Ion Max

APPI Source
User Manual

97055-97021 Revision C February 2009

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Release history: Revision C in February 2009. Revision B in June 2006. Revision A in September
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Software version: Xcalibur 2.0

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Electric Shock: This instrument uses

high voltages that can cause personal
injury. Before servicing, shut down the
instrument and disconnect the instrument
from line power. Keep the top cover on
while operating the instrument. Do not
remove protective covers from PCBs.

Chemical: This instrument might contain

hazardous chemicals. Wear gloves when
handling toxic, carcinogenic, mutagenic,
or corrosive or irritant chemicals. Use
approved containers and proper
procedures to dispose waste oil.

Heat: Before servicing the instrument,

allow any heated components to cool.

Fire: Use care when operating the system

in the presence of flammable gases.

Eye Hazard: Eye damage could occur

from splattered chemicals or flying
particles. Wear safety glasses when
handling chemicals or servicing the
instrument.

General Hazard: A hazard is present that

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Also, this symbol appears on the
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When the safety of a procedure is

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 Contents

Preface ............................................................................................. xi
Safety and Special Notices..........................................................xi
Contacting Us...........................................................................xii

Chapter 1 Introduction..........................................................................................1
Atmospheric Pressure Chemical Ionization .................................3
Atmospheric Pressure Photoionization ........................................6
Combined APCI and APPI .........................................................9
What Types of Buffers Should I Use? What Types Should I
Avoid? ....................................................................................10
How Should I Set Up the Mass Spectrometer for Various LC
Flow Rates? ............................................................................11

Chapter 2 Functional Description.....................................................................13

APCI Source .............................................................................14
PhotoMate Light Source ...........................................................17

Chapter 3 Setting Up the Ion Source for Acquiring Data in

APCI/APPI/MS/MS Mode23
Removing the ESI Probe ...........................................................24
Removing the Ion Max Ion Source Housing .............................26
Installing the APCI Probe .........................................................27
Installing the PhotoMate Light Source......................................30
Installing the Ion Max Ion Source Housing ..............................33

Chapter 4 Optimizing the LCQ Deca XP MAX MS Detector with Your

Analyte37
Setting Up the Inlet for Tuning Using High-Flow Infusion ......38
Setting Up the MS Detector for APCI/APPI/MS Operation.....42
Optimizing the Tune of the MS Detector Automatically in
APCI/APPI/MS Mode ...........................................................45
Saving the Tune Method ..........................................................47
Cleaning the MS Detector After Tuning in APCI Mode...........49

Chapter 5 Optimizing the LTQ MS Detector with Your Analyte ..................51

Thermo Scientific APPI Souce User Manual ix

Contents

Setting Up the Inlet for Tuning Using High-Flow Infusion ......52

Setting Up the MS Detector for APCI/APPI/MS Operation.....55
Optimizing the Tune of the MS Detector Automatically in
APCI/APPI/MS Mode ...........................................................58
Saving the APCI/APPI/MS Tune Method ................................61
Cleaning the MS Detector After Tuning in APCI Mode...........63

Chapter 6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with

Your Analyte65
Setting Up to Introduce Sample by Auto Loop Injection
in APCI Mode ..........................................................................67
Setting Up to Optimize in APCI/APPI/MS/MS
Mode with Your Compound.....................................................71
Optimizing in APCI/APPI/MS/MS Mode
Automatically with Your Compound ........................................77
Saving the Tune Method ..........................................................82
Cleaning the Mass Spectrometer After Tuning
in APCI Mode ..........................................................................84

Chapter 7 Maintenance ..................................................................................... 87

Maintaining the APCI Probe ....................................................88
Maintaining the PhotoMate Light Source .................................92
Cleaning and Polishing the Window of the VUV Lamp ........92
Replacing the VUV Lamp......................................................95

Chapter 8 Replaceable Parts ............................................................................ 99

Appendix A Installing the PhotoMate Light Source Adapter Ring.............. 103

Appendix B Reserpine Solution Formulations................................................ 109

Reserpine Stock Solution ........................................................111
LCQ Deca XP MAX Reserpine Sample Solution ....................112
LTQ Reserpine Sample Solution.............................................113
TSQ Quantum Ultra Reserpine Sample Solution....................114

Index ................................................................................................. 115

x APPI Souce User Manual Thermo Scientific

 P

Preface
This guide describes how to set up and install the PhotoMate® light source on the Ion
Max ion source housing with an APCI probe. It also describes how to optimize the
tune of your instrument after you have installed the Ion Max APPI source.

Safety and Special Notices

Make sure you follow the precautionary statements presented in this guide. The safety and
other special notices appear in boxes.

Safety and special notices include the following:

CAUTION Highlights hazards to humans, property, or the environment. Each CAUTION

notice is accompanied by an appropriate CAUTION symbol.

IMPORTANT Highlights information necessary to prevent damage to software, loss of

data, or invalid test results; or might contain information that is critical for optimal
performance of the system.

Note Highlights information of general interest.

Tip Highlights helpful information that can make a task easier.

Thermo Scientific APPI Source User Manual xi

Preface
Contacting Us

Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need.

Y To contact Technical Support

Phone 800-532-4752
Fax 561-688-8736
E-mail [email protected]
Knowledge base www.thermokb.com

Find software updates and utilities to download at mssupport.thermo.com.

Y To contact Customer Service for ordering information

Phone 800-532-4752
Fax 561-688-8731
E-mail [email protected]
Web site www.thermo.com/ms

Y To copy manuals from the Internet

Go to mssupport.thermo.com and click Customer Manuals in the left margin of the

window.

Y To suggest changes to documentation or to Help

Send an e-mail message to the Technical Publications Editor at

[email protected].

xii APPI Source User Manual Thermo Scientific

 Chapter 1 Introduction

The Ion Max™ ion source is a member of the Thermo Scientific family of
mass spectrometer ion sources.

Your Ion Max APCI/APPI combination probe allows you to perform

successful qualitative and quantitative analysis on a wide range of
compounds, including steroids, peptides, basic drug entities, and pesticides.
You can use APPI and APCI to study compounds that are not readily
ionized by electrospray ionization (ESI). See Figure 1.

You can operate your APCI/APPI combination probe using the following
ionization techniques:

• Atmospheric pressure chemical ionization (APCI)

• Atmospheric pressure photoionization (APPI)

• Combined APCI and APPI

Thermo Scientific APPI Souce User Manual 1

1 Introduction

10,000

ESI

1,000

APPI
MW

100 APCI

10
Nonpolar Ionic
Polarity

Figure 1. Ranges of applicability of APPI, APCI, and ESI

2 APPI Souce User Manual Thermo Scientific

 1 Introduction
Atmospheric Pressure Chemical Ionization

Atmospheric Pressure Atmospheric pressure chemical ionization (APCI) is a soft ionization

Chemical Ionization technique, but not as soft as ESI. APCI is used to analyze compounds of
medium polarity that have some volatility.

In APCI, ions are produced and analyzed as follows:

1. The APCI nozzle sprays the sample solution into a fine mist of droplets.

2. The droplets are vaporized in a high temperature tube (the vaporizer).

3. A high voltage is applied to a needle located near the exit end of the
tube. The high voltage creates a corona discharge that forms reagent ions
through a series of chemical reactions with solvent molecules and
nitrogen sheath gas.

4. The reagent ions react with sample molecules to form sample ions.

5. The sample ions enter the mass spectrometer and are analyzed.

Figure 1 shows the APCI process for positive adduct ion formation.

APCI is a gas phase ionization technique. Therefore, the gas phase acidities
and basicities of the analyte and solvent vapor play an important role in the
APCI process.

In the positive-ion mode, sample ionization occurs in a series of reactions

that start with the electron-initiated cation formation. Typical examples of
primary, secondary, and adduct ion formation are shown below:

Primary ion formation

e- + N2 → N2+. + 2e-

Secondary ion formation

N2+. + H2O → N2 + H2O+.

H2O+. + H2O → H3O+ + HO.

Proton transfer

H3O+ + M → (M + H)+ + H2O

In negative-ion mode, (M − H)- is typically formed by the abstraction of a

proton by OH-.

Thermo Scientific APPI Souce User Manual 3

1 Introduction
Atmospheric Pressure Chemical Ionization

APCI is typically used to analyze small molecules with molecular weights up

to about 1500 u. APCI is a very robust ionization technique. It is not
affected by minor changes in most variables, such as changes in buffers or
buffer strength.

APCI Nozzle
Atmospheric
Pressure
Region
AP
CI

+10 V
Pr

Ion Sweep
ob

Pressure
Cone
e

= 1 Torr

Ion
Chemical
Transfer
Ionization
Capillary
M (M+H) +
S SM
SM M S
SMSMSM
SS H O+ HO
3 2

Corona
Discharge
Needle
(+3 TO +5 kV)

H 20 H 20+
Corona Corona
Discharge Discharge
Needle H 20+ Region
(+3 TO +5 kV) H 20+ H 20+ (Plasma)

- N 2+ N 2+
e -
e
+
++ +
++ -
N2+ e- N 2+e

Figure 2. APCI process in the positive ion polarity mode

You can use APCI in positive or negative ion polarity mode. For most
molecules, the positive-ion mode produces a stronger ion current. This is
especially true for molecules with one or more basic nitrogen (or other basic)
atoms. An exception to the general rule is that molecules with acidic sites,
such as carboxylic acids and acid alcohols, produce more negative ions than
positive ions.

4 APPI Souce User Manual Thermo Scientific

 1 Introduction
Atmospheric Pressure Chemical Ionization

Although, in general, fewer negative ions are produced than positive ions,
negative ion polarity is sometimes the mode of choice. This is because the
negative ion polarity mode sometimes generates less chemical noise than
does the positive mode. Thus, selectivity might be better in the negative ion
mode than in the positive ion mode.

Thermo Scientific APPI Souce User Manual 5

1 Introduction
Atmospheric Pressure Photoionization

Atmospheric Pressure Atmospheric pressure photoionization (APPI) is also a soft ionization

Photoionization technique. In APPI an ion is generated from a molecule when it interacts
with a photon from a source of light such as the Syagen PhotoMate® light
source. APPI generates molecular ions for molecules that have an ionization
potential below the photon energy of the light being emitted by the light
source.

In APPI, ions are produced and analyzed as follows:

1. The nozzle sprays the sample solution into a fine mist of droplets.

2. The droplets are vaporized in a high temperature tube (the vaporizer).

3. The analyte molecule interacts with the light from the PhotoMate light
source. The analyte molecule M is ionized to a molecular ion M+ if the
ionization potential of the analyte is less than the photon energy hν:

4. M + hν → M+ + e−

5. In the presence of protic solvents, the analyte ion may extract a

hydrogen to form an (M + H)+ ion:

6. M+ + S → (M + H)+ + (S − H)

7. The analyte ions pass through the ion transfer capillary, enter the mass
spectrometer, and are analyzed.

Molecules including steroids, basic-drug entities, and pesticides have

ionization potentials below the threshold and protonated molecules are
generated in the LC/MS experiment. APPI reduces fragmentation because
only a small amount of energy is deposited in the molecule. Molecules such
as the nitrogen sheath and auxiliary gas and the simple solvents used for
LC/MS are not ionized because their ionization potentials are greater than
the photon energy. The result is selective ionization of analyte versus
background. See Figure 2 and Figure 3.

6 APPI Souce User Manual Thermo Scientific

 1 Introduction
Atmospheric Pressure Photoionization

Gases in air,
solvent molecules Fragment ion
thresholds

Molecular ion

Energy
thresholds

Drugs and other

compounds

hν

Photoionization
Figure 3. Energetics of photoionization

Agricultural
compounds
Drugs MeOH, AcCN
Chlorinated-solvents

Steroids
H2O, CO2, O2, N2

Ionized Not Ionized

Threshold
Figure 4. Illustration of selective photoionization

The PhotoMate light source uses a krypton lamp that emits photons with
energies of 10.0 and 10.6 eV. Molecules with ionization potentials less than
10 eV ionize to form M+ or (M + H)+, while those with greater ionization
potentials do not. Figure 4 shows ionization potentials of typical
compounds and solvents.

Thermo Scientific APPI Souce User Manual 7

1 Introduction
Atmospheric Pressure Photoionization

Krypton 10.0 eV, 10.6 eV

Ionization Potentials (IP) Solvent Ionization Potentials (IP)

Anthracene 7.4 eV Toluene 8.82 eV

Fluoranthene 7.8 eV Acetone 9.70 eV
Caffeine 8.0 eV
4-Nitrotoluene 9.5 eV

10.0 eV
Methanol 10.85 eV
Acetonitrile 12.19 eV
Water 12.61 eV

Figure 5. Ionization potentials of typical compounds and solvents

8 APPI Souce User Manual Thermo Scientific

 1 Introduction
Combined APCI and APPI

Combined APCI and You can easily change between APCI, APPI, and combined APCI and APPI
APPI techniques by turning on the corona discharge needle, the PhotoMate light
source, or both. See Table 1. You turn the light source on and off by using
the On/Off switch on the light source. You turn the corona discharge needle
on and off by using the Xcalibur software. This allows you to quickly
determine which technique yields the best ion signal.

Table 1. Light source and corona discharge needle status for APPI, APCI, and
combined APCI/APPI modes
PhotoMate Light Corona Discharge
Ionization Technique
Source Needle
APPI On Off
APCI Off On
Combined APCI and On On
APPI

Thermo Scientific APPI Souce User Manual 9

1Introduction
What Types of Buffers Should I Use? What Types Should I Avoid?

What Types of Buffers Use volatile buffers, when possible, to obtain the highest performance for
Should I Use? What your assays. Many volatile buffer solutions are available that can be used
instead of nonvolatile ones. Volatile buffer solutions can include the
Types Should I Avoid? following:

• Acetic acid

• Ammonium acetate

• Ammonium formate

• Ammonium hydroxide

• Triethylamine (TEA)

Many LC applications use nonvolatile buffers such as phosphate and borate

buffers. However, it’s best to avoid the use of these nonvolatile buffers with
the mass spectrometer. Nonvolatile buffers can block the capillary in the
probe and can cause salt buildup in the nozzle, compromising the integrity
of the spray.

10 APPI Souce User Manual Thermo Scientific

 1 Introduction
How Should I Set Up the Mass Spectrometer for Various LC Flow Rates?

How Should I Set Up The APCI/APPI combination probe can generate ions from liquid flows1 of
the Mass 50 μL/min to 2.0 mL/min. This flow range allows you to use microbore
LC, analytical LC, and semipreparative LC.
Spectrometer for
Various LC Flow As you change the rate of flow of solvents entering the mass spectrometer,
Rates? you need to adjust several parameters. For APCI and APPI, you need to
adjust the ion transfer capillary temperature, the vaporizer temperature, and
the gas flow rates for the sheath gas and auxiliary gas.

In general, an increase in the rate of liquid flowing into the mass

spectrometer requires a higher temperature of the ion transfer capillary and
vaporizer and a higher gas flow rate.

Table 2 provides starting guidelines for operating in the APPI, APCI, or

combined APCI/APPI mode. Chapter 4, 5 or 6 (depending upon your
instrument) will help you to optimize these settings for your specific
compound.

Table 2. Guidelines for setting operating parameters for APPI, APCI, and combined APCI/APPI modes *
LC Flow Rate Capillary Vaporizer Auxiliary Gas
Sheath Gas (psi)
(mL/min) Temperature (°C) Temperature (°C) (arbitrary units)
0.2 to 2.0 Typical setting: Typical setting: Required. Not required, but
150 to 225 400 to 550 Typical setting: usually helps to reduce
40 to 100 solvent background
ions
Typical setting:
0 to 20
*For
thermally labile compounds you might need to use a lower vaporizer temperature and a lower flow rate.

1
Flows below 200 μL/min require more care to maintain a stable spray.

Thermo Scientific APPI Souce User Manual 11

 Chapter 2 Functional Description

This chapter describes the principal components of the APCI/APPI

combination probe.

The APCI/APPI combination probe forms gas phase sample ions from
sample molecules that are contained in solution. You can operate the
APCI/APPI combination probe using either atmospheric pressure chemical
ionization (APCI), atmospheric pressure photoionization (APPI), or both.

The APCI/APPI combination probe includes:

• APCI Source

• PhotoMate Light Source

Thermo Scientific APPI Souce User Manual 13

2 Functional Description
APCI Source

APCI Source The APCI probe ionizes the sample by atmospheric pressure chemical
ionization. The APCI probe accommodates liquid flows of 100 μL/min to
2 mL/min without splitting. See Figure 6. The APCI probe includes the
APCI sample tube, nozzle, sheath gas and auxiliary gas plumbing, and
vaporizer. See Figure 7 and Figure 8. Sample and solvent enter the APCI
nozzle through the sample tube. The sample tube is a short section of 0.10
mm ID fused silica tubing that extends from the sample inlet to 1 mm past
the end of the nozzle. The manifold houses the APCI nozzle and includes
the sheath gas and auxiliary gas plumbing. The APCI nozzle sprays the
sample solution into a fine mist. The sheath gas and auxiliary gas plumbing
deliver dry nitrogen gas to the nozzle. The droplets in the mist then enter
the vaporizer. The vaporizer flash vaporizes the droplets at temperatures up
to 500 °C.

Ion Transfer APCI

Capillary Probe

Corona
Needle

Ion Transfer
Capillary Entrance

Figure 6. APCI probe, showing the corona discharge needle and ion transfer
capillary

Typical vaporizer temperatures are 350 to 450 °C for flow rates of 0.1 to
2 mL/min. The sample vapor is swept toward the corona discharge needle
by the flow of the sheath and auxiliary gasses.

The corona discharge needle assembly is mounted inside of the Ion Max
API source housing. The tip of the corona discharge needle is positioned
near the vaporizer. A high potential (typically ±3 to ±5 kV) is applied to the

14 APPI Souce User Manual Thermo Scientific

 2 Functional Description
APCI Source

corona discharge needle to produce a corona discharge current of up to

100 μA. (A typical value of the corona discharge current is 5 μA.) The
corona discharge from the needle produces reagent ion plasma primarily
from the solvent vapor. The sample vapor is ionized by ion-molecule
reactions with the reagent ions in the plasma.

APCI requires a constant source of electrons for the ionization process.

Thus, the corona discharge current is set to a specific value and regulated.
The potential applied to the corona discharge needle varies, as needed, to
provide the required current.

Vaporizer
Heater Cable
Socket

APCI Nozzle 0.312 ID O-ring

Ceramic Heater Tube
0.500 ID
1/16 Viton
O-Ring

Sample
Inlet Fitting

Sample Tube

Figure 7. Cross sectional viewof the APCI probe

Thermo Scientific APPI Souce User Manual 15

2 Functional Description
APCI Source

Vaporizer Heater
Cable Socket

Guide Pin

Retention Flange
Flat Side
APCI Nozzle Assembly
Retention Flange

Figure 8. APCI probe exterior

16 APPI Souce User Manual Thermo Scientific

 2 Functional Description
PhotoMate Light Source

PhotoMate Light The light source is a Syagen PhotoMate vacuum ultraviolet (VUV) light
Source source. The assembly is mounted on the left side of the Ion Max ion source
housing using a specially designed adapter ring.

The PhotoMate light source includes the following components. See

Figure 9 through Figure 11.

• Power supply

• Electronics PCB

• VUV lamp

• Lamp shield

• Box fan

• Lamp On/Off switch

• Safety interlocks

• Remote LEDs

• Window

Thermo Scientific APPI Souce User Manual 17

2 Functional Description
PhotoMate Light Source

Figure 9. PhotoMate light source installed in the Ion Max ion source housing,
side view

18 APPI Souce User Manual Thermo Scientific

 2 Functional Description
PhotoMate Light Source

Figure 10. PhotoMate light source installed in the Ion Max ion source housing,
front view

Box Fan

Electronics PCB

Lamp Shield

VUV Lamp

Figure 11. PhotoMate light source (internal components)

Thermo Scientific APPI Souce User Manual 19

2 Functional Description
PhotoMate Light Source

The power supply provides +48 V dc power for the electronics PCB and fan.
The LTQ MS detector and TSQ Quantum Ultra mass spectrometer can
both supply this power through a DB-15 cable connection. The LTQ MS
detector is also able to control the lamp status through the connection. The
LCQ Deca XP MAX requires that this power be supplied via an external
power supply, which is also connected using the DB-15 connection.

The electronics PCB contains electronic circuitry for driving the VUV
lamp, a photodiode for detecting light emitted by the VUV lamp, and a
thermocouple for monitoring the temperature. The electronics PCB also
powers the status LEDs.

The VUV lamp is an electrodeless, quartz cell with a magnesium fluoride

window. (The window is transparent to VUV light, but the quartz is not.)
The VUV lamp is filled with krypton gas. The lamp emits radiation at
10.0 eV and 10.6 eV.

Minimize the chance of breaking the VUV lamp by doing the following:

• Always wear clean gloves when you handle the VUV lamp.
Fingerprints on the lamp can cause the lamp to fail when it is in use.

• Do not spray solvent on the VUV lamp while it is hot. The VUV
lamp can crack.
• Do not leave the LC or other liquid delivery device on while the mass
spectrometer is in Standby. The absence of sheath and auxiliary gas
can cause the hot lamp to break upon contact with liquids.

The lamp shield protects the VUV lamp.

The box fan cools the electronics PCB and prevents heat from the vaporizer
from damaging the electronics PCB. The fan draws cool air into the light
source. The fan runs at all times – even if the lamp is off.

CAUTION Never disconnect the power cord from the PhotoMate light
source or disconnect the PhotoMate power supply from line power while
the vaporizer is hot. Without power, the fan will stop running and heat
from the vaporizer could damage the electronics PCB.

The lamp On/Off switch turns on and off the power to the circuitry that
powers the VUV lamp. The box fan remains on at all times and is not
controlled by the lamp On/Off switch.

The safety interlock switch prevents the light source from operating when
not attached to the Ion Max ion source housing.

20 APPI Souce User Manual Thermo Scientific

 2 Functional Description
PhotoMate Light Source

The remote status light-emitting diode (LED) is located on the front of the
light source. The LED is illuminated green if the APPI source is connected
to an instrument that has remote control of the lamp status (the LTQ MS
detector). When the Remote LED is illuminated, the switch on the light
source is inactive and will not turn the lamp on and off. When the lamp is
not illuminated, the instrument to which it is connected has no control of
the lamp status and the lamp must be turned on and off with the switch on
the source (TSQ Quantum Ultra mass spectrometer and LCQ Deca XP
MAX MS detector).

The front window in the Ion Max ion source housing allows you to verify
that the light source is working properly. You can see purple light if the light
source is working properly. If the light is red (due to exposure to ambient
nitrogen) then the lamp is broken.

Thermo Scientific APPI Souce User Manual 21

 Chapter 3 Setting Up the Ion Source for
Acquiring Data in
APCI/APPI/MS/MS Mode

This chapter provides information on setting up the ion source for acquiring
data in the APCI/MS/MS mode.

This chapter contains the following sections:

• Removing the ESI Probe

• Removing the Ion Max Ion Source Housing

• Installing the APCI Probe

• Installing the PhotoMate Light Source

• Installing the Ion Max Ion Source Housing

Thermo Scientific APPI Souce User Manual 23

3 Setting Up the Ion Source for Acquiring Data in APCI/APPI/MS/MS Mode
Removing the ESI Probe

Removing the ESI To remove the ESI source

Probe
1. Place the LC/MS system in Standby:

a. Stop the flow of solvent to the ESI source.

Note The following procedures are intended for use with all systems. If
you have questions regarding the operation of your MS system, please
refer to the appropriate system-specific manuals. This might include the
Getting Started and Hardware manuals for your system. For information
on installation and maintenance of other Ion Max probes, please refer to
the Ion Max API Source Hardware Manual.

Note The following procedures are intended for use with all systems. If
you have questions regarding the operation of your MS system, please
refer to the appropriate system-specific manuals. This might include the
Getting Started and Hardware manuals for your system. For information
on installation and maintenance of other Ion Max probes, please refer to
the Ion Max API Source Hardware Manual.

b. Turn off the ESI spray voltage.

c. Click on the On/Standby button on the toolbar to place the mass
spectrometer in Standby.
On Standby
Note If your ESI probe does not already have a sample tube (fused-silica
capillary) and safety sleeve attached, you need to follow the procedure for
installing a sample tube and PEEK safety sleeve that is outlined in the
topic Installing a New Fused-Silica Sample Tube and PEEK Safety Sleeve
in the Ion Max API Source Hardware Manual.

2. Disconnect the sample transfer tubing from the stainless steel ZDV
fitting (grounding union). See Figure 12.

3. Remove the 8 kV cable from the ESI needle high voltage receptacle as
follows: (See Figure 12.)

4. Unlock the cable by twisting the locking ring counter-clockwise.

5. Unplug the 8 kV cable from the ESI needle high voltage receptacle.

6. Disconnect the AUX Gas fitting (green) from the auxiliary gas inlet (A)
on the probe manifold. (Figure 12)

7. Disconnect the Sheath Gas fitting (blue) from the sheath gas inlet (S) on
the probe manifold.

24 APPI Souce User Manual Thermo Scientific

 3 Setting Up the Ion Source for Acquiring Data in APCI/APPI/MS/MS Mode
Removing the ESI Probe

8. Remove the stainless steel ZDV fitting (Grounding Union) from the
grounding bar on the ion source housing.

PEEK ESI
Safety Interlock
Sleeve Socket

Grounding Auxiliary
Bar Gas
Fitting

Grounding 8 kV
Union Cable

Sheath Sample
Gas Inlet
Fitting

Sample Probe
Transfer Locking
Tubing Lever

Figure 12. Ion Max ion source housing with ESI probe installed

9. Unlock the probe locking lever by twisting the lever open to its widest
position.

10. Carefully pull the probe straight back in the port in the housing until it
meets with the slot in the ESI interlock block. The guide pin on the
probe manifold will prevent you from twisting the probe until the pin is
aligned with the slot in the ESI interlock block.

11. After the probe is all the way back and aligned with the slot, turn the
probe 45 degrees counter-clockwise to free the probe from the
alignment notch. Be careful not to break the fused-silica sample tube or
PEEK safety sleeve.

12. Pull the probe straight out to remove it from the ion source housing.

13. Store the ESI probe in its original shipping container.

Thermo Scientific APPI Souce User Manual 25

3 Setting Up the Ion Source for Acquiring Data in APCI/APPI/MS/MS Mode
Removing the Ion Max Ion Source Housing

Removing the Ion Max Remove the Ion Max ion source housing to access the ion sweep cone.
Ion Source Housing
Note Disconnect any external liquid lines connected to the ion source
housing before removing the ion source housing.

To remove the ion source housing

1. Remove the drain tube from the ion source housing drain. See
Figure 13.

2. Rotate the ion source housing locking levers 90 degrees to release the ion
source housing from the ion source mount assembly.

3. Remove the ion source housing by it pulling straight off the ion source
mount assembly.

4. Place the housing in a safe location for temporary storage.

Cover Retaining Screws

Ion Source
Housing
Locking
Lever(s)

Ion Source
Housing
Drain

Cover Retaining Screws Probe Alignment Screw

Figure 13. Ion Max ion source, showing details of components

26 APPI Souce User Manual Thermo Scientific

 3 Setting Up the Ion Source for Acquiring Data in APCI/APPI/MS/MS Mode
Installing the APCI Probe

Installing the APCI To install the APCI probe

Probe
1. Install the corona needle

CAUTION AVOID INJURY. The corona discharge needle is very sharp

and can puncture your skin. Handle it with care.

a. Unlock the ion source housing door by turning the locks 90 degrees
so that the knobs are horizontal.
b. Open the ion source housing door.
c. Using pliers, grasp the needle by the gold plated contact and push
the needle straight into the socket. See Figure 14.

Gold
Plated
Contact

Figure 14. Corona needle, view from rear

d. Make sure that the tip of the needle is aligned with the path of travel
between the APCI probe and the ion source interface on the
instrument.
e. Close and lock the ion source housing door.

2. Connect the 8 kV cable to the corona needle high voltage receptacle:

a. Plug the 8 kV cable into the corona needle high voltage receptacle
on the right side of the top of the ion source housing.
b. Lock the cable by twisting the locking ring clockwise.

3. Be sure to unlock the probe locking lever (widest open position) before
attempting to install the probe.

Thermo Scientific APPI Souce User Manual 27

3 Setting Up the Ion Source for Acquiring Data in APCI/APPI/MS/MS Mode
Installing the APCI Probe

4. Insert the APCI probe into the port in the ion source housing Align the
guide pin on the probe body at a 45 degree angle from the ESI interlock
block. See Figure 15.

Vaporizer Heater
Cable Socket

Sheath Gas
Inlet Guide Pin

Sample Inlet Auxilary

Fitting Gas Inlet

Figure 15. APCI probe

5. Push the probe into the port until the guide pin meets with the locking
ring on the housing.

6. Turn the probe 45 degrees clockwise and align the guide pin with the
slot in the ESI interlock block (you might need to pull the probe
towards you slightly to properly align the pin with the notch).

7. After you have turned the probe far enough to align the pin with the
alignment notch at the rear of the port, push the probe straight in until
the guide pin stops at the bottom of the alignment notch.

8. Seat the probe all the way down into the alignment notch.

9. Lock the probe in place by twisting the probe locking lever towards the
front of the housing. (Closing the probe locking lever towards the rear of
the ion source housing may make it difficult to unlock.)

10. Unplug the vaporizer heater cable from the ESI interlock plug on the
ion source housing.

11. Connect the vaporizer heater cable to the vaporizer heater cable socket
on the APCI probe.

28 APPI Souce User Manual Thermo Scientific

 3 Setting Up the Ion Source for Acquiring Data in APCI/APPI/MS/MS Mode
Installing the APCI Probe

12. Connect the Auxiliary gas line (green colored fitting) to the inlet on the
APCI probe marked A.

13. Connect the Sheath gas line (blue colored fitting) to the inlet on the
APCI probe marked S.

14. Connect the sample transfer line to the APCI probe inlet.

CAUTION Prevent solvent waste from backing up into the ion source
and mass spectrometer. Always ensure that liquid in the drain tube is
able to drain to a waste container and that the outlet of the drain tube is
above the level of liquid in the waste container.

The APCI source is now properly installed in the Ion Max ion source
housing.

Thermo Scientific APPI Souce User Manual 29

3 Setting Up the Ion Source for Acquiring Data in APCI/APPI/MS/MS Mode
Installing the PhotoMate Light Source

Installing the If the APPI assembly is already installed

PhotoMate Light
• If you have an LCQ Deca XP MAX MS Detector, follow the operating
Source procedures in Chapter 4, “Optimizing the LCQ Deca XP MAX MS
Detector with Your Analyte.” .

• If you have an LTQ MS Detector, follow the operating procedures in

Chapter 5, “Optimizing the LTQ MS Detector with Your Analyte.” .

• If you have an TSQ Quantum mass spectrometer, follow the operating

procedures in Chapter 6, “Optimizing the TSQ Quantum Ultra Mass
Spectrometer with Your Analyte.” .

If the APPI assembly is not installed

1. Remove the screws holding the window retainer ring

CAUTION If you have operated your APCI probe recently, be sure to

allow it to cool completely before installing the PhotoMate light source.
The APCI probe and corona needle may be hot

The corona needle is sharp. If you are installing the APPI assembly with
the APCI probe installed, be careful not to poke yourself with the
needle.

2. Carefully remove the retainer ring, while keeping your free hand under
the side of the Ion Max ion source housing to be sure that the window
does not fall out and break. If the window does not come out with the
retainer ring, you might need to push gently on the window from inside
the Ion Max ion source housing (Figure 16).

30 APPI Souce User Manual Thermo Scientific

 3 Setting Up the Ion Source for Acquiring Data in APCI/APPI/MS/MS Mode
Installing the PhotoMate Light Source

Figure 16. Removing the small viewport window

3. Place the window, retainer ring and screws in a secure place.

Note While inserting the PhotoMate light source into the Ion Max ion
source housing, be sure to watch that the APPI lamp does not contact
the corona discharge needle or the ceramic heater tube on the APCI
probe.

4. Carefully align the PhotoMate light source so that the locking tab on the
bottom of the APPI assembly aligns with the notch in the APPI adapter
ring (Figure 17).

5. Secure the PhotoMate light source with two of the hex head screws.

Thermo Scientific APPI Souce User Manual 31

3 Setting Up the Ion Source for Acquiring Data in APCI/APPI/MS/MS Mode
Installing the PhotoMate Light Source

Notch Tab

Figure 17. Aligning the tab on the PhotoMate light source with the adapter ring

32 APPI Souce User Manual Thermo Scientific

 3 Setting Up the Ion Source for Acquiring Data in APCI/APPI/MS/MS Mode
Installing the Ion Max Ion Source Housing

Installing the Ion Max To reinstall the Ion Max ion source housing
Ion Source Housing
1. Carefully align the two guide pin holes on the rear of the ion source
housing with the ion source housing guide pins on the mass
spectrometer, and carefully press the ion source housing onto the ion
source mount. See Figure 18 and Figure 19.

Ion Source Housing

Locking Levers

Guide Ion Source

Pin Holes Housing Drain

Figure 18. Rear view of the Ion Max ion source housing (PhotoMate light source
not shown)

Thermo Scientific APPI Souce User Manual 33

3 Setting Up the Ion Source for Acquiring Data in APCI/APPI/MS/MS Mode
Installing the Ion Max Ion Source Housing

Ion Source
Housing
Guide Pins

Figure 19. Ion source mount showing ion source housing guide pins

2. Rotate the ion source housing locking levers 90 degrees to lock the ion
source housing onto the ion source mount assembly.

CAUTION Prevent solvent waste from backing up into the ion source
and mass spectrometer. Always ensure that liquid in the drain tube is
able to drain to a waste container and that the outlet of the drain tube is
above the level of liquid in the waste container.

34 APPI Souce User Manual Thermo Scientific

 3 Setting Up the Ion Source for Acquiring Data in APCI/APPI/MS/MS Mode
Installing the Ion Max Ion Source Housing

CAUTION Do not vent the API source drain tube (or any vent tubing
connected to the waste container) to the same fume exhaust system to
which you have connected the forepumps. The analyzer optics can
become contaminated if the API source drain tube and the (blue)
forepump exhaust tubing are connected to the same fume exhaust
system.

Your laboratory must be equipped with at least two fume exhaust

systems. Route the (blue) forepump exhaust tubing to a dedicated fume
exhaust system. Route the drain tube from the API source to a waste
container. Vent the waste container to a dedicated fume exhaust system.

3. Reinstall the ion source drain tube as follows:

a. Connect the 1-in. ID Tygon tubing (P/N 00301-22922) to the ion

source housing drain fitting.
b. Attach the free end of the hose to a waste container. Ideally, the
waste container should be vented to a fume exhaust system.

4. Complete the installation:

• For LCQ Deca XP MAX MS detectors:

Connect the external power supply of the PhotoMate light source to
the DB-15 connector on the PhotoMate light source.

• For LTQ MS detectors:

Connect the female end of the communications cable to the DB-15
connector on the PhotoMate light source. Connect the other end of
the cable to the female connector on the front of the LTQ MS
detector, just to the right of where the Ion Max ion source housing
mounts to the detector.

• For TSQ Quantum Ultra mass spectrometers:

Connect the female end of the communications cable to the DB-15
connector on the PhotoMate light source. Connect the other end of
the cable to the female connector on the front of the mass
spectrometer, just to the rigIon Max ion sourceIon Max ion sourceht
of where the Ion Max ion source housing mounts to the detector.
You also have the option to connect the DB-15 connector to the
external power supply that is included with your APPI source
instead of using the TSQ Quantum Ultra’s power connector.

The APCI/APPI source is now properly installed on the mass spectrometer.

Thermo Scientific APPI Souce User Manual 35

To optimize the tune of your mass spectrometer proceed to one of the
following chapters:

• If you have an LCQ Deca XP MAX MS detector, refer toChapter 4,

“Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte.”

• If you have an LTQ MS detector, refer to Chapter 5, “Optimizing the

LTQ MS Detector with Your Analyte.” .

• If you have an TSQ Quantum Ultra mass spectrometer, refer to Chapter

6, “Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your
Analyte.” .
 Chapter 4 Optimizing the LCQ Deca XP
MAX MS Detector with Your
Analyte

This chapter provides information on optimizing the tune of your LCQ

Deca XP MAX MS detector in the APCI/APPI/MS high flow mode. It is
not necessary to recalibrate the MS detector when you switch to
APCI/APPI/MS operation. You can use the calibration settings you
obtained from the successful automatic calibration procedure you
performed in the ESI/MS mode.

For APCI/APPI/MS operation you open a default tune method located in

your C:\Xcalibur\methods folder, in this case APCIhighflow.LCQTune. From
this starting point, you optimize automatically the tube lens offset voltage,
capillary voltage, and ion transfer capillary temperature for your particular
analyte.

Note The following procedures assume that you are familiar with your
XP Plus instrument and the Tune Plus window. If you need information,
refer to the LCQ Deca XP MAX online help, LCQ Deca XP MAX
Getting Connected, or the LCQ Deca XP MAX Hardware Manual.

Ensure that you have completed the procedures in the sections that
describe how to calibrate your instrument in ESI mode, and have
properly set up your APCI/APPI source.

This chapter includes the following sections:

• Setting Up the Inlet for Tuning Using High-Flow Infusion

• Setting Up the MS Detector for APCI/APPI/MS Operation

• Optimizing the Tune of the MS Detector Automatically in

APCI/APPI/MS Mode

• Saving the Tune Method

• Cleaning the MS Detector After Tuning in APCI Mode

Thermo Scientific APPI Souce User Manual 37

4 Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte
Setting Up the Inlet for Tuning Using High-Flow Infusion

Setting Up the Inlet The plumbing connections for the APCI/APPI/MS sample introduction
for Tuning Using from the syringe pump are shown in Figure 20.
High-Flow Infusion To make the plumbing connections for APCI/APPI/MS sample
introduction from the syringe pump into solvent flow from an LC

1. Connect a 4 cm (1.5 in) segment of Teflon tubing with a (brown)

Fingertight fitting and a (brown) ferrule to the (black) LC union. (See
Figure 21.)

Load a clean, 500-μL Unimetrics syringe (P/N 00301-19012) with 420 μL

of a 1 ng/μL solution of reserpine or your analyte of interest. (Refer to
Appendix B: Reserpine Solution Formulations for a procedure for making
the reserpine tuning solution.)

2. Insert the needle of a syringe into the segment of Teflon tubing, and
place the syringe in the syringe holder of the syringe pump.

From LC

LC Tee
Union

To Waste

Syringe Pump

Figure 20. APCI/APPI/MS plumbing connections for sample introduction from the syringe pump into solvent flow from an
LC

3. Connect a fused-silica infusion line from the (black) LC union to the

(black) LC Tee union:

38 APPI Souce User Manual Thermo Scientific

 4 Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte
Setting Up the Inlet for Tuning Using High-Flow Infusion

a. Connect the infusion line (P/N 00106-10504) with a (brown)

Fingertight fitting and a (brown) ferrule to the free end of the LC
union (Figure 20).
b. Connect the other end of the infusion line with a (red) Fingertight
fitting and a (brown) ferrule to the side arm of the LC Tee union.

LC Union Fingertight Fitting

(P/N 00101-18202) (P/N 00101-18081)

Ferrule Teflon Tube

(P/N 00101-18196) (P/N 00301-22803)

Figure 21. APCI/APPI/MS plumbing connections for the syringe pump

Note To cut the PEEK tubing used to connect your LC to the

divert/inject valve and the divert/inject valve to the APCI source, use a
PEEK tubing cutter. This ensures that the tubing is cut straight. In
addition, make sure your LC fittings, ferrules, and PEEK tubing are
installed properly. By using these precautions, you prevent void (dead)
volumes. The exclusion of void volumes is critical to microbore LC.
Also, void volumes affect the quality of the MS detector signal.

PEEK Tubing LC Tee Union PEEK Tubing

(P/N 00301-22912) (P/N 00101-18204) (P/N 00301-22912)
From Divert /
Inject Valve

Stainless Steel
Ferrule
Stainless
Steel Nut Ferrules
(P/N 00101-18196)

Infusion Line
Ferrules Fused-Silica Capillary
(P/N 00101-18120) (P/N 00106-10504)

Fingertight Fingertight
Fitting Fittings
(P/N 00101-18195) (P/N 00101-18081)
From LC Union

Figure 22. APCI/APPI/MS plumbing connections for the LC Tee union

Thermo Scientific APPI Souce User Manual 39

4 Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte
Setting Up the Inlet for Tuning Using High-Flow Infusion

4. Connect a segment of PEEK tubing from the (black) LC Tee union to

the APCI LC inlet (Figure 22).

a. Use a PEEK tubing cutter to cut a 4 cm (1.5 in.) length of the PEEK
tubing.
b. Connect the PEEK tubing with a (brown) Fingertight fitting and a
(brown) ferrule to a free end of the (black) LC Tee union.
c. Connect the other end of the PEEK tubing with a (red) Fingertight
fitting and a (brown) ferrule to the LC inlet located on the APCI
probe.

5. Connect an appropriate length of PEEK tubing (transfer line from the

divert/inject valve) from the divert/inject valve to the LC Tee union:
(Figure 22).

a. Connect a length of PEEK tubing with a (stainless steel) nut and a

(stainless steel) ferrule to port 3 of the divert/inject valve.
b. Connect the other end of the PEEK tubing with a (brown)
Fingertight fitting and a (brown) ferrule to the free end of the LC
Tee union.

6. Connect an appropriate length of PEEK tubing (transfer line from the

LC) from the divert/inject valve to the LC:

a. Connect a length of PEEK tubing with a (stainless steel) nut and a

(stainless steel) ferrule to port 2 of the divert/inject valve.
b. Connect the other end of the PEEK tubing with a proper fitting and
a ferrule to the outlet of the LC.

7. Connect an appropriate length of PEEK tubing (waste line) from the

divert/inject valve to a waste container:

a. Connect a length of PEEK tubing with a (stainless steel) nut and a

(stainless steel) ferrule to port 1 of the divert/inject valve.
b. Insert the other end of the PEEK tubing into a suitable waste
container.

CAUTION Prevent solvent waste from backing up into the API ion
source and MS detector. Always ensure that the PVC drain hose is above
the level of liquid in the waste container.

8. Connect an appropriate length of 1-in. (2.5 cm) OD Tygon tubing hose

to the Ion Max ion source housing drain fitting. Attach the other end of

40 APPI Souce User Manual Thermo Scientific

 4 Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte
Setting Up the Inlet for Tuning Using High-Flow Infusion

the hose to a suitable waste container. Ideally, the waste container should
be vented to a fume exhaust system.

Thermo Scientific APPI Souce User Manual 41

4 Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte
Setting Up the MS Detector for APCI/APPI/MS Operation

Setting Up the MS To set up the MS detector for APCI/APPI/MS operation on the XP Plus
Detector for
1. In Tune Plus, click on the On/Standby button to take the MS detector
APCI/APPI/MS out of Standby mode and turn it on. The MS detector begins scanning,
Operation and applies the high voltage to the corona needle, and shows a real-time
display in the Spectrum view.

Standby 2. Open the APCITune.LCQTune Tune Method, the Tune Method for
On
high-flow APCI operation:

a. Choose File > Open to display the Open dialog box.

b. Scroll down until you see the folder C:\Xcalibur\methods. Then,
select the file APCITune.LCQTune.
c. Click on OK to open the file. XP Plus downloads the Tune Method
parameters to the MS detector.

3. Verify that XP Plus opened the Tune Method, as follows:

a. Choose Setup > Change API Source Type to specify the

APCI source. Then, in the Change Source Type dialog box, which
appears, select the APCI option button.
b. Click on OK to return to the Tune Plus window.
c. On the Instrument Setup toolbar, click on the API Source button to
open the APCI Source dialog box (Figure 23).
d. Verify that the settings in your dialog box are similar to those shown
in Figure 23.
• To operate in APPI mode only, set the discharge current to zero.

• To operate in APCI/APPI or APCI mode only set the discharge

current to 5 μA.

e. Click on OK to close the dialog box.

4. If you are operating in APPI or APCI/APPI mode, turn the APPI lamp
on. Verify that the lamp is operating by observing the lamp through the
front window of the Ion Max ion source housing.

42 APPI Souce User Manual Thermo Scientific

 4 Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte
Setting Up the MS Detector for APCI/APPI/MS Operation

Figure 23. APCI Source dialog box, showing the proper settings for a typical
high flow experiment

5. Define the scan parameters for tuning the MS detector in the

APCI/APPI/MS mode:

a. On the Control/Scan Mode toolbar, click on the Define Scan

button to open the dialog box (Figure 24).
b. In the Scan Description group box, select the Mass Range: Normal
option button to specify a mass range of m/z 50 to 2000.
c. Select the Scan Mode: MS option button to select the MS scan
mode. Note that XP Plus sets the MSn power to 1.
d. Click on the Scan Type: SIM option button to select the SIM data
type. Note that XP Plus sets the Total Scan Ranges to 1.
e. In the Scan Time group box, in the Total Microscans spin box,
enter 1 to set the total number of microscans to 1.
f. In the Input Method group box, select the Center/Width option
button to make available the Center Mass and Width text boxes in
the Scan Ranges group box. (Refer to steps 4h and 4i, below.)
g. In the [Ion] Source Fragmentation group box, confirm that the Turn
On check box is not selected ( ) to specify that the ion source
fragmentation option is turned off.
h. In the Scan Ranges group box, in the Center Mass text box, enter
609.2 to set the center mass for the scan range to m/z 609.2.
i. In the Width text box, enter 2 to set the width of the scan range to
m/z 2.

Thermo Scientific APPI Souce User Manual 43

4 Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte
Setting Up the MS Detector for APCI/APPI/MS Operation

j. Ensure that the settings in your Define Scan dialog box are the same
as those shown in Figure 24.
k. Click on OK to save the MS detector scan parameters and return to
the Tune Plus window.

6. If you are operating in APCI/APPI or APPI only modes, turn on the

APPI source:

a. Turn on the power to the APPI lamp by flipping the switch on the
PhotoMate light source housing to the On position.
b. Verify that the lamp is operating by looking through the front
window of the Ion Max ion source housing.

7. On the Control/Scan Mode toolbar, click on the Centroid/Profile

button to toggle the data type to centroid. (The picture on the button
should be the same as that shown here).

8. Click on the Positive/Negative button to toggle the ion polarity mode to

positive. (The picture on the button should be the same as that shown
here).

You have now completed setting up your MS detector for APCI/APPI/MS

operation.

Figure 24. Define Scan dialog box, showing typical settings for APCI/APPI/MS operation

44 APPI Souce User Manual Thermo Scientific

 4 Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte
Optimizing the Tune of the MS Detector Automatically in APCI/APPI/MS Mode

Optimizing the Tune of You can optimize the tune of the MS detector automatically for APCI
the MS Detector operation.
Automatically in The most important parameters that affect the signal quality during
APCI/APPI/MS Mode APCI/APPI/MS operation are the vaporizer temperature, ion transfer
capillary temperature, capillary voltage, tube lens offset voltage, gases, and
solution flow rate. If any one of these parameters is changed, you need to
re-optimize the MS detector parameters. (You can use the Semi-Automatic
tune procedure to tune the MS detector on individual parameters.)

Use the following procedure to optimize the MS detector automatically on

the reserpine peak at m/z 609.2 at your particular flow rate, for example,
1 mL/min. (Refer to Table 2 on page 1-11 for guidelines about flow rates
and temperatures.)

To optimize the MS detector automatically on the reserpine peak at m/z

609.2 at your particular flow rate

1. On the Control/Scan Mode toolbar, click on the Tune button to display

the Automatic tuning page in the Tune dialog box.

2. In the Mass spin box, enter 609.2 to specify that you want to tune on
the peak at m/z 609.2.

3. Ensure that the Divert/Inject valve is in the Detector position:

a. Click on the Divert/Inject Valve button to open the dialog box.

b. Select the Detector option button, and then click Close to return to
Tune Plus.

4. Start the automatic tuning procedure from the Tune dialog box:

a. Click Start. A message box displays the following message:

b. Please ensure that the 500 microliter syringe is full.
c. Ensure the syringe pump contains at least 420 μL of the 1 ng/μL
reserpine tuning solution.
d. Click OK to close the message box and return to the Tune Plus
window.

5. On the File/Display toolbar, click on the Graph View button to display

the view.

6. Observe the Tune Plus window and the Tune dialog box. While
automatic tuning is in progress, LCQ Deca XP MAX displays various

Thermo Scientific APPI Souce User Manual 45

4 Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte
Optimizing the Tune of the MS Detector Automatically in APCI/APPI/MS Mode

tests in the Spectrum and Graph views in the Tune Plus window and
displays various messages in the Status group box in the Tune dialog
box. Your Tune Plus window should now look similar to the one shown
in Figure 25.

You have now successfully tuned the MS detector in APCI/APPI/MS mode

for the compound reserpine (or your analyte of interest). Leave the LC
pumps on (with a flow rate of approximately 1 mL/min), leave the
APCIhighflow.LCQTune file open in the Tune Plus window and go on to the
next topic: Saving the APCI/APPI/MS Tune Method.

Figure 25. Tune Plus window with the Tune dialog box, showing the Automatic page

46 APPI Souce User Manual Thermo Scientific

 4 Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte
Saving the Tune Method

Saving the Tune You can save the settings you just obtained in a tune method specific to your
Method particular analyte and solvent flow rate. (In this case, you save settings
obtained using reserpine.) You can recall the tune method and use it as a
starting point for optimizing the MS detector on reserpine at a different
flow rate.

Note Save the Tune Method while the MS detector is On.

To save the APCI/APPI/MS tune method

1. Choose File > Save As to display the Save As dialog box. See Figure 26.

Figure 26. Save As dialog box, showing files in the folder C:\Xcalibur\methods

2. In the Save In list box, select the C:\Xcalibur\methods folder.

3. Click on the File Name text box, and then enter APCImyTune to name
the Tune Method APCImyTune.LCQTune.

Thermo Scientific APPI Souce User Manual 47

4 Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte
Saving the Tune Method

4. Click Save to save the Tune Method and return to the Tune Plus
window. Note that the Tune Method is named APCImyTune.LCQTune.

Before you acquire data, go to the next topic: Cleaning the MS Detector
after Tuning in APCI Mode.

48 APPI Souce User Manual Thermo Scientific

 4 Optimizing the LCQ Deca XP MAX MS Detector with Your Analyte
Cleaning the MS Detector After Tuning in APCI Mode

Cleaning the MS To clean the MS detector after tuning on your analyte of interest
Detector After Tuning
1. Click on the On/Standby button to put the MS detector in Standby
in APCI Mode mode. When the MS detector is in Standby, the LCQ Deca XP MAX
MS detector turns off the vaporizer heater, corona discharge voltage, and
syringe pump. The MS detector stops scanning and freezes the displays
OnStandby for the Spectrum and Graph views.

CAUTION Always place the MS detector in Standby (or Off ) before you
open the API source to atmospheric oxygen. The presence of oxygen in
the ion source when the MS detector is On could be unsafe. (The LCQ
Deca XP MAX MS detector automatically turns off when you open the
API source, however, it is best to take this added precaution.)

2. Remove the syringe from the syringe pump holder,:

a. Squeeze the blue buttons, and pull back on the syringe pump handle
to free the syringe.
b. Remove the syringe from the holder.
c. Disconnect the tip of the syringe needle from the Teflon tubing.

3. Clean the syringe thoroughly:

a. Clean the syringe with a solution of 5% formic acid in water.

b. Rinse the syringe with a solution of 50:50 methanol / water.
c. Use acetone to rinse the syringe. Repeat this step several times.

CAUTION AVOID BURNS. The APCI vaporizer heater can reach

temperatures of 600 ×C. Always allow the APCI probe to cool to
ambient temperature, for approximately 20 min, before handling or
removing the APCI probe from the APCI flange

CAUTION AVOID INJURY. The corona discharge needle is very sharp

and can puncture your skin if you handle it without caution.

4. Remove the Ion Max ion source housing as described in the topic
“Removing the Ion Max Ion Source Housing” on page 26.

5. Flush the sample transfer line, sample tube, and APCI probe thoroughly
with a solution of 5% formic acid in water (or with another appropriate
solvent):

Thermo Scientific APPI Souce User Manual 49

 Note The solvent that you use to flush the sample transfer line, sample
tube, and APCI probe assembly depends on the solvent system you use
to dissolve your samples. For example, if you are using a buffered
solution of a high concentration, an acidic solution is appropriate.

a. Fill a clean, 250 μL Unimetrics syringe with an appropriate solvent.

b. While holding the plunger of the syringe in place, carefully insert
the needle of the syringe into the free end of the Teflon tube.
c. Flush the sample transfer line, sample tube, and APCI probe with
the solution by slowly depressing the syringe plunger. Visually check
that the solution is exiting the tip of the APCI probe on the inside of
the probe assembly. Use a lint-free tissue to gently remove the excess
solution as it exits the probe.
d. Remove the needle of the syringe from the Teflon tube.

6. Repeat step 5 with a solution of 50:50 methanol / water.

7. Reinstall the Ion Max ion source housing as described in topic

“Installing the Ion Max Ion Source Housing” on page 33.

Your LCQ Deca XP MAX MS detector is now ready to perform

experiments in APCI/APPI mode. For information regarding the
maintenance of the Ion Max APPI source refer to Chapter 7,
“Maintenance.”
 Chapter 5 Optimizing the LTQ MS
Detector with Your Analyte

This chapter provides information on optimizing the tune of your LTQ MS

detector in the APCI/APPI/MS high flow mode. It is not necessary to
recalibrate the MS detector when you switch to APCI/APPI/MS operation.
You can use the calibration settings you obtained from the successful
automatic calibration procedure you performed in the ESI/MS mode.

For APCI/APPI/MS operation you simply open a default Tune Method

located in your C:\Xcalibur\methods folder, in this case
APCIhighflow.LTQTune. From this starting point, you optimize
automatically the tube lens voltage for your particular analyte. The capillary
voltage and ion transfer capillary temperature can then be optimized
manually to enhance ion transmission.

Note The following procedures assume that you are familiar with your
LTQ instrument and the Tune Plus window. If you need information,
refer to the LTQ online Help, LTQ Getting Connected, and/or LTQ
Hardware Manual.

Ensure that you have completed the procedures in the sections that
describe how to calibrate your instrument in ESI mode, and have
properly set up your APCI/APPI source.

This chapter includes the following sections:

• Setting Up the Inlet for Tuning Using High-Flow Infusion

• Setting Up the MS Detector for APCI/APPI/MS Operation

• Optimizing the Tune of the MS Detector Automatically in

APCI/APPI/MS Mode

• Saving the APCI/APPI/MS Tune Method

• Cleaning the MS Detector After Tuning in APCI Mode

Thermo Scientific APPI Souce User Manual 51

5 Optimizing the LTQ MS Detector with Your Analyte
Setting Up the Inlet for Tuning Using High-Flow Infusion

Setting Up the Inlet To make the plumbing connections for APCI/APPI/MS sample
for Tuning Using introduction from the syringe pump into solvent flow from an LC
High-Flow Infusion 1. Connect a 4 cm (1.5 in) segment of Teflon tubing with a (brown)
FingerTight fitting and a (brown) ferrule to the (black) LC union
(Figure 27).

LC Union Fingertight Fitting

(P/N 00101-18202) (P/N 00101-18081)

Ferrule Teflon Tube

(P/N 00101-18196) (P/N 00301-22803)

Figure 27. APCI/APPI/MS plumbing connections for the syringe pump

2. Load a clean, 500-μL Unimetrics syringe with 450 μL of a 125 fg/μL

solution of reserpine or your analyte of interest. (Refer to Appendix B:
Reserpine Solution Formulations for a procedure for making the
reserpine tuning solution.)

3. Insert the needle of a syringe into the segment of Teflon tubing, and
place the syringe in the syringe holder of the syringe pump.

4. Connect a fused-silica infusion line from the (black) LC union to the

(black) LC Tee union:

a. Connect the infusion line with a (brown) fingertight fitting and a

(brown) ferrule to the free end of the LC union. See Figure 28.
b. Connect the other end of the infusion line with a (red) fingertight
fitting and a (brown) ferrule to the side arm of the LC Tee union.

52 APPI Souce User Manual Thermo Scientific

 5 Optimizing the LTQ MS Detector with Your Analyte
Setting Up the Inlet for Tuning Using High-Flow Infusion

PEEK Tubing LC Tee Union PEEK Tubing

(P/N 00301-22912) (P/N 00101-18204) (P/N 00301-22912)
From Divert /
Inject Valve

Stainless Steel
Ferrule
Stainless
Steel Nut Ferrules
(P/N 00101-18196)

Infusion Line
Ferrules Fused-Silica Capillary
(P/N 00101-18120) (P/N 00106-10504)

Fingertight Fingertight
Fitting Fittings
(P/N 00101-18195) (P/N 00101-18081)
From LC Union

Figure 28. APCI/APPI/MS plumbing connections for the LC Tee union

Note To cut the PEEK tubing used to connect your LC to the

divert/inject valve and the divert/inject valve to the APCI source, use a
PEEK tubing cutter. This ensures that the tubing is cut straight. In
addition, make sure your LC fittings, ferrules, and PEEK tubing are
installed properly. By using these precautions, you prevent void (dead)
volumes. The exclusion of void volumes is critical to microbore LC.
Also, void volumes affect the quality of the MS detector signal.

5. Connect a segment of PEEK tubing from the (black) LC Tee union to

the APCI LC inlet: (Figure 28.)

a. Use a PEEK tubing cutter to cut a 4 cm (1.5 in.) length of the PEEK
tubing.
b. Connect the PEEK tubing with a (brown) fingertight fitting and a
(brown) ferrule to a free end of the (black) LC Tee union.
c. Connect the other end of the PEEK tubing with a (red) fingertight
fitting and a (brown) ferrule to the LC inlet located on the APCI
probe.

6. Connect an appropriate length of PEEK tubing (transfer line from the

divert/inject valve) from the divert/inject valve to the LC Tee union:
(Figure 28.)

Thermo Scientific APPI Souce User Manual 53

5 Optimizing the LTQ MS Detector with Your Analyte
Setting Up the Inlet for Tuning Using High-Flow Infusion

a. Connect a length of PEEK tubing with a (stainless steel) nut and a

(stainless steel) ferrule to port 3 of the divert/inject valve.
b. Connect the other end of the PEEK tubing with a (brown)
fingertight fitting and a (brown) ferrule to the free end of the LC
Tee union.

7. Connect an appropriate length of PEEK tubing (transfer line from the

LC) from the divert/inject valve to the LC:

a. Connect a length of PEEK tubing with a (stainless steel) nut and a

(stainless steel) ferrule to port 2 of the divert/inject valve.
b. Connect the other end of the PEEK tubing with a proper fitting and
a ferrule to the outlet of the LC.

8. Connect an appropriate length of PEEK tubing (waste line) from the

divert/inject valve to a waste container:

a. Connect a length of PEEK tubing with a (stainless steel) nut and a

(stainless steel) ferrule to port 1 of the divert/inject valve.
b. Insert the other end of the PEEK tubing into a suitable waste
container.
The LC plumbing connections are now properly made for APCI/APPI/MS
sample introduction from the syringe pump into solvent flow from an LC.

54 APPI Souce User Manual Thermo Scientific

 5 Optimizing the LTQ MS Detector with Your Analyte
Setting Up the MS Detector for APCI/APPI/MS Operation

Setting Up the MS To set up the MS detector for APCI/APPI/MS operation on the LTQ MS
Detector for detector.
APCI/APPI/MS 1. In Tune Plus, click on the On/Standby button to take the MS detector
Operation out of Standby mode and turn it on. The MS detector begins scanning
and applies high voltage to the corona needle and shows a real-time
display in the Spectrum view.

OnStandby 2. Open the APCIhighflow.LTQTune Tune Method, the Tune Method for
high-flow APCI operation:

a. Choose File > Open to display the Open dialog box.

b. Scroll down until you see the folder C:\Xcalibur\methods. Then,
select the file APCIhighflow.LTQTune.
c. Click OK to open the file. The Tune Method parameters are
uploaded to the MS detector.

3. Verify that the LTQ MS detector opened the Tune Method:

a. On the Instrument Setup toolbar, click on the API Source button to

open the APCI/APPI Source dialog box (Figure 29).
b. Verify that the settings in your dialog box are similar to those shown
in Figure 29. Set the APCI or APPI mode:
• To operate in APPI mode only, set the discharge current to 0
and select the APPI Lamp On check box.

• To operate in APCI/APPI mode, set the corona discharge to

your desired value and select the APPI Lamp On check box
(Figure 29).

• To operate in APCI mode only, set the corona discharge to your

desired value and make sure that the APCI Lamp on check box
is not selected (Figure 29).

c. Click OK to close the APCI/APPI Source dialog box.

d. Verify that the lamp is operating by looking through the front
window of the Ion Max housing. You can see purple light if the light
source is working properly.

Thermo Scientific APPI Souce User Manual 55

5 Optimizing the LTQ MS Detector with Your Analyte
Setting Up the MS Detector for APCI/APPI/MS Operation

Figure 29. APCI/APPI Source dialog box, showing the proper settings for a
typical high flow experiment

4. Define the scan parameters for tuning the MS detector in the

APCI/APPI/MS mode,:

a. On the Control/Scan Mode toolbar, click on the Define Scan

button to open the Define Scan dialog box. See Figure 30. (If your
dialog box appears different from the one shown in the figure, it is
probably because the advanced settings are not displayed. You can
turn on the advanced settings as follows: In Tune Plus, choose
ScanMode, and then click Advanced Scan Features to select the
option.)
b. In the Scan Description group box, in the Mass Range list box,
select Normal to allow for a selection of mass ranges between m/z
150 to 2000.
c. In the Scan Rate list box, select Normal to specify a normal scan rate.
d. In the Scan Type list box, select SIM to specify a selected ion
monitoring scan.
e. In the Scan Time group box, in the Microscans spin box, enter 1 to
set the total number of microscans to 1.
f. In the Max. Inject Time spin box, enter 200.000 to specify a 200 ms
maximum injection time.

56 APPI Souce User Manual Thermo Scientific

 5 Optimizing the LTQ MS Detector with Your Analyte
Setting Up the MS Detector for APCI/APPI/MS Operation

Figure 30. Define Scan dialog box, showing typical settings for APCI/APPI/MS operation

g. In the Source Fragmentation group box, confirm that the On check

box is not selected ( ) to specify that the ion source fragmentation
option is turned off.
h. In the Scan Ranges group box, in the Input list box, select
Center/Width to make available the Center Mass and Width text
boxes in the Scan Ranges table.
i. In the Scan Ranges table, in the Center Mass text box, enter 609.20
to set the center mass for the scan range to m/z 609.20.
j. In the Width text box, enter 2.00 to set the width of the scan range
to m/z 2.00.
k. Ensure that the settings in your Define Scan dialog box are the same
as those shown in Figure 30.
l. Click OK to apply the MS detector scan parameters and to close the
Define Scan dialog box.

5. On the Control/Scan Mode toolbar, click Centroid/Profile to toggle

the data type to centroid. The picture on the button should be the same
as that shown here.

6. Click Positive/Negative to toggle the ion polarity mode to positive. The

picture on the button should be the same as that shown here.

You have now completed setting up your MS detector for APCI/APPI/MS

operation.

Thermo Scientific APPI Souce User Manual 57

5 Optimizing the LTQ MS Detector with Your Analyte
Optimizing the Tune of the MS Detector Automatically in APCI/APPI/MS Mode

Optimizing the Tune of You can optimize the tune of the MS detector automatically for APCI
the MS Detector operation.
Automatically in The most important parameters that affect the signal quality during
APCI/APPI/MS Mode APCI/APPI/MS operation are the vaporizer temperature, ion transfer tube
temperature, API gas flows, and solution flow rate. If any one of these
parameters is changed, you need to re-optimize MS detector parameters.
(You can use the Semi-Automatic tune procedure to tune the MS detector
on individual parameters.)

Use the following procedure to optimize the MS detector automatically on

the reserpine peak at m/z 609.2 at your particular flow rate, for example,
400 μL/min. (Refer to Table 2 for guidelines about flow rates and
temperatures.)

1. On the Control/Scan Mode toolbar, click on the Tune button to display

the Automatic tuning page. See Figure 31.

2. In the What to Optimize On group box, select the Mass option button
to make active the Mass spin box.

3. In the Mass spin box, enter 609.2 to specify that you want to tune on
the peak at m/z 609.2.

4. Ensure that the Divert/Inject valve is in the Detector position:

a. Click on the Divert/Inject Valve button to open the Divert/Inject

Valve dialog box.
b. Select the Detector option button, and then click Close to return to
Tune Plus.

5. Start the automatic tuning procedure from the Tune dialog box:

a. Click Start. A message box displays the following message:

b. Please ensure that the 500 microliter syringe is full.
c. Ensure the syringe pump contains at least 450 μL of the 125 fg/μL
reserpine tuning solution.
d. Click OK to close the message box and return to the Tune Plus
window.

6. On the File/Display toolbar, click on the Graph View button to display

the view.

58 APPI Souce User Manual Thermo Scientific

 5 Optimizing the LTQ MS Detector with Your Analyte
Optimizing the Tune of the MS Detector Automatically in APCI/APPI/MS Mode

Figure 31. Tune dialog box, showing the Automatic tuning page

7. Observe the Tune Plus window and the Tune dialog box. While
automatic tuning is in progress, the LTQ MS detector displays various
tests in the Spectrum and Graph views in the Tune Plus window and
displays various messages in the Status group box in the Tune dialog
box. Your Tune Plus window should now look similar to the one shown
in Figure 32.

You have now successfully tuned the MS detector in APCI/APPI/MS mode

for the compound reserpine (or your analyte of interest). Leave the LC
pumps on (with a flow rate of approximately 400 μL/min), leave the
APCIhighflow.LCQTune file open in the Tune Plus window and go on to the
next topic: Saving the APCI/APPI/MS Tune Method.

Thermo Scientific APPI Souce User Manual 59

5 Optimizing the LTQ MS Detector with Your Analyte
Optimizing the Tune of the MS Detector Automatically in APCI/APPI/MS Mode

Figure 32. Tune Plus window with the Tune dialog box, showing the Automatic tuning page

60 APPI Souce User Manual Thermo Scientific

 5 Optimizing the LTQ MS Detector with Your Analyte
Saving the APCI/APPI/MS Tune Method

Saving the You can save the settings you just obtained in a Tune Method specific to
APCI/APPI/MS Tune your particular analyte and solvent flow rate (in this case, the settings
obtained using reserpine). You can recall the Tune Method and use it as a
Method starting point for optimizing the MS detector on reserpine at a different
flow rate.

Note Save the Tune Method while the MS detector is still On.

To save your APCI/APPI/MS Tune Method

1. Choose File >Save As to display the Save As dialog box. Figure 33.

2. In the Save In list box, select the C:\Xcalibur\methods folder.

3. Click on the File Name text box, and then enter APPImyTune to name
the Tune Method APPImyTune.LTQTune.

Figure 33. Save As dialog box, showing files in the folder C:\Xcalibur\methods

Thermo Scientific APPI Souce User Manual 61

5 Optimizing the LTQ MS Detector with Your Analyte
Saving the APCI/APPI/MS Tune Method

4. Click Save to save the Tune Method and close the Save As dialog box.
Note that the Tune Method is named APPImyTune.LTQTune.

Before you acquire data, go to the next topic: Cleaning the MS Detector
After Tuning in APCI Mode.

62 APPI Souce User Manual Thermo Scientific

 5 Optimizing the LTQ MS Detector with Your Analyte
Cleaning the MS Detector After Tuning in APCI Mode

Cleaning the MS Use the following procedure to clean the MS detector after tuning on your
Detector After Tuning analyte of interest.
in APCI Mode 1. Click on the On/Standby button to put the MS detector in Standby
mode. When the MS detector is in Standby, the LTQ MS detector turns
off the vaporizer heater, corona discharge voltage, and syringe pump.
The MS detector stops scanning and freezes the displays for the
OnStandby Spectrum and Graph views.

CAUTION Always place the MS detector in Standby (or Off ) before you
open the API source to atmospheric oxygen. The presence of oxygen in
the ion source when the MS detector is On could be unsafe. The LTQ
MS detector automatically turns off when you open the API source;
however, it is best to take this added precaution.

2. Remove the syringe from the syringe pump holder, as follows:

a. Squeeze the blue buttons and pull back on the syringe pump handle
to free the syringe.
b. Remove the syringe from the holder.
c. Disconnect the tip of the syringe needle from the Teflon tubing.

3. Clean the syringe thoroughly:

a. Clean the syringe with a solution of 5% formic acid in water.

b. Rinse the syringe with a solution of 50:50 methanol / water.
c. Use acetone to rinse the syringe. Repeat this step several times.

CAUTION AVOID BURNS. The APCI vaporizer heater can reach

temperatures of 600 ×C. Always allow the APCI probe to cool to
ambient temperature, for approximately 20 min, before handling or
removing the APCI probe from the APCI flange.

CAUTION AVOID INJURY. The corona discharge needle is very sharp

and can puncture your skin if you handle it without caution.

4. Remove the Ion Max ion source housing as described in the topic
“Removing the Ion Max Ion Source Housing” on page 26.

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5 Optimizing the LTQ MS Detector with Your Analyte
Cleaning the MS Detector After Tuning in APCI Mode

5. Flush the sample transfer line, sample tube, and APCI probe thoroughly
with a solution of 5% formic acid in water (or with another appropriate
solvent), as follows:

Note The solvent that you use to flush the sample transfer line, sample
tube, and APCI probe assembly depends on the solvent system you use
to dissolve your samples. For example, if you are using a buffered
solution of a high concentration, an acidic solution is appropriate.

a. Fill a clean, 250 μL Unimetrics syringe with an appropriate solvent.

b. While holding the plunger of the syringe in place, carefully insert
the needle of the syringe into the free end of the Teflon tube.
c. Flush the sample transfer line, sample tube, and APCI probe with
the solution by slowly depressing the syringe plunger. Visually check
that the solution is exiting the tip of the APCI probe on the inside of
the probe assembly. Use a lint-free tissue to gently remove the excess
solution as it exits the probe.
d. Remove the needle of the syringe from the Teflon tube.

6. Repeat step 5 with a solution of 50:50 methanol / water.

7. Reinstall the Ion Max ion source housing as described in topic

“Installing the Ion Max Ion Source Housing” on page 33.

Your LTQ MS detector is now ready to perform experiments in APCI/APPI

mode. Please refer to Chapter 7, “Maintenance.” for information regarding
the maintenance of the Ion Max APPI source.

64 APPI Souce User Manual Thermo Scientific

 Chapter 6 Optimizing the TSQ Quantum
Ultra Mass Spectrometer
with Your Analyte

This chapter provides information on fine tuning your TSQ Quantum

Ultra in the APCI/APPI/MS/MS mode using your analyte as the tuning
compound. You optimize the sensitivity of the mass spectrometer for your
analyte with an automatic tuning procedure.

This chapter contains the following sections:

• Setting Up to Introduce Sample by Auto Loop Injection in APCI Mode

• Setting Up to Optimize in APCI/APPI/MS/MS Mode with Your

Compound

• Optimizing in APCI/APPI/MS/MS Mode Automatically with Your

Compound

• Saving the Tune Method

• Cleaning the Mass Spectrometer After Tuning in APCI Mode

The Tune Methods that are provided with your TSQ Quantum Ultra are
useful for a wide range of applications. They can often be used without
further tuning of your mass spectrometer. However, for certain applications
you might need to optimize several mass spectrometer parameters. For
instance, the parameters that affect APCI performance and signal quality are
as follows:

• Discharge current

• APCI vaporizer temperature

• Sheath gas pressure

• Auxiliary gas flow rate

• Capillary temperature

• Tube lens offset voltage

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6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte

The optimum settings for these parameters depend on the solvent flow rate
and on the structure of your analyte. In general, you need to fine tune the
mass spectrometer parameters whenever you change the solvent flow rate
conditions of your particular application. When you optimize the mass
spectrometer parameters using the automatic tuning procedure, the
procedure adjusts all the parameters listed above and the voltages applied to
the ion optics until the ion transmission of your analyte is maximized.

Note Ensure that you have performed the TSQ Quantum Ultra tuning
and calibration procedure within the previous three months before you
optimize the tune for your compound. If you need to tune and calibrate
the system, refer to your TSQ Quantum Ultra Getting Started manual
and the procedure in Chapter 3: Tuning and Calibrating the Mass
Spectrometer in ESI/MS/MS Mode.

To optimize the mass spectrometer for your compound in the

APCI/APPI/MS/MS mode do the folowing:

• Set up the syringe pump and divert/injection valve for auto loop
injection.

• Set up the mass spectrometer for your specific compound from the Tune
Master.

• Run the automatic compound optimization procedure to fine tune the

mass spectrometer parameters that are compound dependent.

• Save the new Tune Method.

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 6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte
Setting Up to Introduce Sample by Auto Loop Injection in APCI Mode

Setting Up to The following procedure describes how to introduce your compound by

Introduce Sample by auto loop injection. The plumbing connections for APCI/MS sample
introduction from the syringe pump into the solvent flow from an LC
Auto Loop Injection in are shown in Figure 34.
APCI Mode
Note You can use the reserpine sample solution described in Appendix
B: Reserpine Solution Formulations, or you can use your compound of
interest.

From LC

To Waste

Sample Inlet
Fitting

Figure 34. APCI/MS plumbing connections for sample introduction by auto loop injection into the solvent flow from an LC

To make the plumbing connections for APCI/MS sample introduction

from the syringe pump into the solvent flow from an LC

1. Remove the syringe from the syringe pump holder:

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6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte
Setting Up to Introduce Sample by Auto Loop Injection in APCI Mode

a. Lift the handle off the syringe while depressing the black release
button on the syringe pump handle.
b. Remove the syringe.
c. Remove the tip of the syringe needle from the end of the Teflon tube
on the syringe adapter assembly(Figure 35).

LC Union Fingertight fitting

(00101-18202) (00101-18081)

Ferrule Teflon Tube

(00101-18196) (00301-22915)

Figure 35. Syringe and syringe adapter assembly

2. Remove the sample transfer line installed between the syringe adapter
assembly and the APCI probe.

3. Install a sample transfer line between the syringe adapter assembly and
the divert/inject valve:

a. Connect an appropriate length of tubing to the LC union on the

syringe adapter assembly.
b. Connect the other end of the tubing fitted with a nut and a ferrule
to port 5 of the divert/inject valve (Figure 36).

From Syringe
1 Lo 5
op
2 4
3

To Ion Source
To Waste
From LC

Figure 36. Divert/inject valve, showing plumbing for auto loop injection

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 6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte
Setting Up to Introduce Sample by Auto Loop Injection in APCI Mode

Note To minimize the possibility of cross-contamination, use a different

syringe and a different sample transfer line for your tuning and
calibration solution than you do for your samples and compound
optimization solution.

4. Load a clean, 500-μL Unimetrics syringe with 420 μL of the 2 pg/μL

reserpine sample solution. (Refer to Appendix B: Reserpine Solution
Formulations for the procedure for preparing the reserpine solution.)

Note Be sure to wipe off the tip of the needle with a clean, lint-free
tissue before reinserting it into the syringe adapter assembly to minimize
the possibility of cross-contamination of the assembly.

5. While holding the plunger of the syringe in place, carefully reinsert the
tip of the syringe needle into the end of the Teflon tube on the syringe
adapter assembly (Figure 35).

6. Place the syringe into the syringe holders of the syringe pump.

7. While squeezing the black release button on the syringe pump handle,
push the handle down until it just contacts the syringe plunger.

8. Install a sample transfer line between the divert/inject valve and the
APCI probe:

a. Gather the necessary fittings for installing a sample transfer line

(Figure 37).
b. Connect an appropriate length of tubing fitted with a nut and a
ferrule to port 3 of the divert/inject valve (Figure 36)
c. Connect the other end of the tubing with a FingerTight fitting and a
ferrule to the sample inlet fitting (LC inlet) (Figure 34).

Stainless Steel Nut Fingertight Fitting

(2522-0066) (00101-18195)

To Divert/ To APCI Probe

Inject Valve LC Inlet

Stainless Steel
Ferrule PEEK Tubing Ferrule
(2522-3830) (00301-22912) (00101-18196)

Figure 37. Sample transfer line, installed between the divert/inject valve and
the APCI probe

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6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte
Setting Up to Introduce Sample by Auto Loop Injection in APCI Mode

9. Install a 5 μL sample loop with nuts and ferrules between ports 1 and 4
of the divert/inject valve.

10. Install a solvent line between the LC system and the divert/inject valve:

a. Connect an appropriate length of tubing with a proper fitting and a

ferrule to the outlet of the LC system.
b. Connect the other end of the tubing with a nut and ferrule to port 2
of the divert/inject valve.

11. Install a waste line on the divert/inject valve and direct the outlet to a
waste container:

a. Connect an appropriate length of tubing with a nut and ferrule to

port 6 of the divert/inject valve (port 6 is labeled with the Rheodyne
logo ).
b. Insert the other end of the tubing into the waste container.
You have completed setting up to introduce your compound by auto loop
injection. Go to the next section: Setting Up to Optimize in
APCI/APPI/MS/MS Mode with Your Compound.

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 6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte
Setting Up to Optimize in APCI/APPI/MS/MS Mode with Your Compound

Setting Up to Optimize To set up the mass spectrometer to optimize automatically on your

in APCI/APPI/MS/MS compound in APCI/APPI/MS/MS mode
Mode with Your 1. Click the On/Standby button on the Control/Scan Mode toolbar to
Compound turn on the mass spectrometer.

2. Tune Master must be placed in the APCI source mode before analyzing
samples with the APCI source. Choose Setup > Change Ion Source >
On Standby APCI to place Tune Master in the APCI source mode.

3. If desired, open an existing Tune Method:

a. On the File / Display toolbar, click on the Open File button to

display the Open dialog box.
b.
c. Confirm that the path is C:\Xcalibur\methods and then select the
desired file.
d. Click Open to open the file. Tune Master downloads the Tune
Method parameters to the mass spectrometer.

4. Click the Optimize Compound Dependent Devices button on the

Control / Scan Mode toolbar to display the Optimize Compound
Dependent Devices view in the top right corner of the workspace
(Figure 38).

Figure 38. Optimize Compound Dependent Devices view, APCI settings

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6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte
Setting Up to Optimize in APCI/APPI/MS/MS Mode with Your Compound

Note You might find that the presence of chemical contamination in the
APCI vaporizer creates chemical noise in the mass spectrum. If this
occurs, recondition the APCI vaporizer. To recondition the APCI
vaporizer, you start LC solvent flow, elevate the temperature of the APCI
vaporizer, and increase the sheath gas and auxiliary gas pressures for
approximately 30 min to drive off the chemical contamination.

Typical values used for reconditioning the APCI vaporizer are as follows:

LC flow rate = 400 mL/min

Vaporizer temperature = 600 ×C
Sheath gas pressure = 80 psi
Auxiliary gas flow rate = 15 units

5. Set the values for the compound dependent devices:

a. Ensure that Discharge Current is selected in the Device Display box.

b. In the Optimize Compound Dependent Devices view, set the APCI
or APPI mode:
• To operate in APPI mode only, set the discharge current to 0
and select the APPI Lamp On check box.

• To operate in APCI/APPI mode or APCI mode only, enter 4.0

in the Device spin box to set the discharge current to 4.0 μA.

c. Set the temperature of the APCI vaporizer:

i. In the Device Display box, click APCI Vaporizer Temperature.
This changes the Device spin box label to APCI Vaporizer
Temperature and enables you to set the APCI vaporizer
temperature.
ii. In the Device box, enter 500 to set the vaporizer temperature to
500 °C.
d. Set the pressure of the sheath gas:
i. Click Sheath Gas Pressure in the Device Display box.
ii. Enter 30 in the Device box to set the sheath gas pressure to
30 psi.
e. Set the flow rate of the auxiliary gas:
i. Click Aux Valve Flow in the Device Display box.
ii. Enter 0 in the Device box to set the auxiliary gas flow rate to
0 units.

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 6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte
Setting Up to Optimize in APCI/APPI/MS/MS Mode with Your Compound

f. Set the temperature of the ion transfer capillary:

i. Click Capillary Temperature in the Device Display box.
ii. Enter 350 in the Device spin box to set the capillary temperature
to 350 °C.
g. Set the ion source fragmentation (CID) collision energy:
i. Click Source CID in the Device Display box.
ii. Enter 0 in the Device box to set the collision energy to 0 V.
h. Set the collision pressure:
i. Click Collision Pressure in the Device Display box.
ii. Enter 1.5 in the Device spin box to set the collision pressure to
1.5 mTorr.
i. Set the collision energy:
i. Click Collision Energy in the Device Display box.
ii. Enter -38 in the Device spin box to set the collision energy to
-38 eV.
j. Set the Quad MS/MS bias voltage:
i. Click Quad MS/MS Bias in the Device Display box.
ii. Enter -3.0 in the Device box to set the bias voltage to -3.0 V.
Ensure that the readbacks in the Device Display box are approximately
equal to the set values. You might need to wait for a few minutes for the
capillary and vaporizer temperatures to stabilize at their set values.

6. If you are operating in APCI/APPI or APPI only modes, turn on the

APPI source as follows:

a. Turn on the power to the APPI lamp by flipping the switch on the
PhotoMate light source housing to the On position.
b. Verify that the lamp is operating by looking through the front
window of the Ion Max ion source housing.

7. Configure the Syringe Pump to automatically inject the reserpine

sample solution into the sample loop:

a. Choose Setup > Syringe Pump & Sample Loop to display the
Syringe Pump and Sample Loop view in the top right corner of the
workspace (Figure 39).

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6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte
Setting Up to Optimize in APCI/APPI/MS/MS Mode with Your Compound

Figure 39. Syringe Pump and Sample Loop view, showing auto loop injection
setup

b. Select the Off option button in the Syringe Flow Control group box
to turn off the syringe pump.
• If you are using either a Unimetrics or Hamilton syringe, go to
step 7.c.

• If you are not using either a Unimetrics or Hamilton syringe, go

to step 7.e.

c. In the Syringe Type group box, select the Unimetrics (or Hamilton)
option button to specify a Unimetrics (or Hamilton) syringe.
d. In the Syringe Size group box, select 500 (or the size of your syringe)
from the Volume list box to specify that the volume of your syringe
is 500 μL.
When you specify the syringe type and syringe volume, Tune Master
automatically sets the proper syringe ID value. Go to step 7.f.

e. If you are using a make of syringe other than Unimetrics or

Hamilton, you need to manually specify the syringe ID by doing the
following:
i. Select the Other option button in the Syringe Type group box.
This specifies that you are using a syringe other than Unimetrics
or Hamilton syringe and enables the Syringe ID spin box.
ii. In the Syringe Size group box, select the volume of your syringe
from the Volume list box.

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 6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte
Setting Up to Optimize in APCI/APPI/MS/MS Mode with Your Compound

iii. Enter the inner diameter of your syringe in the Syringe ID

spin box.
f. In the Sample Loop box, enter 5 in the Sample Loop Size box to
specify a loop size of 5 μL.
g. Click Apply to apply these settings. The syringe pump is now
configured to fill the sample loop with the appropriate amount of
sample.

8. Start the flow of solvent:

a. On the Control / Scan Mode toolbar, click on the AS/LC Direct

Control button to display the Inlet Direct Control view in the top
right corner of the workspace (Figure 40).

Figure 40. Inlet Direct Control view, showing high flow setup

Note The following procedure assumes that isopropyl alcohol and

HPLC grade water are in the solvent bottles labeled A and B,
respectively.

b. Set up the Surveyor MS Pump to deliver a solution of 50:50

isopropyl alcohol / water at 1000 μL/min:
i. In the Inlet Direct Control view, in the Solvents Proportions
(%) and Flow Rate group box, enter 50 in the text box labeled A
to specify a delivery proportion of 50% solvent A.
ii. Enter 50 in the box labeled B to specify a delivery proportion of
50% solvent B.

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6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte
Setting Up to Optimize in APCI/APPI/MS/MS Mode with Your Compound

iii. In the Flow Rate box, enter 1000 to set a flow rate of
1000 μL/min.
c. In the Direct Control Panel group box, click the Start button to
start the Surveyor MS pump.
The system is now set up to automatically deliver reserpine to the ion source
for optimizing the mass spectrometer with your compound.

Next you will optimize the compound dependent devices for your
compound in APCI/APPI/MS/MS mode as discussed in the next section:
Optimizing in APCI/APPI/MS/MS Mode Automatically with Your
Compound.

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 6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte
Optimizing in APCI/APPI/MS/MS Mode Automatically with Your Compound

Optimizing in Optimize the mass spectrometer to maximize the ion transmission of your
APCI/APPI/MS/MS compound. Optimization is performed to fine tune compound dependent
parameters such as discharge current, capillary temperature, and tube lens
Mode Automatically offset. It is recommended that you optimize the mass spectrometer after it
with Your Compound has been successfully tuned and calibrated.

To automatically optimize the mass spectrometer in the

APCI/APPI/MS/MS mode for the reserpine transition from m/z 609.281 to
m/z 195.066

1. On the Control / Scan Mode toolbar, click Compound Optimization

Workspace to display the Compound Optimization workspace
(Figure 41).

Figure 41. Compound Optimization workspace, APCI mode

2. In the Compound Optimization view in the top left corner of the

workspace, ensure that the Single Sample page is displayed.

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6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte
Optimizing in APCI/APPI/MS/MS Mode Automatically with Your Compound

3. Set the optimization parameters for monitoring the reserpine transition

from m/z 609.281 to m/z 195.066:

a. Select Optimization Modes: SRM to optimize a selected reaction

(Figure 42).
b. Select Optimization Options: Standard to tune the default
selection of devices. The tube lens offset and collision energy are the
default compound sensitive devices that are optimized in this
configuration.
c. In the Optimization table, enter the parent mass 609.281 to set the
parent mass of the SRM reaction to the ion at m/z 609.281.
d. Enter the product mass 195.066 to set the product mass of the SRM
reaction to the ion at m/z 195.066.
Note You need to select inlet type option button appropriate to the inlet
mode you use to introduce your sample into the mass spectrometer. This
procedure uses the Auto Loop Injection option.

e. In the Inlet Types box, select the Auto Loop Injection option
button to have the TSQ Quantum Ultra automatically inject the
optimization solution.

Figure 42. Compound Optimization view

4. Click Start to start the automatic tuning procedure.

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 6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte
Optimizing in APCI/APPI/MS/MS Mode Automatically with Your Compound

Note If the syringe runs out of sample during the compound

optimization procedure, the instrument pauses the automatic tuning and
displays the message: Syringe out of sample, Reload and click OK. If this
occurs, reload the syringe and click on OK to continue the optimization.

The message Finish compound optimization is displayed in the Status box

in the Compound Optimization view when the compound
optimization has completed successfully (Figure 43).

• If the compound optimization procedure finishes without errors and

the breakdown curve of the 195.066 fragment is Gaussian-shaped
(Figure 44) or is a smooth, positive-sloped curve, go to step 6.

• If errors occur during the compound optimization procedure or the

breakdown curve of the 195.066 fragment oscillates, contains
multiple peaks, or is excessively noisy, go to step 5.

Figure 43. Compound Optimization workspace, showing the successful completion of compound optimization

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6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte
Optimizing in APCI/APPI/MS/MS Mode Automatically with Your Compound

Figure 44. Breakdown curve of reserpine showing the relative intensity of the product ion at m/z 195.066 as a function of
collision energy

5. If errors occurred during the compound optimization procedure, restore

the previous mass spectrometer compound sensitive device settings by
completing the following steps:

a. Click Undo to restore the prior device settings.

b. Click Accept to reload the prior device settings to the mass
spectrometer.
c. Troubleshoot and correct the situation that caused the optimization
to fail.
d. Go to step 4 of this procedure and restart the compound
optimization procedure.

6. Click Accept to accept the results of the compound optimization.

Note Save the Tune Method while the mass spectrometer is On if any of
the ion source parameters have been changed from their initial settings.

7. Save the Tune Method file by doing the following:

a. Click Save Tune As to open the Save As dialog box.

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 6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte
Optimizing in APCI/APPI/MS/MS Mode Automatically with Your Compound

b. Enter a file name (such as APCI_reserpine, or the name of your

compound) for your Tune Method file in the File Name text box.
c. Click Save to save the Tune Method file.
If the file name that you entered in step 7.b is already in use, a message
box appears and asks whether you want to replace the existing file.

• If you do want to overwrite the existing file, click Yes.

• If you do not want to overwrite the existing file, click No. Then,
change the name in the File Name text box and click Save.

The mass spectrometer is now optimized in APCI/APPI/MS/MS mode for

the compound reserpine (or for your compound).

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6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte
Saving the Tune Method

Saving the Tune You can save the settings obtained in a tune method specific to your
Method particular analyte and solvent flow rate. These settings can be recalled to be
used again. Using the example of the last section, the settings obtained using
reserpine would be saved. This tune method can be recalled and used as a
starting point for optimizing the mass spectrometer on reserpine at a
different flow rate.

Note Save the Tune Method while the mass spectrometer is On.

To save your APCI/APPI/MS tune method

1. Choose File > Save As to display the Save As dialog box (Figure 45).

Figure 45. Save As dialog box, showing files in the folder C:\Xcalibur\methods

2. In the Save In list box, select the C:\Xcalibur\methods folder.

3. Click the File Name text box, and then enter APCImyTune to name the
Tune Method APCImyTune.TSQTune.

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 6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte
Saving the Tune Method

4. Click Save to save the Tune Method, and return to the Tune Plus
window. Note that the Tune Method is named APCImyTune.TSQTune.

Before you acquire data, go to the next topic: Cleaning the Mass
Spectrometer After Tuning in APCI Mode.

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6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte
Cleaning the Mass Spectrometer After Tuning in APCI Mode

Cleaning the Mass Use the following procedure to clean the mass spectrometer after tuning on
Spectrometer After your analyte of interest.
Tuning in APCI Mode 1. Click on the On/Standby button to put the mass spectrometer in
Standby mode. When the mass spectrometer is in Standby, the TSQ
Quantum Ultra mass spectrometer turns off the vaporizer heater, corona
discharge voltage, and syringe pump. The mass spectrometer stops
OnStandby scanning and freezes the displays for the Spectrum and Graph views.

CAUTION Always place the mass spectrometer in Standby (or Off )

before you open the API source to atmospheric oxygen. The presence of
oxygen in the ion source when the mass spectrometer is On could be
unsafe. (The TSQ Quantum Ultra mass spectrometer automatically
turns off when you open the API source; however, it is best to take this
added precaution.)

2. Remove the syringe from the syringe pump holder:

a. Squeeze the blue buttons, and pull back on the syringe pump handle
to free the syringe.
b. Remove the syringe from the holder.
c. Disconnect the tip of the syringe needle from the Teflon tubing.

3. Clean the syringe thoroughly:

a. Clean the syringe with a solution of 5% formic acid in water.

b. Rinse the syringe with a solution of 50:50 methanol / water.
c. Use acetone to rinse the syringe. Repeat this step several times.

CAUTION AVOID BURNS. The APCI vaporizer heater can reach

temperatures of 600 ×C. Always allow the APCI probe to cool to
ambient temperature, for approximately 20 min, before handling or
removing the APCI probe from the APCI flange.

CAUTION AVOID INJURY. The corona discharge needle is very sharp

and can puncture your skin if you handle it without caution.

4. Remove the Ion Max ion source housing as described in “Removing the
Ion Max Ion Source Housing” on page 26.

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 6 Optimizing the TSQ Quantum Ultra Mass Spectrometer with Your Analyte
Cleaning the Mass Spectrometer After Tuning in APCI Mode

5. Flush the sample transfer line, sample tube, and APCI probe thoroughly
with a solution of 5% formic acid in water (or with another appropriate
solvent):

Note The solvent that you use to flush the sample transfer line, sample
tube, and APCI probe assembly depends on the solvent system you use
to dissolve your samples. For example, if you are using a buffered
solution of a high concentration, an acidic solution is appropriate.

a. Fill a clean, 250 μL Unimetrics syringe with an appropriate solvent.

b. While holding the plunger of the syringe in place, carefully insert
the needle of the syringe into the free end of the Teflon tube.
c. Flush the sample transfer line, sample tube, and APCI probe with
the solution by slowly depressing the syringe plunger. Visually check
that the solution is exiting the tip of the APCI probe on the inside of
the probe assembly. Use a lint-free tissue to gently remove the excess
solution as it exits the probe.
d. Remove the needle of the syringe from the Teflon tube.

6. Repeat step 5 with a solution of 50:50 methanol / water.

7. Reinstall the Ion Max ion source housing as described in “Installing the
Ion Max Ion Source Housing” on page 33.

Your TSQ Quantum Ultra mass spectrometer is now ready to perform

experiments in APCI/APPI mode. For information regarding the
maintenance of the Ion Max APPI source please refer to Chapter 7,
“Maintenance.”

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 Chapter 7 Maintenance

This chapter describes routine APCI/APPI combination probe maintenance

procedures that must be performed to ensure optimum performance of the
probe. Most of the procedures involve cleaning. It is your responsibility to
maintain the APCI/APPI combination probe by performing the routine
maintenance procedures on a regular basis, as they are described in this
chapter.

The APCI/APPI combination probe requires minimal maintenance.

Periodically, you need to clean the components of the APCI/APPI
combination probe to remove salts or other contaminants. The frequency of
cleaning depends on the types and amounts of samples and solvents that are
introduced into the system.

This chapter contains the following sections:

• Maintaining the APCI Probe

• Maintaining the PhotoMate Light Source

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7 Maintenance
Maintaining the APCI Probe

Maintaining the APCI The APCI probe requires a minimum of maintenance. The APCI sample
Probe tube (100-μm ID fused-silica tubing) is pre-loaded at the factory. However,
if the sample tube becomes obstructed with salt precipitates or is broken,
you need to replace it. Also, you might need to remove and clean the APCI
nozzle.

Figure 7 and Figure 8 on Figure 9 show the major components of the APCI
probe.

Note You should flush the APCI probe at the end of each working day
by flowing a 50:50 methanol / water solution from the LC through the
APCI source.

Wear clean gloves when you handle APCI probe components.

The following procedures are discussed in this section:

• Removing the APCI Nozzle

• Cleaning the APCI Probe Components

• Removing the APCI Sample Tube

• Installing a New APCI Sample Tube

• Reassembling the APCI Probe

Removing the APCI Nozzle To remove the APCI nozzle from the APCI probe

CAUTION Do not break the APCI sample tube. In step 1, carefully pull
the APCI nozzle straight back from the APCI probe to prevent the
sample tube from touching the sides. If the sample tube hits the sides of
the vaporizer, it can break.

CAUTION AVOID BURNS. At operating temperatures, the APCI

vaporizer can severely burn you! The APCI vaporizer typically operates
between 350 and 500 ×C. Always allow the heated vaporizer to cool to
room temperature (for approximately 20 min) before you touch or
remove these components.

See Figure 8 for the location of parts.

1. Place the instrument in Standby mode.

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 7 Maintenance
Maintaining the APCI Probe

2. Hold onto the APCI probe body with one hand and grasp the head of
the APCI nozzle assembly. Rotate the head of the nozzle assembly until
the flat sides of the head are facing towards the retention flanges (See
Figure 8). The nozzle assembly is now free of the probe.

3. Carefully pull the nozzle assembly straight out of the APCI probe.

4. Place the assembly on a clean, lint free tissue.

Cleaning the APCI Probe To clean the APCI probe components

Components
1. Remove the APCI nozzle from the probe body.

2. Check the condition of the O-rings on the APCI nozzle.

3. Clean the interior APCI components (excluding the ceramic heater)

with a 50:50 solution of HPLC-grade methanol and distilled/deionized
water and a lint-free swab. Dry the components with nitrogen gas and
place them on a lint free tissue.

4. Reinstall any O-rings you have removed while cleaning.

If you do not want to replace the APCI sample tube, reinstall the APCI
nozzle (P/N 97055-60089) as described in the topic “Reassembling the
APCI Probe” on page 91.

Removing the APCI Sample Tube To remove the APCI sample tube from the APCI manifold

1. With a 3/8-in. open-end wrench, remove the sample tube inlet fitting
(P/N 70005-20250), 0.239-in. ID O-ring (P/N 00107-04000), and
sample tube from the APCI manifold (Figure 46).

2. Remove the exit-end nut (P/N 70005-20220), 0.016-in. ID, PEEK

ferrule (P/N 00101-18120), and sample tube from the sample tube inlet
fitting.

3. Discard the old sample tube.

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7 Maintenance
Maintaining the APCI Probe

0.312 in. ID O-ring

0.500 in. ID 1/16 Viton O-Ring

APCI Nozzle

Fused Silica
Sample Tube

10-32 PEEK Fitting

0.016 in. ID PEEK Ferrule
0.239 in. ID 1/16 Viton O-Ring
APCI Flange Fitting

Figure 46. APCI sample tube connection

Installing a New APCI Sample To install a new APCI sample tube

Tube
1. Use a fused-silica cutting tool to cut a piece of 100 μm ID, 390 μm OD
fused-silica tubing (P/N 00106-10498) to a length of approximately
15 cm (6 in.). Ensure that you squarely cut the ends of the fused-silica
tubing.

2. Slide the PEEK fitting (P/N 70005-20220) and ferrule

(P/N 00101-18120) onto the length of the fused-silica tubing. See
Figure 46.

3. Check the condition of the 0.239-in. ID O-ring (P/N 00107-04000) on

the sample tube inlet fitting. Replace it if necessary.

4. Insert the fused-silica tubing into the sample tube inlet fitting.

5. Slide the PEEK fitting and ferrule down the fused-silica tubing and into
the sample tube inlet fitting.

6. Tighten the PEEK fitting to secure the new sample tube (fused-silica
tubing).

90 APPI Souce User Manual Thermo Scientific

 7 Maintenance
Maintaining the APCI Probe

7. Use a fused-silica cutting tool to cut the exit end of the sample tube so
that approximately 1 mm protrudes past the tip of the APCI nozzle. See
Figure 47.

1 mm

Figure 47. Proper position of the exit end of the APCI sample tube

Reassembling the APCI Probe To reassemble the APCI probe

1. With one hand holding the APCI probe body to keep the probe from
turning, carefully insert the APCI nozzle into the APCI probe.

2. With the flat sides of the APCI nozzle head facing upwards towards the
retention flanges on the probe body, seat the nozzle head completely flat
against the probe.

3. To secure the APCI nozzle in the probe, rotate the head of the nozzle 90
degrees to secure the round sides of the nozzle head in the retention
flanges.

To reinstall the probe in the Ion Max API source housing, see “Installing the
APCI Probe” on page 27.

Thermo Scientific APPI Souce User Manual 91

7 Maintenance
Maintaining the PhotoMate Light Source

Maintaining the This section includes the following topics for cleaning and replacing
PhotoMate Light components of the PhotoMate light source:
Source • Cleaning and Polishing the Window of the VUV Lamp

• Replacing the VUV Lamp

Cleaning and Polishing Typically, flowing a 50:50 methanol / distilled water solution from the LC
the Window of the VUV through the APCI/APPI combination probe at the end of each working day
will clean the VUV lamp.
Lamp
In some instances, the VUV lamp window might require additional
cleaning or polishing. (A weak ion signal might indicate a build up of salts
or other contaminants on the VUV lamp window.)

To clean or polish the VUV lamp window

CAUTION AVOID BURNS. The APCI vaporizer heater can reach

temperatures of 600 ×C. Always allow the APCI/APPI combination
probe to cool to ambient temperatures before handling or removing the
APCI/APPI combination probe.

1. Ensure that the MS system is in Standby and the LC flow has been
halted.

2. Unplug the power/communication cable from the PhotoMate light

source.

3. Open the front door of the Ion Max ion source housing.

CAUTION Do not apply solvent to the VUV lamp while it is hot. The
VUV lamp can crack.

AVOID INJURY. The corona discharge needle is very sharp. Use

caution when cleaning the VUV lamp.

4. Use a cotton swab that is soaked with LC solvents to wash the window
(end) of the VUV lamp. Ensure that no lint remains on the lamp.

92 APPI Souce User Manual Thermo Scientific

 7 Maintenance
Maintaining the PhotoMate Light Source

5. Inspect the window of the VUV lamp:

• If no material remains on the window, close and secure the front door of
the Ion Max ion source housing and proceed with your application.

• If you were unable to remove all material from the window, you need to
remove the VUV lamp and polish the window. Continue with step 7.

CAUTION Always wear clean gloves when you are handling a functional
VUV lamp. Fingerprints on the lamp can cause the lamp to fail when it
is in use.

6. While wearing clean gloves, grasp the VUV lamp and pull the lamp out.

• If you are able to remove the VUV lamp, go to step 10.

• If you are having trouble removing the lamp, you need to push it out
from the top. Go to step 7.

7. Remove the PhotoMate light source by removing the retaining screws

that hold the assembly to the adapter ring, then pulling the assembly
straight out until it is free from the Ion Max ion source housing.

8. Remove the box top from the PhotoMate light source:

a. Remove the light source power cord from the light source.
b. Remove the 4 Phillips screws that secure the box top to the light
source.
c. Remove the box top from the electronics PCB, but keep the fan
power cable connected.

9. Insert an Allen key into the lamp hole in the electronics PCB. See
Figure 48. Gently push out the VUV lamp with the Allen key.

Thermo Scientific APPI Souce User Manual 93

7 Maintenance
Maintaining the PhotoMate Light Source

Lamp Hole

Figure 48. Light source with box top removed, showing the lamp hole

10. Dip a cotton swab in isopropyl alcohol, then dip the wet swab in
aluminum oxide polishing compound (5 micron powder).

11. Polish the lamp window with the swab and polishing compound until
the material is removed.

12. Use another cotton swab soaked in isopropyl alcohol to remove the
polishing compound from the lamp window.

13. While wearing clean gloves, install the VUV lamp by pushing it all the
way to the stopping position in the light source assembly.

14. If necessary, reinstall the box top:

a. Tip the box top forward and make sure the lamp On/Off switch
passes through the hole in the box top. Then push the box top down
over the fan connector.
b. Reinstall the four screws to secure the box top.
c. Reconnect the light source power cord to the light source.

15. If necessary, reinstall the PhotoMate light source in the Ion Max ion
source housing.

94 APPI Souce User Manual Thermo Scientific

 7 Maintenance
Maintaining the PhotoMate Light Source

Replacing the VUV Lamp You can minimize the chance of breaking the VUV lamp by doing the
following:

• Always wear clean gloves when you are handling the VUV lamp.
Fingerprints on the lamp can cause the lamp to fail when it is in use.

• Do not spray solvent on the VUV lamp while it is hot. The VUV lamp
can crack.

If the VUV lamp beaks or fails, use the following procedures to replace it:

• Removing the Old VUV Lamp

• Installing the New VUV Lamp

Removing the Old VUV Lamp To remove the old VUV lamp

1. Place the lamp On/Off switch in the Off (O) position.

2. Turn off the flow of liquid from the LC (or other sample introduction
device) to the APCI/APPI combination probe:

3. Put the mass spectrometer in Standby mode

CAUTION AVOID BURNS. At operating temperatures, the APCI

vaporizer, ion sweep cone, spray cone, and ion transfer capillary can
severely burn you! The APCI vaporizer typically operates at
400 to 600 ×C and the ion sweep cone, spray cone, and ion transfer
capillary typically operate at 100 to 300 ×C.

Allow the heated vaporizer, ion sweep cone, spray cone, and ion transfer
capillary to cool to room temperature, for approximately 20 min, before
you touch or remove these components.

4. Open the lid of the APCI/APPI combination probe.

CAUTION Always wear clean gloves when you are handling a functional
VUV lamp. Fingerprints on the lamp can cause the lamp to fail when it
is in use.

5. While wearing clean gloves, grasp the VUV lamp and pull the lamp out.

• If you are able to remove the VUV lamp, go to the next section
Installing the New VUV Lamp.

Thermo Scientific APPI Souce User Manual 95

7 Maintenance
Maintaining the PhotoMate Light Source

• If you are having trouble removing the lamp, you need to push it out
from the top.

6. Remove the box top from the PhotoMate light source:

a. Remove the light source power cord from the light source.
b. Remove the 4 Phillips screws that secure the box top to the light
source.
c. Remove the box top from the electronics PCB, but keep the fan
power cable connected.

7. Insert an Allen key into the lamp hole in the electronics PCB. See
Figure 48 on page 94. Gently push out the VUV lamp with the Allen
key.

Installing the New VUV Lamp To install the new VUV lamp

CAUTION Always wear clean gloves when you are handling a functional
VUV lamp. Fingerprints on the lamp can cause the lamp to fail when it
is in use.

1. While wearing clean gloves, install a new VUV lamp by pushing it all
the way to the stopping position in the light source assembly.

2. If necessary, reinstall the box top:

a. Tip the box top forward and make sure the lamp On/Off switch
passes through the hole in the box top. Then push the box top down
over the fan connector.
b. Reinstall the four screws to secure the box top.
c. Reconnect the light source power cord to the light source.

3. Close and secure the lid of the APCI/APPI combination probe housing.

4. Place the lamp On/Off switch in the On position.

96 APPI Souce User Manual Thermo Scientific

 7 Maintenance
Maintaining the PhotoMate Light Source

5. Check that the Lamp On and Drive On LEDs illuminate. Look through
the Ion Max window and verify that the VUV lamp is on.

Note If the Drive On and Lamp On LEDs do not illuminate, verify that
the front door of the Ion Max ion source housing is secured. The front
door of the source housing must be closed and locked to engage the
interlock.

Thermo Scientific APPI Souce User Manual 97

 Chapter 8 Replaceable Parts

This chapter contains part numbers for replaceable and consumable parts
for the Ion Max APCI probe and Photomate light source. To ensure proper
results in servicing the ion source, order only the parts listed or their
equivalent. Please refer to the figures on the subsequent pages for the
location of each part listed.

The replaceable parts are as follows:

APPI Lamp Kit.............................................................. OPTON-20026

APPI circuit assembly & fan, Ion Max .......................... 00950-10010
Cable, APPI, Ion Max ................................................... 00950-10011
APPI lamp .................................................................... 00950-10002
APPI power supply........................................................ 00950-10012
APCI Probe ................................................................... OPTON-20012
APCI Probe Nozzle Assembly ............................................ 97055-60089
Ferrule, 0.016 ID PEEK HPLC .................................... 00101-18120
Tubing, fused silica 150 μm ID X 390 μm OD ............ 00106-10498
O-ring, 0.239 in. ID 1/16 in. Viton.............................. 00107-04000
O-ring, 0.312 in. ID 1/16 in......................................... 00107-04500
O-ring, 0.500 in. ID 1/16 in.Viton............................... 00107-05600
Fitting, 10-32 male nut PEEK....................................... 70005-20220
Fitting, APCI flange ...................................................... 70005-20250
Nozzle, APCI probe ...................................................... 97055-20221

Thermo Scientific APPI Souce User Manual 99

8 Replaceable Parts

APCI Probe

Ion Max Ion Source Housing

Photomate Light Source

Figure 49. Ion Max ion source housing, showing the APCI probe and PhotoMate light source

100 APPI Souce User Manual Thermo Scientific

 8 Replaceable Parts

Vaporizer Heater
Cable Socket

Guide Pin

Retention Flange
Flat Side
APCI Nozzle Assembly
Retention Flange

Figure 50. APCI Probe Assembly (OPTON-20012)

00107-04500
00107-05600

97055-20221

00106-10468

7005-20220
00101-18120
00107-04000
70005-20250

Figure 51. APCI probe nozzle assembly (P/N 97055-60089)

Thermo Scientific APPI Souce User Manual 101

 Appendix A Installing the PhotoMate
Light Source Adapter Ring

This chapter provides information on installing the Photomate light source

adapter ring in the Ion Max ion source housing. You only need to perform
this procedure the first time you use your source. If you do not want to use
the APPI lamp for a particular experiment, you can install the smaller
viewport window that fits within the Photomate light source adapter ring.
There is no need to remove the ring when not in APPI mode as long as the
small viewport window is installed.

Install the APPI adapter ring as follows:

1. Stop the flow of sample solution from the LC.

2. Place the MS detector in standby.

3. Remove the currently installed API probe as described in the Ion Max
API Source Hardware Manual.

4. Unscrew and remove the probe alignment screw on the left side of the
Ion Max ion source housing. See Figure 52.

5. Using the special hex head wrench provided with your APPI source,
remove the four retaining screws from the left hand side Ion Max ion
source housing cover.

6. Pull the cover straight out and free from the Ion Max ion source
housing.

7. Remove the two screws that hold the Ion Max viewport frame in place.
Be careful not to allow the window to fall free and break. See Figure 53.

8. Align the APPI adapter ring so that the flat side fits against the rear of
the Ion Max ion source housing and so that both holes in the ring align
with the holes in the Ion Max ion source housing. Secure the ring with
the two screws that you removed from the viewport frame. See
Figure 54.

Thermo Scientific APPI Souce User Manual 103

A Installing the PhotoMate Light Source Adapter Ring

9. Replace the source housing cover and secure the cover with all four hex
head screws.

10. Replace the probe alignment screw in the Ion Max ion source housing.

11. Complete the installation:

• If you are going to proceed with an APPI experiment, install the

APCI probe and PhotoMate light source as described in Chapter 3,
“Setting Up the Ion Source for Acquiring Data in
APCI/APPI/MS/MS Mode” .

or

• If you will not be performing an APPI experiment at this time,

complete steps 12 to 14 before continuing with your experiments.
Do not attempt to operate any Ion Max ion source without the
viewport window installed.

12. Carefully install the small viewport window in the APPI adapter ring.
See Figure 55.

13. Secure the retainer ring with four hex head screws. See Figure 56.

14. Reinstall your API probe in the Ion Max ion source housing.

You are now ready to perform ESI or APCI experiments or to install the
PhotoMate light source.

104 APPI Souce User Manual Thermo Scientific

 A Installing the PhotoMate Light Source Adapter Ring

Cover Retaining Screws

Cover Retaining Screws Probe Alignment Screw

Figure 52. Left side of the Ion Max ion source housing, showing the probe
alignment screw and cover retaining screws

Thermo Scientific APPI Souce User Manual 105

A Installing the PhotoMate Light Source Adapter Ring

Viewport Frame Screws

Figure 53. Ion Max ion source housing with left cover removed, showing the
viewport frame and screws

106 APPI Souce User Manual Thermo Scientific

 A Installing the PhotoMate Light Source Adapter Ring

Figure 54. Aligning the APPI adapter ring

Figure 55. Inserting the small viewport window into the APPI adapter ring

Thermo Scientific APPI Souce User Manual 107

A Installing the PhotoMate Light Source Adapter Ring

Figure 56. Completed APPI adapter ring installation

108 APPI Souce User Manual Thermo Scientific

 Appendix B Reserpine Solution
Formulations

This appendix provides instructions for preparing the tuning and calibration
solution and the reserpine solution that is used to optimize the tune of the
mass spectrometer.

The sections in this appendix are as follows:

• Reserpine Stock Solution

• LCQ Deca XP MAX Reserpine Sample Solution

• LTQ Reserpine Sample Solution

• TSQ Quantum Ultra Reserpine Sample Solution

CAUTION AVOID EXPOSURE TO POTENTIALLY HARMFUL

MATERIALS. Always wear protective gloves and safety glasses when you
use solvents or corrosives. Also, contain waste streams and use proper
ventilation. Refer to your supplier's Material Safety Data Sheet (MSDS)
for the proper handling of a particular solvent.

Always take safety precautions when you handle chemicals and unknown
samples. READ AND UNDERSTAND THE HAZARDS OF THE
CHEMICALS USED IN THE FOLLOWING PREPARATIONS.
Dispose of all laboratory reagents by the appropriate method for a specific
reagent or solvent.

Material Safety Data Sheets (MSDS) provide summarized information on

the hazards and toxicity of specific chemical compounds. MSDSs also
provide information on the proper handling of compounds, first aid for
accidental exposure, and procedures for the remedy of spills or leaks.
Producers and suppliers of chemical compounds are required by law to
provide their customers with the most current health and safety information
in the form of an MSDS. Read the MSDSs for each chemical you use.
Examples of potentially hazardous chemicals used in procedures throughout
this manual are as follows:

Thermo Scientific APPI Souce User Manual 109

B Reserpine Solution Formulations

• Acetic acid

• Methanol

• Reserpine

Follow the directions given below to prepare a stock solution of reserpine.

Then, use serial dilutions of the stock solution to make the compound
optimization solution.

110 APPI Souce User Manual Thermo Scientific

 B Reserpine Solution Formulations
Reserpine Stock Solution

Reserpine Stock Prepare 10 mL of a 1 μg/μL Reserpine Stock Solution in 1% acetic acid

Solution
15. Carefully weigh 10 mg of Reserpine.

16. Transfer the 10 mg of reserpine into a 10 mL volumetric flask.

17. Add 1% acetic acid in methanol until the 10 mL mark is reached.

18. Mix the solution thoroughly.

19. Transfer the solution to a clean dry vial.

20. Label the vial Reserpine Stock Solution (1 μg/μL).

Thermo Scientific APPI Souce User Manual 111

B Reserpine Solution Formulations
LCQ Deca XP MAX Reserpine Sample Solution

LCQ Deca XP MAX Prepare 1 mL of the sample solution of 1 pg/μL (8.2 fmol/μL) in a solution
Reserpine Sample of 1% acetic acid in methanol
Solution 1. Pipette 1 mL of reserpine stock solution (1 μg/μL) into a 10 mL
volumetric flask and bring the volume up to the 10mL mark using
methanol (1% acetic acid). Mix the resulting solution thoroughly and
label it as Reserpine (100 ng/μL).

2. Place 75 mL of methanol (1% acetic acid) into a clean 100 mL

volumetric flask.

3. Using the 10 μL syringe provided in the accessories kit or a calibrated

pipette, add 5 μL of the Reserpine (100 ng/μL) solution to the 75 mL of
methanol (1% acetic acid) in the 100 mL volumetric flask.

4. Rinse the pipette twice with the 75 mL of methanol (1% acetic acid)
contained in the volumetric flask by dipping the pipette tip into the
solution and rinsing it back into the flask.

5. Carefully bring up this volume with methanol (1% acetic acid) until the
lower part of the meniscus is level with the 100 mL marking.

6. Mix this solution thoroughly. Label it as Reserpine (5 pg/μL)

7. Add 20 mL of the Reserpine (5 pg/μL) to another clean 100 mL

volumetric flask, and carefully bring up this volume with methanol
(1% acetic acid) until the lower part of the meniscus is level with the
100 mL marking.

8. Mix the solution thoroughly.

9. This is the LCQ Deca XP MAX Reserpine Sample Solution (1 pg/μL).

112 APPI Souce User Manual Thermo Scientific

 B Reserpine Solution Formulations
LTQ Reserpine Sample Solution

LTQ Reserpine Prepare 1 mL of the sample solution of 125 fg/μL (205 amol/μL) in
Sample Solution 1% acetic acid in 50:50 methanol / water

1. Pipette 1 mL of reserpine stock solution (1 μg/μL) into a 10 mL

volumetric flask and bring the volume up to the 10 mL mark using
methanol (1% acetic acid). Mix the resulting solution thoroughly and
label it as Reserpine (100 ng/μL).

2. Place 75 mL of methanol (1% acetic acid) into a clean 100 mL

volumetric flask.

3. Using the 10 μL syringe provided in the accessories kit or a calibrated

pipette, add 5 μL of the Reserpine (100 ng/μL) solution to the 75 mL of
methanol (1% acetic acid) in the 100 mL volumetric flask.

4. Rinse the pipette twice with the 75 mL of methanol (1% acetic acid)
contained in the volumetric flask by dipping the pipette tip into the
solution and rinsing it back into the flask.

5. Carefully bring up this volume with methanol (1% acetic acid) until the
lower part of the meniscus is level with the 100 mL marking.

6. Mix this solution thoroughly. Label it as Reserpine (5 pg/μL)

7. Add 20 mL of the Reserpine (5 pg/μL) to another clean 100 mL

volumetric flask, and carefully bring up this volume with methanol
(1% acetic acid) until the lower part of the meniscus is level with the
100 mL marking.

8. Mix the solution thoroughly.

9. Label this Reserpine (1 pg/μL).

10. Transfer 100 μL of the 1 pg/μL solution into a clean polypropylene

tube.

11. Add 700 μL of 1% acetic acid in 50:50 methanol / water to the tube.

12. Mix this solution (125 fg/μL) thoroughly.

13. Label the tube LTQ Reserpine Sample Solution (125 fg/μL) and store it in
a refrigerator until it is needed.

Thermo Scientific APPI Souce User Manual 113

B Reserpine Solution Formulations
TSQ Quantum Ultra Reserpine Sample Solution

TSQ Quantum Ultra Prepare 1 mL of the 200 fg/μL (0.329 fmol/μL) reserpine compound
Reserpine Sample optimization solution in 1% acetic acid in methanol
Solution 1. Pipette 1 mL of reserpine stock solution (1 μg/μL) into a 10 mL
volumetric flask and bring the volume up to the 10mL mark using
methanol (1% acetic acid). Mix the resulting solution thoroughly and
label it as Reserpine (100 ng/μL).

2. Place 75 mL of methanol (1% acetic acid) into a clean 100 mL

volumetric flask.

3. Using the 10 μL syringe provided in the accessories kit or a calibrated

pipette, add 5 μL of the Reserpine (100 ng/μL) solution to the 75 mL of
methanol (1% acetic acid) in the 100 mL volumetric flask.

4. Rinse the pipette twice with the 75 mL of methanol (1% acetic acid)
contained in the volumetric flask by dipping the pipette tip into the
solution and rinsing it back into the flask.

5. Carefully bring up this volume with methanol (1% acetic acid) until the
lower part of the meniscus is level with the 100 mL marking.

6. Mix this solution thoroughly. Label it as Reserpine (5 pg/μL)

7. Add 20 mL of the Reserpine (5 pg/μL) to another clean 100 mL

volumetric flask, and carefully bring up this volume with methanol
(1% acetic acid) until the lower part of the meniscus is level with the
100 mL marking.

8. Mix the solution thoroughly.

9. Label this Reserpine (1 pg/μL).

10. Transfer 200 μL of the 1 pg/μL solution into a clean polypropylene

tube.

11. Add 800 μL of 1% acetic acid in methanol to the tube.

12. Label the vial TSQ Quantum Ultra Reserpine Sample Solution
(200 fg/μL) and store it in a refrigerator until it is needed.

114 APPI Souce User Manual Thermo Scientific

Index
A molecular weight range 2
operating parameters 11
APCI
APCI process 4 APPI/APCI combination probe
maintenance 87
discussed 3
operating parameters 11 atmospheric pressure chemical ionization
plumbing for sample input See APCI
Tee to LC 38 atmospheric pressure photoionization
tuning procedure 38 See APPI
APCI manifold auto loop injection
location 15 APCI
APCI nozzle plumbing for 67
reinstalling 89 auxiliary gas
removing 89 settings for APPI and APCI 11
APCI probe
cleaning 89
corona discharge needle 15 B
description 14
box fan
disassembling 88
description 20
figure 14
location 19
maintenance 88
nozzle 14 buffers, LC
discussion 10
reassembling 91
removing 88
vaporizer 14
vaporizer temperature 14 C
APCI sample tube CAUTIONS
connection 90 avoid sharp needle 92
installation 91 avoiding burns
installing 90 from APCI vaporizer 49, 63, 84, 88
removing 89 avoiding injury from corona discharge needle 27
replacing 88 Ion Max ion source
APCI Source dialog box exposing to atmosphere 49, 63, 84
displaying 55 ion source, exposing to oxygen 49, 63, 84
figure 56 ion transfer capillary, avoiding burns 88
APCI Source dialog box. Cautions
figure 43 changing API probes 20
APCI vaporizer disconnecting PhotoMate power cord 20
avoiding burns from (CAUTION) 88 handling VUV lamp 93, 95, 96
cross sectional view 15 solvent waste backing into API2 source housing 40
reconditioning (note) 72 solvent waste backing into ion source housing 29, 34
APCI/MS venting ESI source 35
compound optimization 65 VUV lamp, breaking 20
setting up LTQ for 55 chemicals
APPI reserpine sample solution, preparing 114
discussed 6 cleaning procedures
molecular polarity range 2 APCI probe components 88, 89

Thermo Scientific APPI Souce User Manual 115

Index: D

VUV lamp 92 APCI process 4

cleaning, LCQ Deca XP MAX 49 APCI sample tube connection 90
cleaning, LTQ 63 APCI Source dialog box 43, 56
cleaning, TSQ Quantum Ultra 84 Define Scan dialog box, APCI settings 44
combined APCI and APPI Ion Max ion source housing 33
corona needle status (table) 9 plumbing
discussed 9 Tee union, APCI 38
light source status (table) 9 plumbing for
divert/inject valve to APCI probe 69
compound optimization
LC/APCI/MS mode 65 divert/inject valve, for auto loop injection 68
Save As d.b. 47, 82
setting up mass spectrometer for 71
Save As dialog box 61
setting up syringe pump for 67
syringe adapter assembly 68
solutions, preparing 110
Tune dialog box
computer terms
settings for automatic tuning 59
directories 47, 82
Tune Master views
files 47, 82
Inlet Direct Control 75
contamination of Optimize Compound Dependent Devices 71
APCI source, cleaning (note) 72
Syringe Pump and Sample Loop 74
syringe (note) 69 Tune Master workspaces
corona discharge needle Compound Optimization 77
description 15 Tune Plus window
discharge current 15 Automatic page, Tune dialog box 46, 59
figure 14
fused-silica tubing
corona discharge needle, avoiding injury from 27 APCI, installing 90

D G
Define Scan dialog box 44 Graph view
displaying 56 displaying 58
dialog boxes freezing 49, 63, 84
APCI Source 43, 56 guidelines
Define Scan 44 mass spectrometer operation (table) 11
Save As 47, 47, 61, 61, 82, 82
Tune 46, 59, 59
divert/inject valve
plumbing for auto loop injection 68 I
procedure 67 interlocks
description 20
Ion Max ion source
E exposing to atmosphere (CAUTION) 49, 63, 84
ion source
electromagnet compatibility iii ESI
electronics PCB high voltage connector 33
discussion 20 nitrogen gas connections 33
location 19 removing 24
ion transfer capillary
avoiding burns from (CAUTION) 88
F optimizing temperature of
discussion 51, 58
FCC compliance iii
temperatures for APPI and APCI 11
Figures
APCI plumbing for Tee 39, 53 ionization modes 1
atmospheric pressure chemical ionization (APCI) 3

116 APPI Souce User Manual Thermo Scientific

 Index: L

ionization potentials 8 opening predefined 42

MS detector
maintenance overview 87
setting up for APCI/MS operation 42
L
lamp
cleaning and polishing 92
installation 96 N
location 19 Notes
removing 95 avoiding contamination of syringe 69
replacing 95 cutting PEEK tubing 39, 53
lamp on/off switch optimizing on compound of interest 67
description 20 reconditioning the APCI 72
location 18 removing contamination from APCI 72
LC saving Tune Method 80
flow rates 11 selecting appropriate inlet type 78
using buffers, discussion 10 solvents 50, 64, 85
LCQ Deca XP MAX nozzle
cleaning for normal operation 49 APCI, reinstalling 89
LCQ Deca XP Plus system APCI, removing 89
replaceable parts 99
LEDs
location 18, 18 O
light source
operating parameters (APPI and APCI) 11
description 17
figure 18
internal components 19
LEDs 21 P
maintenance 92 PEEK tubing
safety interlocks 21 cutting (note) 39
light source power cord PEEK tubing, cutting (note) 53
location 18
PhotoMate 17
LTQ
PhotoMate light source 18
cleaning for normal operation 63
description 17
setting up for APCI/MS operation 55
figure 18
internal components 19
LEDs 21
M maintenance 92
maintenance safety interlocks 21
APCI probe 88 plumbing for
APCI probe components, cleaning 89 divert/inject valve 69
APCI sample tube, installing 90 auto loop injection 68
light source 92 syringe pump, Tee to LC, APCI 38
overview 87, 87 power supply
maintenance procedures discussion 20
cleaning and polishing VUV lamp 92 procedures
overview 87 cleaning
replacing the VUV lamp 95 LCQ Deca XP MAX, after tuning and calibrating 49
mass spectrometer LTQ, after tuning and calibrating 63
ionization modes 1 TSQ Quantum Ultra, after tuning and calibrating 84
operational guidelines (table) 11 compound optimization, APCI/MS mode 77
installing ESI source 23
methods, Tune
optimizing

APPI Souce User Manual Thermo Scientific 117

Index: R

LCQ Deca XP MAX, APCI Tune 45 reserpine 113

TSQ Quantum Ultra, APCI Tune 65 solvents (note) 50, 64, 85
optimizing, APCI tune 58 status LEDs
preparing reserpine solutions 110 location 18, 18
removing ESI source 24 syringe
saving Tune Method 47, 61, 80, 82 adapter assembly 68
setting up syringe pump
LCQ Deca XP MAX installing syringe into 52
for APCI/MS operation 42 plumbing 52, 54
inlet for APCI tuning 38 removing syringe from 49, 63, 84
LTQ setting up for compound optimization 67
for APCI/MS operation 55 starting 58
TSQ Quantum Ultra stopping 49, 63, 84
for compound optimization 71
system
syringe pump for compound optimization 67 replaceable parts 99
setting up hardware
for tuning and calibrating 23
tuning
LCQ Deca XP MAX T
automatically, APCI/MS mode 45 Tables
LTQ corona discharge needle status 9
automatically in APCI/MS mode 58 light source status 9
operation parameter guidelines 11
temperatures
R APCI vaporizer 14
TSQ Quantum Ultra
regulatory compliance iii
cleaning for normal operation 84
Remote LED
description 21 Tune dialog box
figure 59
replacement procedures
showing settings for automatic tuning (figure) 59
sample tube, APCI 88
Tune Method, saving 47, 61, 82
reserpine, preparing solutions 110
Tune Plus window
tuning 46
tuning results 59
S
safety interlocks
description 20 U
safety standards iii
user interface
sample solutions Tune Master
ESI, reserpine 112 changing syringe pump and sample loop parameters 73
sample solutions, reserpine, preparing 113 direct control of Surveyor LC system 75, 75
sample tube manually changing device parameters 72
APCI, installing 90 manually changing scan parameters 78
APCI, removing 89 optimizing in the APCI/MS mode 77
APCI, replacing 88 optimizing in the ESI/MS mode 78
Save As dialog box 47, 61, 82 preparing for optimizing 71, 76
saving saving the Tune Method 80
files 47, 82 switching between ESI and APCI operation 71
saving Tune Method 47
sheath gas
settings for APPI and APCI 11
solutions, preparing

118 APPI Souce User Manual Thermo Scientific

 Index: V

V
vaporizer
APCI probe, description 14
location 15
temperature 14
temperatures for APPI and APCI 11
voltages
corona discharge needle 14
VUV lamp
cleaning and polishing 92
discussion 20
installation 96
location 19
removing 95
replacing 95

APPI Souce User Manual Thermo Scientific 119