Duo Spray Ion Source

DuoSpray
Ion Source
Operators Manual
Part Number: 1005699 B

December 2002
This document contains information proprietary and confidential to MDS Sciex, a

division of MDS Inc., and is for customer use in the operation and maintenance of
MDS Sciex equipment or is for vendor use in the specification, fabrication, and
manufacture of MDS Sciex designed component parts. Any other use, disclosure to
third parties, or reproduction of the information contained herein is strictly
forbidden, except as MDS Sciex may authorize in writing.
Equipment that may be described in this document is protected under one or more
patents filed in the United States, Canada, and other countries. Additional patents are
pending.
Software that may be described in this document is furnished under a license
agreement. It is against the law to copy, modify, or distribute the software on any
medium, except as specifically allowed in the license agreement. Furthermore, the
license agreement may prohibit the software from being disassembled, reverse
engineered, or decompiled for any purpose.
Portions of this document may make reference to other manufacturers products,
which may contain parts that are patented and may contain parts whose names are
registered as trademarks and/or function as trademarks. Any such usage is intended
only to designate those manufacturers products as supplied by Applied Biosystems/
MDS Sciex for incorporation into its equipment and does not imply any right and/or
license to use or permit others to use such product names as trademarks.
All products and company names mentioned herein may be the trademarks of their
respective owners.
Applied Biosystems/MDS Sciex makes no warranties or representations as to the
fitness of this equipment for any particular purpose and assumes no responsibility or
contingent liability, including indirect or consequential damages, for any use to
which the purchaser may put the equipment described herein, or for any adverse
circumstances arising therefrom.
Applied Biosystems/MDS Sciex is a joint venture between Applera Corporation and
MDS Sciex, the instrument technology division of MDS Inc.
For Research Use Only. Not for use in diagnostic procedures.
Equipment built by MDS Sciex, a division of MDS Inc.,

at 71 Four Valley Dr., Concord, Ontario, Canada L4K 4V8.
MDS Sciex and Applied Biosystems are ISO 9001 registered.
2002 Applied Biosystems/MDS Sciex, Joint Owners. All rights reserved.
Printed in Canada.
ISO
9001
REGISTERED
COMPANY
Contents
Foreword . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
About This Manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Audience . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . viii
How This Manual Is Organized . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . viii
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .ix
Labels and Warnings on Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .ix
Technical Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Chapter 1: Introducing the DuoSpray Ion Source . . . . . . . . . . . . . . 1

Why Use the Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Choosing the Technique to Use . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Multi-period methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Multi-experiment methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Choosing an Ion Source Probe. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

TIS Probe. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
APCI Probe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Parts of the Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

TIS Probe. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
APCI Probe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Switching Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Valve Controller . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Valve Mounting Bracket . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Specifications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
DuoSpray Ion Source Housing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
iii
Contents
DuoSpray Ion Source Operators Manual

Ion Source Probe Adjustments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Ion Source Interlocks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Source Exhaust System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Ionization Process . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
TIS Inlet Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
APCI Inlet Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Probe Temperature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Corona Discharge Characteristics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Chapter 2: Installing the Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Installing Source Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Installing the Valve Mounting Bracket . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Installing the Switching Valve Controller . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Installing the TIS and APCI Probes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Installing the Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Chapter 3: Operating the Source . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Introducing the Sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Optimizing the Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
TIS Optimization Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Optimizing the TIS Probe Position . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Optimizing TIS Nebulizer and Heater Gas Flow . . . . . . . . . . . . . . . . . . . . . . 28
Optimizing Turbo Temperature and Solvent Composition . . . . . . . . . . . . . . . 28
APCI Optimization Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Optimizing the APCI Probe Position . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Optimizing the Needle Current . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Optimizing Probe Temperature and Solvent Composition . . . . . . . . . . . . . . . 32
Setting the Software Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Setting up Instrument-Specific Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Setting up Compound-Specific Parameters. . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Setting up Source-Specific Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Needle Current . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Nebulizer Gas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Heater Gas. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Temperature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Declustering Potential. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Curtain GasTM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Solvent Composition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
iv
Contents
Tuning Your Source Manually . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

Displaying the Tune Method Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Building a Tuning Method. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Acquiring Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Warming Up the Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

Operating Tips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Controlling the DuoSpray Ion Source Temperature . . . . . . . . . . . . . . . . . . . . 43
Chapter 4: DuoSpray Testing Procedures . . . . . . . . . . . . . . . . . . . . 45

System Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Instrument Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Injector Setup. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Materials Required. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Mobile Phase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Preparing The Test Solution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Equipment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Gases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
DuoSpray Performance Tests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

Testing the TurboIonSpray Probe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Specification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Testing the APCI Probe. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Specification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Chapter 5: Maintaining the Source . . . . . . . . . . . . . . . . . . . . . . . . . 53

Maintenance Schedule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Tools Required. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Cleaning the Switching Valve and Source Probes . . . . . . . . . . . . . . . . . . . . . 54
Replacing Source Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

Replacing the Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Replacing the Probes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Replacing the Switching Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Replacing the Turbo Heater . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Replacing the Corona Discharge Needle Tip . . . . . . . . . . . . . . . . . . . . . . . . . 59
Replacing the Corona Discharge Needle . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Adjusting the Corona Discharge Needle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Replacing the Electrode Tube . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Replacing the PEEK Tubing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Contents
Appendix A: Source Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

Appendix B: Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Appendix C: Consumables and Spares. . . . . . . . . . . . . . . . . . . . . . 73
vi
Foreword
The DuoSprayTM Ion Source Operators Manual contains the instructions
required to install, operate, and maintain the DuoSpray ion source for the API
4000 LC/MS/MS mass spectrometer.
About This Manual

This manual provides an overview of the DuoSpray ion source, and contains
the information necessary to perform the following procedures:
Install and operate the DuoSpray ion source
Perform routine maintenance procedures on the source
The manual also provides information on optimizing the DuoSpray ion

source, as well as troubleshooting tips. This manual is not designed to instruct
operators on procedures for conducting mass spectrometry or the repair and
servicing of the mass spectrometer itself. If the source requires repair or
replacement beyond what is described in this manual, contact an Applied
Biosystems Customer Service Representative.
Note: All instrument locations specified in the photographs in this manual
are stated when viewing the source from the front.
Audience
The DuoSpray Ion Source Operators Manual is targeted to operators who are
familiar with mass spectrometry but are new to the DuoSpray Ion source. This
manual is designed to provide information to both junior and senior lab
technicians, and scientists.
vii
Any person using an Applied Biosystems/MDS Sciex mass spectrometer

system should be fully trained in its safe operation as well as in laboratory
procedures. All warnings should be followed implicitly as failure to do so
could result in serious injury.
Conventions
Within the scope of this manual, the following conventions are used:
WARNING! Indicates an operation that may cause personal injury if
precautions are not followed.
WARNING! All standard safety precautions regarding high voltages,
vacuum systems, and electrostatic discharge must be followed to
prevent personal injury or damage to the instrument.
WARNING! If hazardous, biohazardous, or radioactive materials are
injected into the instrument, all appropriate safety precautions should
be taken. If these materials have been used, the instrument should be
handled according to the material safety regulations in the country of
use (for example, WHMIS).
WARNING! Indicates that the probes and source housing may reach
high temperatures. Follow the stated procedures to avoid injury.
CAUTION! Indicates an operation that may cause damage to the
instrument if precautions are not followed.
Note: Emphasizes significant information in a procedure or description.
How This Manual Is Organized

This DuoSpray Ion Source Operators Manual is organized as follows:
Chapter 1 - Introducing the DuoSpray Ion Source This section provides a
general introduction to the DuoSpray Ion Source. It includes an overview of
the ionization process and sample introduction theory.
viii
Chapter 2 - Installing the Source This section provides information on how

to install the source and optimize its parameters for multi-period and multiexperiment methods.
Chapter 3 - Operating the Source This section provides step-by-step
procedures for operating the TIS and APCI probes.
Chapter 4 - DuoSpray Testing Procedures This section details the materials
required and the procedures for testing the performance of the DuoSpray
source.
Chapter 5 - Maintaining the Source This section details the procedures for
maintaining the source, and for replacing consumable parts.
Appendix A provides a list of the default parameters and voltages for the
DuoSpray ion source.
Appendix B provides a list of typical problems you may encounter when
operating the source, and ways to resolve them.
Appendix C provides a list of spare parts for the source and its components.
Related Documentation
Additional operational information regarding the instrument on which the
source is installed is available in the API 4000 LC/MS/MS Hardware Manual,
the Analyst Operators Manual and online Help.
Information on configuring the instruments peripheral devices is available in
the Peripheral Devices Setup Manual, and online Help.
Labels and Warnings on Source

The DuoSpray Ion Source bears the following labels and warnings:
Patent notice label
High voltage and High temperature warning labels
Assembly number and serial number label
System Approval label
ix
Technical Support
Applied Biosystems/MDS Sciex and its representatives maintain a staff of
fully-trained service and technical specialists strategically located throughout
the world. They can answer questions pertaining to the source.
For technical support and other information please contact your Customer
Service Representative or consult the Applied Biosystems/MDS Sciex Web
site:
www.appliedbiosystems.com
1
Introducing the DuoSpray
Ion Source
The DuoSpray ion source for the API 4000 LC/MS/MS platform combines
TurboIonSpray (TIS) and Atmospheric Pressure Chemical Ionization (APCI)
probes in a single source housing. The instrument uses a low dead volume
switching valve under software control to rapidly divert the sample flow to
either the TIS or APCI probe. This ability to direct sample streams into either
probe allows you to set up experiments that incorporate both ionization
processes on a single sample stream, maximizing sensitivity over the full
range of compound polarities during an analyis.
DuoSpray ion source
Introducing the DuoSpray Ion Source
Why Use the Source

Applications for the DuoSpray ion source include qualitative method
development, and quantitative analysis.
The DuoSpray ion source is used for mass spectrometry in the identification
of unknown compounds, the quantitation of known compounds, and the
elucidation of structural information and chemical properties of molecules.
By having two ion probes, each generating different streams of data collected
with different ionization modes, you can perform multi-experiment methods
using a single quadrupole scan, product ion scan, neutral loss scan, or
precursor ion scan.
Probe switching during LC elution allows the use of multi-period methods
based on Multiple Reaction Monitoring (MRM) or Selected Ion Monitoring
(SIM) scan modes, at period-based switching that allows the selection of the
optimal temperatures for each probe.
The DuoSpray ion source:
Allows the rapid development of more universal analytical methods,

broadening the capability to collect all the information from a single
injection.
Facilitates the migration of analytical methods developed for other LC/

MS/MS instruments.
Provides improved flexibility in open access environments, allowing a

more complete range of methods.
Choosing the Technique to Use

The switching capability of the DuoSpray ion source is ideally suited for
investigative and broad spectrum analyses, allowing you to determine the
optimum technique and parameter settings for the compound you are testing.
Multi-period methods
Period-based switching from the TurboIonSpray (TIS) to the Atmospheric
Pressure Chemical Ionization (APCI) probe during a multi-period scan
provides completion of all cycles on one probe before switching to the other
probe.
Multi-experiment methods
In a multi-experiment method, switching between the two probes over the
course of a scan occurs as the valve moves the sample from one probe to
another on the completion of each cycle.
Choosing an Ion Source Probe

The TIS and APCI probes provide a range of capability for testing samples,
particularly with the switching valve which allows both multi-period and
multi-experiment methods. The TurboIonSpray probe and the coronadischarge APCI probe each work best for compounds of different polarity.
Choose the probe and method that are most suitable for the compound in your
sample stream flow.
TIS Probe
The TIS probe is ideally suited for LC/MS/MS analyses. The sensitivity gains
that are achieved with this technique are both flow rate and analyte dependent.
The TIS probe increases ionization efficiency at higher flow rates. This results
in improved sensitivity. Sensitivity is compound dependent, and compounds
with extremely high polarity and low surface activity usually show the
greatest sensitivity increases. The TIS technique is mild enough to be used
with labile compounds, such as peptides, proteins, and thermally labile
pharmaceuticals.
The difference between conventional IonSpray and TIS is that, in TIS, the
ionization of the sample is achieved with additional heater gas that is
delivered to aid in the desolvation of the spray. The TIS heater will operate
only if a minimum desolvation gas flow is established. Typically, the TIS
probe is used at flow rates greater than 40 L/min.
APCI Probe
The APCI probe is ideally suited for creating simple APCI spectra for MS/MS
experiments. It is also good for rapid sample introduction by flow injection
with or without a liquid chromatograph (LC) column.
The APCI probe offers an additional method of introducing samples to the
API 4000. The APCI probe generates ions representative of the molecular
composition of the sample. Where the TIS probe produces ions by the process
of ion evaporation, the APCI probe vaporizes the sample prior to inducing
3
ionization by a process called atmospheric pressure chemical ionization

(APCI). This process is induced by a corona discharge needle as the ions pass
through the ion source housing to the interface region. This process leaves the
molecular constituents of the sample intact.
The APCI probe can accept the entire effluent from as low as 50 L/min to a
wide bore column (2000 L/min) without splitting. The rapid desolvation and
vaporization of the droplets and entrained analyte minimizes thermal
decomposition and preserves molecular identity for ionization by the corona
discharge needle. Buffers are readily tolerated by the source without
significant contamination and the flash vaporization of the sprayed effluent
allows up to 100% water to be used without difficulty. Overall, the APCI
probe is a stable inlet that is used extensively for high-throughput analyses of
complex and dirty samples since it is less sensitive to ion suppression effects.
Parts of the Source

This section describes the following parts of the DuoSpray ion source:
TIS probe
APCI probe
Switching valve
Valve controller
Mounting bracket
TIS Probe
The TIS probe is an ion source that converts a liquid sample into gas phase
ions. Samples introduced through the TurboIonSpray tip are nebulized by a jet
of gas from a high-voltage sprayer, creating a mist of small, highly-charged
droplets. The TIS probe is located centrally adjacent to a turbo heater that
sprays heated dry ultrahigh purity (UHP) nitrogen. The combination of
IonSpray effluent and the heated dry gas from the turbo sprayer are projected
at a 90 angle to the orifice.
Bronze retaining ring
Electrode tip
Electrode adjustment nut
TIS probe
APCI Probe
The APCI probe is an ion source that produces ions by nebulizing the liquid
sample in a heated tube, causing the finely dispersed sample drops to
vaporize. This process leaves the molecular constituents of the sample intact.
The molecules are ionized through a process called atmospheric pressure
chemical ionization (APCI) induced by a corona discharge needle as they pass
through the ion source housing into the orifice in the curtain plate.
Bronze retaining ring
Electrode tip
Electrode adjustment nut
APCI probe
Switching Valve
The switching valve is a mechanism, under software control, that can rapidly
switch the sample stream from one probe to another during a scan. The valve
contains a rotor with channels that divert the sample stream into the tubing
5
leading to the probe that was specified in the acquisition method at the speed
set for each cycle. For accurate valve switching, the shortest cycle time is one
second. Faster switching speeds will shorten the life and ultimately damage
the switching valve.
Switching valve and motor on mounting bracket
Valve Controller
The valve controller controls the valve motor and thus the switching speed
and frequency. It is powered by an external direct plug-in low voltage power
supply, and the control cable is connected to the sources port at the back of the
instrument.
Valve controller
Valve Mounting Bracket

The valve mounting bracket holds the valve and motor assembly in place on
top of the instrument, next to the source.
Specifications
The following table indicates the specifications of the DuoSpray ion source.
TIS Components
APCI Components
Ion source temperature

range
Probe temperature from

0750 C
Probe temperature from

50750 C
Liquid chromatography
Interfaces to any liquid chromatography system
Nebulizer gas (Gas 1)

Heater gas (Gas 2)
Zero grade air regulated to 100 psi
DuoSpray Ion Source Housing

The housing contains the following ports:
An APCI housing tower for the APCI probe and heater, on the left.
A TIS housing tower for the TIS probe, in the center.
A turbo heater port to the right of the TIS housing tower.
A window port to provide a side view of the probes.
A source exhaust port on the bottom.
A pressure relief port on the side.
DuoSpray Ion Source Components as viewed from the front of the source
Tempered glass windows on the side and at the end of the housing let the
operator see the probes and nebulized sample stream in the interior of the
housing.
The source housing mounts onto the front end of the mass spectrometer
vacuum chamber and is held in position by two metal rods that are rotated
with locking arms. The ion source probes and the source housing can be
quickly and easily removed without tools to provide convenient access to the
vacuum interface. If the probes are not properly installed in the source
housing, or the source housing itself is not properly installed, an interlock
disables the instrument's high-voltage power supply.
Gas, high voltage, and electrical connections to the installed ion source probes
enter through the front plate of the interface and connect internally through
the source housing. When the ion source probes are inserted into the housing,
all electrical and gas connections are made. Only the sample lines need to be
connected manually to the switching valve and probes.
A passive, positive-pressure exhaust system exhausts ion source gases

through a source exhaust port to reduce sample carryover and reduce
chemical background noise. The source exhaust port connects through an
exhaust chamber and a source exhaust pump to a customer-supplied exhaust
vessel and exhaust ventilation system.
Ion Source Probe Adjustments

The TIS probe can be adjusted vertically using the vertical adjustment
micrometer on the front of the TIS tower. It can be adjusted horizontally using
the horizontal micrometer on the side of the TIS tower.
The APCI probe can be adjusted vertically only, using the vertical adjustment
micrometer on the front of the APCI tower.
For both probes, a black electrode adjustment nut mounted in the handle of
each probe raises and lowers the sample electrode in relation to the nebulizing
jet(s) to produce an optimal signal.
Ion Source Interlocks

The system controller controls the source exhaust system, a safety feature that
isolates the sample vapors and exhaust products from the laboratory
environment. If the source housing is not installed, the instrument's highvoltage power supply is disabled. Also, if the instrument senses a gas fault
then the high voltage is turned off.
Source Exhaust System

WARNING! Ensure proper operation of the laboratory exhaust system
prior to performing analytical measurements with this instrument.
All ion sources produce both sample and solvent vapors. These vapors are a
potential hazard to the laboratory environment. The source exhaust system is
designed to safely remove and allow for the appropriate handling of the ion
source exhaust products.
WARNING! Take all necessary precautions to ensure the safe disposal
of the source exhaust gas.
The ion source housing operates at slightly above atmospheric pressure due to
the entrance of the curtain gasTM and the heater gas into the housing. The
9
slightly positive gas pressure tends to move waste gases through the exit port
of the housing into the exhaust chamber that is mounted under the housing.
Waste liquids from the housing also drain into this chamber. The chamber
content is evacuated by the source exhaust pump located in the front bulkhead
assembly. The waste is collected into a waste container that is connected to a
customer-supplied ventilation system.
The TIS and the APCI probes produce a large volume of exhaust products
because both use additional volumes of gas and both use heat to produce ions.
As a result, the use of the source exhaust system is an essential component of
the DuoSpray ion source. When the source is installed, the system will not
operate unless the source exhaust system is operating.
WARNING! You must ensure that the source exhaust system is properly
connected, particularly if samples containing toxic or highly volatile
chemicals, or solvents are being analyzed. A minimum 20% positive
oxygen flow into the laboratory is also recommended.
A pressure switch mounted on the source exhaust pump measures the pressure
in the source exhaust line. If the pressure in the line rises above the set point
while the probes are installed, the instruments high-voltage power supply is
disabled.
Before each use, test the pressure switch for the exhaust line by shutting off
the source exhaust gas supply. If the hose is connected to a forced ventilation
system, disconnect the hose from the drain bottle. Fault messages will be
displayed on the monitor indicating the source exhaust gas is off, which
verifies that the pressure switch is working. If the fault messages are not
displayed the pressure switch is defective and the source must not be used. A
service call is mandatory.
If the above procedure is not followed, the ion source pressure sensor may
inadvertently allow the system to operate when the ion source is not being
properly exhausted. If the source is not properly exhausted, vapor can escape
through the heated nebulizer probe and condense within the probe's electrical
wiring. This could cause a short circuit and the possibility of a fire if
flammable solvents are used.
10
Ionization Process
Samples are normally introduced to the instrument in a flowing liquid stream
through a TIS and/or APCI ion source. The ion source probe produces gas
phase ions that are subjected to mass spectrographic analysis by the
instrument.
TIS
The TurboIonSpray (TIS) probe utilizes a turbo (heater gas) sprayer to blow
hot, dry ultrahigh purity (UHP) nitrogen. The TIS probe is located centrally
adjacent to a turbo heater placed at a 45 angle to the side. The combination of
IonSpray effluent and the heated dry gas from the turbo sprayer are projected
at a 90 angle to the orifice.
The interaction between the IonSpray and the turbo heater helps focus the TIS
stream and increases the rate of droplet evaporation resulting in an increased
ion signal. The heated gas increases the efficiency of ion evaporation resulting
in increased sensitivity (that is, produces higher ion intensities) and the ability
to handle higher liquid sample flow rates.
A high-velocity flow of nebulizer gas shears droplets from the liquid sample
stream in the IonSpray inlet. Using the variable high voltage applied to the
sprayer, a net charge is applied to each droplet and aids in the droplet
dispersion. Ions of a single polarity are preferentially drawn into the droplets
by the high voltage as they are separated from the liquid stream. The
separation, however, is incomplete, therefore each droplet contains many ions
of both polarities. Ions of one polarity are predominant in each droplet, and
the difference between the number of positively or negatively-charged ions
results in the net charge. Only the excess ions of the predominant polarity are
available for ion evaporation, and only a fraction of these actually evaporate.
The polarity and concentration of excess ions depends on the magnitude and
polarity of the high-voltage potential applied to the sprayer tip. For example,
when a sample contains arginine in a water-acetonitrile solution and a positive
potential is applied to the sprayer, the excess positive ions will be H+ and
MH+ arginine.
The TurboIonSpray can generate multiple-charged ions from compounds that
have multiple charge sites, such as peptides and oligonucleotides. This is
useful when observing high molecular-weight species where the multiple
charges produce ions of a mass-to-charge (m/z) value within the mass range
of the instrument. This allows routine molecular-weight determinations of
compounds in the kilodalton (kDa) range.
11
Ion Evaporation
Each charged droplet contains solvent and both positive and negative ions, but
with ions of one predominant polarity. As a conducting medium, excess
charges reside at the droplets surface. As the solvent evaporates, the electrical
field at the surface of the droplet increases due to the decreasing radius of the
droplet.
If the droplet contains excess ions and enough solvent evaporates from the
droplet, a critical field is reached at which ions are emitted from the surface.
Eventually, all of the solvent will evaporate from the droplet, leaving a dry
particle consisting of the nonvolatile components of the sample solution.
Ion evaporation
Only compounds that ionize in the liquid solvent can be generated as gas
phase ions in the ion source. The efficiency and rate of ion generation depends
on the solvation energies of the specific ions. Ions with lower solvation
energies are more likely to evaporate than ions with higher solvation energies.
Given that the solvation energies for most organic molecules are unknown,
the sensitivities of any given organic ion to ion evaporation is difficult to
predict. The importance of solvation energy is evident because surfactants
that concentrate at the surface of a liquid can be detected very sensitively.
APCI
The basis for past incompatibilities in linking liquid chromatography (LC)
with mass spectrometry (MS) arise from difficulties converting relatively
involatile molecules in solution in a liquid into a molecular gas without
inducing excessive decomposition. The APCI probe process of gently
nebulizing the sample into finely dispersed small droplets in a heated ceramic
tube ensures the rapid vaporization of the sample so that the sample molecules
12
are not decomposed. The ceramic tube is heated by a 300 W element.

e-
NO
H 2O
N2
O2
+
N2
N2
N+
4
H2 O
NO
H2 O
H 2O
+
H3 O
NO (H2 O)
H2 O
H2 O
O2 (H2 O)
H2 O
+
H3 O (H2 O)
H2 O
+
O2
H 2O
H2 O
NO+(H2 O)
NO (H2 O)3
H2 O
O2 (H2 O)2
H2 O
H2 O
H3 O (H2 O)2
H 2O
H3 O (H2 O)n
APCI reaction flow diagram
The above diagram shows the reaction flow of the atmospheric pressure
chemical ionization (APCI) process for reactant positive ions (the proton
hydrates, H3O+[H2O]n). This sequence is derived from experimental results
summarized by Huertas and Fontan (Huertas, M.L. and J. Fontan 1975
Evolution Times of Tropospheric Positive Ions, Atmospheric Environ. 9,
1018.).
The major primary ions N2+, O2+, H2O+, and NO+ are formed by the electron
impact of corona-created electrons on the major neutral components of air.
Although NO is normally not a major constituent of clean, ambient air, the
concentration of this species in the source is enhanced due to neutral reactions
initiated by the corona discharge.
13
Samples that are introduced through the APCI probe are sprayed, with the aid
of a nebulizing gas, into the heated ceramic tube. Within the tube, the finely
dispersed droplets of sample and solvent undergo a rapid vaporization with
minimal thermal decomposition. The gentle vaporization preserves the
molecular identity of the sample.
The gaseous sample and solvent molecules pass into the DuoSpray source
housing where the ionization by APCI is induced by a corona discharge
needle attached to the end of the ceramic tube. The sample molecules are
ionized by colliding with the reagent ions created by the ionization of mobile
phase solvent molecules. The vaporized solvent molecules ionize to produce
the reagent ions [X+H]+ in the positive mode and [X-H]- in the negative mode.
It is these reagent ions that produce stable sample ions when they collide with
the sample molecules.
Atmospheric pressure chemical ionization (APCI)
The sample molecules are ionized through a process of proton transfer in the
positive mode and by either electron transfer or proton transfer in the negative
mode. The energy for the APCI ionization process is collision dominated
because of the relatively high (atmospheric) pressure of the API source.
Note: For reverse phase applications, the reagent ions consist of protonated
solvent molecules in the positive mode and solvated oxygen ions in the
negative mode. With favorable thermodynamics, the addition of modifiers
changes the reagent ion composition. For example, the addition of acetate
buffers or modifiers can make the acetate ion, [CH3COO]-, the primary
14
reagent in the negative mode. Ammonium modifiers may make protonated

ammonia [NH4]+ the primary reagent in the positive mode.
Through collisions, an equilibrium distribution of certain ions (for example,
protonated water cluster ions) is maintained. The likelihood of premature
fragmentation of the sample ions in the ion source is reduced given the
moderating influence of solvent clusters on the reagent ions and the relatively
high gas pressure in the source. As a result, the ionization process yields
primarily molecular product ions for mass analysis in the mass spectrometer.
Ionization Region
APCI ionization region
The preceding figure shows the general location of the ion-molecule reactor
of the API source. The slanted lines in the figure indicate a wall-less reactor.
A self-starting corona discharge ion current in the microampere range is
created as a result of the electric field between the discharge needle and the
curtain plate. Primary ions, for example, N2+ and O2+ are created by the loss of
electrons that originate in the plasma in the immediate vicinity of the
discharge needle tip. The energy of these electrons is moderated by a number
of collisions with gas molecules before attaining an energy where their
effective ionization cross-section allows them to ionize neutral molecules
efficiently.
15
The primary ions, in turn, generate intermediate ions that finally lead to the
formation of sample ions. Ions of the chosen polarity drift under the influence
of the electric field in the direction of the curtain plate and through the gas
curtain into the mass analyzer. The whole ion formation process is collision
dominated because of the relatively high (atmospheric) pressure of the API
source. Except in the immediate vicinity of the discharge needle tip, where the
strength of the electric field is greatest, the energy imparted to an ion by the
electric field is small in comparison with the ions own thermal energy.
Through collisions, an equal distribution of certain ions (for example,
protonated water cluster ions) is maintained. Any excess energy that an ion
may acquire in the ion-molecule reaction process is thermalized. Through the
process known as collisional stabilization, many of the product ions are fixed,
even though many subsequent collisions occur. Both product ion and reactant
ion formation are governed by equilibrium conditions at 760 torr
(atmospheric) operating pressure.
Note: The API source functions as a wall-less reactor since the ions that pass
from the source to the vacuum chamber and eventually to the CEM ion
detector never experience collisions with a wallonly collisions with other
molecules. Ions are also formed outside the designated API source, but are not
detected and are eventually neutralized by interacting with a wall surface.
The temperature of the probe is an important factor for APCI probe operation.
The temperature must be set high enough to ensure a rapid evaporation. At a
sufficiently high operating temperature, the droplets are vaporized quickly so
that organic molecules are desorbed from the droplets with minimal thermal
degradation. If, however, the temperature is set too low, the evaporation
process is slower and pyrolysis, or decomposition, may occur before
vaporization is complete. To preserve the molecular identity, the temperature
of the probe must be set to ensure rapid evaporation. Operating the APCI
probe at temperatures above the optimal temperature may cause thermal
decomposition of the sample.
16
TIS Inlet Description

The TIS operation consists of an IonSpray probe with a turbo (heater gas)
spray, as shown in the following figure.
TIS schematic
All electrical and gas connections are made through the DuoSpray ion source
housing. This includes Gas 1 as nebulizer gas, Gas 2 as turbo gas, a
high-voltage connection, heater element and temperature sensors, and
electrical interlock connections. The micrometer head allows the probe to be
adjusted vertically up to 13 mm, and horizontally up to 10 mm for optimum
performance. Only the sample lines need to be connected manually to the
probes.
The turbo heater temperature is set in Analyst through the TEM parameter.
The TEM parameter value and the actual value of the heater temperature is
the same (for example, TEM 350 is equal to 350 C at the heater).
The TIS probe temperature, which is set using the application software, is
maintained by the temperature control board (TCB) mounted inside the main
console. The TCB adjusts the flow of power to the heater element as a
function of the difference between the actual heater temperature and the
temperature setting. The probe temperature is monitored by a sensor
embedded in the heater element that maintains the temperature at the TEM
setting. The operating temperature for the probe is up to a maximum of
750 C.
The operating temperature should be adjusted relative to LC mobile phase
composition, analyte, and flow rate.
17
APCI Inlet Description

The sprayer probe consists of 100 m (0.004" ID) stainless steel tubing
surrounded by a flow of nebulizer gas. The liquid sample flow is pumped
through the sprayer where it is nebulized into a ceramic tube surrounded by a
heater. The inner wall of the ceramic tube is maintained at a temperature of
about 100 to 250 C. A high velocity jet of nebulizer gas (Gas 1) flows around
the electrode to disperse the sample as a mist of fine particles. It moves
through the ceramic vaporization tube into the reaction region of the ion
source past the corona discharge needle where the sample molecules are
ionized.
Probe Temperature
The probe temperature is controlled by the sensor embedded in the probe. The
temperature control board adjusts the flow of power to the heater element as a
function of the difference between the actual heater temperature and the
temperature setting at the applications computer.
Corona Discharge Characteristics

The corona discharge in the APCI source is formed by three major electric
fields and fluid flow elements:
1. Corona discharge needle
2. Curtain plate
3. Orifice lens
The purpose of the corona discharge is to produce ionization of the trace
species, or sample gas. Primary ions, which are formed as a result of the
discharge, are converted by collisional processes to final ion-molecule
reaction products.
The operator has the ability to set the corona discharge setting at the
applications computer by adjusting the value of needle current (NC), which is
normally set to 2 in Analyst.
18
2
Installing the Source
This section of the manual describes the requirements and procedures for
installing the DuoSpray ion source.
Because the DuoSpray ion source is a new optional component for the API
4000 mass spectrometer, installation consists of upgrading an existing
instrument to accommodate the DuoSpray ion source, or installing a
DuoSpray ion source-ready API 4000 instrument along with the DuoSpray
ion source and possibly other optional sources.
If your instrument bears assembly # 1005760 (found on the back of the
instrument), your instrument is ready to accept the DuoSpray ion source.
Installing Source Components

Operator installation consists of installing the switching valve mounting
bracket, connecting the switching valve controller, inserting the probes into
the source housing, and mounting the housing on the instrument.
Installing the Valve Mounting Bracket

A DuoSpray-ready API 4000 instrument has been modified to accept the
switching valve mounting bracket.
To install the switching valve mounting bracket

1. Ensure the instrument has been turned off.
2. Using a 5mm Allen key, loosen the 2 upper bolts holding the interface
assembly to the vacuum chamber.
19
3. Align the slots on the bottom of the mounting bracket over the bolts and
slide it down into position.
4. Tighten the bolts hand tight.
5. Connect the exhaust tube to the exhaust port on the valve, and to the
waste container.
Installing the Switching Valve Controller

To complete the installation of the switching valve, you must connect the
controller.
The switching valve controller assembly consists of a 24 V external DC
power supply and electrical cord, a 2-position actuator control module, and
connecting cables.
To install the switching valve controller

1. Plug the 24 V external DC power supply into the wall.
2. Connect the power supply cord to the 2-position actuator control module.
The red LED A and B lights may not illuminate until the controller is
completely connected and has initialized after a few actuations.
3. Connect the cable from the controller to the valve motor on the mounting
bracket.
4. Connect the second cable from the controller to the sources port on the
back of the instrument. You should now see that one of the A and B LED
lights is on. When the valve operates, these lights will indicate the
position of the valve and will illuminate respectively as the valve switches
positions.
Installing the TIS and APCI Probes

When first installing the source, install the probes before you install the
source on the instrument. Always switch the instrument to standby mode
before removing the probes or source housing.
The probes are inserted and secured into their respective ports in the top of the
housing. Each probe is designed to fit only into its receptacle. The probes can
be inserted and removed separately as required. See Replacing the Probes
on page 55 for instructions.
20
To install the probes

1. Insert the APCI probe into the APCI housing tower located on the left
side of the source housing, positioning it so that the raised plastic post fits
into the groove on the probe.
CAUTION! To avoid damaging the probe, do not allow the protruding
electrode tip in the probe or the corona discharge needle to touch
any part of the source housing.
2. Gently push down on the probe so that the contacts engage with those in
the tower.
3. Turn the bronze retaining ring over the probe, push it down to engage its
threads with the threads on the source tower, and then screw the ring
down all the way. The micrometer knob on the front of the housing tower
is used to adjust the probe vertical position.
4. Insert the TIS probe into the TIS housing tower located on the top of the
source housing, positioning it so that the raised plastic post fits into the
groove on the probe.
CAUTION! To avoid damaging the probe, do not allow the protruding
electrode tip in the probe to touch any part of the source housing.
5. Gently push down on the probe so that the contacts engage with those in
the tower. Turn the bronze retaining ring over the probe, push it down to
engage its threads with the threads on the source tower, and then screw
the ring down all the way. The micrometer knobs on the front and side of
the housing tower, respectively, are used to adjust the horizontal and
vertical positions.

The DuoSpray ion source is designed to be easily set into place on the
instrument. Both the ion source probes and housing can be quickly and easily
removed without tools to allow access to the vacuum interface.
21
To install the source

1. Place the DuoSpray ion source housing straight in against the vacuum
interface, ensuring that the two metal rods on the housing insert into the
vacuum interface.
2. Rotate the two black locking arms on either side of the housing
downwards to secure the housing.
3. Attach the sample inlet line from the column to the center valve port,
labelled L.
4. Attach the .005 ID PEEK tubing lines from the valve ports to the probes.
Ensure the 30 cm-long PEEK tubing runs from the TIS probe to the valve
port labelled T; the 45 cm-long PEEK tubing runs from the APCI probe to
the valve port labelled A.
Note: PEEK tubing lengths have been preadjusted to minimize pressure
variations. Do not alter the PEEK tubing relative lengths.
22
Black
locking
arm
Installing the DuoSpray ion source housing
When the DuoSpray ion source is installed, the instrument recognizes the
source and displays the source identification on all Analyst software
interface screens where applicable.
23
24
3
Operating the Source
This chapter describes the procedures for operating the DuoSpray ion source.
WARNING! Some surfaces on the source become hot during operation. Use
caution when installing or removing the source or the heated probe.

Introducing the Sample

The liquid sample stream is pumped to the ion source by an LC pump or a
syringe drive. Flow rates are determined by the chromatography or the
volume of the sample available. If introduced by an LC pump, the sample
may be injected directly into mobile phase through a loop injector, flow
injection analysis (FIA), or via a separation column (LC/MS).
25
The specific requirements of the sample inlet and ion source are:
To quantitatively transfer the liquid sample to the ion source inlet without
loss and with minimal dead volume.
To generate gas phase ions that are representative of the molecular

composition of the sample with minimal fragmentation.
It is important for the instrument operator to apply appropriate analytical

procedures and practices so that external dead volumes are minimized. Proper
procedures help ensure chromatographic integrity and analytical
reproducibility. It is also important that samples are sufficiently prefiltered so
that the capillary tubing in the inlets is not blocked by particles, precipitated
samples, or salts.
Optimizing the Source

The following sections outline the practical considerations when optimizing
probe performance.
TIS Optimization Procedures

TIS performance depends on the following factors:
Sprayer position in relation to the orifice
Nebulizer tip position in relation to the nebulizing jet
Nebulizer gas
Heater gas flow and temperature
Solvent composition
Optimum performance on standard compounds is relatively easy to achieve

and only a little adjusting or tuning is required once the probe is optimized.
With experience, the operator will develop a personal optimization method
that works best. In general, once the probe is installed and optimum factors
have been determined, little or no readjustment of the values is necessary on a
day-to-day basis. If the probe is removed, it is recommended that it be
re-optimized after it is reinstalled.
CAUTION! If the TIS voltage is set too high, a blue glow can be seen at
the tip of the TIS probe indicating a corona discharge. This will result in
decreased sensitivity and stability of the ion signal.
26
CAUTION! If the instrument is to be left unattended while in operation,

ensure that LC shut-off is in use to prevent flooding of the DuoSpray ion
source housing.
Optimizing the TIS Probe Position

The position of the TIS probe relative to the orifice in the curtain plate, and
the position of the sample tube relative to the nebulizing jet are important
factors in optimizing TIS performance. The position of the sprayer affects
sensitivity and signal stability, and it should always be moved in small
increments.
Looking through the window of the DuoSpray ion source housing provides
the best view of the spray trajectory. At lower flow rates, the probe could be
adjusted to its lowest position. Higher flow rates will require that the probe be
positioned higher than the orifice. The curtain plate orifice should remain
clear of solvent or solvent drops at all times.
Changing from low solvent flow rates (5 L/min) to high solvent flow rates
(3000 L/min) may require that the TIS be repositioned higher to ensure
proper evaporation of droplets and efficient ionization for sampling through
the orifice of the mass spectrometer. This may also require a temperature
adjustment.
Also, as the aqueous composition of the carrier solvent increases at high flow
rates (3000 L/min), the spray becomes more visible. Refer to the table in
Appendix A for recommended starting settings for the TIS probe.
Multiply charged proteins and peptides introduced at a few microliters per
minute usually require the sprayer to be much higher than the curtain plate
orifice.
To optimize the TIS probe position

1. Start with the probe in the middle location of the horizontal plane (setting
of 5) and at the highest position on the vertical plane (setting of 0). The
TIS probe can be adjusted horizontally and vertically.
2. Infuse or inject the analyte of interest.
3. Using small increments, move the probe up and down, left and right until
optimal sensitivity is achieved. The TIS probe may optimize slightly to
27
either side of the orifice. The probe vertical position depends on flow rate
(higher flow rate, higher vertical position).
4. Adjust the black electrode adjustment nut on the handle of the ion source
to move the electrode tube with respect to the nebulizer tube. Typically, a
0.5 to 1.0 mm protrusion of the electrode from the nebulizer tube will
ensure stable and optimum operating conditions.
Note: Optimization needs to be done if the combination of analyte, flow
rate, and composition changes. However, the optimal settings will remain
constant for any given combination of the above.
Optimizing TIS Nebulizer and Heater Gas Flow

Optimize nebulizer gas (Gas 1) for best signal stability and sensitivity.
Typically, the software provides a pressure of 40 to 60 psi. The heater gas
(Gas 2) aids in the evaporation of solvent, which helps to increase the
ionization of the sample. However, too high a temperature can cause
premature vaporization of the solvent at the TIS probe tip, especially if the
probe is set too low (setting of 5 to 13 mm), which will result in signal
instability and a high chemical background noise. Similarly, a high heater gas
flow could produce a noisy or unstable signal. Typically a value of 30 to
50 psi is used for Gas 2.
To optimize Gas 1 and Gas 2

1. In Analyst, Tune Method Editor, open the parameter table dialog box for
your method.
2. Select a starting value for Gas 1.
3. Select a starting value for Gas 2.
4. Adjust each value as required to obtain accurate results.
Optimizing Turbo Temperature and Solvent

Composition
The quantity and type of sample affects the optimal TIS temperature. At
higher flow rates the optimal temperature increases.
A more significant factor is the composition of the solvent. As the organic
content of the solvent increases, the optimal probe temperature should
decrease. With solvents consisting of 100% methanol or acetonitrile, the
probe performance may optimize as low as 500 C. Aqueous solvents
28
consisting of 100% water at flows approximately 1000 L/min require a

maximum probe temperature of 750 C. Normal optimization is usually
performed in increments of 50 C.
The TIS probe is normally used with sample flow rates of 40 to 1000 L/min.
The heat is used to increase the rate of evaporation and this improves
ionization efficiency resulting in increased sensitivity. For recommended
temperatures, see the table Parameter optimization for TIS probe on page 66.
Commonly used solvents and modifiers are acetonitrile, methanol, propanol,
water, acetic acid, formic acid, ammonium formate, and ammonium acetate.
The modifiers such as triethyl amine (TEA), sodium phosphate,
trifluoroacetic acid (TFA), and dodecyl sodium sulfate are not commonly
used because they complicate the spectrum with their ion mixtures and cluster
combinations. They may also suppress the strength of the target compounds
ion signal. The standard concentration of ammonium formate or ammonium
acetate is from 2 to 10 mmol/L for positive ions and 2 to 50 mmol/L for
negative ions. The concentration of the organic acids is 0.1 to 0.5% by
volume.
To optimize turbo heater temperature

your method.
2. Select the TIS source from the dropdown list.
3. Enter a starting value for the temperature parameter.
4. Adjust the temperature parameter as required for accurate results.
APCI Optimization Procedures

Optimization of the APCI probe should begin with a warm-up stage, to allow
the probe to heat prior to initiating the liquid sample flow. The
30-minute warm-up eliminates the possibility that solvent vapors may
condense in a cold probe.
29
To warm up the APCI probe

CAUTION! If the instrument is to be left unattended while in operation,
ensure that LC shut-off is in use to prevent flooding of the DuoSpray ion
source housing.
your method.
2. Select the APCI source from the dropdown list.
3. Set the curtain gas value to 10 psi. It is suggested that you operate the
APCI with curtain gas settings adjusted to the highest flow rate possible
without signal loss.
4. Set the nebulizer gas (Gas 1) to 20 psi.
5. Set the heater temperature (TEM) to 400 oC.
CAUTION! The ceramic heater needs to be warmed slowly to avoid
thermal shock to the heating element.
6. Let the APCI probe warm up for 30 minutes.

7. Connect the LC solvent line from the injector or autosampler to the LC
connection on the probe. Turn on the pump.
It takes approximately ten minutes before the APCI probe reaches a
temperature at which the solvent mist is cleared from the source housing.
Several parameters impact the performance of the APCI probe. Optimize the
performance while injecting a known compound (reserpine is recommended),
and monitor the signal of the known ion. Adjust the parameters to maximize
the signal-to-noise ratio as shown in the table in Appendix A.
30
Optimizing the APCI Probe Position

The position of the sprayer, as shown in the following figure, affects
sensitivity and signal tability and should always be changed in small
increments.
APCI (Heated Nebulizer) probe position
Looking through the window of the DuoSpray ion source housing provides
the best view of the probe position. At low flow rates, the probe could be
adjusted closer to the orifice. Higher flow rates require that the probe be
positioned farther away from the orifice. The curtain plate orifice should
remain clear of solvent or solvent drops at all times. The corona needle is
attached to the housing and should be adjusted so that the tip of the needle
points right at the center of the probe.
31
You can adjust the black electrode adjustment nut on the handle to raise and
lower the sample tube in relation to the nebulizing jet to produce an optimal
signal.
To optimize the APCI probe position

1. Start with the probe in the middle location. The APCI probe can be
adjusted vertically only, using the adjustment knobs on each probe.
2. Using small increments move the probe away from or toward the orifice
until optimal sensitivity is achieved.The APCI probe optimizes toward
the orifice plate.
3. Adjust the black electrode adjustment nut on the handle of the ion source
to move the electrode tube with respect to the nebulizer tube.
Note: Optimization needs to be done if the combination of analyte, flow
rate, and composition changes. However, the optimal settings will remain
constant for any given combination of the above.
Optimizing the Needle Current

The needle current (NC) applied to the corona discharge needle usually
optimizes over a broad range (that is, 1 to 5 A in positive mode).
To optimize, start at a value of one and increase until you achieve the best
signal-to-noise ratio. If no changes in signal are observed when increasing the
current, it is best to leave the current at the lowest setting that provides the
best sensitivity (for example, 2 A).
Optimizing Probe Temperature and Solvent

Composition
The quantity and type of solvent affects the optimal APCI probe temperature.
At higher flow rates the optimal temperature increases. A more significant
factor is the composition of the solvent. As the organic content of the solvent
increases, the optimal probe temperature should decrease. With solvents
consisting of 100% methanol or acetonitrile the probe performance may
optimize at temperature as low as 400 C at flow rates of 1000 L/min.
Aqueous solvents consisting of 100% water set at flows of approximately
2000 L/min require a minimum probe temperature of 700 C. Normal
optimization is usually performed in increments of 50 C.
32
The APCI probe is normally used with sample flow rates of 1000 L/min but
may be used with flows from 50 L/min to 2 mL/min. Heat is used to
vaporize the sample and solvent sprayed into the DuoSpray ion source
housing. If the temperature is set too low, the vaporization will be incomplete
and large, visible droplets are expelled into the housing. However, setting the
temperature too high induces thermal degradation of the sample. The optimal
temperature is the lowest setting that ensures the complete vaporization of the
sample.
WARNING! Do not remove the probe from the source housing or the housing
from the instrument while either is hot. Allow at least ten minutes for the
source and probes to cool.
Commonly used solvents and modifiers are acetonitrile, methanol, propanol,

water, acetic acid, formic acid, ammonium formate and ammonium acetate.
Modifiers such as triethyl amine (TEA), sodium phosphate, trifluoroacetic
acid (TFA), and dodecyl sodium sulfate are not commonly used because they
complicate the spectrum with their ion mixtures and cluster combinations.
They may also suppress the strength of the target compound ion signal. The
standard concentration of ammonium formate or ammonium acetate is from 2
to 10 mmol/L for positive ions and 2 to 50 mmol/L for negative ions. The
concentration of the organic acids is 0.1 to 0.5% by volume.
WARNING! The source exhaust pump must be vented to either an external
fume hood or an external source.
Setting the Software Parameters

This section describes the procedures for setting up compound- and sourcespecific parameters using Analyst.
Setting up Instrument-Specific Parameters

Setting up instrument parameters is only necessary on a periodic basis, either
on initial installation, or if you need to recalibrate the instrument. This process
is not required for each analysis. Once you assign optimum instrument
parameters for a particular analysis, they become the working parameters
describing the control parameters for the instrument. For further information,
see the online Help in Analyst for the API 4000 mass spectrometer.
33
Setting up Compound-Specific Parameters

Each time you quantitate a new compound, you need to begin at this step and
define the analysis conditions for the compound. You can set up
compound-specific parameters in two different ways: automatically using the
Quantitation Optimization wizard or manually using Manual Tune. For these
procedures, see the online Help in Analyst for the API 4000 mass
spectrometer.
Setting up Source-Specific Parameters

Source-specific parameters can be optimized for the LC conditions used
during analysis. These parameters are accessed either by selecting the Source/
Gas tab in the Manual Tune Method Editor window, or by clicking Edit
Parameters in the Method Editor window in Acquire mode.
Software parameters are set for each experiment, which is a sequence of
measurements for the mass spectrometer. One or more experiments can be
grouped to make a period that contains one or more cycles. The DuoSpray ion
source supports both multi-period and multi-experiment methods.
The Analyst software provides the capability to select either of the two probes
on a per experiment basis. All of the data acquired using the DuoSpray ion
source is clearly identified by the probe used to acquire the data, TIS or APCI
(Heated Nebulizer).
Needle Current
The DuoSpray ion source is current-controlled rather than
voltage-controlled. Specify the appropriate current for your acquisition
method, regardless of source selection position.
Nebulizer Gas
This gas is used to generate a fine aerosol spray. Optimize for signal stability
and sensitivity. Typical values range from 20 to 60 and depend on sample
flow rate. A higher flow rate requires a higher Gas 1 setting.
Heater Gas
In the TIS probe, the heater gas (Gas 2) aids in the evaporation of solvent,
which aids in increasing the ionization of the sample. The higher the liquid
flow or the higher the aqueous composition of the solvent, the higher the
34
heater gas temperature and gas flow required. However, for the TIS probe too
high a temperature can cause premature vaporization of the solvent, and result
in a high chemical background noise, while too high a heater gas flow can
produce a noisy or unstable signal.
In the DuoSpray ion source, Gas 2 is also used as a nebulizer gas for APCI.
Temperature
The liquid flow rate, quantity, composition, and type of sample affect the
optimal spray temperature. At higher flow rates, the optimal temperature
increases. A more significant factor is the composition of the solvent. As the
organic content of the solvent increases, the optimal probe temperature should
decrease. With solvents consisting of 100% methanol or acetonitrile, the
probe performance may optimize as low as 300 C. Normal optimization is
usually performed in increments of 50 C. Aqueous solvents consisting of
100% water at flows of approximately 1 mL/min require a probe temperature
of 750 C.
The TurboIonSpray is normally used with sample flow rates of 40 to

1000 L/min.
The APCI is normally used with sample flow rates of 1 mL/min but has
been used with flows from 50 L/min to 2 mL/min.
The heat is used to vaporize the sample spray generated in the ion source
housing, to increase the rate of evaporation thus improving ionization
efficiency resulting in increased sensitivity.
If the temperature is set too low the vaporization is incomplete and visible
large droplets are expelled into the housing. However, setting the temperature
too high can induce thermal degradation of the sample. The optimal
temperature is the lowest setting that ensures the complete vaporization of the
sample. For recommended settings, see the TIS Suggested Operating Settings
table in Appendix A.
Declustering Potential
Optimal declustering potential voltage should be set high enough to reduce
the chemical noise, but low enough to avoid fragmentation. Start with the
declustering potential (DP) at 20 V.
Note: The fragmentation energy of a compound is a function of its structure
and molecular weight. Generally, lower molecular weight compounds require
less energy lower declustering potential to induce fragmentation. For
35
some labile compounds, DP values of between 5 and 10 may be required with

the TurboIonSpray.
In general terms, the higher the declustering potential voltage the greater the
energy imparted to the ions entering the analyzing region of the mass
spectrometer. The energy helps to decluster the ions and to reduce the
chemical noise in the spectrum, resulting in an increase in signal-to-noise, or
sensitivity. Increasing the voltage beyond optimal conditions can induce
fragmentation before the ions enter the mass filters, resulting in a decrease in
sensitivity. In some instances, fragmentation is a valuable tool that provides
additional structural information.
Curtain GasTM
The curtain gas ensures a stable, clean environment for the sample ions
entering the mass spectrometer. The gas curtain prevents ambient air or
solvent from entering the analyzer region of the instrument while permitting
the sample ions to be directed into the vacuum chamber by the electrical fields
generated between the vacuum interface and the spray needle. The presence
of the solvent vapor or other non-gaseous compounds in the analyzer region
of the mass spectrometer contaminates the Q0 rod set causing a reduction in
Q0 resolution, stability and sensitivity, and an increase in chemical
background noise.
In order to prevent instrument contamination the curtain gas flow should be
optimized at the highest possible setting that does not result in a significant
reduction in signal intensity.
Solvent Composition
Commonly used solvents are:
Acetonitrile
Methanol
Propanol
Water
Commonly used modifiers are:
36
Acetic acid
Formic acid
Ammonium formate
Ammonium acetate
Not commonly used modifiers:
Triethyl amine (TEA)
Sodium phosphate
Trifluoroacetic acid (TFA)
Sodium dodecyl sulfate
These are not commonly used because they complicate the spectrum with
their ion mixtures and cluster combinations. They may also suppress the
strength of the target compound ion signal.
The standard concentration of ammonium formate or ammonium acetate is
from 2 to 10 mmol/L for positive ions and 2 to 50 mmol/L for negative ions.
The concentration of the organic acids is 0.1% to 0.5% by volume for the TIS
probe and 0.1% to 2.0% by volume for the APCI probe.
Tuning Your Source Manually

Manual tuning allows users with expert knowledge of the instrument and
source to manually adjust the source parameters, working parameters, and
other options to get the best performance from the instrument. Principal tools
for performing manual tuning are
Ramping a parameter. This feature allows you to automatically ramp a
selected compound-dependent parameter while viewing the results.
Optimizing working parameters manually. This allows you to change the
value of one or more compound-dependent parameters as the experiment
progresses. You can increase or decrease the value or values.
The Tune Method Editor allows you to perform manual tuning operations,
such as creating a method, acquiring data, ramping a parameter, and manually
optimizing a parameter.
37
Displaying the Tune Method Editor

The Tune Method Editor consists of two panes and several buttons above the
panes.
State
Parameter
Edit
Acquisition
Method
Editor
Tune Method Editor window
The State Parameter Editor on the left has four tabs, including, the
Source/Gas tab, the Compound tab, the Resolution tab, and the Detector
tab.
The Acquisition Method Editor pane is on the right. This pane displays
various tabs depending on the method (MS, Syringe Pump, or LC), and
the types of peripheral devices configured to work with the mass
spectrometer.
To display the Tune Method Editor
38
Double-click Manual Tuning on the Navigation bar.
Building a Tuning Method

To build a tuning method you must perform the following steps:
1. Reserve the acquisition queue for tuning.
2. Create a mass spectrometry (MS) method, and if required, a liquid
chromatography (LC) method and a syringe pump method.
You can create an LC acquisition method, an MS acquisition method, or a
syringe pump acquisition method in manual tuning mode. You can save and
use these methods when building an acquisition batch. After creating an
acquisition method in manual tuning, you are ready to acquire data. For more
information, see To create an MS acquisition method on page 39, or To
add an LC acquisition method on page 40, or To add a syringe pump
acquisition method on page 40.
To reserve the acquisition queue for tuning
From the Tools menu, click Tuning Instrument.

The Tuning icons become available on the toolbar and Navigation bar.
To create an MS acquisition method

1. On the Tools menu, click Manual Tuning.
The Tune Method Editor opens.
2. From the method list, select MS Method.
3. Click the MS tab.
4. Choose the Scan type and configure values for all of the parameters as
required.
Note: Different parameters are displayed depending on the Scan type
selected. For more information, see the online Help topic describing the
MS tab for each scan type.
5. Type the Duration, number of Cycles, and the period Delay Time.
6. Click the Advanced MS tab.
7. Configure values for all of the parameters as required.
Note: Different parameters are displayed depending on the scan type
selected on the MS tab. For more information, see the online Help topic
describing the Advanced MS tab for each scan type.
39
8. Click the Source/Gas tab and edit the values for the parameters.
9. Click the Compound tab and edit the values for the parameters.
You can now either save your method or acquire data.
SeeAcquiring Data on page 41.
To add an LC acquisition method

1. On the Tools menu, choose Manual Tuning.
The Tune Method Editor appears.
2. From the method list, select LC Method.
3. Click the LC Pump Gradient tab.
4. Type the values for the flow rate, gradient, and other parameters displayed
in the table.
5. Click the Limits tab.
6. Type the values for maximum pressure, minimum pressure, shutdown
time, and any other parameters displayed on the tab.
To add a syringe pump acquisition method

1. On the Tools menu, choose Manual Tuning.
The Tune Method Editor appears.
2. From the method list, select Syringe Pump Method.
3. On the Syringe Pump Properties tab, type the Syringe Diameter.
4. Type the Flow Rate value.
5. Select the Unit for the flow rate.
6. To start the syringe pump, click Start Syringe Pump.
The syringe pump starts. The label on the Start Syringe Pump button
changes to Stop Syringe Pump.
7. To change the flow rate while the pump is on, type the Flow Rate value
and then click Set Flow Rate.
40
Acquiring Data
After you have created a method using the Tune Method Editor you can start
data acquisition.
To acquire data
1. Create an MS acquisition method, and, if required, an LC method or a
syringe pump method.
2. Click Start (if you want Analyst to name the data file) or Acquire (if you
want to name the sample and data file).
If you clicked Start, the Start button becomes the Stop button; go to
step 4.
If you clicked Acquire, go to step 3.
3. In the Acquire to Disk dialog box, type the name of the sample and the
name of the data file where the results will be stored, and then click OK.
Data acquisition starts.
The TIC and corresponding mass spectrum are appended to the Tune
Method Editor as separate panes.
4. Right-click on the TIC pane to display the following three options:
If you select Open File the file currently displayed in the window
opens with Explore and allows you to use the tools available in
Explore.
If you select Fixed Intensity Display, the Fixed Intensity Display

dialog box opens, and you can specify the y-axis maximum intensity
in cps.
If you highlight an area of interest in the pane and then select

Normalize to Selection, you can perform a y-axis zoom.
5. Right-click on the mass spectrum to display the following Explore

options:
If you select Open File, the file currently displayed in the window
opens with Explore and allows you to use all the tools available in
Explore.
If you select Acquire Product, you can acquire the product of the
highest intensity mass in the region that was selected.
41
If you select Fixed Intensity Display, the Fixed Intensity Display

dialog box opens, and you can specify the y-axis maximum intensity
in cps.
If you highlight an area of interest in the pane and then select

Normalize to Selection, you can perform a y-axis zoom.
If there are multiple mass windows, you can select a particular mass
window or the entire mass range in the MS pane by selecting All
Mass Ranges.
Warming Up the Source

Operation of the source should begin with a warm-up stage to allow the
housing to heat prior to initiating the liquid sample at high flow rates. A
warm-up period eliminates the possibility that solvent vapors may condense
in a cold probe. The ceramic heater in the APCI probe needs to be warmed
slowly to avoid thermal shock to the heating element, and the TIS probe also
needs to be warmed prior to use.
To warm up the source and probes

1. In Analyst, Tune Method Editor, accept the default curtain gas value of 10
psi.
We suggest that you operate the APCI (HN) probe with curtain gas
settings adjusted to the highest flow rate possible without signal loss.
2. Set the nebulizer gas (Gas 1) to 20 psi.
3. Set the heater gas (Gas 2) to 15 psi.
4. In the Working Parameters file, set the heater temperature (TEM) to
400 C.
5. Let the source warm up for 30 minutes or until the housing is warm to the
touch.
6. Connect the LC solvent line from the injector or autosampler to the LC
connection on the valve.
7. In Analyst, select the APCI (HN) probe.
8. Turn on the pump.
It takes approximately ten minutes before the APCI probe reaches a
temperature at which the solvent mist is cleared from the source housing.
42
Operating Tips
1. When running the TurboIonSpray run the curtain gas at as high a flow
rate as possible without decreasing the signal. This helps to:
Prevent penetration of the curtain gas, which can produce a noisy

signal.
Prevent contamination of the orifice
Increase the overall signal to noise ratio.
2. The liquid spray from the TurboIonSpray should be directed away from
the orifice in order to:
Prevent contamination of the orifice.
Prevent piercing of the curtain gas, which can create an unstable

signal.
Prevent electrical shorting due to the presence of the liquid.
3. The higher the liquid flow, or the higher the aqueous composition of the
solvent, the higher the temperature and heater gas (Gas 2) flow required.
However, too high a temperature can cause thermal degradation of the
compound, and result in a high chemical background noise, while too
high a heater gas flow can produce a noisy, or unstable signal.
Controlling the DuoSpray Ion Source Temperature

The temperature controller monitors and maintains the temperature of the
turbo heater, and the APCI heater. A thermal sensor senses the actual heater
temperature and transmits it to the temperature controller board.
The operating temperature range for the probes is up to 750 C.
WARNING! Do not remove the probe from the source housing or the housing
from the instrument while either is hot. Allow at least ten minutes for the
source and probes to cool.
43
44
4
DuoSpray Testing
Procedures
The DuoSpray Performance Tests in this chapter will indicate the level of
performance of the DuoSpray source. Meeting the test specifications will
ensure that the source is operating at an optimal performance level. These
tests should be run in any of the following three situations:
After the DuoSpray is first installed.
After performing major maintenance to the instrument or source.
Any time the customer is required to reassess the performance of the

DuoSpray source (i.e. before starting a project, or as part of a standard
operating procedure).
WARNING! Throughout the TIS and APCI (HN) tests, the source housing
and the probes become very hot. Handle with extra care to avoid injury.
CAUTION! The Curtain Gas should be run as high as possible to avoid
contamination of the test instrument.
This chapter contains the following:
System Setup on page 46
Materials Required on page 47
DuoSpray Performance Tests on page 49
45
DuoSpray Testing Procedures
System Setup
This section provides the information required to prepare the system for the
performance testing procedures.
Instrument Setup
Ensure that the host instrument has passed all specifications for Q1 PPG and
Reserpine (Q1 and MS/MS) testing and that it is fully optimized for
sensitivity. For the Reserpine Q1 and MS/MS infusion test, you will require a
100 pg/L solution.
The initial setup/verification procedures (CEM optimization, verifying peak
width with mass calibration and ion spray) must be performed before
collecting any analytical data. Please refer to the Analyst online Help for
details.
WARNING! Do not spray sample (liquid) directly at the orifice. Ensure
that the curtain gas is always run as high a possible without loss of
sensitivity to avoid contamination of the ion optics.
The curtain gas should be run as high as possible, one number below the point
where the ion intensity starts to decrease.
Injector Setup
A dedicated injector with a 5 L loop and a 10 L syringe for the test solution
is required. A blank injection is required prior to the DuoSpray test.
Different syringes must be designated and labeled for each sample in order to
minimize cross contamination.
46
Materials Required
The following materials are required for testing performance of the DuoSpray
Ion Source.
Mobile Phase
Solvent: 70% acetonitrile (HPLC grade) and 30% deionized distilled water
The Reserpine solution for TIS and APCI tests consists of 10 pg/L of
Reserpine dissolved in mobile phase of 70/30 Acetonitrile/Water
and 2 mM Ammonium Acetate and 0.1% Formic Acid.
Preparing The Test Solution

The test solution to be used for performance testing is 10 pg/L Reserpine in
mobile phase.
To prepare the test solution

Important! Both polypropylene vials used in this procedure must be flushed
and sonicated with methanol prior to their use.
1. Prepare a 1 mg/mL stock in 50/50 methanol and ethyl acetate from
Reserpine powder in a 4 mL brown glass vial.
2. Add 100 L of stock to 9.9 mL of methanol in a 30 mL polypropylene
Wheaton vial and vortex to yield a 10 ng/L solution.
3. Add 100 L of the 10 ng/L solution to 100 mL of the mobile phase in a
125 mL polypropylene Wheaton vial and vortex to yield the 10 pg/L test
solution.
Equipment
The following equipment is required.
PE 250/HP LC pump or equivalent with 8125 Reodyne injector (5 L

loop)
PEEK tubing 1/16" o.d. 0.005" ID
Analyst 1.3 and epack 1, or later version
47
DuoSpray source (TIS and APCI probes)
Syringe 2501000 L
Gases
Ensure the following gases are available.
Zero Air (< 0.1 ppm hydrocarbons, e.g. CH4)
Gas withdrawal liquid nitrogen

Verify the following gas connections to the instrument:
Curtain gas supply is nitrogen at 60 psi
Source exhaust is Zero Air at 55 psi
Gas 1 is Zero Air at 105 psi
Gas 2 is Zero Air at 105 psi
CAUTION! All test solutions must be kept refrigerated. If for any reason
they are left out of the refrigerator for longer than 48 hours new
solutions must be used.
Safety
Refer to all applicable Material Safety Data Sheets for any necessary
precautions before handling chemical solutions or solvents. Before
performing the tests, the technician must be sufficiently trained on operation
and safety procedures.
48
DuoSpray Performance Tests

The procedures in this section should be carried out with reference to the
Installing the Source and Operating the Source chapters earlier in this
manual.
Testing the TurboIonSpray Probe

Before running the performance test, select the TIS probe from the Source
Parameter dropdown list and ensure that the following parameters are set for
your instrument and the TIS probe.
TIS Test Procedure Parameter Settings
Parameter
Curtain Gas (CUR)
Gas1
Gas2
Needle Current (NC)
Temperature (C)
DP
Nominal Value
10
35
40
3
700
100
Recommended Range
10 to 20
20 to 70
30 to 80
1 to 8
700 to 750
70 to 140
In the Acquisition Method window of Analyst, set the following scan

parameters.
Scan Parameters
Parameter
Scan Mode
Q1
Q3
Scan Time
Duration
Value
MRM
609.2
195.1
200 ms
10 minutes
Note: Do not introduce any solvent flow before verifying that the source has
reached the temperature setting.
To test the TIS performance

1. In Analyst, select the Method file optimized for Reserpine MS/MS.
2. Set the HPLC pump to deliver 0.2 mL/min, using the mobile phase
detailed above.
49
3. Connect the pump to the source through an injector equipped with a 5 L

loop.
4. Over fill the 5 L loop with 30-40 L 10 pg/L Reserpine solution, while
optimizing the nebulizer gas (Gas1), turbo gas (Gas2), curtain gas, and
needle current for sensitivity and stability of the signal.
5. Optimize the electrode protrusion through the tube, as well as the vertical
and horizontal position of the probe.
6. Once the source is optimized, inject 30-40 L of 10 pg/L of Reserpine
solution while monitoring m/z 609/195.
7. Make a total of three injections and record the intensities.
The three injections should resemble the following figure:
Specification
The three injections of the 10 pg/L solution of Reserpine must have
intensities greater than:
For 0.2 mL/min: 1.25 105 cps/injection at 609/195
Background noise should not exceed 100 cps.
If the source does not meet specification, verify that the instrument performs
to specification with the dedicated source installed, and that the test solution
has been prepared correctly. If the instrument performance and the test
solution have been verified and the source does not meet specification, call
your local Customer Service Representative.
50
Testing the APCI Probe

Before running the performance test, select the APCI (HN) probe from the
Source Parameter dropdown list and ensure that the following parameters are
set for your instrument and the APCI probe.
APCI (HN) Test Procedure Parameter Settings
Parameter
Curtain Gas (CUR)
Gas1
Gas2
Needle Current
(NC)
Temperature (C)
DP
Nominal Value
10
25
40
3
Recommended Range
10 to 20
20 to 50
40
1 to 8
350
100
300 to 550
70 to 140
In the Acquisition Method window of Analyst, set the following scan

parameters.
Scan Parameters
Parameter
Scan Mode
Q1
Q3
Scan Time
Duration
Value
MRM
609.2
195.1
100 ms
10 minutes
Note: Do not introduce any solvent flow before verifying that the source has
reached the temperature setting.
To test the APCI Performance

1. In Analyst, select the Method file optimized for TIS.
2. Set the HPLC pump to deliver 1 mL/min, using the mobile phase detailed
above.
3. Connect the pump to the source through an injector equipped with a 5 L
loop.
51
4. Over fill the 5 L loop with 3040 L 10 pg/L Reserpine solution, while
optimizing the turbo gas (Gas2), curtain gas, and needle current for
sensitivity and stability of the signal.
5. Optimize the electrode protrusion through the tube, as well as the vertical
and horizontal position of the probe.
6. Once the source is optimized, inject 3040 L of 10 pg/L of Reserpine
solution while monitoring m/z 609/195.
7. Make a total of three injections and record the intensities.
Specification
The three injections of the 10 pg/L solution of Reserpine must have
intensities greater than:
For 1 mL/min: 5.5 104 cps/injection at 609/195
Background noise should not exceed 100 cps.
If the source does not meet specification, verify that the instrument performs
to specification with the dedicated source installed, and that the test solution
has been prepared correctly. If the instrument performance and the test
solution have been verified and the source does not meet specification, call
your local Customer Service Representative.
Upon completion of the performance tests, stop the LC pump, set the
temperature to zero, and allow the probes to cool down.
52
5
Maintaining the Source
This chapter describes procedures for maintaining the DuoSpray ion source in
good working condition.
CAUTION! Use only the recommended cleaning or decontamination
methods, to avoid damaging the equipment.
Maintenance Schedule
Periodic gas leakage tests should be performed, along with general
maintenance inspection by the operator to ensure safe operation of the
instrument. Carry out regular cleaning procedures to maintain the DuoSpray
ion source, its probes, and the switching valve in good operating condition.
Frequency of cleaning depends on the compounds you test and the amount of
time each probe may be idle while containing a sample stream.
Tools Required
The following tools are required for carrying out maintenance of the source:
9/64" Allen key (supplied)
5 mm Allen key
2.5 mm Allen key
6.3 mm crescent wrench
53
Phillips screwdriver
Slotted screwdriver
Cleaning the Switching Valve and Source Probes

The following valve flushing procedure should be performed after using a
mobile phase that contains high buffer/salt concentrations.
We recommend periodic flushing of the source, regardless of type of
compounds sampled. This can be done easily by setting up a method in
Analyst specifically for conducting a flushing operation.
To clean the switching valve and sprayer tubes

Important! Ensure that both probes and sample lines are flushed thoroughly.
1. Switch to buffer/salt free mobile phase composition (i.e., 50/50
water/acetonitrile or 50/50 water/methanol).
2. In Analyst, set TEM between 500 and 600, and GS1 and GS2 to at least
40. Ensure TEM setpoint is reached.
3. Flow buffer/salt free mobile phase through the valve, sample lines and
both probes at 1 mL/min for about 10 to 15 minutes.
Replacing Source Components

The following procedures will help you in replacing source components
during maintenance.
Replacing the Source

The DuoSpray ion source is designed to be easily removed and reinstalled as
necessary.
To remove the source

1. Complete any ongoing scans or abort a scan in progress by selecting
Abort Sample command from the Acquire menu.
2. Stop the sample flow to the ion source by turning off the flow pump.
3. Rotate the two black locking arms upward to loosen the housing.
4. Pull the source housing straight away from the vacuum chamber.
54
To reinstall the source

1. Line the source up with the vacuum chamber and push into place.
2. Rotate the two black locking arms downward to secure the source.
Replacing the Probes

The following procedure describes how to remove and reinstall either of the
ion source probes.
To remove the ion source probes

WARNING! Follow this procedure to avoid contact with the high
voltages applied to the corona discharge needle and the curtain plate.
WARNING! Do not remove a probe from the source while it is hot. Allow
at least ten minutes for the source and probes to cool.
Important! The source probes are interlocked. The instrument will not run
unless both probes are installed and the DuoSpray ion source is locked into
place.
Abort Sample command from the Acquire menu, and place the
instrument in standby mode.
2. Stop the sample flow to the ion source by turning off the flow pump.
3. Remove the PEEK tubing from the ion source probe.
4. Unscrew the bronze retaining ring.
5. Gently pull the ion source probe straight up out of the housing. Do not
allow the tip of the probe to touch anything as you remove it or store it.
Place the probe aside in a safe area.
To reinstall the ion source probes

1. Slide the ion source probe straight down into the housing, taking care not
to allow the tip of the probe to touch anything.
2. Tighten the bronze retaining ring.
3. Reattach the PEEK tubing to the ion source probes.
55
Replacing the Switching Valve

The valve has wear components that require routine preventative maintenance
to ensure uninterrupted service.
A polymer based rotor seal can be replaced should the seal fail or become
contaminated. Concentrations of particulates on the rotor can damage the
valve surface. Before installing a new rotor, clean the valve body using an
ultrasonic bath for approximately 5 minutes. Allow the valve body to dry.
Switching valve
56
To remove the rotor

1. Ensure that the valve has been depressurized by shutting down the sample
flow.
2. Unscrew the knurled nut on the front of the valve and pull it away from
the valve.
3. Using a pencil magnet, pull the rotor out of the valve. The rotor is located
directly behind the knurled nut.
To reinstall the rotor

1. Using a pencil magnet, reinstall the rotor, taking care not to scratch the
mirrored surface inside the valve or touch the seal on the rotor.
2. Replace the knurled fitting on the front of the valve and tighten by hand
until the end stop is reached.
3. As an administrator, log into Analyst and reset the valve cycling counter
in the Mass Spectrometer status information area. The counter tracks
valve usage. It should be reset every time the rotor is replaced, or
according to specific laboratory procedures.
Switching valve counter reset
57
Replacing the Turbo Heater

The following procedures describe how to remove and reinstall the turbo
heater.
To remove the turbo heater

Abort Sample command from the Acquire menu.
2. Allow sufficient time for the turbo heater to cool down, then remove the
PEEK tubing, and ion source as described in To remove the source on
page 54
3. Using a 2.5mm Allen key, loosen the screw on the cap of the turbo heater.
4. Using a Phillips screwdriver, unscrew the four screws and set them aside.
5. Pull the turbo heater straight out of the turbo heater port.
To reinstall the turbo heater

voltages applied to the corona discharge needle and the curtain
plate.
WARNING! Allow at least ten minutes for the source and probes to
cool.
1. Push the turbo heater straight into the turbo heater port.
2. Using a Phillips screwdriver, place and tighten the four screws on the
turbo heater.
3. Replace the cap, and tighten using a 2.5mm Allen key.
4. Replace the ion source onto the instrument.
5. Reattach the PEEK tubing.
58
Replacing the Corona Discharge Needle Tip

Over time, the tip of the corona discharge needle may become corroded and
need to be replaced.
When removing and replacing the corona discharge needle tip, care must be
taken to ensure your safety from the high voltages applied to the ion source
probe. Always place the instrument in Standby mode before removing the
source.
To replace the corona discharge needle tip


Abort Sample command from the Acquire menu, and place the instrument
in standby mode.
2. Allow sufficient time for the probe to cool down, then remove the PEEK
tubing, ion source probes, and DuoSpray source as described in To
remove the source on page 54.
3. Turn the source so the open back is facing you.
4. Press down on the PEEK adjuster knob on the top of the source tower.
The corona discharge needle extends.
5. Holding the corona discharge needle tip between thumb and forefinger,
with the other hand rotate the PEEK adjuster knob anti-clockwise to
unscrew the tip.
6. Gently remove the corona discharge needle tip.
7. Holding a new tip between thumb and forefinger, with the other hand,
press down on the PEEK adjuster knob to extend the corona discharge
needle.
8. With the PEEK adjuster knob held down, place the tip on the extended
corona discharge needle and turn the knob clockwise to tighten the tip.
You can now insert the ion source probes, place the source housing on the
instrument, attach the PEEK tubing, and begin optimization procedures.
59
Replacing the Corona Discharge Needle

Occasionally, the corona discharge needle tip may become so corroded that it
must be cut off the corona discharge needle. Should this occur, you will need
to replace the corona discharge needle.
When removing and replacing the corona discharge needle, care must be
taken to ensure your safety from the high voltages applied to the ion source
probe. Always place the instrument in Standby mode before removing the
source.
To replace the corona discharge needle


Abort Sample command from the Acquire menu, and place the instrument
in standby mode.
2. Allow sufficient time for the probe to cool down, then remove the PEEK
tubing, ion source probes, and DuoSpray source as described in To
remove the source on page 54.
3. Turn the source so the open back is facing you.
4. Gently pull the PEEK adjuster knob to remove the corona discharge
needle from the ceramic sleeve, taking care not to break the sleeve.
5. Unscrew the PEEK adjuster knob from the corona discharge needle.
6. Place the PEEK adjuster knob on a new corona discharge needle and
insert the needle into the sleeve.
7. Tighten the PEEK adjuster knob until a firm connection is made.
You can now replace the corona discharge needle tip, insert the ion source
probes, place the source housing on the instrument, attach the PEEK tubing,
and begin optimization procedures.
60
Adjusting the Corona Discharge Needle

When using the APCI probe, ensure that the corona discharge needle is
pointing toward the orifice.
To adjust the corona discharge needle

voltages applied to the corona discharge needle and the curtain
plate.
1. Use a slotted screwdriver to adjust the plastic screw on the top of the
needle.
2. Look through the glass window to ensure that the needle is aligned with
the tip facing the orifice.
If further adjustment is needed

1. Remove the DuoSpray ion source as described in To remove the source
on page 54.
WARNING! Never operate the source with the APCI corona
discharge needle facing away from the orifice as arcing may occur.
2. Turn the source so that the back is facing toward you.

3. Turn the needle so that the tip is pointing toward you. This orients the
corona discharge needle toward the curtain plate when the source is
remounted on the instrument.
You can now remount the source.
61
Replacing the Electrode Tube

The electrode tube on either the TIS or the APCI probes may become blocked
or produce an uneven spray. If flushing the probe does not clear the blockage,
replace the tube using the following procedure.
To change a blocked tube

WARNING! The source may be hot for several minutes after it is
removed from the instrument. Allow the source to cool prior to working
on it.
1. Place the instrument in standby mode.

2. Unscrew the metal ring holding the probe in the source.
3. Gently remove the probe from the source.
4. Unscrew and remove the metal probe fitting at the top of the probe. The
electrode can now be removed from the probe.
5. Place a new electrode tube in the fitting and screw into the union. Ensure
that the sprayer tube is placed as far as it can go into the union to
guarantee a leak-proof seal.
6. Place the metal tube back into the probe.
7. Place the metal probe fitting over the union and tighten. This fitting must
be tightened by hand as far as it will go to ensure the proper protrusion of
the metal sprayer tube tip at the end of the probe.
8. Replace the probe into the source.
The source is now ready for use again.
Replacing the PEEK Tubing

Ensure you have stopped the sample flow as described in Replacing the
Source on page 54 and that any remnant gas has been exhausted through the
source exhaust.
Note: PEEK tubing lengths have been preadjusted to minimize pressure
variations. Do not alter the PEEK tubing relative lengths. See Appendix C for
a complete list of parts.
62
To replace the PEEK tubing

1. Disconnect the PEEK tubing from the valve and the ion probe.
2. Replace the PEEK tubing with the same length of tubing used previously.
The correct length of .005" ID tubing must be used for each probe: 30cm
for the TIS probe, 45cm for the APCI probe.
You can now resume the sample flow.
63
64
Appendix A: Source
Parameters
This section describes the typical operating parameters for the DuoSpray Ion
Source.
TIS Suggested Operating Settings

The following table provides recommended operating conditions for the
TurboIonSpray at three different flow rates. For each flow rate, the curtain gas
(from setting 11 to 45 at the applications computer) should be as high as
possible. The solvent composition used for optimization was 50/50
water/acetonitrile. These conditions represent a starting point from which to
optimize the TurboIonSpray. By an iterative process, the various settings can
be optimized using flow injection analysis to obtain maximum signal-to-noise
for the compound of interest.
TIS suggested operating settings
Flow
Rate
(L/min)
Turbo
Probe
Heater
Gas (GS2)
Nebulizer
Gas (GS1)
Scale
Position
L/min
Psi
Psi
40
300
(200-500)
6
(4-8)
65
(40-90)
20
(10-30)
6-10
4-6
200
650
(500-700)
7
(4-8)
70
(40-90)
40
(30-70)
3-6
4-6
65

TIS suggested operating settings
Flow
Rate
(L/min)
1000
Turbo
Probe
700
(600-750)
Heater
Gas (GS2)
8
(4-8)
80
(40-90)
Nebulizer
Gas (GS1)
70
(50-80)
Scale
Position
1-5
4-6
V = vertical position
H = horizontal position
Note: The lower the number in the Position column, the farther away from
the orifice the probe is positioned.
Parameters
The following table lists parameters for optimizing the performance of the
TIS probe.
Parameter optimization for TIS probe
Parameter
66
Operational
range
Typical values
LC flow
5 to 50 L/
min
200 L/min
1000 L/min
5 to 3000 L/
min
Gas 1
nebulizer gas
30 to 40 psi
40 to 60 psi
40 to 60 psi
0 to 90 psi
Gas 2turbo
gas
50 psi
50 psi
50 psi
0 to 90 psi
Temperature*
100 to 200 C
425 to 650 C
550 to 750 C
Up to 750 C
DP**
70 V
70 V
80 V
5 to 400 V
Curtain gas
10 psi
10 psi
10 psi
10 to 50 psi
Probe vertical
y-axis
position
10 to 13 mm
0 to 2 mm
0 mm
0 to 13 mm

Parameter optimization for TIS probe
Parameter
Probe
horizontal
x-axis
position
Operational
range
Typical values
5 to 8 mm
5 to 8 mm
5 to 8 mm
0 to 10 mm
* Optimum temperature values depend on the compound and mobile phase

composition (higher aqueous content requires higher temperature).
** DP value is compound dependent.
The following table lists parameters for optimizing the performance of the
APCI probe.
Parameter optimization for the APCI probe
Parameter
Nominal value
Operational range
LC Flow
1000 L/min
200 to 2000 L/min
NC
2 A (positive),
-2 A (negative)
1 to 5 A (positive),
-1 to -5 A (negative)
Gas 1
30 psi
0 to 90 psi
Temperature*
400 C
100 to 750 C
DP
60 V (positive),
-60 V (negative)
0 to 400 V
Curtain gas
10 psi
10 to 50 psi
Probe vertical y-axis

position
4 mm
Scale 0 to 13 mm
* Temperature value is compound-dependent.
67
68
Appendix B:
Troubleshooting
This section contains information on some typical problems you may
encounter when using the DuoSpray Ion Source.
Possible Problems
Problem
Symptom
Possible Cause
Solution
Instrument does
not run
Instrument does
not run
Probe is missing
Install both probes

in their correct
locations
Instrument will
not go into
standby (yellow)
mode
Instrument will
not go into
standby (yellow)
mode
Probes are not

connected
securely
Remove and
replace probes
Heater doesnt
work
Shows HN source
in Analyst
F3 Fuse is blown
Replace F3 fuse. If
the F3 fuse is OK,
there is a short
between the
wiring and the
housing. Contact
your service
representative
Valve doesnt turn
Valve doesnt turn
Ground has been

left off.
Reattach ground
on valve assembly
69

Possible Problems
70
Problem
Symptom
Possible Cause
Solution
Valve doesnt turn
Valve doesnt turn
Cables or valve
controller are not
connected
Check/reattach
cables and connect
valve controller
Valve doesnt turn
Valve doesnt turn
Valve controller
cable has been
connected to
Auxiliary I/O port
instead of sources
port.
Disconnect the
valve controller
cable from the
instrument, and
reconnect it to
sources port
Spray is not
uniform
Spray is not
uniform
Electrode tube
may be blocked.
Replace electrode
tube. See
Replacing the
Electrode Tube
on page 62
Poor sensitivity
Poor sensitivity
Too high voltage

can induce
fragmentation
before the ions
enter the mass
filters.
Use one probe

type at a time;
optimize curtain
gas
Poor sensitivity
Poor sensitivity
Presence of
solvent vapor or
other known
compounds in
analyzer region
Optimize curtain
gas
High background
noise
High background
noise
Temperature too
high
Optimize heater
gas flow
High background
noise
High background
noise
High heater gas

flow
Optimize heater
gas flow
High background
noise
High background
noise
Buildup of
particles or salts
on the valve
Flush valve

Possible Problems
Problem
Symptom
Possible Cause
Solution
High background
noise
High background
noise
Valve rotor has

been scored
Replace valve;
See
Replacing the
Switching Valve
on page 56
Leaking valve
Dirty area
underneath the
valve, or obvious
leakage
Scored valve rotor

or buildup of
particles or salts.
Replace valve;
See
Replacing the
Switching Valve
on page 56
Arcing or sparks
Arcing or sparks
Corona discharge
needle position is
incorrect
Turn corona
discharge needle
toward the curtain
plate, and away
from the stream of
heater gas
71
72
Appendix C: Consumables
and Spares
The following tables list parts included in the consumable parts kit (part
number 1005603) as well as spare parts for the DuoSpray ion source.
Consumables Kit (p/n 1005603)
Item
Part No.
Descritpion
Quantity
016316
PEEK tubing, Red, 1/16 o.d. x .005

bore, 100 cm
100 cm
016325
PEEK fitting, Brown, 10-32 x 1/16

inch
025388
Electrode, Nebulizer
025392
Electrode, TuroIonSpray
027471
PEEK Graph-tite fitting, Black, 1/16

inch.
1005601
PEEK tubing kit to connect to TIS

probe, 30 cm
1005602
PEEK tubing kit to connect to APCI

probe, 45 cm
025348
PEEK union in probe
73

Consumables Kit (p/n 1005603)
Item
Part No.
Descritpion
Quantity
003403
O-ring for probe PEEK union
10
026626
Spring for probe
Item
Part No.
Descritpion
Quantity
1005151
Valve replacement head
1005152
Valve rotor
1006177
APCI Corona discharge needle tip
1006174
APCI Corona discharge needle rod
027497
Gold plated spring for HV connection
027013
Spring for corona discharge needle
Spares
74

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DuoSpray

Part Number: 1005699 B

This document contains information proprietary and confidential to MDS Sciex, a

Equipment built by MDS Sciex, a division of MDS Inc.,

Chapter 1: Introducing the DuoSpray Ion Source . . . . . . . . . . . . . . 1

Choosing an Ion Source Probe. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Parts of the Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

DuoSpray Ion Source Operators Manual

Chapter 2: Installing the Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Chapter 3: Operating the Source . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Setting the Software Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

DuoSpray Ion Source Operators Manual

Tuning Your Source Manually . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

Warming Up the Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

Chapter 4: DuoSpray Testing Procedures . . . . . . . . . . . . . . . . . . . . 45

DuoSpray Performance Tests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

Chapter 5: Maintaining the Source . . . . . . . . . . . . . . . . . . . . . . . . . 53

Replacing Source Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

DuoSpray Ion Source Operators Manual

Appendix A: Source Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

About This Manual

Install and operate the DuoSpray ion source

Perform routine maintenance procedures on the source

The manual also provides information on optimizing the DuoSpray ion

DuoSpray Ion Source Operators Manual

Any person using an Applied Biosystems/MDS Sciex mass spectrometer

Note: Emphasizes significant information in a procedure or description.

How This Manual Is Organized

DuoSpray Ion Source Operators Manual

Chapter 2 - Installing the Source This section provides information on how

Labels and Warnings on Source

Patent notice label

High voltage and High temperature warning labels

Assembly number and serial number label

System Approval label

DuoSpray Ion Source Operators Manual

DuoSpray ion source

Introducing the DuoSpray Ion Source

DuoSpray Ion Source Operators Manual

Why Use the Source

Allows the rapid development of more universal analytical methods,

Facilitates the migration of analytical methods developed for other LC/

Provides improved flexibility in open access environments, allowing a

Choosing the Technique to Use

DuoSpray Ion Source Operators Manual

Introducing the DuoSpray Ion Source

Choosing an Ion Source Probe

Introducing the DuoSpray Ion Source

DuoSpray Ion Source Operators Manual

ionization by a process called atmospheric pressure chemical ionization

Parts of the Source

DuoSpray Ion Source Operators Manual

Introducing the DuoSpray Ion Source

Bronze retaining ring

Bronze retaining ring

Introducing the DuoSpray Ion Source

DuoSpray Ion Source Operators Manual

Switching valve and motor on mounting bracket

DuoSpray Ion Source Operators Manual

Introducing the DuoSpray Ion Source

Valve Mounting Bracket

Ion source temperature

Probe temperature from

Probe temperature from