part of the source)
Grounding union holder
(part of the source)
For APCI mode, this path
through the grounding
union is optional.
(The parts are in the
Source LC Connection
Kit.)
Grounding union
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Connecting the Inlet Plumbing
Setting Up the Inlet Plumbing
Setting Up the Inlet for High-Flow Infusion
Table 9 lists the plumbing connections required to set up the system for a high-flow infusion
experiment. (You can make the connections in any order.)
Table 9. Connections for high-flow infusion
Connection
Location
Reference
1
Connect the syringe to the union Tee.
Connecting the Syringe to the
Union Tee
2
Connect the LC pump to the union Tee.
Connecting the LC pump to
the Union Tee
3
Connect the union Tee to the divert/inject Connecting the Union Tee to
valve.
the Divert/Inject Valve
4
Connect port 1 of the divert/inject valve to Connecting the Divert/Inject
a waste container.
Valve to a Waste Container
5
For H-ESI mode, connect the union Tee to Connecting the Union Tee to
the grounding union. For APCI mode,
the API Source
connect the union Tee directly to the
sample inlet.
6
For H-ESI mode, connect the grounding
union to the sample inlet of the H-ESI
spray insert.
Connecting the Grounding
Union to the H-ESI Spray
Insert
Connecting the Syringe to the Union Tee
 To connect the syringe to the union Tee
1. Set up the syringe pump; see “Setting Up the Syringe Pump.”
2. Use red PEEK tubing (infusion line) to connect the LC union to the union Tee as follows
(Figure 11):
• Using a two-piece fingertight fitting, connect one end of the tubing to the free end of
the LC union that connects to the syringe.
• Using a two-piece fingertight fitting, connect the other end to the union Tee.
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Connecting the Inlet Plumbing
Setting Up the Inlet Plumbing
Figure 11. Plumbing connection between the LC union and the union Tee
Two-piece fingertight fitting
LC union
Union Tee
Two-piece fingertight fitting
Red PEEK tubing
Connecting the LC pump to the Union Tee
 To connect the LC pump to the divert/inject valve
• Using an appropriate fitting, connect a length of red PEEK tubing to the outlet of the
LC pump.
• Using a two-piece fingertight fitting, connect the other end of the tubing to the
union Tee (Figure 12).
Figure 12. Plumbing connection between the union Tee and the divert/inject valve
Connect this end to the
LC pump.
Union Tee
Sample input to port 6 on
the divert/inject valve
Two-piece fingertight fitting
to union Tee
One-piece fingertight fitting
to port 6
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Connecting the Inlet Plumbing
Setting Up the Inlet Plumbing
Connecting the Union Tee to the Divert/Inject Valve
 To connect the union Tee to the divert/inject valve
• Using a one-piece fingertight fitting, connect a length of red PEEK tubing to the
union Tee (Figure 12).
• Using a one-piece fingertight fitting, connect the other end of the tubing to port 6 of
the divert/inject valve.
Connecting the Divert/Inject Valve to a Waste Container
 To connect the divert/inject valve to a waste container
• Using a one-piece fingertight fitting, connect a length of the Teflon tubing to port 1
of the divert/inject valve.
• Insert the other end of the tubing into a suitable waste container.
Connecting the Union Tee to the API Source
 To connect the union Tee to the API source
1. Using a fingertight fitting and a ferrule, connect a length of red PEEK tubing to the
union Tee (Figure 13).
Figure 13. Plumbing connection between the union Tee and the grounding union
Union Tee
Red PEEK tubing
Two-piece
fingertight fitting
Grounding
union
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Two-piece
fingertight fitting
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3
Connecting the Inlet Plumbing
Setting Up the Inlet Plumbing
2. Do one of the following to connect the other end of the tubing:
• For H-ESI mode, use a two-piece fingertight fitting to connect the other end of the
tubing to the grounding union (Figure 10).
For instructions on how to connect the other end of the grounding union, see
“Connecting the Grounding Union to the H-ESI Spray Insert.”
–or–
• For APCI mode, use a two-piece fingertight fitting to connect the other end of the
tubing directly to the sample inlet of the APCI spray insert.
Note The plumbing path through the grounding union of the API source is
optional for APCI mode. A knurled nut secures the grounding bar to the API
source housing. You do not need to remove the grounding bar if you choose not
to use that plumbing path in the APCI mode.
This completes the inlet setup for the high-flow infusion technique.
Setting Up the Inlet for Manual or Auto-Loop Injections
Figure 14 shows the inlet plumbing connection to introduce sample into the API source by
using manual or auto-loop injection.
 To set up the inlet for loop injections
1. Do one of the following:
• To load sample automatically with the syringe pump, set up the syringe pump; see
“Setting Up the Syringe Pump.” Using a red PEEK infusion line, make the following
connections:
–
Using a two-piece fingertight fitting, connect one end of the infusion line to the
free end of the LC union that connects to the syringe.
–
Using a one-piece fingertight fitting, connect the other end to port 2 of the
divert/inject valve.
–or–
• To load sample manually with a hand-held syringe, connect the needle port to port 2
of the divert/inject valve (Figure 14).
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Connecting the Inlet Plumbing
Setting Up the Inlet Plumbing
Figure 14. Divert/inject valve setup for manual loop injection
Port 2 to a loop
filler (needle port)
Sample loop from
port 1 to port 4
Port 6 to the LC pump
1
3
Port 3 to a waste
container
6
4
5
Port 5 to the grounding union (H-ESI
mode) or the spray insert’s sample
inlet (APCI mode)
2. Connect a sample loop from port 1 to port 4 of the divert/inject valve.
3. Use red PEEK tubing to connect port 6 of the divert/inject valve to the LC pump as
follows:
• Using an appropriate fitting and ferrule, connect one end of the tubing to the outlet
of the LC pump.
• Using a one-piece fingertight fitting, connect the other end to port 6 of the
divert/inject valve.
4. Connect port 5 of the divert/inject valve to the API source:
a. Using a one-piece fingertight fitting, connect a length of red PEEK tubing to port 5
of the divert/inject valve.
b. Depending on whether you installed the H-ESI or APCI spray insert, do one of the
following:
• For H-ESI mode, use a two-piece fingertight fitting to connect the other end of
the red PEEK tubing that connects to port 5 of the divert/inject valve to the
grounding union.
For instructions on how to connect the other end of the grounding union, see
“Connecting the Grounding Union to the H-ESI Spray Insert.”
–or–
• For APCI mode, connect the other end of the red PEEK tubing to the sample
inlet of the APCI spray insert (Figure 15). Or, you can connect the tubing to the
installed grounding union and associated flow path (Figure 10 or Figure 16).
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3 Connecting the Inlet Plumbing
Setting Up the Inlet for an LC/MS System with an Autosampler
Figure 15. Plumbing connections for manual loop injection (APCI mode)
Loop filler (needle port)
APCI spray
insert
Port 6 of the
divert/inject valve to
the LC pump
Port 3 to waste
Port 5 of the divert/inject
valve to the sample inlet of
the APCI spray insert
5. Use Teflon tubing to connect port 3 of the divert/inject valve to a waste container as
follows:
• Using a Rheodyne fitting, connect one end of the tubing to port 3 of the divert/inject
valve.
• Place the other end into an appropriate waste container.
This completes the inlet setup for the manual and auto-loop injection techniques.
Setting Up the Inlet for an LC/MS System with an Autosampler
This section describes how to connect the inlet plumbing to introduce sample into the API
source from the autosampler in an LC system.
 To connect the inlet plumbing for an LC/MS system with an autosampler
1. Use red PEEK tubing to connect port 6 of the divert/inject valve to the outlet of the
autosampler as follows:
• Using an appropriate fitting and ferrule, connect one end of the tubing to the outlet
of the autosampler.
• Using a one-piece fingertight fitting, connect the other end to port 6 of the
divert/inject valve.
2. Use Teflon tubing to connect port 1 of the divert/inject valve to a waste container as
follows:
• Using a Rheodyne fitting, connect one end of the tubing to port 1 of the divert/inject
valve.
• Place the other end into an appropriate waste container.
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Connecting the Inlet Plumbing
Connecting the Grounding Union to the H-ESI Spray Insert
3. Do one of the following to connect port 5 of the divert/inject valve to the API source:
• For H-ESI mode, use a one-piece fingertight fitting to connect a length of red PEEK
tubing between port 5 of the divert/inject valve and the grounding union.
For instructions on how to connect the other end of the grounding union, see
“Connecting the Grounding Union to the H-ESI Spray Insert.”
–or–
• For APCI mode, use a one-piece fingertight fitting to connect a length of red PEEK
tubing between port 5 of the divert/inject valve and the sample inlet of the APCI
spray insert.
This completes the inlet setup for using an autosampler in an LC/MS system.
Connecting the Grounding Union to the H-ESI Spray Insert
Figure 16 shows the connection between the grounding union and the sample inlet of the
H-ESI spray insert. The grounding union is not required for the APCI mode plumbing.
CAUTION To prevent electric shock, verify that the grounding union is made of stainless
steel. A grounding union made of a nonconductive material, such as PEEK, creates an
electric shock hazard.
Figure 16. Plumbing connections for the grounding union (H-ESI mode)
For APCI mode, the grounding
union and this plumbing path
are not required.
H-ESI spray insert
Sample input
Grounding union installed in
the grounding union holder
(bar)
API source housing
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4
Using the Syringe Pump and Divert/Inject Valve
This chapter describes the external syringe pump and divert/inject valve that ship with the
TSQ Endura or TSQ Quantiva mass spectrometer. For information about installing these
components, refer to the TSQ Endura and TSQ Quantiva Getting Connected Guide.
Contents
• Syringe Pump
• Divert/Inject Valve
Syringe Pump
The external Chemyx™ Fusion 100T syringe pump delivers sample solution from an installed
syringe, through the sample transfer line (red PEEK), and into the API source. The motorized
pusher block (Figure 17) depresses the syringe plunger at the flow rate specified in the data
system. (The default flow rate for calibration is 5 μL/min.)
You can start and stop the syringe pump from the data system; refer to the data system Help
for instructions. You can also start and stop the syringe pump by pressing the syringe pump
buttons.
Note If you choose to provide a syringe pump other than the Fusion 100T, ensure that it
can provide a steady, continuous flow of 1–5 μL/min.
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Using the Syringe Pump and Divert/Inject Valve
Divert/Inject Valve
Figure 17. Syringe pump setup (top view)
Teflon
tubing
Fingertight
fittings
LC union, internal view
Syringe pump
Red PEEK
tubing
Pusher block
Release
knob
Syringe
holder
Syringe
Divert/Inject Valve
The external Rheodyne MX Series II™ divert/inject valve is a 6-port motorized valve that
switches between two positions. In the first position, port one connects internally to port two,
port three connects to port four, and port five connects to port six. In the second position, the
valve rotates one position so that port one connects internally to port six, port two connects to
port three, and port four connects to port five. Figure 18 shows the valve’s internal flow paths
for both positions.
The Method Editor in the Xcalibur application identifies the valve’s two positions as “1–2”
(port 1 to 2) and “1–6” (port 1 to 6).
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Using the Syringe Pump and Divert/Inject Valve
Divert/Inject Valve
Figure 18. Divert/inject valve positions
Internal connection path
(light gray)
2
1
2
Port 1 internally switches between port 2
(position 1–2) and port 6 (position 1–6, shown).
1
Valve screw
6
3
4
5
Position 1–2
3
6
4
5
Position 1–6
Configurations
You can configure (plumb) the divert/inject valve as a loop injector (for flow injection
analysis) or as a divert valve. The divert valve can switch the solvent front, gradient endpoint,
or any portion of the LC run to waste. Figure 19 shows both of these configurations.
In the loop injector valve configuration, the valve switches between these two positions:
• Load (position 1–2)—The sample loop is isolated from the solvent stream. Solvent flow
from the LC pump enters and exits the valve through ports five and six, respectively.
When you load the sample into port two, the sample enters and exits the sample loop
through ports one and four, respectively. As you overfill the sample loop, the excess
sample exits the valve through port three to waste.
• Inject (position 1–6)—The sample loop is open to the solvent stream. The solvent flow
from the LC pump flushes sample out of the sample loop, and then exits through port six
into the API source.
In the divert valve configuration, the valve switches between these two positions:
• Detector (position 1–2)—Solvent flow from the LC pump enters the valve through port
five and exits through port six into the API source.
• Waste (position 1–6)—Solvent flow from the LC pump enters the valve through port five
and exits through port four to waste.
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Using the Syringe Pump and Divert/Inject Valve
Divert/Inject Valve
Figure 19. Divert/inject valve plumbed as a loop injector and as a divert valve
Sample loop
Sample input
1
2
6
3
Waste
4
1
2
6
3
4
5
5
API source
API source
Waste
LC pump
LC pump
Loop injector
(Position 1–2 with load configuration)
Divert valve
(Position 1–2 with detector configuration)
Controlling the Divert/Inject Valve
You can control the divert/inject valve as follows:
• Use the mass spectrometer’s data system to specify the parameters in the Divert Valve
Properties pane of the Method Editor. For instructions, refer to the Xcalibur Method
Editor Help.
• Use the valve’s control buttons (Figure 20) to divert the LC flow between the mass
spectrometer and waste when the valve is in the divert valve configuration, or switch
between load and inject modes when the valve is in the loop injector configuration. For
instructions, refer to the manufacturer’s manual.
Figure 20. Divert/inject valve (front view)
Valve position indicator
Six-port, two-position valve
Valve control buttons
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Preparing the System for Calibration
This chapter describes how to prepare the TSQ Endura or TSQ Quantiva system before you
calibrate the mass spectrometer.
IMPORTANT You must pump down the instrument for the full 15 hours before you start
the instrument calibration process.
Contents
• Pumping Down the Mass Spectrometer
• Setting Up the Syringe Pump for Direct Infusion
• Setting Up the Mass Spectrometer for Calibration
Pumping Down the Mass Spectrometer
To help optimize the performance of the mass spectrometer, pump down the vacuum system
for at least 15 hours.
 To pump down the mass spectrometer
1. Check that the forepumps’ exhaust tubing connect to the exhaust system and that any
valves in the exhaust path are open.
2. Turn on the forepumps’ power switches.
3. Place the electronics service switch in the Service Mode (down) position (Figure 21).
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Preparing the System for Calibration
Pumping Down the Mass Spectrometer
Figure 21. Power entry module (right side of the instrument)
Electronics service
switch
Main Power
switch
4. Turn on the Main Power switch.
The LEDs on the front panel remain off.
5. Verify that the forepumps are running and that there are no leaks in the connection
between the forepumps and the mass spectrometer.
6. Wait 1 hour.
7. Place the electronics service switch in the Operating Mode (up) position.
The mass spectrometer’s restart sequence begins. The Power LED on the front panel turns
green, and the Vacuum, Communication, and System LEDs remain off. When the
instrument startup process is complete, the Vacuum and Communication LEDs are green
and the System LED is yellow.
8. Open the Status pane in the Tune window (see page 68), click the downward arrow, and
then choose By Board (Figure 22).
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Pumping Down the Mass Spectrometer
Figure 22. By Board page in the Status pane
Opens and closes the
selected pane.
Includes the source
vacuum gauges.
Click to select By Function
or By Board.
9. Check the readback values for the source pressure gauges as follows:
• Double-click Source Board, and then verify that the Source Pressure and Analyzer
Pressure readback values are below the operating threshold limits (see Table 10).
Table 10. Threshold limits for the vacuum pressure gauges
Instrument
Source pressure (Torr)
TSQ Endura
2.5
TSQ Quantiva
4.5
Analyzer pressure (Torr)
9.0 × 10–6
Normal readback measurements show a green square ( ). If the vacuum pressure
values are normal, follow the next procedure “Setting Up the Syringe Pump for
Direct Infusion.”
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Preparing the System for Calibration
Setting Up the Syringe Pump for Direct Infusion
Setting Up the Syringe Pump for Direct Infusion
Use the syringe pump to infuse the calibration solution directly into the H-ESI source. For
information about the syringe pump, see “Syringe Pump” on page 33.
IMPORTANT To minimize the possibility of cross-contamination, use a different syringe
and length of PEEK tubing for each type of solution.
 To set up the syringe pump for direct infusion of the calibration solution
1. Turn on the syringe pump’s power switch.
The power switch is located on the back of the device.
2. In the Tune window, place the mass spectrometer in Standby mode.
3. Load a clean, 500 μL syringe with 500 μL of the ESI positive calibration solution.
For a list of provided solutions, see “Chemical Kit.”
Note To minimize the possibility of cross-contamination of the assembly, be sure to
wipe off the tip of the needle with a clean, lint-free tissue before reinserting it into the
syringe adapter assembly (Figure 8).
4. Plumb the inlet for direct infusion as follows:
a. Follow steps 2–5 in “To set up the syringe for infusion or high-flow infusion
experiments” on page 24.
b. Follow steps 2 and 3 in “To connect an infusion line between the LC union and the
grounding union” on page 25.
CAUTION To prevent electric shock, verify that the grounding union is made of
stainless steel and is completely inserted into the grounding union holder.
Go to the next section, “Setting Up the Mass Spectrometer for Calibration.”
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5 Preparing the System for Calibration
Setting Up the Mass Spectrometer for Calibration
Setting Up the Mass Spectrometer for Calibration
Before you calibrate the mass spectrometer, set up the operational parameters.
CAUTION Before beginning normal operation of the mass spectrometer each day, verify
that there is sufficient nitrogen for the API source. If you run out of nitrogen, the mass
spectrometer automatically turns off to prevent atmospheric oxygen from damaging the
source. The presence of oxygen in the source when the mass spectrometer is on can be
unsafe. In addition, if the mass spectrometer turns off during an analytical run, you might
lose data.
 To set up the mass spectrometer for calibration
1. In the Tune window, place the mass spectrometer in On mode.
2. Open the Ion Source page in the Ion Source pane, and then do the following:
a. In the Current LC Flow (μL/min) box, enter 3.
b. Click Get Defaults, and then click Apply.
The Tune application sets the default parameters for the H-ESI source.
3. Set the syringe pump parameters as follows:
a. Click the dropdown arrow,
syringe parameters box.
, next to the Syringe On/Off button to open the
b. In the Flow Rate (μL/min) box, type 3.
c. In the Volume (μL) list, select 500.
The Tune application automatically sets the internal diameter (ID) for the syringe
volume.
d. Click Syringe On (Off ) to start the syringe pump.
4. Click Positive (Negative) to select the positive ion polarity mode.
5. Click Standard Pressure Mode (Intact Protein Mode) to select the standard pressure
mode.
6. Verify that the system readback is normal (see page 69).
This completes the setup for calibrating the mass spectrometer. Go to Chapter 6,
“Establishing a Stable Ionization Spray.”
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Preparing the System for Calibration
Setting Up the Mass Spectrometer for Calibration
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Establishing a Stable Ionization Spray
Before you calibrate the mass spectrometer, make sure that you establish stable ionization
spray conditions. The intensity and stability of the ionization spray largely depend on the
performance of the API source.
IMPORTANT
• Failure to maintain a stable spray might compromise the data quality or result in a
poor calibration or diagnostic result.
• If the spray becomes unstable with your analyte solution, return to this chapter to
evaluate the spray stability.
Contents
• Evaluating the Spray Stability
• Optimizing the API Source Parameters
Evaluating the Spray Stability
Use the Plot Chromatogram tool (
) to evaluate the API source’s ionization spray.
 To evaluate the spray stability
1. Open the Tune window.
2. Set up the system to use the calibration solution as follows:
a. Verify that the syringe contains the appropriate calibration solution.
b. In the Tune window, verify the following syringe and instrument settings:
–
2 μL/min in the Current LC Flow box
–
500 μL/min flow rate and 500 μL syringe volume
–
Positive ion polarity mode
–
Profile data type
c. Go to step 4.
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Establishing a Stable Ionization Spray
Evaluating the Spray Stability
3. (Optional) Set up the system to use an analyte solution as follows:
• Verify that the LC device or the syringe contains a sufficient amount of the analyte.
• Open the Ion Source page in the Ion Source pane, and verify the value in the Current
LC Flow (μL/min) box.
4. Place the mass spectrometer in On mode (see page 69).
The mass spectrometer begins scanning and applies high voltage to the spray insert. A
real-time mass spectrum appears in the Tune window.
5. Turn on the flow for the solution as follows:
• For the calibration solution, click Syringe On (Off ) to start the syringe pump.
–or–
• For an analyte solution, turn on the flow from the LC device or the syringe pump.
A real-time plot of the solution’s mass spectrum appears.
6. Plot the full total ion current (TIC) and relative standard deviation (RSD) graphs as
follows:
a. Click the Plot Chromatogram icon,
box (Figure 23).
, to open the Plot Chromatogram dialog
Figure 23. Plot Chromatogram dialog box with the TIC option selected
b. Select the Spray Stability check box to monitor the relative standard deviation
(RSD) of the desired ion current.
c. Select the TIC option.
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Establishing a Stable Ionization Spray
Optimizing the API Source Parameters
d. Click OK to plot the TIC chromatogram.
The Plot Chromatogram tool generates a real-time graph (plot) of the full TIC where
you can observe the signal stability and the effects of changes to various parameters.
The tool also generates a real-time graph of the RSD of the 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.
7. Observe the RSD graph, and review the signal stability rating and maximum %RSD
value.
Table 11 lists the criteria for a stable spray in either positive or negative ion polarity mode.
Table 11. Recommended %RSD values and ratings for the calibration solutions
Ion polarity mode
Acceptable signal
stability rating
Maximum %RSD (threshold)
Positive
Excellent or Good
15
Negative
Excellent or Good
15
8. If the signal stability rating is poor or the %RSD value is above the threshold, follow the
procedure in the next section, “Optimizing the API Source Parameters.”
IMPORTANT Thermo Fisher Scientific recommends that you optimize the API source
parameters only if the preceding spray evaluation determines that the ionization spray is
unstable.
This completes the spray stability evaluation.
Optimizing the API Source Parameters
If the ionization spray is unstable, follow the procedure in this section to optimize the API
source parameters.
IMPORTANT Thermo Fisher Scientific recommends that you optimize the API source
parameters only if the preceding spray evaluation determines that the ionization spray is
unstable.
 To optimize the API source parameters
1. Verify that the syringe has a sufficient amount of the calibration solution.
2. In the Tune window, click Syringe On (Off ) to start the syringe pump.
For an analyte solution, turn on the flow from the syringe pump or the LC device.
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Establishing a Stable Ionization Spray
Optimizing the API Source Parameters
3. Open the Optimization page of the Ion Source pane, and then do the following:
a. Select the Polarity Ion Spray Voltage (V) option (Figure 24).
Figure 24. Optimization page of the Ion Source pane
Optimization tab
(selected)
b. In the Signal Type list, select TIC.
c. Click Optimize.
The status area displays the message “Optimization In Progress.” After Tune
completes the optimization, the optimized value and the Accept and Reject buttons
appear.
d. Click Accept.
The Report Generation Options dialog box opens (Figure 25).
Figure 25. Report Generation Options dialog box
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Establishing a Stable Ionization Spray
Optimizing the API Source Parameters
e. Select an option, and then click OK.
Tip To turn off the Report Generation Options dialog box, see “Setting the Tune
Preferences” on page 72.
4. Optimize the remaining source parameters.
5. (Optional) Save the parameters’ state in the Favorites pane (see page 76). For additional
information about the Favorites pane, refer to the Tune Help.
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Establishing a Stable Ionization Spray
Optimizing the API Source Parameters
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Performing the Tune, Calibration, or Calibration
Check
This chapter describes how to tune, calibrate, or check the calibration of the TSQ Endura and
TSQ Quantiva MSs in H-ESI mode. The tune, calibrate, and calibration evaluation
procedures require that you infuse the calibration polytyrosine 1-3-6 calibration solution into
the instrument at a steady flow rate.
Contents
• Performing System Tune and Calibration
• Spray Stability Evaluation
• System Tune and Check
• Check Mass Position and Resolution
• Calibrate Mass Position and Resolution
• Detector Gain Calibration
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Performing the Tune, Calibration, or Calibration Check
Performing System Tune and Calibration
Performing System Tune and Calibration
Calibration parameters are instrument parameters that affect the mass accuracy and
resolution. Calibrate the TSQ Endura and TSQ Quantiva MSs in H-ESI mode before
acquiring data in H-ESI or APCI mode. Generally, you must calibrate the mass spectrometer
every one to three months of operation for optimum performance over the entire mass range
of the mass analyzer.
Tune parameters are instrument parameters that affect the magnitude of the ion signal. There
are two types of tune parameters: mass dependent and compound dependent.
• Mass-dependent tune parameters include the rf voltage of the rf lens, the dc offset
voltages of multipoles M00 and M0, and the dc offset voltages of lenses L11, L12, L21,
L23, L31, L33, and L4.
• Compound-dependent tune parameters include the spray voltage (H-ESI or NSI mode)
or spray current (APCI mode), sheath gas pressure, auxiliary gas pressure, sweep gas
pressure, vaporizer temperature, and ion transfer tube temperature. Use the Optimization
page of the Ion Source pane to optimize the spray voltage or spray current, sheath gas
pressure, auxiliary gas pressure, and sweep gas pressure for your compound, whenever you
change experiments. See Chapter 8, “Optimizing the API Source Parameters.”
Note The Tune application writes the calibration parameters and the mass-dependent
tune parameters to the calibration file. It writes the compound-dependent tune
parameters to a change record in the History pane. You can rename and save the change
record to the Favorites pane for future use in the Tune application or the Method Editor.
See “Using the History Pane” on page 75.
 To perform system tune and calibration
1. Set up to infuse the polytyrosine 1-3-6 calibration solution at 2 μL/min into the API
source. See “Setting Up the Syringe Pump for Direct Infusion.”
2. Click Calibration to display the Calibration Status page, and then click Calibrate to
display the Calibration Options pane (Figure 26).
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Performing the Tune, Calibration, or Calibration Check
Spray Stability Evaluation
Figure 26. Calibration – Options page
3. Clear the Skip Spray Stability Evaluation check box.
4. Under Quad Selection, select the Q1MS, Q3MS, or Both option.
5. Under System Tune and Calibration Options, select one of the following options:
• System Tune and Check
• Check Mass Position and Resolution
• Calibrate Mass Position and Resolution
• Detector Gain Calibration
6. Click Start.
7. When the procedure is complete, select a report generation option and click OK.
Note When it completes a calibration, the mass spectrometer writes the calibration
parameters to a calibration file, which overwrites the previous calibration file. You
cannot replace or modify the calibration file.
Spray Stability Evaluation
The spray stability evaluation generates real-time graphs of both the TIC and the RSD of
the TIC. See “Evaluating the Spray Stability” on page 43. The %RSD must be less than
15 percent for the spray stability evaluation to pass.
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Performing the Tune, Calibration, or Calibration Check
System Tune and Check
System Tune and Check
When you select the System Tune and Check option (Figure 26), the mass spectrometer
maximizes the ion signal by optimizing the rf voltage of the rf lens, the dc offset voltages of
multipoles M00 and M0, and the dc offset voltages of lenses L11, L12, L21, L23, L31, L33,
and L4. The system optimizes for polytyrosine 1, 3, and 6, and for quadrupoles Q1 and Q3.
Figure 27 shows the M00 multipole offset voltage optimization for polytyrosine 1, 3, and 6.
After the optimizations are complete, the system performs a mass position and resolution test.
For a description of the multipoles and lenses, refer to the TSQ Quantiva and TSQ Endura
Hardware Manual.
Figure 27. Normalized intensity as a function of the M00 multipole offset voltage
Check Mass Position and Resolution
On a regular basis, run the check mass position and resolution evaluation by selecting its
check box (Figure 26). If the evaluation fails, run the mass position and resolution calibration.
During the mass position and resolution evaluation, the Tune application compares the
measured isotopic peaks of polytyrosine 1-3-6 (red curve) with the theoretical isotopic peaks
(blue curve). Figure 28 shows the experimental (red curve) and theoretical (blue curve)
isotopic peaks of the polytyrosine trimer at a peak width of m/z 0.4. This procedure repeats
for the polytyrosine 1, 3, and 6, for m/z 0.4 and 0.7 peak widths, and for quadrupoles Q1 and
Q3.
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Performing the Tune, Calibration, or Calibration Check
Check Mass Position and Resolution
Figure 28. Isotopic peaks of the polytyrosine trimer at a peak width of m/z 0.4
Figure 29 shows the error range boxes for polytyrosine 1, 3, and 6. The y axis is the error range
of the peak widths from the expected peak width of m/z 0.4 (in mDa), and the x axis is the
error range of the mass positions from the expected mass position (in mDa). The mass
spectrometer measures the peak width and mass position over a large number of scans. The
error ranges boxes must be within ±20 mDa from the expected peak width and mass positions
for the evaluation to pass.
Figure 29. Error range of the polytyrosine 1-3-6
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Performing the Tune, Calibration, or Calibration Check
Calibrate Mass Position and Resolution
Calibrate Mass Position and Resolution
Use the Calibrate Mass Position and Resolution option (Figure 26) if the mass position and
resolution evaluation fails. During the mass position and resolution calibration, the
calibration procedure varies the rf and dc voltages that it applies to quadrupoles Q1 and Q3 to
best fit the measured peak widths and positions of the polytyrosine isotopic peaks (red curve
in Figure 28) to the theoretical peak widths and positions of those peaks (blue curve in
Figure 28). This procedure repeats for polytyrosine 1, 3, and 6, for m/z 0.4 and 0.7 peak
widths, and for quadrupoles Q1 and Q3.
Detector Gain Calibration
The detector gain decreases as the electron multiplier ages. The detector gain calibration
increases the voltage on the electron multiplier to maintain a gain of 5 × 105 for MS mode
and 2 × 106 for MS/MS mode. Select the Detector Gain option (Figure 26) if you notice a
falloff of the ion signal intensity.
You can now start using your analyte solution for data acquisition.
IMPORTANT Before you start using your analyte, follow the procedure “To flush the inlet
components” on page 81.
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8
Optimizing the API Source Parameters
This chapter describes how to optimize the API source parameters, including those that are
compound-dependent, such as the spray voltage or spray current and the pressures for the API
gases that maximize the ion signal of your analyte.
Contents
• Setting Up the Plumbing for Compound Optimization
• Determining the Initial API Source Settings
• Optimizing the RF Lens Voltage
• Optimizing the Collision Energy
Setting Up the Plumbing for Compound Optimization
Use the high-flow infusion technique to introduce the analyte into the mass spectrometer’s
API source. The high-flow infusion technique uses a Tee union to direct the analyte from the
syringe pump into an LC flow that is appropriate (flow rate and composition) for your
experiment. For plumbing instructions, see “Setting Up the Inlet for High-Flow Infusion.”
Proceed to the next section, Determining the Initial API Source Settings.
Determining the Initial API Source Settings
Use the Ion Source page of the Ion Source pane to determine the initial spray voltage,
pressures for the API gases, ion transfer tube temperature, and vaporizer temperature for the
LC flow rate of your experiment. These initial API source settings provide a starting point for
optimizing system performance. The optimal settings for your application depend on the
compounds of interest, the solvent matrix, and the chromatographic conditions.
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Optimizing the API Source Parameters
Determining the Initial API Source Settings
 To determine the initial API source settings
1. Open the Tune window.
2. Click Ion Source to display the Ion Source page of the Ion Source pane.
3. In the Current LC Flow (μL/min) box, type the flow rate (for example, 200) and click
Get Defaults.
Figure 30 shows the Ion Source page with the initial API source settings that are
appropriate for the 200 μL/min flow rate.
Figure 30. LC flow rate of 200 μL/min on the Ion Source – Ion Source page
4. Click Apply.
The Tune application makes a change record in the History pane. Proceed to the next section,
Optimizing the RF Lens Voltage.
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Optimizing the RF Lens Voltage
Optimizing the RF Lens Voltage
The rf lens transfers ions from the API source to the ion optics. Use the Define Scan –
Optimization page to find the optimum rf lens voltage for transmitting a precursor ion
through the rf lens.
Note The rf lens voltage is a mass-dependent tune parameter until you run the rf lens
voltage optimization. After that it is a compound-dependent tune parameter.
The magnitude of the rf lens voltage affects the mass spectrum as follows:
• Decreases the rf lens voltage, which does the following:
–
Decreases the amount of fragmentation of fragile ions in the rf lens.
–
Decreases the transmission of high m/z ions through the rf lens and increases the
transmission of low m/z ions.
• Increases the rf level, which does the following:
–
Increases the amount of fragmentation of fragile ions in the rf lens.
–
Increases the transmission of high m/z ions through the rf lens and decreases the
transmission of low m/z ions.
 To optimize the rf lens voltage
1. Set up the system for direct infusion or high-flow infusion (see “Setting Up the Inlet
Plumbing” on page 24).
2. Introduce the compound into the instrument at a steady flow rate.
3. Click Define Scan, and then click the Optimization tab to display the Optimization
page (Figure 31).
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Optimizing the API Source Parameters
Optimizing the RF Lens Voltage
Figure 31. Define Scan – Optimization page showing the rf lens voltage optimization settings
4. Specify the mass input option, either Formula or m/z.
5. Enter a name for the compound.
6. Specify the charge state.
7. Select the Precursor - Optimize RF Lens check box.
8. Click Optimize.
Figure 32 shows the intensity of the polytyrosine trimer ion signal (m/z 508.2) as a
function of the rf lens voltage. The optimization algorithm determined that the optimum
rf lens voltage is 118.0 V.
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Optimizing the Collision Energy
Figure 32. RF optimization for the polytyrosine trimer ion
After the optimization is complete, the optimized value, and the Accept and Reject
buttons appear.
9. Click Accept to accept the optimized value or Reject to reject it.
Optimizing the Collision Energy
The collision energy determines the product ion intensities from collision-induced
dissociation (CID) of the precursor ions in an MS/MS experiment. Use the Define Scan –
Optimization page to find the optimum collision energy for the MS/MS transitions of a single
precursor ion. The following example uses the polytyrosine trimer ion as the precursor ion.
 To optimize the collision energy
1. Set up the system for direct infusion or high-flow infusion (see “Setting Up the Inlet
Plumbing” on page 24).
2. Introduce the compound into the instrument at a steady flow rate.
3. Click Define Scan, and then click the Optimization tab to display the Optimization
page.
Figure 33 shows the settings for the collision energy optimization of the m/z 508.2 to 299
MS/MS transition of the polytyrosine trimer ion.
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Optimizing the API Source Parameters
Optimizing the Collision Energy
Figure 33. Define Scan – Optimization page showing the collision energy optimization
settings
4. Specify the mass input option for the precursor ion.
5. Enter a name for the compound.
6. Specify the charge state of the precursor ion.
7. Select the Product check box.
8. Select the CID gas pressure (in milliTorr).
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Optimizing the Collision Energy
9. Select the input option:
• Select Unknown Product Ions to optimize the collision energy for the top n most
intense product ions.
• Select Known Product Ions to optimize the collision energy for the product ions
that you list in the Product Mass table.
10. Click Optimize.
The Tune application plots the product ion intensity as a function of collision energy and
determines the optimum collision energy. Figure 34 shows the intensity of the m/z 508.2
to 299.15 MS/MS transition of the polytyrosine trimer ion as a function of the collision
energy (top) and the MS/MS spectrum of the polytyrosine trimer ion (bottom). The
optimization algorithm determined that the optimum collision energy is 24.0 V.
Figure 34. Collision energy optimization curve and MS/MS spectrum of the polytyrosine
trimer ion
After the optimization is complete, the optimized value, and the Accept and Reject
buttons appear.
11. Click Accept to accept the optimized value or Reject to reject it.
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Optimizing the API Source Parameters
Optimizing the Collision Energy
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Acquiring Sample Data
This chapter describes how to use the Tune application to manually acquire sample data and
how to use the Xcalibur data system to set the start (trigger) instrument before you run an
instrument method to acquire sample data.
Note
• Before you begin the analysis of the sample solution, make sure that you have
calibrated the mass spectrometer in H-ESI mode within the last three months.
• The data system computer automatically saves the acquired data to its hard drive.
Contents
• Using the Tune Application to Acquire Sample Data
• Using the Xcalibur Data System to Acquire Sample Data
Using the Tune Application to Acquire Sample Data
 To acquire a sample data file
1. Open the Data Acquisition pane (Figure 35), and then do the following:
a. (Optional) To change the destination folder for the raw data file, click the Browse
icon.
The default folder location is in C:\Thermo\Data.
b. In the File Name box, type reserpine (or the name of the analyte).
If the base file name already exists in the save location, the Tune application adds a
time-stamp suffix that consists of the year (YYYY), month (MM), day (DD), and
time (HHMMSS).
c. In the Sample Name box, type the name of the analyte (or other suitable label).
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Acquiring Sample Data
Using the Tune Application to Acquire Sample Data
d. In the Comment box, type a comment about the experiment.
For example, describe the ionization mode, scan type, scan rate, sample amount, or
method of sample introduction. The data system includes the comment in the header
information for the raw data file.
You can also add this information to reports created with the Xcalibur XReport
reporting application. To open this application, choose Start > All Programs >
Thermo Xcalibur > XReport.
e. Under Timed Acquisition, select the Continuously option (acquires data until you
stop the acquisition).
Figure 35. Data Acquisition pane in the Tune window
Start/stop the data
acquisition recording.
Click to open/close the
Data Acquisition pane.
File name box
2. Click Record to start data acquisition.
After the Tune parameters reach their specified settings, the data acquisition process
begins and the small circle on the Record button turns red (
).
3. When you are ready, click Record again to stop the acquisition.
The small circle on the Record button turns gray (not recording).
For more information about reviewing the acquired data, refer to the Thermo Xcalibur Qual
Browser User Guide or the Qual Browser Help.
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9 Acquiring Sample Data
Using the Xcalibur Data System to Acquire Sample Data
Using the Xcalibur Data System to Acquire Sample Data
Thermo Scientific mass spectrometry applications, such as the Xcalibur data system, can
control the connected external device. If the Xcalibur application can control the external
device, it selects the autosampler as the default start (trigger) instrument for a sequence run. If
the Xcalibur application cannot control the external device, it selects the mass spectrometer as
the start instrument, which means that you must change the start instrument to the
appropriate instrument as part of the Xcalibur sequence setup.
Follow these procedures:
1. To select the external start instrument
2. To acquire a data file by using the Xcalibur data system
 To select the external start instrument
1. Open the Xcalibur data system, and then choose View > Sequence Setup View to open
the Sequence Setup window.
2. Open the sequence that you want to run as follows:
a. Click the Open button and browse to the appropriate folder.
b. Select the sequence (.sld) file and click Open.
3. Choose Actions > Run Sequence or Actions > Run This Sample to open the Run
Sequence dialog box (Figure 36).
The Yes in the Start Instrument column indicates the default start instrument for the
sequence run.
Figure 36. Run Sequence dialog box (partial) showing the selected start instrument
The LC device is the start instrument.
Change Instruments
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9
Acquiring Sample Data
Using the Xcalibur Data System to Acquire Sample Data
4. If Yes appears in the Start Instrument column for the mass spectrometer or if you need to
change the start instrument to another device, click Change Instruments to open the
Change Instruments In Use dialog box (Figure 37).
Figure 37. Change Instruments In Use dialog box showing the MS as the start instrument
a. In the Start Instrument column, click the blank field to the right of the appropriate
triggering device (typically an autosampler) to move “Yes” to that field.
b. Click OK.
5. In the Run Sequence dialog box, complete the remaining selections.
6. Click OK.
This completes the start instrument setup.
 To acquire a data file by using the Xcalibur data system
For instructions, refer to the Instrument Setup and Sequence Setup topics in the Xcalibur
Help.
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A
Using Basic Tune Functions
This appendix describes some of the basic Tune functions that are used throughout this guide.
You enable several of the functions by pressing a toggle button. For additional information
about the Tune window, refer to the Tune Help.
Contents
• Opening the Tune Window
• Setting the Instrument Power Mode
• Checking the Instrument Readback Status
• Controlling the Syringe Pump
• Setting the Data Type
• Setting the Ion Polarity Mode
• Setting the Tune Preferences
• Using the Mass List Table in the Define Scan Pane
• Using the History Pane
• Using the Favorites Pane to Save System Settings
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Using Basic Tune Functions
Opening the Tune Window
Opening the Tune Window
 To open the Tune window
From the Windows taskbar, choose Start > All Programs > Thermo Instruments >
model x.x Tune (Figure 38).
For information about the buttons and icons in the Tune application and what they
control, refer to the Tune Help.
Figure 38. Tune window showing the Define Scan – Scan page
Three power mode icons
(On/Standby/Off)
Manual data
acquisition
Instrument readback
status
Chromatogram view
Spectrum view
Define Scan – Scan page
Plot Chromatogram tool
Controls for the graphs
Panes: Status, History, and Favorites
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A Using Basic Tune Functions
Setting the Instrument Power Mode
Setting the Instrument Power Mode
Use the three power mode icons in the Tune window (Figure 38) to set the mass
spectrometer’s power mode (on, standby, or off ).
Before you remove the API source or the spray insert, always place the system in standby
mode. The mass spectrometer then automatically switches to off mode.
In standby mode, the System LED on the front panel turns yellow and the mass spectrometer
turns off the electron multipliers, conversion dynodes, 8 kV power to the API source, main rf
voltage, and ion optic rf voltages. The auxiliary, sheath, and sweep gas flows remain on and
return to their standby default settings (2 arbitrary). For a list of the on/off status of the
components under varying power conditions, refer to Chapter 3 in the TSQ Endura and
TSQ Quantiva Hardware Manual.
 To set the instrument power mode
Click the icon for the power mode that you want (Figure 39).
The center of the selected icon changes from white to green.
Figure 39. Power mode icons showing the selected icon (mode)
On mode
Standby mode
Off mode
Checking the Instrument Readback Status
The system readback icon is located in the top, right corner of the Tune window. Table 12 lists
the various readback states.
Table 12. Instrument readback icons and their meanings (Sheet 1 of 2)
Icon
Thermo Scientific
Background color
Meaning
Green
The system parameters are within tolerance.
Green
The system is initializing.
Amber
One or more settings are changing.
Red
An error has occurred.
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Using Basic Tune Functions
Controlling the Syringe Pump
Table 12. Instrument readback icons and their meanings (Sheet 2 of 2)
Icon
Background color
Meaning
Gray
The API source is off.
Dark gray
There is no communication between the
mass spectrometer and the data system.
Controlling the Syringe Pump
Follow these procedures, as applicable:
• To turn the syringe pump on or off
• To set the syringe pump parameters
 To turn the syringe pump on or off
Click Syringe On (Off ) to switch between on and off (Figure 40).
Figure 40. Toggle button for the syringe modes
 To set the syringe pump parameters
1. Click the dropdown arrow,
parameter box (Figure 41).
, next to the Syringe On/Off button, to open the syringe
Figure 41. Syringe parameter box
2. Type the parameter values that you want.
The Tune application automatically saves the values.
3. Click the dropdown arrow again or click elsewhere in the Tune window to close the
syringe parameter box.
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Setting the Data Type
Setting the Data Type
 To set the data type
Click Centroid (Profile) to select the data type that you want (Figure 42).
Figure 42. Toggle button for the data types
Centroid data type
Profile data type
Setting the Ion Polarity Mode
 To set the ion polarity mode
Click Positive (Negative) to select the polarity mode that you want (Figure 43).
Figure 43. Toggle button for the instrument polarity modes
Positive polarity
Thermo Scientific
Negative polarity
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Setting the Tune Preferences
Setting the Tune Preferences
You can set a few preferences for how the Tune application works.
 To set the Tune preferences
1. Click the Options icon, and then choose Tune Preferences to open the Tune Preferences
dialog box (Figure 44).
Figure 44. Tune Preferences dialog box
2. Under General and Report Content Options, select all check boxes that apply.
3. In the center under Report Options, select one of the options, and then click OK.
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A Using Basic Tune Functions
Using the Mass List Table in the Define Scan Pane
Using the Mass List Table in the Define Scan Pane
The mass list table appears when you select the SIM Scan (Q1), SIM Scan (Q3), or SRM scan
type in the Define Scan pane. Use this table to specify scan parameters. To set different scan
parameters for the precursor ions, add the parameters to the table.
• To add a row to the table
• To delete a row from the table
• To delete multiple rows from the table
• To add or remove scan parameters from the table
 To add a row to the table
Do one of the following:
• Click the Add Row icon,
.
• Right-click the table, and then choose Add Row from the shortcut menu.
 To delete a row from the table
1. Select the row number to highlight the entire row.
2. Do one of the following:
• Click the Delete Selected Rows icon,
.
• Right-click the selected row, and then choose Delete Selected Rows from the
shortcut menu.
• Press the DELETE key on your keyboard.
 To delete multiple rows from the table
1. Select the first row’s number to highlight the entire row.
2. Do one of the following:
• For an adjacent row or group of sequential rows, hold down the SHIFT key and
select another row number.
• For an adjacent row or nonsequential rows, hold down the CTRL key and select each
additional row number.
3. Do one of the following:
• Click the Delete Selected Rows icon,
.
• Right-click the selected row, and then choose Delete Selected Rows from the
shortcut menu.
• Press the DELETE key on your keyboard.
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Using the Mass List Table in the Define Scan Pane
 To add or remove scan parameters from the table
Click the Table icon once to add the adjacent scan parameter to the table (Figure 45).
Click it again to remove the parameter from the table.
Figure 45. Q3 Resolution selected and added to the SRM Table
Q3 Resolution
is selected.
Q3 Resolution appears in the table.
 To import a mass list from a file
1. Click Import to open the Open dialog box.
2. Browse to an XML or a CVS (Microsoft Excel™) file, and then click Open.
The list of mass-to-charge ratio values appears in the table.
 To export a mass list to a file
1. Complete the list of mass-to-charge ratio values.
2. Click Export to open the Save As dialog box.
3. Browse to a location, enter a file name, and then select a file type (.csv, .txt, or .xml).
4. Click Save.
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Using the History Pane
Using the History Pane
When you click Apply in the Ion Source pane or the Define Scan pane, the Tune application
adds a change record to the History pane (Figure 46). The change record records all changes
to the instrument state that originated from the Tune application.
Change records in the History pane work as follows:
• The Tune application creates a change record when you change parameters in one of the
Ion Source or Define Scan panes and then click Apply.
• The History pane displays the change records as subitems under the date that they were
created. The maximum number of change records is 100.
• Click a change record to display its parameters, or right-click it and choose Load from the
shortcut menu. Parameters that are colored red differ from their default values.
• Double-click a change record to submit its parameters to the mass spectrometer, or
right-click it and choose Apply from the shortcut menu.
• A change record is inactive if the API source type of the change record differs from the
current API source type.
Figure 46. History pane
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Using the Favorites Pane to Save System Settings
Using the Favorites Pane to Save System Settings
You can manually save the current settings for the API source and scan parameters in the
Favorites pane.
• To create a favorite state
• To load only or apply a favorite state
• To rename a favorite state
• To delete a favorite state
 To create a favorite state
1. In the Tune window, modify the parameters in one of the Ion Source or Define Scan
panes.
2. Click Apply or Export.
3. Click the Favorites tab to display the Favorites pane (Figure 47).
Figure 47. Favorites pane
4. Click Save Current State, and then type a unique name in the box (Figure 48).
Figure 48. State name box
State name box
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A Using Basic Tune Functions
Using the Favorites Pane to Save System Settings
5. Click Save Current State again to save the state.
The most recent state appears at the top of the User Settings list.
 To load only or apply a favorite state
Under User Settings, right-click the state name, and then choose one of the following
from the shortcut menu:
• Load to only display the key parameters in the applicable parameter boxes.
• Apply to submit the key parameters to the mass spectrometer.
You can click Apply without first loading the parameters.
 To rename a favorite state
1. Under User Settings, right-click the state name, and then choose Rename from the
shortcut menu.
2. Type a different name and press ENTER.
 To delete a favorite state
Under User Settings, right-click the state name, and then choose Delete from the
shortcut menu.
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B
Flushing the Inlet Components
This appendix describes how to flush the inlet components (sample transfer line, sample tube,
and spray insert) after both the positive and negative calibration processes, and also before you
change from one analyte solution to another.
In addition, Thermo Fisher Scientific recommends that you clean the ion sweep cone, spray
cone, and ion transfer tube, on a regular basis to prevent corrosion and to maintain optimum
performance of the API source. A good practice is to wash or flush the ion sweep cone and ion
transfer tube at the end of each operating day after you pump a solution of 50:50
methanol/water from the LC system through the inlet components. If you use a mobile phase
that contains a nonvolatile buffer or inject high concentrations of sample, you might need to
clean these parts more often. Be aware that it is not necessary to vent the system to flush the
ion sweep cone and ion transfer tube.
For instructions on how to clean the ion sweep cone, spray cone, and ion transfer tube, refer
to Chapter 6 in the TSQ Endura and TSQ Quantiva Hardware Manual.
CAUTION When the ion transfer tube is installed, do not flush it with cleaning solution,
which flushes the residue into the mass spectrometer.
Contents
• Supplies
• Flushing the Inlet Components after Calibration
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B
Flushing the Inlet Components
Supplies
Supplies
Table 13 lists the necessary supplies for flushing and cleaning specific components.
CAUTION Avoid exposure to potentially harmful materials.
By law, producers and suppliers of chemical compounds are required to provide their
customers with the most current health and safety information in the form of Material
Safety Data Sheets (MSDSs) or Safety Data Sheets (SDSs). The MSDSs and SDSs must
be freely available to lab personnel to examine at any time. These data sheets describe the
chemicals and summarize information on the hazard and toxicity of specific chemical
compounds. They also provide information on the proper handling of compounds, first
aid for accidental exposure, and procedures to remedy spills or leaks.
Read the MSDS or SDS for each chemical you use. Store and handle all chemicals in
accordance with standard safety procedures. Always wear protective gloves and safety
glasses when you use solvents or corrosives. Also, contain waste streams, use proper
ventilation, and dispose of all laboratory reagents according to the directions in the MSDS
or SDS.
Table 13. Flushing and cleaning supplies
Description
Part number
Gloves, nitrile
Fisher Scientific™ 19-120-2947a
Unity Lab Services:
• 23827-0008 (size medium)
• 23827-0009 (size large)
a
80
Acetone, LC/MS-grade
Fisher Scientific: AX0120-2
Methanol, LC/MS-grade
Fisher Scientific: A456-1
Water, LC/MS-grade
Fisher Scientific: W6-1
Multiple sizes are available.
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B Flushing the Inlet Components
Flushing the Inlet Components after Calibration
Flushing the Inlet Components after Calibration
This section describes how to flush the inlet components (sample transfer line, sample tube,
and spray insert) with the syringe after calibration. For best results, follow this procedure
before you acquire data on an analyte.
Tip You can also use an LC pump to flush the 50:50 methanol/water solution through the
inlet components to the API source at a flow rate of 200–400 μL/min for approximately
15 minutes.
 To flush the inlet components
1. Turn off the flow from the syringe pump (see page 70).
2. Place the mass spectrometer in Standby mode (see page 69).
3. Remove the syringe from the syringe pump as follows:
a. Lift the syringe holder off of the syringe.
b. Press the pusher block’s release knob and slide the block to the left.
c. Remove the syringe from the holder.
d. Carefully remove the syringe needle from the Teflon tube on the syringe adapter
assembly (Figure 8).
4. Clean the syringe as follows:
a. Rinse the syringe with a solution of 50:50 methanol/water.
b. Rinse the syringe with acetone several times.
5. Flush the sample transfer line, sample tube, and spray insert as follows:
a. Load the cleaned syringe with a solution of 50:50 methanol/water (or another
appropriate solvent).
b. Carefully reinsert the syringe needle into the Teflon tube on the syringe adapter
assembly.
c. Slowly depress the syringe plunger to flush the sample transfer line, sample tube, and
spray insert with the solution.
d. Remove the syringe needle from the syringe adapter assembly.
This completes the procedure to flush the inlet components. Repeat this procedure after you
complete the negative polarity calibrations.
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Flushing the Inlet Components
Flushing the Inlet Components after Calibration
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G
Glossary
A
B
C
D
E
F
G
H
I
J
K
L M N O
P
Q
R
S
T
U
V W X
Y
Z
A
C
APCI spray current The ion current carried by the
charged particles in the APCI source. The APCI
corona discharge voltage varies, as required, to
maintain the set spray current.
centroid data Data used to represent mass spectral
peaks in terms of two parameters: the centroid (the
weighted center of mass) and the intensity. The data
is displayed as a bar graph. The normalized area of
the peak provides the mass intensity data.
API source The sample interface between the liquid
chromatograph (LC) and the mass spectrometer
(MS).
atmospheric pressure chemical ionization (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, forming a reagent gas.
atmospheric pressure ionization (API) Ionization
performed at atmospheric pressure by using
atmospheric pressure chemical ionization (APCI),
heated-electrospray (H-ESI), or nanospray ionization
(NSI).
atmospheric pressure photoionization (APPI) A
soft ionization technique that shows an ion generated
from a molecule when it interacts with a photon
from a light source.
auxiliary gas The outer-coaxial gas (nitrogen) that
assists the sheath (inner-coaxial) gas in dispersing
and/or evaporating sample solution as the sample
solution exits the ESI or APCI (optional) spray
insert.
Thermo Scientific
charge state The imbalance between the number of
protons (in the nuclei of the atoms) and the number
of electrons that a molecular species (or adduct ion)
possesses. If the species possesses more protons than
electrons, its charge state is positive. If it possesses
more electrons than protons, its charge state is
negative.
collision energy The energy used when ions collide
with the collision gas.
collision gas A neutral gas used to undergo collisions
with ions.
collision-induced dissociation (CID) A method of
fragmentation where ions are accelerated to highkinetic energy and then allowed to collide with
neutral gas molecules such as argon. The collisions
break the bonds and fragment the ions into smaller
pieces.
conversion dynode A highly polished metal surface
that converts ions from the mass analyzer into
secondary particles, which enter the electron
multiplier.
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Glossary: divert/inject valve
D
H
divert/inject valve A valve on the mass spectrometer
that can be plumbed as a loop injector or as a divert
valve.
heated-electrospray (H-ESI) A type of atmospheric
pressure ionization that converts ions in solution into
ions in the gas phase by using electrospray (ESI) in
combination with heated auxiliary gas.
E
electron multiplier A device used for current
amplification through the secondary emission of
electrons. Electron multipliers can have a discrete
dynode or a continuous dynode.
electrospray (ESI) A type of atmospheric pressure
ionization that is currently the softest ionization
technique available to transform ions in solution into
ions in the gas phase.
electrospray ionization (ESI) See electrospray (ESI).
F
flow rate, syringe pump status The syringe pump
injection flow rate in milliliters per minute (mL/min)
or microliters per minute (μL/min) for the current
sample, as defined in the current experiment method.
heated-electrospray ionization (H-ESI) See heatedelectrospray (H-ESI).
high performance liquid chromatography (HPLC)
Liquid chromatography where the liquid is driven
through the column at high pressure. Also known as
high pressure liquid chromatography.
I
ion detection system A high sensitivity, off-axis
system for detecting ions. It produces a high signalto-noise ratio (S/N) and allows for switching of the
voltage polarity between positive ion and negative
ion modes of operation. The ion detection system
includes two ±12 kVdc conversion dynodes and a
discrete dynode electron multiplier.
ion optics Focuses and transmits ions from the API
source to the mass analyzer.
forepump The pump that evacuates the foreline. A
rotary-vane pump is a type of forepump. It might
also be referred to as a backing, mechanical, rotaryvane, roughing, or vacuum pump.
ion polarity mode The mass spectrometer can operate
in either of two ion polarity modes: positive or
negative.
fragment ion A charged dissociation product of an
ionic fragmentation. Such an ion can dissociate
further to form other charged molecular or atomic
species of successively lower formula weights.
ion sweep cone A removable cone-shaped metal cover
that fits on top of the API ion transfer tube and acts
as a physical barrier to protect the entrance of the
tube.
full-scan type Provides a full mass spectrum as
opposed to the selected ion monitoring (SIM) scan
type, which produces only one mass. With the fullscan type, the mass analyzer is scanned from the first
mass to the last mass without interruption. Also
known as single-stage full-scan type.
isolation window The baseline width of a window for
a mass peak (or peak cluster) of interest for an MS/
MS or MSn scan.
L
LC pump A high pressure solvent pump in the LC
that provides the pressure on the input side of a
column to drive the eluent and sample through the
column.
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Glossary: lens
lens An element that provides focusing of the ion
beam.
M
mass analysis A process that produces a mixture of
ionic species that is then separated according to the
mass-to-charge ratios (m/z) of the ions to produce a
mass spectrum.
mass analyzer A device that determines the mass-tocharge ratios (m/z) of ions by one of a variety of
techniques.
mass spectrometer An instrument that ionizes sample
molecules and then separates the ions according to
their mass-to-charge ratio (m/z). The resulting mass
spectrum is a characteristic pattern for the
identification of a molecule.
mass spectrum A graphical representation (plot) of
measured ion abundance versus mass-to-charge ratio.
The mass spectrum is a characteristic pattern for the
identification of a molecule and is helpful in
determining the chemical composition of a sample.
mass-to-charge ratio (m/z) An abbreviation used to
denote the quantity formed by dividing the mass of
an ion (in Da) by the number of charges carried by
the ion. For example, for the ion C7H72+,
m/z = 45.5.
molecular ion An ion formed by the removal (positive
ion) or addition (negative ion) of one or more
electrons to/from a molecule without fragmentation
of the molecular structure.
MS scan modes Scan modes where only one stage of
mass analysis is performed. The scan types used with
the MS scan modes are full-scan type and selected
ion monitoring (SIM) scan type.
N
nano liquid chromatography (nanoLC) Liquid
chromatography with typical flow rates of
10–1000 nL/min and 10–150 μm diameter
columns.
Thermo Scientific
nanoelectrospray ionization (nanoESI or NSI) A
type of electrospray (ESI) that accommodates very
low flow rates of sample and solvent at 1–20 nL/min
(for static nanoelectrospray) or 100–1000 nL/min
(for dynamic nanoelectrospray, which is also called
nanoESI nanoLC gradient separation).
nanoESI nanoLC gradient separation Employs
microscale capillary columns to separate the analytes
in complex mixtures. The sample is loaded onto a
column using an injection valve or a gas pressure
vessel. The mixture components are then eluted by a
solvent gradient and pumped through the emitter.
nanoESI (NSI) spray current The flow of charged
particles in the nanoESI (NSI) source. The voltage
on the NSI spray needle supplies the potential
required to ionize the particles.
nanoESI (NSI) spray voltage The high voltage that is
applied to the spray needle in the nanoESI (NSI)
source to produce the NSI spray current as liquid
emerges from the nozzle. The NSI spray voltage is
selected and set; the NSI spray current varies.
nanospray ionization (NSI) See nanoelectrospray
ionization (nanoESI or NSI).
P
precursor ion An electrically charged molecular
species that can dissociate to form fragments. The
fragments can be electrically charged or neutral
species. A precursor ion can be a molecular ion or an
electrically charged fragment of a molecular ion.
precursor mass The mass-to-charge ratio of a
precursor ion. The location of the center of a target
precursor-ion peak in mass-to-charge ratio (m/z)
units.
product ion An electrically charged fragment of an
isolated precursor ion.
product mass The mass-to-charge ratio of a product
ion. The location of the center of a target production
peak in mass-to-charge ratio (m/z) units.
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Glossary: profile data
profile data Data representing mass spectral peaks as
point-to-point plots, with each point having an
associated intensity value.
Q
qualitative analysis Chemical analysis designed to
determine the identity of the components of a
substance.
quantitative analysis Chemical analysis designed to
determine the quantity or concentration of a specific
substance in a sample.
R
relative standard deviation (RSD) A measure of the
dispersion of a group of measurements relative to the
mean of the group. Relative standard deviation is
expressed as a percentage of the average value. The
percent relative standard deviation is calculated as:
%RSD = 100   S  X 
where S is the standard deviation and X is the sample
mean.
retention time (RT) The time after injection at which
a compound elutes. The total time that the compound
is retained on the chromatograph.
selected ion monitoring (SIM) scan type A scan type
where the mass spectrometer acquires and records ion
current at only one or a few selected mass-to-charge
ratio values.
sheath gas The inner coaxial gas (nitrogen), which is
used in the API source to help nebulize the sample
solution into a fine mist as the sample solution exits
the H-ESI or APCI nozzle.
signal-to-noise ratio (S/N) The ratio of the signal
height (S) to the noise height (N). The signal height
is the baseline corrected peak height. The noise
height is the peak-to-peak height of the baseline
noise.
source See API source.
static nanoelectrospray A device that performs
continuous analysis of small analyte solution volumes
over an extended period of time.
sweep gas Nitrogen gas that flows out from behind
the sweep cone in the API source. Sweep gas aids in
solvent declustering and adduct reduction.
syringe pump A device that delivers a solution from a
syringe at a specified rate.
T
total ion current (TIC) The sum of the ion current
intensities across the scan range in a mass spectrum.
S
sample loop A loop of calibrated volume that is used
to perform flow injection analysis.
scan Comprised of one or more microscans. Each
microscan is one mass analysis (ion injection and
storage/scan-out of ions) followed by ion detection.
After the microscans are summed, the scan data is
sent to the data system for display and/or storage.
The process of ramping the amplitude of the rf and
dc voltages on the multipole rods in the mass
analyzer to transmit ions from the lowest mass to the
highest mass of a specified scan range.
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I
Index
A
APCI mode
description 3
plumbing connection, direct infusion 25
spray insert, installing 16
API source
cautions 12
high voltage connector 14
installing or removing 11
solvent waste container, connecting 11
spray insert 16
APPI mode, selecting the spray insert 16
auto-loop injection
schematic 22
setup 29
uses 19
autosampler injection 31
B
buffers, description 6
buttons, on/standby/off 68
C
Calibration pane
See panes, Calibration Options
calibration parameters 50
caution symbols, description xviii
Change Instruments In Use dialog box 66
cleaning
inlet components 81
ion sweep cone 79
ion transfer tube 79
spray cone 79
syringe 81
compliance
FCC iii–iv
regulatory iii
Thermo Scientific
contacting us xviii
contamination, preventing 23, 40
D
data acquisition
button 64
Tune 63
Xcalibur 66
Data Acquisition pane 64
data type, setting 71
Define Scan pane
See panes, Define Scan
direct infusion
connecting the plumbing for 25
description 20
schematic 22
directive, WEEE v
divert/inject valve
configurations
as divert valve 35
as loop injector 35
schematic of 36
controlling 36
description 34
positions 35
schematic 22
valve position indicator 36
documentation
accessing xiv
downloading xiv
related xiv
E
electromagnetic compatibility iii
EMC compliance iii
TSQ Endura and TSQ Quantiva Getting Started Guide
87
Index: F
F
L
favorite states
saving as 76
using to set parameters 76
Favorites pane 76
FCC compliance iii–iv
figures, list of xi
flow rates, setting 4
flow-injection analysis, description 21
flushing inlet components 81
forepump, fume exhaust system cautions 12
LC pump, connecting to the divert/inject valve 28
LC union xvi
LC with autosampler injection, schematic 22
LC/MS experiments, connecting the plumbing for 31
LC/MS operational guidelines
APCI mode 5
H-ESI mode 5
NSI mode 5
loop injection
connecting the plumbing for 29
liquid chromatography description, and 21
G
gas flow rates, adjusting for LC flow rate 4
grounding (ZDV) union xvi, 29
H
H-ESI mode
description 2
plumbing connection, direct infusion 25
spray insert, installing 16
high-flow infusion
connecting the plumbing for 26
description 20
schematic 22
History pane 75
HPLC with autosampler injection
schematic 22
uses 21
I
infusion line, connecting to grounding union 25
ion polarity mode, setting 71
Ion Source pane
See panes, Ion Source
ion sweep cone, cleaning 79
ion transfer tube
cleaning 79
temperature, adjusting for LC flow rate 4
K
kits
Chemical xvii
MS Calibration xv
Performance Specification xvi
88
TSQ Endura and TSQ Quantiva Getting Started Guide
M
manual loop injection
schematic 22
setup 29
uses 19
mass list
exporting from Tune 74
importing into Tune 74
mass spectrometers
API source, installing or removing 11
calibration parameters 50
flow rates, setting 4
plumbing connections 19
power modes, setting 69
pumping down the vacuum 37
sample introduction techniques 19
spray insert, installing or removing 16
tune parameters 50
MSDS 6
MSn setting table, using 73
N
NSI mode, description 4
O
optimization
API source parameters, general procedure 45
note 45
signal type, list 46
Optimization page
Define Scan pane 58
Ion Source pane 46
Thermo Scientific
Index: P
P
panes
Calibration
Options page 51
Status page 50
Data Acquisition 64
Define Scan
Optimization page 58
Scan page 68
Favorites 76
History 75
Ion Source
Ion Source page 56
Optimization page 46
Status 39
PEEK tubing, special notice 23
plumbing connections, inlet 19
polarity mode
See ion polarity mode, setting
power mode button 68
pump down, MS 37
R
readback status, description 69
record button 64
regulatory compliance iii
Report Generation Options dialog box 46
Run Sequence dialog box (acquisition options) 65
S
safety standards iii
sample introduction techniques
schematic diagrams 22
summary of connections 19
Scan page, Define Scan pane 68
SDS 6
sequence run, start instrument in Xcalibur 65
solvents
description 6
waste 11
source
See API source
spray cone, cleaning 79
spray insert, API source
adjustments
front-to-back 17
rotational 17
installing or removing 16
Thermo Scientific
start instrument
configuring with Xcalibur 65
description 65
Run Sequence dialog box 65
Status pane 39
syringe
adapter assembly 23
avoid contamination 40
cleaning 81
syringe adapter assembly, drawing 34
syringe pump
controlling 70
default flow rate 33
description 33
setting up 24
T
Tune application
opening 68
preferences, setting 72
tune parameters
compound dependent 50
mass dependent 50
U
union types, plumbing
grounding (ZDV) xvi
LC xvi
Tee xvii
V
vaporizer temperature, adjusting for LC flow rate 4
W
waste container, solvent 14
WEEE directive v
X
Xcalibur file type, raw data (.raw) 63
Xcalibur file type, sequence (.sld) 65
Z
ZDV union xvi
TSQ Endura and TSQ Quantiva Getting Started Guide
89
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