User Guide: Turbo V Ion Source for SCIEX QTOF Systems Operator Guide

User Guide: Turbo V Ion Source for SCIEX QTOF Systems Operator Guide
Turbo V™ Ion Source
for SCIEX QTOF Systems
Operator Guide
RUO-IDV-05-1828-A
December 2015
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Contents
Chapter 1 Ion Source Overview.................................................................................................................5
Operational Precautions and Hazards................................................................................................................................5
Ionization Modes...............................................................................................................................................................6
ESI Mode......................................................................................................................................................................6
APCI Mode...................................................................................................................................................................6
Ion Source Components.....................................................................................................................................................7
Probes................................................................................................................................................................................8
Twin ESI Probe.............................................................................................................................................................9
Twin APCI Probe..........................................................................................................................................................9
Gas and Electrical Connections........................................................................................................................................10
Ion Source Sense Circuit...................................................................................................................................................10
Source Exhaust System....................................................................................................................................................11
Contact Us.......................................................................................................................................................................11
Related Documentation...................................................................................................................................................12
Technical Support............................................................................................................................................................12
Chapter 2 Ion Source Installation.............................................................................................................13
Prepare for Installation....................................................................................................................................................13
Install the Probe...............................................................................................................................................................14
Connect the Ion Source Tubing........................................................................................................................................14
Install the Ion Source on the Mass Spectrometer.............................................................................................................15
Sample Inlet Requirements........................................................................................................................................16
Inspect for Leaks..............................................................................................................................................................16
Chapter 3 Ion Source Optimization.........................................................................................................17
Sample Introduction.........................................................................................................................................................17
Method......................................................................................................................................................................17
Flow Rate...................................................................................................................................................................18
Twin ESI Probe Optimization............................................................................................................................................18
Flow Rate and Temperature.......................................................................................................................................18
Set Up the System......................................................................................................................................................19
Prepare the System....................................................................................................................................................19
Set the Starting Conditions........................................................................................................................................19
Optimize the Twin ESI Probe Position........................................................................................................................20
Optimize Source and Gas Parameters and Voltage....................................................................................................20
Optimize the Turbo Heater Temperature....................................................................................................................21
Twin APCI Probe Optimization.........................................................................................................................................21
Set Up the System......................................................................................................................................................22
Prepare the System....................................................................................................................................................22
Set the Starting Conditions........................................................................................................................................23
Optimize Gas 1 and Curtain Gas Flow.......................................................................................................................23
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Contents
Adjust the Position of the Corona Discharge Needle.................................................................................................23
Optimize the Twin APCI Probe Position.....................................................................................................................24
Optimize the Nebulizer Current..................................................................................................................................25
Optimize the APCI Probe Temperature.......................................................................................................................25
Optimization Tips.............................................................................................................................................................25
Chapter 4 Ion Source Maintenance..........................................................................................................27
Remove the Ion Source....................................................................................................................................................28
Clean the Ion Source Surfaces..........................................................................................................................................29
Clean the Probes..............................................................................................................................................................29
Remove the Probe............................................................................................................................................................30
Replace the Twin Electrodes............................................................................................................................................30
Adjust the Electrode Tip Extension...................................................................................................................................31
Replace the Corona Discharge Needle.............................................................................................................................32
Replace the Sample Tubing..............................................................................................................................................34
Chapter 5 Troubleshooting......................................................................................................................35
Appendix A Principles of Operation—Ion Source...................................................................................38
Electrospray Ionization Mode...........................................................................................................................................38
APCI Mode.......................................................................................................................................................................39
APCI Ionization Region..............................................................................................................................................42
Appendix B Source Parameters and Voltages.........................................................................................45
Twin ESI Probe Parameters..............................................................................................................................................45
Twin APCI Probe Parameters...........................................................................................................................................46
Parameter Descriptions....................................................................................................................................................47
Probe Position..................................................................................................................................................................48
Solvent Composition........................................................................................................................................................49
Appendix C Consumables and Spares.....................................................................................................50
Revision History........................................................................................................................................52
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1
Ion Source Overview
TM
The Turbo V ion source can be used for either electrospray ionization (ESI) or atmospheric pressure chemical
ionization (APCI).
The twin ESI probe is used for ESI mode operation. The twin APCI probe is used for APCI mode operation. The
standard probe supplied with the ion source is the twin ESI probe.
The twin probes enable on-demand introduction of calibrant and sample through independent electrodes.
Applications for the ion source include qualitative method development and qualitative and quantitative analysis.
Operational Precautions and Hazards
For regulatory and safety information for the mass spectrometer, refer to the System User Guide.
WARNING! Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Use the
ion source only if you have knowledge of and training in the proper use,
containment, and evacuation of toxic or injurious materials used with the
ion source.
WARNING! Puncture Hazard, Radiation Hazard, Biohazard, or Toxic Chemical
Hazard. Discontinue use of the ion source if the ion source window is cracked
or broken and then contact a SCIEX Field Service Employee (FSE). Any toxic
or injurious materials introduced into the equipment will be present in the
source exhaust output. Dispose of sharps following established laboratory
safety procedures.
WARNING! Hot Surface Hazard. Let the ion source cool for at least 30 minutes before
starting any maintenance procedures. Surfaces of the ion source and the vacuum
interface components become hot during operation.
WARNING! Toxic Chemical Hazard. Wear personal protective equipment, including
a laboratory coat, gloves, and safety glasses, to avoid skin or eye exposure.
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Ion Source Overview
WARNING! Radiation Hazard, Biohazard, Electrical Shock Hazard, or Toxic
Chemical Hazard. In the event of a chemical spill, review product Safety Data
Sheets for specific instructions. Make sure that the system is in Standby mode
before cleaning a spill near the ion source. Use appropriate personal protective
equipment and absorbent wipes to contain the spill and dispose of it following
local regulations.
WARNING! Environmental Hazard. Do not dispose of system components in municipal
waste. Follow local regulations when disposing of components.
WARNING! Electrical Shock Hazard. Avoid contact with the high voltages applied
to the ion source during operation. Put the system in Standby mode before adjusting
the sample tubing or other equipment near the ion source.
Ionization Modes
ESI Mode
ESI produces gas phase ions of analytes in a sample by applying a high voltage to the sample effluent flowing
through a needle. With the aid of heated gas flow, ESI produces single and multiply charged ions in a relatively
mild condition so that it is suitable for a wide range of compounds including small molecules such as drugs or
pesticides, and larger molecules such as peptides, proteins and other biopolymers. The sensitivity depends on the
chemical properties of the analyte, the gas flow rate, the temperature, the voltage, and the mobile phase
composition.
The ESI technique is mild enough to be used with labile compounds, such as peptides, proteins, and thermally
labile pharmaceuticals. It functions with flow rates from 5 μL/min to 3000 μL/min and it vaporizes 100% aqueous
to 100% organic solvents.
Refer to Electrospray Ionization Mode on page 38.
APCI Mode
The APCI mode is suitable for:
• Ionization of compounds that do not readily form ions in solution. These are usually non-polar compounds.
• Creation of simple APCI spectra for LC-MS/MS experiments.
• High-throughput analyses of complex and dirty samples. It is less sensitive to ion suppression effects.
• Rapid sample introduction by flow injection with or without an LC column.
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Ion Source Overview
The APCI technique can be used for volatile and labile compounds with minimal thermal decomposition. The rapid
desolvation and vaporization of the droplets and entrained analyte minimizes thermal decomposition and preserves
molecular identity for ionization by the corona discharge needle. Buffers are readily tolerated by the ion source
without significant contamination and the flash vaporization of the sprayed effluent allows up to 100% water to
be used. The probe can accept the entire effluent, without splitting, at flow rates from 50 μL/min to 3000 μL/min
(through a wide-bore column).
Refer to APCI Mode on page 39.
Ion Source Components
Figure 1-1 Ion Source Components
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Ion Source Overview
Item
Description
1
Sample tubing
2
Corona discharge needle adjustment screw
3
Y-axis micrometer used to position the probe on the vertical axis for ion source sensitivity
adjustments
4
Grounding union
5
One of two source latches that secure the ion source to the mass spectrometer
6
Guide pin
7
X-axis micrometer used to position the probe on the horizontal axis for ion source sensitivity
adjustments
8
Probe tower
9
Retaining ring
10
Calibrant port with fitting
11
Flow module, consisting of calibrant tubing and check valve
12
LC (sample) port with fitting
Probes
The twin ESI and twin APCI probes provide a range of capability for testing samples. Select the probe and method
most suitable for the compounds in the sample.
Table 1-1 Ion Source Specifications
Specification
Twin ESI Probe
Twin APCI Probe
Temperature range
From ambient temperature to 750
°C, depending on liquid flow
From 50 °C to 750 °C, depending on
liquid flow
Liquid chromatography (LC)
Interfaces with any LC system
Gas 1 / Gas 2
Refer to the Site Planning Guide for the mass spectrometer.
The SCIEX OS software identifies which probe is installed and enables the corresponding user controls.
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Ion Source Overview
Twin ESI Probe
The twin ESI probe is 220 mm long. It contains two 100 µm (0.004 inch) inside diameter (i.d.) stainless steel
electrodes and is located centrally, with the two turbo heaters placed at a 45 degree angle to each side.
The sample supply is connected to the port labeled LC and the calibrant is connected to the port labeled Cal.
Analytes (samples or calibrants) introduced through the twin ESI probe are ionized within the tubing by the
application of high voltage (IonSpray voltage). The ions are then nebulized by a jet of compressed zero air, creating
a mist of small, highly-charged droplets. The combination of the IonSpray effluent and the heated dry gas from
the turbo heaters is projected at a 90 degree angle to the ion path.
Figure 1-2 Parts of the Twin ESI Probe
Item
Description
1
Electrode adjustment nut (black collar) that adjusts the extension of the electrode tips
2
Retaining ring that fastens the probe to the probe tower on the ion source housing
3
Electrode tips through which sample or calibrant are sprayed into the sample inlet area of the
ion source
Twin APCI Probe
The twin APCI probe is 125 mm long. It contains two 100 µm (0.004 inch) inside diameter (i.d.) stainless steel
electrodes surrounded by a flow of nebulizer gas (Gas 1).
The sample supply is connected to the port labeled LC and the calibrant is connected to the port labeled Cal.
Analytes (samples or calibrants) are pumped through the sprayer, where they are nebulized in a ceramic tube
containing a heater. The inside wall of the ceramic tube can be maintained at a temperature range of 100 °C to
750 °C and is monitored by the sensor embedded in the heater. A high-velocity jet of nebulizer gas flows around
the electrode tip to disperse the sample as a mist of fine particles. The sample moves through the ceramic
vaporization heater into the reaction region of the ion source and then past the corona discharge needle where
the sample molecules are ionized as they pass through the ion source housing.
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Ion Source Overview
Figure 1-3 Parts of the Twin APCI Probe (TBD)
Item
Description
1
Electrode adjustment nut (black collar) that adjusts the extension of the electrode tips
2
Retaining ring that fastens the probe to the probe tower on the ion source housing
3
Electrode tips through which sample or calibrant are sprayed into the sample inlet area of the
ion source
Gas and Electrical Connections
Gas and low- and high-voltage electrical connections are provided through the front plate of the interface and
connect internally through the ion source housing. When the ion source is installed on the mass spectrometer, all
of the electrical and gas connections are complete.
Ion Source Sense Circuit
An ion source sense circuit disables the high-voltage power supply for the mass spectrometer and the source
exhaust system if:
• The ion source housing is not installed or is improperly installed.
• A probe is not installed.
• The mass spectrometer senses a gas fault.
• A turbo heater has failed.
• The ion source has over-heated.
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Ion Source Overview
Source Exhaust System
WARNING! Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Make
sure that the source exhaust system is connected and functioning, to safely
remove sample vapor exhaust from the laboratory environment. For
requirements for the source exhaust system, refer to the Site Planning Guide.
WARNING! Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Vent the
source exhaust system to either a dedicated laboratory fume hood or an
external ventilation system to prevent hazardous vapors from being released
into the laboratory environment.
WARNING! Fire Hazard. Do not direct more than 3 mL/min of flammable solvent
into the ion source. Exceeding the maximum flow rate can cause solvent to
accumulate in the ion source. Do not use the ion source if the source exhaust system
is not enabled and functioning when the ion source and the probe are properly
installed.
All of the ion sources produce both sample and solvent vapors. These vapors are a potential hazard to the laboratory
environment. The source exhaust system is designed to safely remove and allow for the appropriate handling of
the sample and solvent vapors. When the ion source is installed, the mass spectrometer does not operate unless
the source exhaust system is operating.
A vacuum switch mounted in the source exhaust circuit measures the vacuum in the source. If the vacuum in the
source rises above the set point while the probe is installed, then the system goes into an exhaust fault (Not Ready)
state.
An active exhaust system removes ion source exhaust (gases, solvent, sample vapor) through a drain port without
introducing chemical noise. The drain port connects through a drain chamber and a source exhaust pump to a
drain bottle, and from there to a customer-supplied exhaust ventilation system. For information about the ventilation
requirements for the source exhaust system, refer to the Site Planning Guide.
Contact Us
SCIEX Support
• sciex.com/contact-us
• sciex.com/request-support
Customer Training
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Ion Source Overview
• In North America: [email protected]
• In Europe: [email protected]
• Outside the EU and North America, visit sciex.com/education for contact information.
Online Learning Center
• training.sciex.com
Related Documentation
Documentation for the mass spectrometer can be found on the Customer Reference DVD for the mass
spectrometer.
Documentation for the ion source can be found on the Customer Reference DVD for the ion source.
Technical Support
SCIEX and its representatives maintain a staff of fully-trained service and technical specialists located throughout
the world. They can answer questions about the system or any technical issues that might arise. For more
information, visit the SCIEX Web site at sciex.com.
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Ion Source Installation
WARNING! Electrical Shock Hazard. Install the ion source on the mass spectrometer
as the last step in this procedure. High voltage is present when the ion source is
installed.
The ion source is connected to the vacuum interface and is held in position by two source latches. The interior of
the ion source is visible through the tempered glass window on the front of the ion source.
When the ion source is installed, the SCIEX OS recognizes the ion source and shows the ion source identification.
Required Materials
• Ion source
• Twin ESI probe
• (Optional) Twin APCI probe
• 1/4 inch wrench
• Ion source consumables kit
Prepare for Installation
WARNING! Puncture Hazard. Be careful when handling the electrode. The tips of
the electrodes are extremely sharp.
Tip! Do not discard the empty package. Use it to store the ion source when it is not in use.
• Adjust the electrode adjustment nut on the probe to move the electrodetips inside the electrode tube.
For optimum stability and performance, the electrode tip of the shortest electrode should extend between 0.5 mm
and 1.0 mm from the end of the probe. Refer to Adjust the Electrode Tip Extension on page 31.
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Ion Source Installation
Install the Probe
Prerequisite Procedures
• Remove the Ion Source on page 28
WARNING! Electrical Shock Hazard. Make sure that the ion source is completely
disconnected from the mass spectrometer before proceeding.
CAUTION: Potential System Damage. Do not let the protruding electrode tips or the corona
discharge needle touch any part of the ion source housing, to avoid damaging the probe.
CAUTION: Potential System Damage. Make sure that the corona discharge needle tip is
®
turned away from the aperture if the twin ESI or TurboIonSpray probe is in use.
The probe is not pre-installed in the ion source. Always remove the ion source from the mass spectrometer before
exchanging probes.
If the probe is not properly installed in the ion source, then the high-voltage power for the mass spectrometer and
source exhaust system is turned off.
1. Insert the probe into the tower. Align the hole on the probe with the corona discharge needle adjustment screw
at the top of the ion source. Refer to Ion Source Components on page 7.
2. Gently push down on the probe so that the contacts engage with those in the tower.
3. Turn the retaining ring over the probe, push it down to engage its threads with the threads on the tower, and
then tighten it until it is finger-tight.
4. For the twin APCI probe only, make sure that the corona discharge needle tip is pointed toward the curtain
plate aperture. Refer to Adjust the Position of the Corona Discharge Needle on page 23.
Connect the Ion Source Tubing
WARNING! Electrical Shock Hazard. Do not bypass the grounding union connection.
The grounding union provides grounding between the mass spectrometer and the
sample introduction device.
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Ion Source Installation
WARNING! Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Make
sure that the sample tubing nut is tightened properly before operating this
equipment, to prevent leakage.
Ion Source Components on page 7.
1. Insert a 30 cm piece of red PEEK tubing into the sample tubing nut.
2. Install the sample tubing nut in the LC port at the top of the probe, and then tighten the sample tubing nut
until it is finger-tight. Use a 1/4-inch wrench to tighten it one quarter turn further.
The twin probe has two ports. Be sure to use the port labeled LC.
3. Connect the other end of the tubing to the grounding union on the ion source.
4. Connect the calibrant tubing to the port labeled CAL.
Install the Ion Source on the Mass Spectrometer
WARNING! Electric Shock Hazard. Install the probe in the ion source before installing
the ion source on the mass spectrometer.
WARNING! Crushing Hazard. When installing the ion source, be careful not to pinch
fingers between the ion source and the vacuum interface.
If the ion source probe is not properly installed, then the high-voltage power supply is not available.
1. Make sure that the ion source latches on either side of the ion source are pointing up in the 12 o’clock position.
Refer to Ion Source Components on page 7.
2. Align the ion source with the vacuum interface, making sure that the latches on the ion source are aligned
with the sockets in the vacuum interface.
3. Push the ion source gently against the vacuum interface and then rotate the ion source latches down to lock
the ion source into place.
The mass spectrometer recognizes the ion source and then shows the ion source identification in the SCIEX
OS.
4. Connect the red PEEK tubing from the sample supply device to the grounding union on the ion source.
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Ion Source Installation
Sample Inlet Requirements
• Use appropriate analytical procedures and practices to minimize external dead volumes. The sample inlet
transfers the liquid sample to the ion source inlet without loss and with minimal dead volume.
• Prefilter samples so that the capillary tubing in the sample inlets is not blocked by particles, precipitated
samples, or salts.
• Make sure that all of the connections are tight enough to prevent leaks. Do not over-tighten.
Inspect for Leaks
WARNING! Toxic Chemical Hazard. Wear personal protective equipment, including
a laboratory coat, gloves, and safety glasses, to avoid skin or eye exposure.
Inspect fittings and tubing to make sure that there are no leaks.
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Ion Source Optimization
WARNING! Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Use the
ion source only if you have knowledge of and training in the proper use,
containment, and evacuation of toxic or injurious materials used with the
ion source.
WARNING! Fire Hazard. Do not direct more than 3 mL/min of flammable solvent
into the ion source. Exceeding the maximum flow rate can cause solvent to
accumulate in the ion source. Do not use the ion source if the source exhaust system
is not enabled and functioning when the ion source and the probe are properly
installed.
WARNING! Puncture Hazard, Radiation Hazard, Biohazard, or Toxic Chemical
Hazard. Discontinue use of the ion source if the ion source window is cracked
or broken and then contact a SCIEX Field Service Employee (FSE). Any toxic
or injurious materials introduced into the equipment will be present in the
source exhaust output. Dispose of sharps following established laboratory
safety procedures.
TM
Note: If the IonSpray voltage is too high, then a corona discharge can occur. It is visible as a blue glow at
the tip of the probe. A corona discharge results in decreased sensitivity and stability of the signal.
Optimize the ion source whenever the analyte, flow rate, or mobile phase composition changes.
Several parameters affect the performance of the source. Optimize the performance while injecting a known
compound and monitoring the signal of the known ion. Adjust the micrometer, gas, and voltage parameters to
maximize the signal-to-noise ratio and signal stability.
Sample Introduction
Method
The liquid sample stream is delivered to the ion source by an LC pump. The sample can be injected directly into
the mobile phase using flow injection analysis (FIA) or tee infusion, through a syringe pump (not supplied), or
through a separation column using a loop injector or autosampler.
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Ion Source Optimization
Flow Rate
Sample flow rates are determined by the LC system or syringe pump. The twin ESI probe supports flow rates from
5 µL/min to 3000 µL/min. The twin APCI probe supports flow rates from 50 µL/min to 3000 µL/min.
Twin ESI Probe Optimization
WARNING! Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Make
sure that the source exhaust system is connected and functioning and that
good general laboratory ventilation is provided. Adequate laboratory
ventilation is required to control solvent and sample emissions and to provide
for safe operation of the mass spectrometer.
WARNING! Fire Hazard. Do not direct more than 3 mL/min of flammable solvent
into the ion source. Exceeding the maximum flow rate can cause solvent to
accumulate in the ion source. Do not use the ion source if the source exhaust system
is not enabled and functioning when the ion source and the probe are properly
installed.
CAUTION: Potential System Damage. If the HPLC system connected to the mass spectrometer
is not controlled by the software, then do not leave the mass spectrometer unattended
while in operation. The HPLC system can flood the ion source when the mass spectrometer
goes into Standby mode.
Note: To keep the system clean and at its optimum performance, adjust the probe position when changing the
flow rate.
Tip! It is easier to optimize signal and signal-to-noise with flow injection analysis than with on-column injections.
Flow Rate and Temperature
The sample introduction flow rate and the sample solvent composition affect the optimal twin ESI probe temperature.
A higher flow rate or a higher aqueous content have a higher optimal temperature.
The twin ESI probe is often used with sample flow rates of 40 µL/min to 1000 µL/min. The heat is used to increase
the rate of evaporation which improves ionization efficiency, resulting in increased sensitivity. Extremely low flow
rates of high organic solvent usually do not require increased temperatures. Refer to Source Parameters and
Voltages on page 45.
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Ion Source Optimization
Set Up the System
1. Configure the LC pump to deliver the mobile phase at the required flow rate. Refer to Source Parameters and
Voltages on page 45.
2. Connect the grounding union on the ion source to an LC pump, through an injector equipped with a 5 µL loop,
or to an autosampler.
3. If an autosampler is being used, then configure the autosampler to perform multiple injections.
Prepare the System
1. Start the SCIEX OS software.
2. Open a previously optimized method or create a method based on the compounds.
3. If the ion source has been allowed to cool, then do the following.
a.
Set the Temperature parameter to 450.
b.
Let the ion source warm up for 30 minutes.
The 30-minute warm-up stage prevents solvent vapors from condensing in the cold probe.
4. Start the sample flow and sample injection.
Set the Starting Conditions
1. Type a starting value for Ion Source Gas 1.
For LC pumps, use a value between 40 and 60 for Gas 1.
2. Type a starting value for Ion Source Gas 2.
For LC pumps, use a value between 30 and 50 for Gas 2.
Note: Gas 2 is used with higher flow rates typical with an LC system and in conjunction with increased
temperature.
3. Type the appropriate value in the IonSpray Voltage field.
• Positive mode: 5500
• Negative mode: –4500
4. Type 25 in the Curtain Gas field.
5. Start acquisition.
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Ion Source Optimization
Optimize the Twin ESI Probe Position
WARNING! Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Make
sure that the electrodes protrude beyond the tip of the probe, to prevent
hazardous vapors from escaping from the source. The electrode must not be
recessed within the probe.
After the probe is optimized, it needs only minor adjustment. If the probe is removed, or if the analyte, flow rate,
or solvent composition change, then repeat the optimizing procedure.
1. Look through the window of the ion source housing to view the position of the probe.
2. Use the previous horizontal and vertical micrometer settings or set them to 5 as a starting position.
3. Monitor the signal or signal-to-noise of the analytes in the SCIEX OS.
4. Use the horizontal micrometer to adjust the probe position in small increments to achieve the best signal or
signal-to-noise ratio.
The probe can optimize slightly to either side of the aperture.
5. Use the vertical micrometer to adjust the probe position in small increments to achieve the best signal or
signal-to-noise ratio.
Note: The vertical position of the probe depends on flow rate. At lower flow rates, the probe should be
closer to the aperture. At higher flow rates, the probe should be farther from the aperture.
6. Use the black electrode adjustment cap on the probe to adjust the electrode tip protrusion. Refer to Adjust the
Electrode Tip Extension on page 31.
Note: Make sure that both electrodes protrude from the probe.
Tip! Direct the liquid spray from the twin ESI probe away from the aperture to prevent contamination of the
TM
aperture; to prevent piercing of the Curtain Gas flow, which can create an unstable signal; and to prevent
electrical shorting due to the presence of the liquid.
Optimize Source and Gas Parameters and Voltage
Optimize Ion Source Gas 1 (nebulizer gas) for best signal stability and sensitivity. Ion Source Gas 2 (heater gas)
aids in the evaporation of solvent, which helps to increase the ionization of the sample.
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Ion Source Optimization
Too high a temperature can cause premature vaporization of the solvent at the twin ESI probe tip, especially if
the probe protrudes too far, which results in signal instability and a high chemical background noise. Similarly, a
high heater gas flow can produce a noisy or unstable signal.
TM
Use the lowest IonSpray voltage possible without losing signal. Focus on signal-to-noise and not just signal. If
TM
the IonSpray voltage is too high, then a corona discharge can occur. The discharge is visible as a blue glow at
the tip of the twin ESI probe. This will result in decreased sensitivity and stability of the ion signal.
1. Adjust Ion Source Gas 1 and Ion Source Gas 2 in increments of 5 to achieve the best signal or
signal-to-noise ratio.
2. Increase the value in the Curtain Gas field until the signal begins to decrease.
Note: To prevent contamination, use the highest value for CUR possible without sacrificing sensitivity. Do
TM
not set CUR lower than 25. This helps to prevent penetration of the Curtain Gas flow, which can produce
a noisy signal; prevent contamination of the aperture; and increase the overall signal-to-noise ratio.
3. Adjust Ion Spray Voltage in increments of 500 V to maximize signal-to-noise.
Optimize the Turbo Heater Temperature
The optimal heater temperature is compound-dependent, flow rate-dependent, and mobile phase
composition-dependent. The higher the flow rate and the higher the aqueous composition, the higher the optimized
temperature.
When optimizing the source temperature, make sure that the ion source equilibrates to the new temperature
setting.
• Adjust the Temperature value in increments of 50 °C to 100 °C to achieve the best signal or signal-to-noise
ratio.
Twin APCI Probe Optimization
WARNING! Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Make
sure that the source exhaust system is connected and functioning and that
good general laboratory ventilation is provided. Adequate laboratory
ventilation is required to control solvent and sample emissions and to provide
for safe operation of the mass spectrometer.
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Ion Source Optimization
WARNING! Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Make
sure that the electrodes protrude beyond the tip of the probe, to prevent
hazardous vapors from escaping from the source. The electrode must not be
recessed within the probe.
CAUTION: Potential System Damage. If the HPLC system connected to the mass spectrometer
is not controlled by the software, then do not leave the mass spectrometer unattended
while in operation. The HPLC system can flood the ion source when the mass spectrometer
goes into Standby mode.
Refer to Twin APCI Probe Parameters on page 46 .
Tip! It is easier to optimize signal and signal-to-noise with flow injection analysis than with on-column injections.
Note: When using the APCI probe, make sure that the corona discharge needle is pointing toward the aperture.
Set Up the System
1. Configure the LC pump to deliver the mobile phase at the required flow rate. Refer to Source Parameters and
Voltages on page 45.
2. Connect the grounding union on the ion source to an LC pump, through an injector equipped with a 5 µL loop,
or to an autosampler.
3. If an autosampler is being used, then configure the autosampler to perform multiple injections.
Prepare the System
1. Start the SCIEX OS software.
2. Open a previously optimized method or create a method based on the compounds.
3. If the ion source has been allowed to cool, then do the following.
a.
Set the Temperature parameter to 450.
b.
Let the ion source warm up for 30 minutes.
The 30-minute warm-up stage prevents solvent vapors from condensing in the cold probe.
4. Start the sample flow and sample injection.
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Ion Source Optimization
Set the Starting Conditions
1. Type 30 in the Ion Source Gas 1 (GS1) field.
2. Type 1 in the Nebulizer Current (NC) field.
3. Start acquisition.
TM
Optimize Gas 1 and Curtain Gas
Flow
1. Adjust Ion Source Gas 1 in increments of five to achieve the best signal or signal-to-noise ratio.
2. Increase the Curtain Gas parameter until the signal starts to decrease.
Note: To prevent contamination, use the highest value for CUR possible without sacrificing sensitivity. Do
TM
not set CUR lower than 25. This helps to prevent penetration of the Curtain Gas flow, which can produce
a noisy signal; prevent contamination of the aperture; and increase the overall signal-to-noise ratio.
Adjust the Position of the Corona Discharge Needle
Required Materials
• Insulated flat-bladed screwdriver
WARNING! Electrical Shock Hazard. Follow this procedure to avoid contact with the
high voltages applied to the corona discharge needle, curtain plate, and turbo
heaters.
When using the twin APCI probe, make sure that the corona discharge needle is pointing toward the aperture.
1. Use an insulated flat-bladed screwdriver to rotate the corona discharge needle adjustment screw on the top
of the needle.
2. Look through the glass window to make sure that the needle is aligned with the tip facing the aperture.
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Ion Source Optimization
Optimize the Twin APCI Probe Position
WARNING! Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Make
sure that the electrodes protrude beyond the tip of the probe, to prevent
hazardous vapors from escaping from the source. The electrode must not be
recessed within the probe.
Make sure that the curtain plate aperture remains clear of solvent or solvent droplets at all times.
The position of the sprayer nozzle affects sensitivity and signal stability. Adjust probe position in small increments
only. At lower flow rates, position the probe closer to the aperture. For higher flow rates, position the probe farther
away from the aperture. After the probe is optimized, it needs only minor adjustment. If the probe is removed, or
if the analyte, flow rate, or solvent composition changes, then repeat the optimization procedure.
Figure 3-1 Sprayer Nozzle Position
Item
Description
1
Corona discharge needle
2
Curtain plate
3
Twin APCI probe
1. Use the previous horizontal and vertical micrometer settings or set them to 5 as a starting position.
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Ion Source Optimization
Note: To avoid reducing the performance of the mass spectrometer, do not spray directly into the aperture.
2. Monitor the signal or signal-to-noise of the analytes in the SCIEX OS.
3. Use the horizontal micrometer to adjust the probe in small increments to achieve the best signal or signal-to-noise
ratio.
Note: Adjust the horizontal micrometer until adequate sensitivity is achieved for both sample and calibrant
ions.
4. Use the vertical micrometer to adjust the probe in small increments to achieve the best signal or signal-to-noise
ratio.
5. Adjust the black electrode adjustment cap on the probe to move the electrode tube in or out of the probe.
Refer to Adjust the Electrode Tip Extension on page 31.
Note: Make sure that both electrodes protrude from the probe.
Optimize the Nebulizer Current
The ion source is controlled by current and not by voltage. Select the appropriate current for the acquisition method,
regardless of ion source selection position.
• Start with a Nebulizer Current value of 1 and then increase it to achieve the best signal or signal-to-noise
ratio.
The nebulizer current applied to the corona discharge needle usually optimizes between 1 µA and 5 µA in
positive mode. If no changes in signal are observed when the current is increased, then leave the current at
the lowest value that provides the best signal or signal-to-noise ratio.
Optimize the APCI Probe Temperature
The quantity and type of solvent affects the optimal APCI probe temperature. At higher flow rates, the optimal
temperature increases.
• Adjust the Temperature value in increments of 50 °C to 100 °C to achieve the best signal or signal-to-noise
ratio.
Optimization Tips
Optimization of the ion source minimizes the need for cleaning of the ion source and vacuum interface components.
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Ion Source Optimization
• Use the highest temperature possible when optimizing compounds. A temperature of 700 °C is common for
many compounds. High temperatures help keep the ion source clean and reduce background noise.
TM
• Use the highest Curtain Gas flow rate (CUR) possible without decreasing the signal. This helps to:
TM
• Prevent penetration of the Curtain Gas flow, which can produce a noisy signal.
• Prevent contamination of the aperture.
• Increase the overall signal-to-noise ratio.
• Direct the liquid spray from the probe away from the aperture to:
• Prevent contamination of the aperture.
TM
• Prevent piercing of the Curtain Gas flow, which can create an unstable signal.
• Prevent electrical shorting due to the presence of the liquid.
TM
• Use the lowest IonSpray voltage possible without losing signal. Focus on signal-to-noise and not just signal.
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Ion Source Maintenance
4
The following warnings apply to all of the maintenance procedures in this section.
WARNING! Hot Surface Hazard. Let the ion source cool for at least 30 minutes before
starting any maintenance procedures. Surfaces of the ion source and the vacuum
interface components become hot during operation.
WARNING! Fire and Toxic Chemical Hazard. Keep flammable liquids away
from flame and sparks and use them only in vented chemical fume hoods or
safety cabinets.
WARNING! Toxic Chemical Hazard. Wear personal protective equipment, including
a laboratory coat, gloves, and safety glasses, to avoid skin or eye exposure.
WARNING! Radiation Hazard, Biohazard, Electrical Shock Hazard, or Toxic
Chemical Hazard. In the event of a chemical spill, review product Safety Data
Sheets for specific instructions. Make sure that the system is in Standby mode
before cleaning a spill near the ion source. Use appropriate personal protective
equipment and absorbent wipes to contain the spill and dispose of it following
local regulations.
WARNING! Electrical Shock Hazard. Avoid contact with the high voltages applied
to the ion source during operation. Put the system in Standby mode before adjusting
the sample tubing or other equipment near the ion source.
WARNING! Puncture Hazard, Radiation Hazard, Biohazard, or Toxic Chemical
Hazard. Discontinue use of the ion source if the ion source window is cracked
or broken and then contact a SCIEX Field Service Employee (FSE). Any toxic
or injurious materials introduced into the equipment will be present in the
source exhaust output. Dispose of sharps following established laboratory
safety procedures.
This section contains general maintenance procedures for the ion source. To determine how often to clean the ion
source or perform preventive maintenance, consider the following:
• Compounds tested
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Ion Source Maintenance
• Cleanliness of the preparation methods
• Amount of time an idle probe contains a sample
• Overall system run time
These factors can cause changes in ion source performance, indicating that maintenance is required.
Make sure that the installed ion source is fully sealed to the mass spectrometer with no evidence of gas leaks.
Regularly inspect the ion source and its fittings for leaks. Clean the ion source components regularly to keep the
ion source in good working condition.
CAUTION: Potential System Damage. Use only the recommended cleaning methods and
materials to avoid damaging the equipment.
Required Materials
• 1/4 inch open-ended wrench
• Flat-bladed screwdriver
• MS-grade methanol
• HPLC-grade deionized water
• Safety glasses
• Breathing mask and filter
• Powder-free gloves (nitrile or neoprene is recommended)
• Lab coat
Remove the Ion Source
1. Stop any ongoing scans.
2. Turn off the sample stream.
3. In the SCIEX OS software, click Standby on the status panel.
4. Wait at least 30 minutes for the ion source to cool.
5. Disconnect the sample tubing from the grounding union.
6. Disconnect the calibrant tubing from the check valve.
7. Turn the two source latches upward to the 12 o'clock position to release the ion source.
8. Pull the ion source gently away from the vacuum interface.
9. Put the ion source on a clean, secure surface.
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Ion Source Maintenance
Note: Nitrogen continues to flow, at a rate of 9 L/min when the mass spectrometer is on.
The ion source can be removed quickly and easily, without tools. Always remove the ion source from the mass
spectrometer before performing any maintenance on the ion source or exchanging the probes.
Clean the Ion Source Surfaces
Prerequisite Procedures
• Remove the Ion Source on page 28
WARNING! Electrical Shock Hazard. Remove the ion source from the mass
spectrometer before starting this procedure. Follow all electrical safe work practices.
Clean the surfaces of the ion source after a spill or when they become dirty.
• Wipe the surfaces of the ion source with a soft, damp, cloth.
Clean the Probes
Flush the ion source periodically, regardless of the type of compounds sampled. Do this by setting up a method
in the SCIEX OS specifically for performing a flushing operation.
1. Change to a mobile phase that is 1:1 water:acetonitrile or 1:1 water:methanol.
2. Adjust the position of the probe so that it is as far from the orifice as possible.
3. In the SCIEX OS software, in the MS Methods workspace, do the following:
a.
Set Temperature between 500 and 600.
b.
Set Ion Source Gas 1 and Ion Source Gas 2 to at least 40.
c.
Set Curtain Gas to the highest setting possible.
d.
Wait until the Temperature setpoint is reached.
4. Make sure that the probe and sample tubing are flushed thoroughly.
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Ion Source Maintenance
Remove the Probe
Prerequisite Procedures
• Remove the Ion Source on page 28
WARNING! Electrical Shock Hazard. Remove the ion source from the mass
spectrometer before starting this procedure. Follow all electrical safe work practices.
CAUTION: Potential System Damage. Do not let the protruding electrode tips or the corona
discharge needle touch any part of the ion source housing, to avoid damaging the probe.
The probe can be removed quickly and easily, without tools. Always remove the ion source from the mass
spectrometer before changing probes or performing maintenance on the probe.
1. Loosen the sample tubing nut and then disconnect the sample tubing from the probe.
2. Loosen the calibrant tubing nut and then disconnect the calibrant tubing from the probe.
3. Loosen the retaining ring that secures the probe on the ion source housing.
4. Gently pull the probe straight up out of the tower.
5. Put the probe on a secure, clean surface.
Replace the Twin Electrodes
Prerequisite Procedures
• Remove the Ion Source on page 28
• Remove the Probe on page 30
WARNING! Electrical Shock Hazard. Remove the ion source from the mass
spectrometer before starting this procedure. Follow all electrical safe work practices.
WARNING! Puncture Hazard. Be careful when handling the electrode. The tips of
the electrodes are extremely sharp.
The probe contains twin electrodes. Replace the twin electrodes when there is a decrease in performance.
This procedure applies to both probes.
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Ion Source Maintenance
1. Remove the electrode adjustment nut and then remove the twin electrodes.
2. Install the twin electrodes inside the probe and then tighten the electrode adjustment nut.
3. Install the probe. Refer to Install the Probe on page 14.
4. Connect the sample tubing.
5. Connect the calibrant tubing.
6. Install the ion source on the mass spectrometer. Refer to Ion Source Installation on page 13.
7. Adjust the electrode tip extension. Refer to Adjust the Electrode Tip Extension on page 31.
Adjust the Electrode Tip Extension
WARNING! Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Make
sure that the electrodes protrude beyond the tip of the probe, to prevent
hazardous vapors from escaping from the source. The electrode must not be
recessed within the probe.
WARNING! Puncture Hazard. Be careful when handling the electrode. The tips of
the electrodes are extremely sharp.
Adjust the electrode tip extension for best performance. The optimal setting is compound-dependent. The distance
that the sample electrode tip protrudes affects the shape of the spray cone, and the shape of the spray cone affects
mass spectrometer sensitivity.
• Adjust the black electrode adjustment cap on the top of the probe to extend or retract the electrode tip. The
sample electrode tip should protrude at least 1.0 mm from the end of the probe.
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Ion Source Maintenance
Figure 4-1 Electrode Tip Extension Adjustment
Item
Description
1
Probe
2
Calibrant electrode
3
Sample electrode
Note: Make sure that both electrodes protrude from the probe.
Replace the Corona Discharge Needle
Prerequisite Procedures
• Remove the Ion Source on page 28
• Remove the Probe on page 30
WARNING! Electrical Shock Hazard. Remove the ion source from the mass
spectrometer before starting this procedure. Follow all electrical safe work practices.
WARNING! Puncture Hazard. Handle the needle with care. The tip of the needle is
extremely sharp.
The corona discharge needle tip might become so corroded that it must be cut off the needle. If this occurs, then
replace the entire corona discharge needle.
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Ion Source Maintenance
1. Rotate the ion source so the open side is accessible.
Figure 4-2 Corona Discharge Needle
Item
Description
1
Exhaust chimney
2
Ceramic sleeve
3
Corona discharge needle tip
2. While holding the corona discharge needle tip between the thumb and forefinger of one hand and the corona
discharge needle with the other hand, rotate the corona discharge needle tip counter-clockwise to loosen and
gently remove the tip.
3. Insert the new needle through the exhaust chimney into the ceramic sleeve as far as possible.
4. Holding a new tip between the thumb and forefinger of one hand and the corona discharge needle with the
other hand, rotate the corona discharge needle tip clockwise to install the tip.
5. Insert the probe and then install the ion source on the mass spectrometer. Refer to Ion Source Installation
on page 13.
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Ion Source Maintenance
Replace the Sample Tubing
Prerequisite Procedures
• Stop the sample flow and make sure that any remaining gas has been removed through the source exhaust
system.
• Remove the Ion Source on page 28.
WARNING! Electrical Shock Hazard. Remove the ion source from the mass
spectrometer before starting this procedure. Follow all electrical safe work practices.
Note: To replace the calibrant tubing, refer to the System User Guide.
Use the following procedure to replace the sample tubing if it has a blockage.
1. Disconnect the sample tubing from the probe and the grounding union.
2. Replace the sample tubing with the same length of tubing used previously.
3. Install the ion source. Refer to Ion Source Installation on page 13.
4. Start the sample flow.
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5
Troubleshooting
Symptom
Possible Cause
The SCIEX OS reports that the mass • The probe is not installed.
spectrometer has gone to a Fault
• The probe is not connected
state.
securely.
Corrective Action
• Install the probe. Refer to Install
the Probe on page 14.
• Reinstall the probe:
1. Remove the probe. Refer to
Remove the Probe on
page 30.
2. Install the probe, making sure
to tighten the retaining ring
securely. Refer to Install the
Probe on page 14.
The spray is not uniform.
The electrode is blocked.
Replace the electrode. Refer to
Replace the Twin Electrodes
on page 30.
Sensitivity is poor.
• The interface components (front • Clean the interface components
end) are dirty.
and then install the ion source.
• Solvent vapor or other unknown • Optimize the Curtain Gas™ flow.
compounds are present in the
Refer to Ion Source
analyzer region.
Optimization on page 17.
During testing, the ion source fails
to meet specifications.
Operator Guide
RUO-IDV-05-1828-A
• The shorter electrode is not
protruding from the probe.
• Adjust the electrode tip
extension. Refer to Adjust the
Electrode Tip Extension on page
31.
• The test solution was not
prepared correctly.
• Confirm that the test solutions
were prepared correctly.
• The mass spectrometer has not
passed the installation tests.
• If the problem cannot be
resolved, then contact the FSE to
perform the installation tests.
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Troubleshooting
Symptom
Possible Cause
Corrective Action
Background noise is high.
• The Temperature (TEM) is too
high.
• Optimize the temperature.
• Optimize heater gas flow.
• The heater gas flow rate (GS2) is
• Clean or replace the ion source
too high.
components, and then condition
• The ion source is contaminated.
the ion source and front end:
1. Move the probe to the
furthest position from the
aperture (vertically and
horizontally).
2. Make sure that the interface
heater is On.
3. Infuse or inject 50:50
methanol:water with a pump
flow of 1 mL/min.
4. In the SCIEX OS, set TEM to
650, GS1 to 60, and GS2 to
60.
5. Set the CUR flow to 45 or
50.
6. Run for a minimum of 2 hours
or preferably overnight for
best results.
Ion source performance has
degraded.
• The probe is not optimized.
• The sample was not prepared
correctly or the sample has
degraded.
• The sample inlet fittings are
leaking.
• Optimize the probe. Refer to
Twin ESI Probe
Optimization on page 18
or Twin APCI Probe
Optimization on page 21.
• Confirm that the sample was
prepared correctly.
• Verify that the fittings are tight
and replace the fittings if leaks
continue. Do not overtighten the
fittings.
• Install and optimize an alternate
ion source. If the issue persists,
then contact an FSE.
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Troubleshooting
Symptom
Possible Cause
Arcing or sparks occur.
The position of the corona discharge Turn the corona discharge needle
needle is incorrect.
toward the curtain plate, and away
from the stream of heater gas. Refer
to Adjust the Position of the
Corona Discharge Needle on
page 23.
Calibrant signal is low.
• The CDS is not connected.
• Check the CDS connections.
• The CDS tubing is blocked.
• Inspect the calibrant tubing for
blockages.
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Corrective Action
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Principles of Operation—Ion
Source
A
Electrospray Ionization Mode
The probe is located centrally between the two turbo heaters, which are placed at a 45-degree angle on either
TM
side of the probe. The combination of IonSpray effluent and the heated dry gas from the turbo heaters is projected
at a 90-degree angle to the aperture in the curtain plate.
Only compounds that ionize in the liquid solvent can be generated as gas phase ions in the source. The efficiency
and rate of ion generation depends on the solvation energies of the specific ions. Ions with lower solvation energies
are more likely to evaporate than ions with higher solvation energies.
TM
The interaction of the IonSpray voltage and the turbo heaters helps focus the stream and increases the rate of
droplet evaporation, resulting in an increased ion signal. The heated gas increases the efficiency of ion evaporation,
resulting in increased sensitivity and the ability to handle higher liquid sample flow rates.
TM
A high-velocity flow of nebulizer gas shears droplets from the liquid sample stream in the IonSpray inlet. Using
the variable high voltage applied to the sprayer, the ion source applies a net charge to each droplet. This charge
aids in the droplet dispersion. Ions of a single polarity are preferentially drawn into the droplets by the high voltage
as they are separated from the liquid stream. However, this separation is incomplete and each droplet contains
many ions of both polarities. Ions of one polarity are predominant in each droplet, and the difference between
the number of positively or negatively charged ions results in the net charge. Only the excess ions of the predominant
polarity are available for ion evaporation, and only a fraction of these actually evaporate.
The probe can generate multiply-charged ions from compounds that have multiple charge sites, such as peptides
and oligonucleotides. This is useful during analysis of high-molecular-weight species where the multiple charges
produce ions of a mass-to-charge (m/z) ratio within the mass range of the mass spectrometer. This allows routine
molecular-weight determinations of compounds in the kiloDalton (kDa) range.
As shown in Figure A-1, each charged droplet contains solvent and both positive and negative ions, but with
ions of one predominant polarity. As a conducting medium, excess charges reside at the surface of the droplet.
As the solvent evaporates, the electrical field at the surface of the droplet increases due to the decreasing radius
of the droplet.
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Principles of Operation—Ion Source
Figure A-1 Ion Evaporation
Item
Description
1
Droplet contains ions of both polarities with one polarity being predominant.
2
As the solvent evaporates, the electrical field increases and the ions move to the surface.
3
At some critical field value, ions are emitted from the droplets.
4
Nonvolatile residue remains as a dry particle.
If the droplet contains excess ions and enough solvent evaporates from the droplet, a critical field is reached at
which ions are emitted from the surface. Eventually, all of the solvent will evaporate from the droplet, leaving a
dry particle consisting of the nonvolatile components of the sample solution.
Because the solvation energies for most organic molecules are unknown, the sensitivities of any given organic ion
to ion evaporation are difficult to predict. The importance of solvation energy is evident because surfactants that
concentrate at the surface of a liquid can be detected very sensitively.
APCI Mode
The basis for past incompatibilities in linking liquid chromatography with mass spectrometry arose from difficulties
converting relatively involatile molecules in solution in a liquid into a molecular gas without inducing excessive
decomposition. The twin APCI probe process of gently nebulizing the sample into finely dispersed small droplets
in a heated ceramic tube results in the rapid vaporization of the sample so that the sample molecules are not
decomposed.
Figure A-2 shows the reaction flow of the APCI process for reactant positive ions (the proton hydrates,
+
H3O [H2O]n).
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Principles of Operation—Ion Source
Figure A-2 APCI Reaction Flow Diagram
+
+
+
+
The major primary ions N2 , O2 , H2O , and NO are formed by the electron impact of corona created electrons
+
on the major neutral components of air. Although NO is normally not a major constituent of clean air, the
concentration of this species in the source is enhanced due to neutral reactions initiated by the corona discharge.
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Principles of Operation—Ion Source
Samples that are introduced through the twin APCI probe are sprayed, with the aid of a nebulizer gas, into the
heated ceramic tube. Within the tube, the finely dispersed droplets of sample and solvent undergo a rapid
vaporization with minimal thermal decomposition. The gentle vaporization preserves the molecular identity of the
sample.
The gaseous sample and solvent molecules pass into the ion source housing where the ionization by APCI is
induced by a corona discharge needle connected to the end of the ceramic tube. The sample molecules are ionized
by colliding with the reagent ions created by the ionization of mobile phase solvent molecules. As shown in Figure
+
–
A-3, the vaporized solvent molecules ionize to produce the reagent ions [X+H] in the positive mode and [X-H]
in the negative mode. It is these reagent ions that produce stable sample ions when they collide with the sample
molecules.
Figure A-3 Atmospheric Pressure Chemical Ionization
Item
Description
1
Sample
2
Primary ions are created in the vicinity of the corona discharge needle
3
Ionization produces predominantly solvent ions
4
Reagent ions react with sample molecules forming clusters
5
Curtain plate
6
Interface
x = solvent molecules; M=sample molecules
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Principles of Operation—Ion Source
The sample molecules are ionized through a process of proton transfer in the positive mode and by either electron
transfer or proton transfer in the negative mode. The energy for the APCI ionization process is collision-dominated
because of the relatively high atmospheric pressure of the ion source.
For reverse phase applications, the reagent ions consist of protonated solvent molecules in the positive mode and
solvated oxygen ions in the negative mode. With favorable thermodynamics, the addition of modifiers changes
the reagent ion composition. For example, the addition of acetate buffers or modifiers can make the acetate ion
–
[CH3COO] the primary reagent in the negative mode. Ammonium modifiers may make protonated ammonia
+
[NH4] the primary reagent in the positive mode.
Through collisions, an equilibrium distribution of certain ions (for example, protonated water cluster ions) is
maintained. The likelihood of premature fragmentation of the sample ions in the ion source is reduced because
of the moderating influence of solvent clusters on the reagent ions and the relatively high gas pressure in the
source. As a result, the ionization process yields primarily molecular product ions for mass analysis in the mass
spectrometer.
APCI Ionization Region
Figure A-4 shows the general location of the ion-molecule reactor of the twin APCI probe. The slanted lines
indicate a wall-less reactor. A self-starting corona discharge ion current in the microampere range is created as a
+
result of the electric field between the discharge needle and the curtain plate. Primary ions, for example, N2 and
+
O2 , are created by the loss of electrons that originate in the plasma in the immediate vicinity of the discharge
needle tip. The energy of these electrons is moderated by a number of collisions with gas molecules before attaining
an energy where their effective ionization cross-section allows them to ionize neutral molecules efficiently.
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Principles of Operation—Ion Source
Figure A-4 APCI Ionization Region
Item
Description
1
Discharge needle tip
2
Sample flow
3
Wall-less reactor
4
Curtain plate aperture
5
Curtain Gas supply
6
Orifice
7
Orifice plate
8
Ceramic tube
TM
The primary ions, in turn, generate intermediate ions that lead to the formation of sample ions. Ions of the chosen
polarity drift under the influence of the electric field in the direction of the curtain plate and through the gas curtain
into the mass analyzer. The whole ion formation process is collision-dominated because of the relatively high
atmospheric pressure of the twin APCI probe. Except in the immediate vicinity of the discharge needle tip, where
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Principles of Operation—Ion Source
the strength of the electric field is greatest, the energy imparted to an ion by the electric field is small in comparison
with the thermal energy of the ion.
Through collisions, an equal distribution of certain ions (for example, protonated water cluster ions) is maintained.
Any excess energy that an ion may acquire in the ion-molecule reaction process is thermalized. Through collisional
stabilization, many of the product ions are fixed, even though many subsequent collisions occur. The formation
of both product ions and reactant ions is governed by equilibrium conditions at 760 torr (atmospheric) operating
pressure.
The twin APCI probe functions as a wall-less reactor because the ions that pass from the source to the vacuum
chamber and eventually to the detector never experience collisions with a wall—only collisions with other molecules.
Ions are also formed outside the designated ion source, but are not detected and are eventually neutralized by
interacting with a wall surface.
The temperature of the probe is an important factor for twin APCI probe operation. To preserve the molecular
identity, the temperature must be set high enough to ensure a rapid evaporation. At a sufficiently high operating
temperature, the droplets are vaporized quickly so that organic molecules are desorbed from the droplets with
minimal thermal degradation. If, however, the temperature is set too low, the evaporation process is slower and
pyrolysis, or decomposition, may occur before vaporization is complete. Operating the twin APCI probe at
temperatures above the optimal temperature may cause thermal decomposition of the sample.
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B
Source Parameters and Voltages
Twin ESI Probe Parameters
The following table shows the recommended operating conditions for the twin ESI probe at three different flow
TM
rates. For each flow rate, the Curtain Gas flow should be as high as possible. The solvent composition used for
optimization was 1:1 water:acetonitrile. These conditions represent a starting point from which to optimize the
probe. Using an iterative process, optimize the parameters using flow injection analysis to achieve the best signal
or signal-to-noise for the compound of interest.
Table B-1 Parameter Optimization for the Twin ESI Probe
Parameters
Typical Values
LC flow rate
5 µL/min to
50 µL/min
Gas 1 (nebulizer gas)
1000 µL/min
5 µL/min to 3000
µL/min
20 psi to 40 40 psi to 60 psi
psi
40 psi to 60 psi
0 psi to 90 psi
Gas 2 (heater gas)
0 psi
50 psi
50 psi
0 psi to 90 psi
IonSpray voltage
5500
5500 V
5500 V
5500 V
Curtain Gas supply
25 psi
25 psi
25 psi
25 psi to 50 psi
Temperature*
0 ºC to 200
ºC
200 ºC to 650 ºC
400 ºC to 750 ºC
Up to 750 ºC
Declustering Potential (DP) Positive: 70 Positive: 70 V
**
V
Negative –70 V
Negative –70
V
Positive: 70 V
Negative –70 V
Positive: 0 V to 400 V
Negative –400 V to 0
V
Probe vertical micrometer
setting
0 to 2
0 to 13
TM
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7 to 10
200 µL/min
Operational Range
2 to 5
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Source Parameters and Voltages
Table B-1 Parameter Optimization for the Twin ESI Probe (continued)
Parameters
Typical Values
Probe horizontal micrometer 4 to 6
setting
4 to 6
Operational Range
4 to 6
0 to 10
* Optimum temperature values depend on the compound and mobile phase composition (higher aqueous content
requires higher temperature). Zero (0) means no temperature is applied.
** DP values depends on the compound.
Twin APCI Probe Parameters
Table B-2 Parameter Optimization for the Twin APCI Probe
Parameter
Typical Value
Operational Range
LC flow rate
1000 µL/min
200 µL/min to 2000 µL/min
Gas 1 (nebulizer gas)
30 psi
0 psi to 90 psi
Curtain Gas supply
25 psi
25 psi to 50 psi
Temperature*
400 ºC
100 ºC to 750 ºC
Nebulizer Current (NC)
Positive: 3 µA
Positive: 0 mA to 5 µA
Negative: –3 µA
Negative: –5 mA to 0 µA
Positive: 60 V
Positive: 0 V to 300 V
Negative: –60 V
Negative: –300 V to 0 V
4
Scale 0 to 13
TM
Declustering Potential (DP)
Probe vertical micrometer setting
* Temperature value depends on the compound.
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Source Parameters and Voltages
Parameter Descriptions
Table B-3 Source-Dependent Parameters
Parameter
Description
®
Ion Source Gas 1
Controls the nebulizer gas for the twin ESI, twin APCI, TurboIonSpray , and APCI probes.
Refer to Principles of Operation—Ion Source on page 38.
Ion Source Gas 2
Controls the heater gas for the ESI probe. The best sensitivity is achieved when the
combination of temperature (TEM) and heater gas (GS2) flow rate causes the LC solvent
to reach a point at which it is nearly all vaporized. To optimize GS2, increase the flow to
obtain the best signal or signal-to-noise ratio if there is a significant increase in
background noise. Too high a gas flow can produce a noisy or unstable signal. Refer to
Principles of Operation—Ion Source on page 38.
Curtain Gas
Controls the flow of gas to the Curtain Gas interface. The Curtain Gas interface is
located between the curtain plate and the orifice. It prevents ambient air and solvent
droplets from entering and contaminating the ion optics, while permitting direction of
sample ions into the vacuum chamber by the electrical fields generated between the
vacuum interface and the spray needle. Contamination of the ion entrance optics reduces
Q0 transmission, stability, and sensitivity, and increases background noise.
TM
TM
Maintain the Curtain Gas flow as high as possible without losing sensitivity.
Temperature
Controls the heat applied to the sample to vaporize it. The optimal temperature is the
lowest temperature at which the sample is vaporized completely.
Optimize in increments of 50 °C.
Temperature - ESI
probe
Controls the temperature of the heater gas in the ESI probe.
The best sensitivity is achieved when the combination of temperature and heater gas(Ion
Source Gas 2) flow rate causes the LC solvent to reach a point at which it is nearly all
vaporized.
As the organic content of the solvent increases, the optimal probe temperature decreases.
With solvents consisting of 100% methanol or acetonitrile, the probe performance might
optimize as low as 300 °C. Aqueous solvents consisting of 100% water at flows of
approximately 1000 µL/min require a maximum probe temperature of 750 °C.
If the temperature is set too low, then vaporization is incomplete and large, and visible
droplets are expelled into the ion source housing.
If the temperature is set too high, then solvent might vaporize prematurely at the probe
tip, especially if the probe is set too low (5 mm to 13 mm).
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Source Parameters and Voltages
Table B-3 Source-Dependent Parameters (continued)
Parameter
Temperature - APCI
probe
Description
Controls the temperature of the APCI probe.
As the organic content of the solvent increases, the optimal probe temperature should
decrease. With solvents consisting of 100% methanol or acetonitrile the probe
performance might optimize at temperatures as low as 400 °C at flow rates of 1000
µL/min. Aqueous solvents consisting of 100% water set at flows of approximately 2000
µL/min require a minimum probe temperature of 700 °C.
If the temperature is set too low, then vaporization is incomplete and large, and visible
droplets are expelled into the ion source housing.
If the temperature is set too high, then thermal degradation of the sample occurs.
Nebulizer Current
Controls the current applied to the corona discharge needle in the APCI probe. The
discharge ionizes solvent molecules, which in turn ionize the sample molecules. For the
APCI probe the current applied to the corona discharge needle usually optimizes over a
broad range (about 1 µA to 5 µA in positive mode). To optimize, start at a value of 1 and
then increase to achieve the best signal or signal-to-noise ratio. If, when the current is
increased, no changes in signal are observed, then leave the current at the lowest setting
that provides the best sensitivity (for example, 2 µA).
IonSpray Voltage
Controls the voltage applied to the sprayer in the ESI probe, which ionizes the sample in
the ion source. The parameter value depends on the polarity, and affects the stability of
the spray and the sensitivity.
Interface Heater
This parameter is always on.
The ihe parameter turns the interface heater on and off. Heating the interface helps
maximize the ion signal and prevents contamination of the ion optics. Unless the
compound the user is analyzing is extremely fragile, we recommend that the user heats
the interface.
Probe Position
The position of the probe can affect the sensitivity of the analysis. Refer to Ion Source Optimization on
page 17 for more information on how to optimize the position of the probe.
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Source Parameters and Voltages
Solvent Composition
The standard concentration of ammonium formate or ammonium acetate is from 2 mmol/L to 10 mmol/L for
positive ions and 2 mmol/L to 50 mmol/L for negative ions. The concentration of organic acids is 0.1% to 0.5%
by volume for the twin ESI probe and 0.1% to 2.0% by volume for the twin APCI probe.
Commonly used solvents are:
• Acetonitrile
• Methanol
• Propanol
• Water
Commonly used modifiers are:
• Acetic acid
• Formic acid
• Ammonium formate
• Ammonium acetate
The following modifiers are not commonly used because they complicate the spectrum with their ion mixtures and
cluster combinations. They might also suppress the strength of the target compound ion signal:
• Triethyl amine (TEA)
• Sodium phosphate
• Trifluoroacetic acid (TFA)
• Sodium dodecyl sulfate
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C
Consumables and Spares
Table C-1 Consumables
PN
Description
016316
TUBE*1 16 OD X .005 BORE
016325
FITTING*PEEK 10 32 X 1 16 INCH
016485
Quantity
Details
cm
Red PEEK tubing (0.005-inch bore).
Refer to Replace the Sample Tubing on
page 34.
1
Brown PEEK fitting. Refer to Replace the
Sample Tubing on page 34.
TUBE* 1 16 OD-0.0025 INCH ID
PEEK
cm
Tan PEEK tubing (0.0025-inch bore).
Refer to Replace the Sample Tubing on
page 34.
019675
FITTING*TEE INSERT .25 BORE
1
Tee insert (0.25 mm bore)
5044626
ASSY* ESI TWIN ELECTRODE
1
Twin ESI probe electrode
5045380
ASSY* APCI TWIN ELECTRODE
1
Twin APCI probe electrode
Table C-2 Spares
PN
Description
Quantity
Details
027947
FRU*KIT NEB NEEDLE
1
Corona discharge needle. Refer to
Replace the Corona Discharge Needle
on page 32.
5041898
KIT* ESI TWIN SPRAYER PROBE
TESTED
1
Twin ESI probe assembly
5041899
KIT* APCI TWIN SPRAYER PROBE
TESTED
1
Twin APCI probe assembly
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Consumables and Spares
Figure C-1 Red PEEK Tubing
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Revision History
Revision
A
Description of Change
First release of document.
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Date
December 2015
Operator Guide
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