SCIEX NanoSpray Manual

NanoSpray®Ion Source
Operator Guide
May 2018RUO-IDV-05-0811-F

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1 Operational Precautions and Limitations...............................................................................................6
Operational Precautions and Hazards................................................................................................................................6
Chemical Precautions.........................................................................................................................................................7
System Safe Fluids.......................................................................................................................................................8
Laboratory Conditions........................................................................................................................................................9
Operating Conditions...................................................................................................................................................9
Performance Specifications..........................................................................................................................................9
Equipment Use and Modification.....................................................................................................................................10
Contact Us.......................................................................................................................................................................10
Related Documentation...................................................................................................................................................11
Technical Support............................................................................................................................................................11
Laser Safety Information..................................................................................................................................................11
Laser Classification....................................................................................................................................................11
Scheduled Maintenance.............................................................................................................................................12
Specifications.............................................................................................................................................................12
Labels on the Ion Source............................................................................................................................................12
2 Ion Source Overview..............................................................................................................................14
3 Ion Source Components.........................................................................................................................15
Camera and Illuminator...................................................................................................................................................16
Ion Source Head...............................................................................................................................................................18
X-Y-Z Positioning Unit.....................................................................................................................................................18
Positioning Rails..............................................................................................................................................................19
NanoSpray®Interface Components.................................................................................................................................20
OptiFlowTM Interface Components...................................................................................................................................20
Requirements...................................................................................................................................................................22
Gases.........................................................................................................................................................................22
Solvents.....................................................................................................................................................................22
4 NanoSpray®III Head Assembly and Installation..................................................................................23
Assemble the NanoSpray®III Head..................................................................................................................................24
Remove the NanoSpray®III Head....................................................................................................................................26
Prepare the Sprayer Fitting..............................................................................................................................................28
Insert the Emitter Tip.......................................................................................................................................................30
Install the NanoSpray III Head on the Bracket.................................................................................................................31
Connect the Sample Line.................................................................................................................................................32
Adjust the Illuminator and Camera..................................................................................................................................34
Adjust and Focus the Camera....................................................................................................................................34
Adjust the Illuminator................................................................................................................................................36
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Contents

Inspect for Leaks..............................................................................................................................................................40
5 Optimize the NanoSpray III Head.........................................................................................................42
6 Ion Source Maintenance........................................................................................................................44
Remove the Ion Source....................................................................................................................................................45
Install the Ion Source.......................................................................................................................................................46
Change Ion Sources.........................................................................................................................................................48
Change to a Different Ion Source (OptiFlowTM Interface Components)......................................................................49
Change to the NanoSpray®Ion Source (OptiFlowTM Interface
Components).............................................................................................................................................................49
Change to a Different Ion Source (NanoSpray®Interface Components)....................................................................49
Change to the NanoSpray®Ion Source (NanoSpray®Interface
Components).............................................................................................................................................................50
Change the Interface Components...................................................................................................................................50
Install the OptiFlowTM Interface Components............................................................................................................50
Remove the Interface Components............................................................................................................................52
Install the Interface Components...............................................................................................................................54
Remove the Monitor........................................................................................................................................................56
Remove the Monitor from the 4500, 5500, 6500, 6500+, and TripleTOF®
Systems......................................................................................................................................................................56
Remove the Monitor from the 3200 and 4000 Series Systems...................................................................................57
Install the Monitor...........................................................................................................................................................57
Install the Monitor 4500, 5500, 6500, 6500+, and TripleTOF®Systems.....................................................................57
Install the Monitor on 3200 and 4000 Series Systems...............................................................................................59
Connect the Monitor Cables............................................................................................................................................60
Bake the Interface............................................................................................................................................................61
Clean the Ion Source........................................................................................................................................................62
Clean the Nano Cell Heater Assembly..............................................................................................................................62
Required Materials ....................................................................................................................................................62
Tools and Supplies Available from the Manufacturer.................................................................................................63
Clean the Assembly....................................................................................................................................................64
7 Troubleshooting.....................................................................................................................................66
Mass Spectrometer Troubleshooting Tips........................................................................................................................66
Syringe Troubleshooting Tips...........................................................................................................................................67
External Pump Troubleshooting Tips................................................................................................................................67
NanoSpray®III Head Troubleshooting Tips......................................................................................................................68
Spray Plume Troubleshooting Tips...................................................................................................................................73
Monitor and Camera Troubleshooting Tips......................................................................................................................73
Emitter Tip Troubleshooting Tips.....................................................................................................................................74
Acquisition Troubleshooting Tips.....................................................................................................................................75
A Principles of Operation.........................................................................................................................78
B Tips for Working with the Ion Source..................................................................................................80
Cleaving an Emitter Tip....................................................................................................................................................80
NanoSpray®III Head........................................................................................................................................................80
Sample Solvent Composition.....................................................................................................................................80
Factors Affecting Optimization..................................................................................................................................80
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Contents

C Connecting the Syringe Using PEEK-lined Fused Silica Tubing..........................................................83
D Source Parameters and Voltages..........................................................................................................87
E Glossary of Symbols...............................................................................................................................88
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Contents

Note: Before operating the system, carefully read all of the sections of this guide.
This section contains general safety-related information. It also describes potential hazards and associated warnings
for the system and the precautions that should be taken to minimize the hazards.
In addition to this section, refer to Glossary of Symbols for information about the symbols and conventions used
in the laboratory environment, on the system, and in this documentation.
Operational Precautions and Hazards
For regulatory and safety information for the mass spectrometer, refer to the safety guide or System User Guide.
WARNING! Ionizing 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! Hot Surface Hazard. Let the NanoSpray®ion source cool for at
least 60 minutes before starting any maintenance procedures. Surfaces of
the ion source 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.
WARNING! Ionizing Radiation Hazard, Biohazard, or Toxic Chemical Hazard.
In the event of a chemical spill, review product Safety Data Sheets for specific
instructions. Use appropriate personal protective equipment and absorbent
wipes to contain the spill and dispose of it following local regulations.
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1
Operational Precautions and
Limitations

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.
Chemical Precautions
WARNING! Ionizing Radiation Hazard, Biohazard, or Toxic Chemical Hazard.
Determine whether decontamination is required prior to cleaning or
maintenance. The customer must decontaminate the system prior to cleaning
or maintenance if radioactive materials, biological agents, or toxic chemicals
have been used with the system.
WARNING! Environmental Hazard. Do not dispose of system components in municipal
waste. Follow local regulations when disposing of components.
WARNING! Biohazard, Toxic Chemical Hazard. Connect the drain tubing to
the mass spectrometer and the source exhaust drain bottle properly, to
prevent leaks.
•Determine which chemicals have been used in the system prior to service and regular maintenance. Refer to
the Safety Data Sheets for the health and safety precautions that must be followed with chemicals. SCIEX
Safety Data Sheets can be found at sciex.com/tech-regulatory.
•Always wear assigned personal protective equipment, including powder-free neoprene or nitrile gloves, safety
glasses, and a laboratory coat.
•Avoid ignition sources when working with flammable materials, such as isopropanol, methanol, and other
flammable solvents.
•Take care in the use and disposal of any chemicals. Potential risk of personal injury if proper procedures for
handling and disposing of chemicals are not followed.
•Avoid skin contact with chemicals during cleaning and wash hands after use.
•Make sure that all exhaust hoses are connected properly and that all connections are functioning as designed.
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Operational Precautions and Limitations

•Collect all spent liquids and dispose of them as hazardous waste.
•Comply with all of the local regulations for the storage, handling, and disposal of biohazardous, toxic, or
radioactive materials.
•(Recommended) Use secondary containment trays beneath the roughing pump, the solvent bottles, and the
waste collection container to capture potential chemical spills.
System Safe Fluids
The following fluids can safely be used with the system.
CAUTION: Potential System Damage. Do not use any other fluid until confirmation is
received from SCIEX that it does not present a hazard. This is not an exhaustive list.
•Organic Solvents
•MS-grade acetonitrile; up to 100%
•MS-grade methanol; up to 100%
•Isopropanol; up to 100%
•HPLC-grade or higher water; up to 100%
•Tetrahydrofuran; up to 100%
•Toluene and other aromatic solvents; up to 100%
•Hexanes; up to 100%
•Buffers
•Ammonium acetate; less than 1%
•Ammonium formate; less than 1%
•Phosphate; less than 1%
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Operational Precautions and Limitations

•Acids and Bases
•Formic acid; less than 1%
•Acetic acid; less than 1%
•Trifluoroacetic acid (TFA); less than 1%
•Heptafluorobutyric acid (HFBA); less than 1%
•Ammonia/ammonium hydroxide; less than 1%
•Phosphoric acid; less than 1%
•Trimethylamine; less than 1%
•Triethylamine; less than 1%
Laboratory Conditions
Operating Conditions
The system is designed to operate safely under these conditions:
•Indoors
•Altitude: Up to 2 000 m (6 560 feet) above sea level
•Ambient temperature: 5 °C (41 °F) to 40 °C (104 °F)
•Relative humidity: 80% for temperatures up to 31 °C (88 °F), decreasing lineraly to 50% at 40 °C (104 °F)
•Mains supply voltage fluctuations: ±10% of the nominal voltage
•Transient overvoltages: Up to the levels of Overvoltage Category II
•Temporary overvoltages on the mains supply
•Pollution degree: Pollution Degree 2
•External power supply rating: 90 VAC to 264 VAC, 47 Hz to 63 Hz, 1 A
Performance Specifications
The system is designed to meet specifications under these conditions:
•An ambient temperature of 15 °C to 30 °C (59 °F to 86 °F)
Over time, the temperature must remain within a range of 4 °C (7.2 °F), with the rate of the change in
temperature not exceeding 2°C (3.6°F) per hour. Ambient temperature fluctuations exceeding the limits might
result in mass shifts in spectra.
•Relative humidity from 20% to 80%, non-condensing
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Operational Precautions and Limitations

Equipment Use and Modification
WARNING! Personal Injury Hazard. Contact the SCIEX representative if product
installation, adjustment, or relocation is required.
WARNING! Electrical Shock Hazard. Do not remove the covers. Removing the
covers might cause injury or malfunctioning of the system. The covers need
not be removed for routine maintenance, inspection, or adjustment. Contact
a SCIEX Field Service Employee (FSE) for repairs that require the covers to be
removed.
WARNING! Personal Injury Hazard. Use SCIEX-recommended parts only. Use of parts
not recommended by SCIEX or use of parts for any purpose other than their intended
purpose can put the user at risk of harm or negatively impact system performance.
Use the mass spectrometer and ion source indoors in a laboratory that complies with the environmental conditions
recommended in the Site Planning Guide.
If the mass spectrometer and ion source are used in an environment or in a manner not prescribed by the
manufacturer, then the protection provided by the equipment might be impaired.
Unauthorized modification or operation of the mass spectrometer and ion source might cause personal injury and
equipment damage, and might void the warranty. Erroneous data might be generated if the mass spectrometer
and ion source is operated either above or below the recommended environmental conditions or operated with
unauthorized modifications. Contact an FSE for information on servicing the system.
Contact Us
SCIEX Support
•sciex.com/contact-us
•sciex.com/request-support
Customer Training
•In North America: [email protected]
•In Europe: [email protected]
•Outside the EU and North America, visit sciex.com/education for contact information.
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Operational Precautions and Limitations

Online Learning Center
•SCIEXUniversity
CyberSecurity
For the latest guidance on cybersecurity for SCIEX products, visit
sciex.com/Documents/brochures/win7-SecurityGuidance.pdf.
Related Documentation
To find software product documentation, refer to the release notes or software installation guide that comes with
the software. Documentation for the hardware products can be found on the Customer Reference DVD that
comes with the system or component.
For the latest versions of the documentation, visit the SCIEX website at sciex.com.
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 website at sciex.com.
Laser Safety Information
This section contains safety information for the laser used in the illuminator for the NanoSpray®III ion source.
Laser Classification
WARNING! Laser Hazard. Do not view the laser output with an optical instrument.
Class 3(R) lasers can cause acute injury to the eyes.
WARNING! Laser Hazard. Follow all local codes, regulations, standards and internal
requirements applicable to laser safety.
WARNING! Laser Hazard. Using equipment and controls or performing procedures
in a manner different from that documented in this manual might result in hazardous
laser radiation exposure.
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Operational Precautions and Limitations

The illuminator used in the ion source is a class 3(R) laser.
Scheduled Maintenance
The illuminator requires no maintenance. Its expected lifetime is 3000 hours (more than 3 years).
Tip! The laser is designed for continuous operation. However, we recommend that the laser be turned off when
not in use, to extend its lifetime.
Specifications
RangeSpecification
Laser Beam
Collimated 37 mm ± 3 mm
Focused distance
0.7 mm ± 0.1 mm x 2.5 mm ± 0.2 mmSpot size
< 0.7 mradDivergence
Output Parameters
655 nm, -10 nm, + 5 nmWavelength
0.25 nm/1 ºC (nominal)Wavelength stability
3.0 mW ± 0.15 mWOutput power
< 1% fluctuation over 60 minutesOutput power stability
(25ºC)
Labels on the Ion Source
In accordance with regulatory requirements, all laser warning labels displayed on the ion source are documented
in this guide. Warnings and labels on the ion source use international symbols.
LocationDefinitionExternal Labels
External. On the top cover.CAUTION: Visible and/or invisible laser
radiation. Avoid eye or skin exposure to
direct or scattered radiation.
External. On the top cover.Complies with 21 CFR 1040.10 and
1040.11 except for deviations pursuant to
Laser Notice No. 50, dated June 24, 2007
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Operational Precautions and Limitations

LocationDefinitionExternal Labels
External. On the top cover.Laser Aperture. Identifies the location of
the aperture through which the laser beam
emerges.
External. On the top cover.Laser Radiation: Avoid direct eye exposure.
Class 3R laser product. Max power: 5 mW;
Wavelength: 650 nm; IEC 60825-1
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Operational Precautions and Limitations

Electrospray ionization (ESI) is a soft ionization technique for mass spectrometry. Nano-flow ESI is particularly
useful when small amounts of valuable sample are available, or when high sensitivity is required.
The NanoSpray®ion source is ideally suited for the analysis of polar, thermally labile compounds by mass
spectrometry. It is an atmospheric pressure ionization (API) source that provides high ionization efficiency for the
transfer of analytes into gas phase ions.
The ion source is intended for continuous sample throughput. It typically uses an external nano LC pump with a
nano LC column for separation, although infusion can also be used. Samples travel along the nano LC column to
the ion source head and then through an open-ended emitter tip. The ion source has an X-Y-Z positioning unit
that can be used to position the emitter tip relative to the curtain plate. The ion source also has a camera that
sends an image to the monitor. The image facilitates the positioning of the emitter tip and observation of the
spray.
Refer to Principles of Operation.
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2
Ion Source Overview

Figure 3-1 Ion Source Components
DescriptionItem
Cover. Laser warning labels (not shown) are located on the top of this cover.1
Ion source interface2
Release pin3
Release latch4
Camera. Refer to Adjust and Focus the Camera.5
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3
Ion Source Components

DescriptionItem
X-Y-Z positioning unit6
Positioning rails7
Sleeve8
X-Y-Z adjustment knobs (micrometers)9
Bracket. The ion source head is installed on the bracket. Refer to NanoSpray®III Head
Assembly and Installation.
10
Protective end cap11
Illuminator. Refer to Adjust the Illuminator.12
Camera and Illuminator
The camera is mounted on a rod connected to the ion source. Use it to focus the image on the monitor and to
reposition the image of the emitter tip and curtain plate.
An illuminator provides light for observing the curtain plate aperture and the emitter tip.
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Ion Source Components

Figure 3-2 Camera and Illuminator
DescriptionItem
Illuminator1
Camera2
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Ion Source Components

Ion Source Head
The bracket holds the ion source head. Figure 3-3 shows the NanoSpray®III bracket, used with the NanoSpray®
III head. The ion source head holds the union that connects the fused silica or nano LC column to the emitter tip.
The mass spectrometer supplies high-voltage power to the ion source head and the union holder.
Figure 3-3 Ion Source and NanoSpray III Head
DescriptionItem
NanoSpray®III bracket1
NanoSpray®III head2
X-Y-Z Positioning Unit
After the X-Y-Z positioning unit, shown in Figure 3-4, is in place against the ion source interface, the position of
the emitter tip can be adjusted with the X-Y-Z axis adjustment knobs. The image shown on the monitor facilitates
the adjustment of the emitter tip position.
Note: The movement of the X-Y-Z positioning unit is limited by the cover. The unit cannot be moved to positions
at the limits of the micrometer range.
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Ion Source Components

Figure 3-4 Controls on the X-Y-Z Positioning Unit
DescriptionItem
Fine Z-axis adjustment knob (movement toward the curtain plate)1
Coarse Z-axis adjustment knob (movement toward the curtain plate)2
Y-axis adjustment knob (vertical movement)3
X-axis adjustment knob (horizontal movement)4
X-Y-Z positioning unit5
Positioning Rails
The ion source has two rails that support the X-Y-Z positioning unit. Move the X-Y-Z positioning unit along these
rails into and out of the operating position. Moving the X-Y-Z positioning unit away from the ion source interface
disconnects the high-voltage supply from the ion source head and allows the ion source head to be removed. The
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Ion Source Components

high-voltage power supply to the ion source head is disconnected until the X-Y-Z positioning unit is pushed
completely into its operating position.
NanoSpray®Interface Components
The ion source housing connects to the NanoSpray®interface components. Refer to Figure 3-5. The interface
components consist of the orifice plate and the curtain plate.
Note: The NanoSpray®interface components for the different mass spectrometers might be physically
interchangeable, but they have different aperture sizes. Be sure to install the correct interface for the mass
spectrometer.
Figure 3-5 NanoSpray®Interface Components
DescriptionItem
Curtain plate aperture1
Curtain plate2
OptiFlowTM Interface Components
The ion source housing connects to the OptiFlowTM interface components. Refer to Figure 3-6. The OptiFlowTM
interface components consist of the nano cell heater assembly and nano cell curtain plate.
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Ion Source Components