Nanospray Flex Series Ion Source User Guide Revision A

Nanospray Flex Series Ion Source User Guide Revision A
Nanospray Flex Series
Ion Source
User Guide
60053-97127 Revision A
March 2016
© 2016 Thermo Fisher Scientific Inc. All rights reserved.
DirectJunction, EASY-nLC, Endura MD, LCQ Deca XP MAX, Nanospray Flex, Nanospray Flex NG,
nanoViper, Q Exactive, and TSQ Quantum Ultra are trademarks; Unity is a registered service mark; and
Exactive, LTQ, Orbitrap, Orbitrap Fusion, Thermo Scientific, TSQ Endura, TSQ Quantiva, and Xcalibur are
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Release history: Rev A, March 2016
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Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
Accessing Documentation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Compatible Mass Spectrometers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Special Notices, Symbols, and Cautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi
Safety Precautions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xii
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xii
Thermo Scientific
Chapter 1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Advantages of Nanoelectrospray . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Offline Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Source Housing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Chapter 2
Assembling the LC Plumbing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
Choosing a One- or Two-Column Configuration . . . . . . . . . . . . . . . . . . . . . . . . 5
Choosing a Stainless Steel or Glass Emitter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Using the nanoViper Fitting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Configurations for a Stainless Steel Emitter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Configurations for a Glass Emitter and Liquid Junction . . . . . . . . . . . . . . . . . . . 9
Additional Resources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Chapter 3
Installing the Nanospray Flex Series Ion Source . . . . . . . . . . . . . . . . . . . . . . . . . .13
Attaching the Ion Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Installing the Cameras and Monitor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Optional Gas Connection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Attaching the DirectJunction Adapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Adjusting the Emitter Tip Position . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Adjusting the Video Picture. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Removing the Nanospray Flex Series Ion Source . . . . . . . . . . . . . . . . . . . . . . . . 20
Chapter 4
Configuring the Mass Spectrometer for NSI Mode . . . . . . . . . . . . . . . . . . . . . . . .21
Configuring the NSI Parameters for the Nanospray Flex NG Source . . . . . . . . 21
Configuring the NSI Parameters for the Nanospray Flex Source . . . . . . . . . . . . 22
Selecting the Source for the LCQ Deca XP Max Mass Spectrometer . . . . . . . . . 22
Chapter 5
Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25
Nanospray Flex Series Ion Source User Guide
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Contents
Chapter 6
Replaceable Parts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .29
Spare Parts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Consumables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Appendix A Contents of the Installation Kits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .31
Appendix B Mounting the UHPLC Liquid Junction Cross . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
Configuration Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Connecting the Plumbing to the UHPLC Liquid Junction Cross . . . . . . . . . . . 35
Mounting the UHPLC Liquid Junction Cross . . . . . . . . . . . . . . . . . . . . . . . . . 36
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F
Figures
Figure 1.
Figure 2.
Figure 3.
Figure 4.
Figure 5.
Figure 6.
Figure 7.
Figure 8.
Figure 9.
Figure 10.
Figure 11.
Figure 12.
Figure 13.
Figure 14.
Figure 15.
Figure 16.
Figure 17.
Figure 18.
Figure 19.
Figure 20.
Figure 21.
Figure 22.
Figure 23.
Figure 24.
Thermo Scientific
Nanospray Flex ion source mounted on a Thermo Scientific mass spectrometer . . 1
Nanospray Flex NG ion source (ES072) with the DirectJunction™ adapter
(ES256) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Nanospray Flex ion source (ES071) with the DirectJunction adapter (ES256) . . . 4
nanoViper fitting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Steps to configure an SS emitter and two columns for HPLC (max. 300 bar) . . . 8
Steps to configure a glass emitter and two columns for HPLC (max. 300 bar) . . . 9
Steps to configure a glass emitter and two columns for UHPLC (over 300
bar) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Examples of the mass spectrometer ion sweep cones . . . . . . . . . . . . . . . . . . . . . 14
Nanospray Flex NG locking levers (top view) . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Nanospray Flex locking levers (top view) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Nanospray Flex NG source housing connection . . . . . . . . . . . . . . . . . . . . . . . . 15
Hex socket-head screw to secure the top camera . . . . . . . . . . . . . . . . . . . . . . . . 16
Gas port on the bottom of the source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
DirectJunction adapter mounted on the XYZ-manipulator arm (Nanospray
Flex) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Diagram showing the 20-degree emitter angle . . . . . . . . . . . . . . . . . . . . . . . . . 18
DirectJunction HV connection (left side view) . . . . . . . . . . . . . . . . . . . . . . . . . 18
Adjustment knobs on the XYZ manipulator (front view) . . . . . . . . . . . . . . . . . 19
Two-column setup example (modified Column Out and Waste In lines and
an analytical column with an external emitter) . . . . . . . . . . . . . . . . . . . . . . . 34
UHPLC fused-silica union (cross section, P/N ES272) . . . . . . . . . . . . . . . . . . . 34
Column Out line and precolumn connected to the PEEK holder . . . . . . . . . . . 35
Using the tightening tool on a knurled nut . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Connections to the UHPLC liquid junction cross (two-column setup). . . . . . . 36
Protective cover (side view) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
UHPLC liquid junction cross with the bottom protective cover . . . . . . . . . . . . 37
Nanospray Flex Series Ion Source User Guide
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Figures
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P
Preface
The Nanospray Flex Series Ion Source User Guide provides installation and configuration
procedures for the Thermo Scientific™ Nanospray Flex™ Series ion sources.
Contents
• Accessing Documentation
• Compatible Mass Spectrometers
• Special Notices, Symbols, and Cautions
• Safety Precautions
• Contacting Us
 To suggest changes to the documentation
Complete a brief survey about this document by clicking the button below.
If you have a printed copy of this document, fill out a reader survey online at
www.surveymonkey.com/s/PQM6P62 or send an email message to the Technical
Publications Editor at [email protected]
Thank you in advance for your help.
Thermo Scientific
Nanospray Flex Series Ion Source User Guide
ix
Preface
Accessing Documentation
In addition to this guide, you can also access the Preinstallation Requirements Guide, Getting
Connected Guide, Getting Started Guide, and Hardware Manual for your specific Thermo
Scientific mass spectrometer (MS) as PDF files from the data system computer.
 To view the product manuals
From the Microsoft™ Windows™ taskbar, choose Start > All Programs > Thermo
Instruments and so on.
 To view user documentation from the Thermo Fisher Scientific website
1. Go to www.thermofisher.com.
2. Click the Services & Support tab.
3. On the right, click Manuals & Protocols.
4. In the Refine Your Search box, search by the product name.
5. From the results list, click the title to open the document in your web browser, save it, or
print it.
To return to the document list, click the browser Back button.
Compatible Mass Spectrometers
Use the Nanospray Flex Series ion source with the appropriate Thermo Scientific MS for
nanoelectrospray (commonly referred to as nanoES or nanospray™) analysis. Table 1 lists
several compatible MSs. For information about your specific instrument, refer to its manuals.
Table 1. Ion sources and compatible mass spectrometers
Ion source model
x
Thermo Scientific mass spectrometer
Nanospray Flex NG™
• Endura MD™
• Orbitrap Fusion™ Series
• TSQ Endura™ and TSQ Quantiva™
Nanospray Flex
•
•
•
•
•
Nanospray Flex Series Ion Source User Guide
Exactive™ and Q Exactive™
Orbitrap™ Series
LTQ™ Series
TSQ Quantum Ultra™
LCQ Deca XP Max™
Thermo Scientific
Preface
Special Notices, Symbols, and Cautions
Make sure you understand the special notices, symbols, and caution labels in this guide. Most
of the special notices and cautions appear in boxes; those pertaining to safety also have
corresponding symbols. For complete definitions, see Table 2.
Table 2. Notices, symbols, labels, and their meanings
Notice, symbol, or label
Meaning
IMPORTANT
Highlights information necessary to prevent damage to
software, loss of data, or invalid test results; or might contain
information that is critical for optimal performance of the
product.
Note
Highlights information of general interest.
Tip
Highlights helpful information that can make a task easier.
Caution: Read the cautionary information associated with this
task.
Chemical hazard: Observe Good Laboratory Practices (GLP)
when handling chemicals. Only work with volatile chemicals
under a fume or exhaust hood. Wear gloves and other protective
equipment, as appropriate, when handling toxic, carcinogenic,
mutagenic, corrosive, or irritant chemicals. Use approved
containers and proper procedures to dispose of waste oil and
when handling wetted parts of the instrument.
Hot surface: Allow any heated components to cool before
touching them.
Risk of electric shock: This instrument uses voltages that can
cause electric shock and personal injury. Before servicing the
instrument, shut it down and disconnect it from line power.
While operating the instrument, keep covers on.
Risk of eye injury: Eye injury can occur from splattered
chemicals, airborne particles, or sharp objects. Wear safety
glasses when handling chemicals or servicing the instrument.
Sharp object: Avoid handling the tip of the emitter.
Trip obstacle: Be aware of cords or other objects located on the
floor.
Thermo Scientific
Nanospray Flex Series Ion Source User Guide
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Preface
Safety Precautions
Observe the following safety precautions when you operate or perform service on the ion
source.
CAUTION Do not perform any servicing other than that contained in this manual. To
avoid personal injury or damage to the instrument, do not perform any servicing other
than that contained in this manual or related manuals unless you are qualified to do so.
CAUTION The Nanospray Flex Series ion source must connect to a certified Thermo
Scientific MS, which supplies high voltage capable of delivering a maximum of 8 kV and
100 μA. If you connect the source to another type of MS, you might impair the
protection provided by the equipment.
CAUTION Be aware of high voltage components. Before you touch a stainless steel
emitter or the liquid flowing through a glass emitter, depending on the plumbing
configuration, make sure that you place the MS in off mode.
CAUTION Avoid personal injury. Before you remove the emitter, make sure that you
depressurize the LC system. Otherwise, the emitter might eject at a high speed and cause
personal injury to you or a nearby person.
Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need. You
can use your smartphone to scan a QR code, which opens your email application or browser.
Contact us
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Nanospray Flex Series Ion Source User Guide
Customer Service and Sales
Technical Support
(U.S.) 1 (800) 532-4752
(U.S.) 1 (800) 532-4752
(U.S.) 1 (561) 688-8731
(U.S.) 1 (561) 688-8736
us.customer-support.analyze
@thermofisher.com
us.techsupport.analyze
@thermofisher.com
Thermo Scientific
Preface
Contact us
Customer Service and Sales
Technical Support
 To find global contact information or customize your request
1. Go to thermofisher.com.
2. Click Contact Us and then select the type of support you need.
3. At the prompt, type the product name.
4. Use the phone number or complete the online form.
 To find product support, knowledge bases, and resources
Go to thermofisher.com/us/en/home/technical-resources.
 To find product information
Go to thermofisher.com/us/en/home/brands/thermo-scientific.
Note To provide feedback for this document:
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• Complete a survey at surveymonkey.com/s/PQM6P62.
Thermo Scientific
Nanospray Flex Series Ion Source User Guide
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Preface
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1
Introduction
The Nanospray Flex Series ion source, shown in Figure 1, maintains excellent spray stability
to ensure efficient evaporation and ionization of the liquid samples—the key to achieving the
highest sensitivity at nano-flow rates.
Key benefits of the Nanospray Flex Series are as follows:
• Flexible, user-friendly design (that is, allows for custom column configurations)
• Single setup for all online and offline nanoflow applications
• Ability to interface with online nanoscale LC separation techniques
Contents
• Advantages of Nanoelectrospray
• Source Housing
• Offline Analysis
Figure 1.
Thermo Scientific
Nanospray Flex ion source mounted on a Thermo Scientific mass spectrometer
Nanospray Flex Series Ion Source User Guide
1
1
Introduction
Advantages of Nanoelectrospray
Advantages of Nanoelectrospray
The use of electrospray ionization (ESI) has evolved as a leading technique for generating
intact, gas-phase ions from thermally labile, polar analytes in solution. In this technique, an
emitter (a capillary tube or needle) induces ionization at a controlled distance from a counter
electrode. Direct current (dc) voltage is applied, either to the needle or to the solvent, to
produce a strong electrical field at the emitter tip. The electric field excites the ions in the
solution as they leave the emitter tip. This interaction results in electrohydrodynamic
disintegration of the fluid, generation of droplets, and formation of an aerosol jet.
Conventional ESI employs flow rates from 1 μL/min to 1 mL/min. Expediting desolvation
and droplet shrinkage often requires a drying gas, thermal heating, or both, due to the high
volume of liquid that exits the emitter. Nanospray ionization (NSI), also known as
nanoelectrospray ionization (nanoESI or NSI), is a form of ESI that employs low rates of 10–
1000 nL/min. NSI (or nanoESI) generally does not require a drying gas or thermal heating.
Compared with ESI, NSI tolerates a wider range of liquid compositions including pure water.
As you lower the flow rate, a lower volume of mobile phase passes through the emitter,
producing smaller aerosol droplets. This makes NSI more effective than conventional ESI at
concentrating the analyte at the emitter tip, producing significant increases in sensitivity as
demonstrated by the signal response of the MS.
Note The MS’s instrument control application uses the terms nanospray and NSI.
Offline Analysis
Through offline analysis, you can extract the maximum amount of information from very
limited amounts of sample. You can also average data extensively to improve the
signal-to-noise ratio and conditions optimized for MS/MS experiments. Using the optional
offline Nano ES ion source head (ES260), you can do the following:
• Work at low flow rates of 10–40 nL/min.
• Use nearly 100 percent of sample.
• Work effectively with sample volumes down to 300 nL.
• Avoid cross-contamination by using disposable emitters.
• Spray from purely aqueous and purely organic solvents.
The offline Nano ES ion source head, which can be ordered separately, includes the necessary
items for offline analysis.
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1
Introduction
Source Housing
Source Housing
The Nanospray Flex NG (Figure 2) or the Nanospray Flex (Figure 3) ion source is easy to
install on the appropriate MS (see Table 1 on page x). For installation instructions, see
Chapter 3.
The source housing includes two locking levers, an observation cylinder, a position-adjustable
column holder, and sliding rails for emitter retraction. Using the observation cylinder, you can
view the emitter tip while you move it into position. To enhance your view of the emitter,
follow the instructions in “Installing the Cameras and Monitor.”
Figure 2.
Nanospray Flex NG ion source (ES072) with the DirectJunction™ adapter (ES256)
Camera focusing
wheel
DirectJunction adapter
Locking lever
(locked position)
Thermo Scientific
Source bottom
Sliding rails to retract
the emitter
Nanospray Flex Series Ion Source User Guide
3
1
Introduction
Source Housing
Figure 3.
Nanospray Flex ion source (ES071) with the DirectJunction adapter (ES256)
Camera light button
DirectJunction
adapter
Locking lever
(locked position)
Source bottom
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Nanospray Flex Series Ion Source User Guide
Sliding rails to retract
the emitter
Thermo Scientific
2
Assembling the LC Plumbing
After you decide how many columns you need for your LC analysis and what type of emitter
to use, follow the applicable procedure in this chapter to assemble the plumbing for the
DirectJunction adapter.
Contents
• Choosing a One- or Two-Column Configuration
• Choosing a Stainless Steel or Glass Emitter
• Using the nanoViper Fitting
• Configurations for a Stainless Steel Emitter
• Configurations for a Glass Emitter and Liquid Junction
• Additional Resources
Choosing a One- or Two-Column Configuration
The Nanospray Flex Series installation kit includes the DirectJunction adapter, which
supports both one- and two-column configurations. The following table describes some of the
advantages for each configuration.
Configuration
One-column
Advantages
• Fewer connections, which minimize any potential peak broadening
that results from dead volumes.
• Enables MS analysis of compounds that elute during sample loading
(as they might not bind to the column material) because the fluid path
leads directly to the instrument.
Two-column
• Use of a shorter pre-analytical column (precolumn). This provides an
increased loading capacity and loading flow rate when compared to
loading sample directly onto the longer analytical column.
• The precolumn acts as a guard column by protecting the analytical
column from particulate matter.
Thermo Scientific
Nanospray Flex Series Ion Source User Guide
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2
Assembling the LC Plumbing
Choosing a Stainless Steel or Glass Emitter
Choosing a Stainless Steel or Glass Emitter
The mass spectrometer energizes the stainless steel (SS) emitter through the high-voltage
(HV) connection on the ion source’s DirectJunction adapter. When you use a glass emitter,
the plumbing configuration includes the Liquid Junction adapter, which energizes the liquid
flow that passes the HV electrode.
SS emitters are more robust than glass emitters and help maintain a stable spray for longer
periods of time.
Glass emitters can have very small openings. However, the very small opening at the emitter
tip often results in stability problems associated with blockage, which means that glass
emitters rarely last as long as the SS emitters.
Some consider glass emitters to be more bio-inert than SS emitters. This might reduce the risk
of nonspecific adsorption of biomolecules and lead to slightly improved sensitivity. However,
the degree of this adsorption, and thus the performance change, depends on the chemical
characteristics of the sample.
IMPORTANT For glass emitters, do the following:
• Place the Liquid Junction adapter on the high-pressure side of the column.
Electrochemical processes that occur at the electrode can otherwise create gas that
leads to spray instability.
• Use glass emitters with small ID emitter tips (less than 20 μm) to create back pressure
in the emitter and avoid outgassing and consequent spray instability.
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2
Assembling the LC Plumbing
Using the nanoViper Fitting
Using the nanoViper Fitting
For some LC instruments, the plumbing connections include several nanoViper™ fittings,
such as the one shown in Figure 4. Although these fittings can withstand
ultra-high-performance LC (UHPLC) backpressures up to ~1034 bar (~15 000 psi), they are
fingertight fittings, which require only very small torques to seal. Therefore, you must follow
the next procedure to avoid damage by overtightening.
Tip Refer to the packing for your nanoViper fittings to determine compatibility with
either the 1000 bar capillaries (beige tubing) or the 1200 bar capillaries (blue tubing).
Figure 4.
nanoViper fitting
PEEK sealing surface
Removable knurled tightening tool
Screw
 To use a nanoViper fitting
1. Insert the nanoViper fitting into the target port and slowly rotate the screw clockwise
until you feel resistance.
2. Using the black knurled fitting tool, tighten the screw clockwise to an angle of
0–45 degrees (1/8-turn).
3. Start operating the system at the desired working pressure and check the backpressure.
4. If the backpressure is too low, check the system for leaks.
For instructions, refer to the LC instrument’s documentation.
5. If the backpressure continues to be too low, return the system to atmospheric pressure.
IMPORTANT To extend the lifetime of the nanoViper fittings, open and close the
connections at only atmospheric system pressures. Opening and closing connections
at high system pressures can reduce the lifetime of the fittings.
6. Tighten the screw by as much as an additional 45 degrees. Do not turn the screw beyond
an angle of 90 degrees from where you felt the initial resistance.
IMPORTANT To prevent damage to the sealing surface of the nanoViper fitting, do
not overtighten the fitting.
Thermo Scientific
Nanospray Flex Series Ion Source User Guide
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2
Assembling the LC Plumbing
Configurations for a Stainless Steel Emitter
Configurations for a Stainless Steel Emitter
Figure 5 (HPLC) shows the recommended configuration of an SS emitter with two columns.
For a one-column configuration, start with Step 2. Make sure that the tubing, sleeves, and
unions are compatible and appropriate for the connection method and pressure range.
IMPORTANT Install the emitter last to avoid damaging its tip.
Figure 5.
Steps to configure an SS emitter and two columns for HPLC (max. 300 bar)
4
Connect the “Column Out” line to the
ZDV union (2-column setup) or to the
HPLC venting Tee (1-column setup).
1
2-column setup only—Insert one or both ends of the precolumn
into PEEK sleeves, and then insert a sleeved end into the ZDV
union and the other end into the HPLC venting Tee.
Note Make sure that the precolumn’s flow arrow points away
from the union.
5
3
Connect the LC “Waste In” line to the HPLC venting Tee.
Insert the venting Tee in the
multipurpose adapter.
2
Insert one or both ends of the analytical column into PEEK
sleeves, and then insert a sleeved end into the second ZDV
union and the other end into the venting Tee.
Note Make sure that the column’s flow arrow points away from
the venting Tee.
Mounting arm
6
Carefully insert the sleeved end of the SS emitter into the ZDV
union. The DirectJunction’s HV clamp holds the emitter.
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Nanospray Flex Series Ion Source User Guide
7
After installing the DirectJunction,
connect its cable to the source’s
bottom.
Thermo Scientific
2 Assembling the LC Plumbing
Configurations for a Glass Emitter and Liquid Junction
Configurations for a Glass Emitter and Liquid Junction
Figure 6 (HPLC) and Figure 7 (UHPLC) show the recommended configurations of a glass
emitter with two columns. For a one-column configuration, start with Step 2. Make sure that
the tubing, sleeves, and unions are compatible and appropriate for the connection method
and pressure range.
IMPORTANT Install the emitter last to avoid damaging its tip.
Figure 6.
Steps to configure a glass emitter and two columns for HPLC (max. 300 bar)
5
Connect the “Column Out” line to the
ZDV union (2-column setup) or the HPLC
venting Tee (1-column setup).
1
2-column setup only—Insert one or both ends of the precolumn
into PEEK sleeves, and then insert a sleeved end into the ZDV
union and the other end into the HPLC liquid junction cross.
Note Make sure that the precolumn’s flow arrow points away
from the union.
3
Connect the liquid junction HV
cable to the junction cross and
the source bottom.
4
Insert the liquid junction cross
in the multipurpose adapter.
6
Connect the LC “Waste In” line to the HPLC liquid junction
cross (ES257).
2
(Option 1 – shown) Insert one or both ends of the analytical
column into PEEK sleeves, and then insert a sleeved end into
the second ZDV union and the other end into the HPLC liquid
junction cross.
(Option 2) Instead of an analytical column, insert a
packed-glass emitter into the HPLC liquid junction cross and
slide the other end through a ZDV union.
Note Make sure that the column’s flow arrow points away from
the liquid junction cross.
Mounting arm
7
Carefully insert the sleeved end of the glass or packed-glass
emitter into the ZDV union. The DirectJunction’s HV clamp
holds the emitter.
Thermo Scientific
8
Do not connect the DirectJunction
cable.
Nanospray Flex Series Ion Source User Guide
9
2
Assembling the LC Plumbing
Configurations for a Glass Emitter and Liquid Junction
Figure 7.
Steps to configure a glass emitter and two columns for UHPLC (over 300 bar)
3
2
Connect the “Column Out” line to the
UHPLC union (2-column setup) or the
UHPLC liquid junction cross (1-column
setup).
2-column setup only—Insert a PEEK sleeve on the unattached
end of the precolumn, and then insert it into the UHPLC
fused-silica union.
Note Make sure that the precolumn’s flow arrow points away
from the union.
1
Assemble and mount the UHPLC
liquid junction cross (ES269); see
Appendix B. Connect the HV cable
to the source’s bottom.
4
(Option 1 – shown) Insert a PEEK sleeve on the unattached
end of the analytical column, and then insert it into a ZDV
union.
(Option 2) Instead of an analytical column, insert a
packed-glass emitter into the UHPLC liquid junction cross and
slide the other end through a ZDV union.
Note Make sure that the column’s flow arrow points away
from the venting Tee.
Mounting arm
5
Carefully insert the sleeved end of the glass or
packed-glass emitter into the ZDV union. The
DirectJunction’s HV clamp holds the emitter.
6
Do not connect the DirectJunction
cable.
IMPORTANT If the columns are less than 360 μm OD, sleeve the ends before inserting
them into the UHPLC liquid junction cross.
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2
Assembling the LC Plumbing
Additional Resources
Note
• Use small ID emitter tips (less than 20 μm) to prevent outgassing in the tip and
subsequent spray instability.
• The packed-glass emitter contains the stationary phase and has dual roles: as the
analytical column and the emitter. The packed-glass emitter is inserted through the
ZDV union, which only holds the emitter in place.
• To use a longer analytical column (greater than 20 cm), coil it between the venting
Tee and ZDV union.
Additional Resources
For general information about configuring Thermo Scientific nanoLC sources, log in (free) to
planetorbitrap.com, choose Library > Scientific Library > Keyword, and search for A1969.
For information about setting up the column assembly for the Thermo Scientific EASY-nLC™
Series instrument, refer to Chapter 5 in the EASY-nLC Series Getting Started Guide.
For information about modifying the EASY-nLC Series instrument before connecting it to
the UHPLC Liquid Junction adapter on the Nanospray Flex Series ion source, refer to
Chapter 4 in the EASY-nLC Series Troubleshooting and Maintenance Guide.
For other LC instruments, refer to their documentation.
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Nanospray Flex Series Ion Source User Guide
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2
Assembling the LC Plumbing
Additional Resources
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3
Installing the Nanospray Flex Series Ion Source
The only tools required to install the Nanospray Flex Series ion source are the hex keys
(provided).
Contents
• Attaching the Ion Source
• Installing the Cameras and Monitor
• Optional Gas Connection
• Attaching the DirectJunction Adapter
• Adjusting the Emitter Tip Position
• Adjusting the Video Picture
• Removing the Nanospray Flex Series Ion Source
Attaching the Ion Source
Follow these procedures to install the Nanospray Flex Series ion source.
CAUTION Before you touch a previously operating source or its components, allow the
system to cool for a minimum of 20 minutes.
 To prepare the mass spectrometer
1. If any other source is installed, remove it from the MS after it has cooled to room
temperature.
For instructions, refer to the instrument documentation.
2. If the ion sweep cone (Figure 8) is installed, remove it from the MS by grasping its outer
ridges and pulling it off.
The spray cone is directly behind the ion sweep cone (Figure 11).
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Nanospray Flex Series Ion Source User Guide
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3
Installing the Nanospray Flex Series Ion Source
Attaching the Ion Source
Figure 8.
Examples of the mass spectrometer ion sweep cones
Ion sweep cone for the Orbitrap Fusion Series MS
Ion sweep cone for the legacy MSs (shown is the
offset orifice type for ESI, H-ESI, and APCI)
 To attach the ion source on the mass spectrometer
1. Follow the procedure “To prepare the mass spectrometer.”
2. Depending on your source type, unlock the source’s locking levers as follows:
• For the Nanospray Flex NG source, rotate the locking levers until they are horizontal
(Figure 9).
Figure 9.
Nanospray Flex NG locking levers (top view)
Unlocked (horizontal) position
–or–
• For the Nanospray Flex source, rotate the locking levers toward the front of the
source (right lever in Figure 10).
Figure 10. Nanospray Flex locking levers (top view)
Locked position
Unlocked (forward) position
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3
Installing the Nanospray Flex Series Ion Source
Installing the Cameras and Monitor
3. Align the two guide pin holes on the back of the source with the guide pins on the front
of the MS (Figure 11).
Figure 11. Nanospray Flex NG source housing connection
MS spray cone
High voltage (HV)
input connector
Guide holes on the back
of the source
Guide pins on the MS ion source
mount assembly
4. Carefully press the source onto the MS, and then lock the locking levers.
Installing the Cameras and Monitor
Follow this procedure to install the cameras and monitor.
 To install the cameras and monitor
1. For the monitor, do the following:
• On the back, attach the BNC adapters to both Video IN ports.
• Connect its power supply between the monitor’s DC 12V IN socket and an electrical
outlet.
2. For the cameras, do the following:
a. Using the 1.5 mm hex key, loosen the hex socket-head screw near the camera
opening, and then insert the camera with its focusing wheel facing toward you
(Figure 12).
b. Using the 1.5 mm hex key, tighten the screw until it touches the camera—do not
overtighten it.
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Nanospray Flex Series Ion Source User Guide
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3
Installing the Nanospray Flex Series Ion Source
Optional Gas Connection
c. Connect the yellow video connector to a BNC adapter on the monitor.
d. Connect the black connector to its power supply, and then connect the power supply
to an electrical outlet.
Figure 12. Hex socket-head screw to secure the top camera
Securement screw
Camera focusing wheel
3. Place the monitor on top of the MS near the source, making sure that it is not too close to
the edge of the instrument.
CAUTION After completing these connections, route all cables and power cords so that
they are not a trip hazard.
Optional Gas Connection
To provide a controlled environment in the spray area, you can optionally connect clean, dry
nitrogen gas with a flow rate of 0–5 L/min to the 1/8 in. OD Swagelok™ fitting on the
bottom of the Nanospray Flex Series ion source.
Figure 13. Gas port on the bottom of the source
HV connector for the DirectJunction
adapter
Swagelok fitting for the gas
connection
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3
Installing the Nanospray Flex Series Ion Source
Attaching the DirectJunction Adapter
Attaching the DirectJunction Adapter
Follow this procedure to attach the DirectJunction adapter to the Nanospray Flex Series ion
source. You can attach the LC plumbing to the adapter before or after you connect the adapter
to the source’s manipulation arm.
 To attach the DirectJunction adapter to the ion source
1. Pull out the bottom of the source to fully expose the XYZ-manipulator arm (Figure 14).
2. Using the 3 mm hex key, loosely attach the DirectJunction adapter to the
XYZ-manipulator arm with the provided screw.
Note The longer screw provided with the DirectJunction is for the Nanospray
Flex NG source, which has a wider manipulator arm.
Figure 14. DirectJunction adapter mounted on the XYZ-manipulator arm (Nanospray Flex)
DirectJunction adapter
Bottom of the
source
Hex socket-head screw on the XYZ-manipulator arm
3. Attach the one- or two-column LC configuration to the adapter as shown in Figure 5,
Figure 6, or Figure 7.
IMPORTANT Avoid handling the emitter tip when you attach the LC plumbing.
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Nanospray Flex Series Ion Source User Guide
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3
Installing the Nanospray Flex Series Ion Source
Attaching the DirectJunction Adapter
4. Elevate the adapter’s free end approximately 20 degrees (Figure 15), and then firmly
tighten the screw.
Figure 15. Diagram showing the 20-degree emitter angle
Sample from
HPLC system
Inlet of MS
Emitter
0–20°
Optimal flow rate of
50–500 nL/min
A
Values for stainless steel or fused-silica emitters:
A = 3–5 mm and the potential on the emitter is 1500–2200 V
5. Attach the HV cable to the socket on the source’s bottom (Figure 16).
The DirectJunction cable (with an SS emitter) or the Liquid Junction cable (with a glass
or packed glass emitter) connects to the bottom of the source.
Figure 16. DirectJunction HV connection (left side view)
DirectJunction adapter
Source bottom
HV connector
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3
Installing the Nanospray Flex Series Ion Source
Adjusting the Emitter Tip Position
Adjusting the Emitter Tip Position
Follow this procedure to make any needed positional adjustments for the emitter tip.
 To adjust the emitter tip position
1. Using the XYZ-manipulator knobs (Figure 17), position the emitter tip almost on-axis
with the ion transfer tube.
2. As you make adjustments, observe the distance on the monitor. If necessary, follow the
procedure “To adjust the video picture.”
Figure 17. Adjustment knobs on the XYZ manipulator (front view)
(X axis) Horizontal emitter
adjustment
(Y axis) Vertical emitter
adjustment
(Z axis) Forward-backward
adjustment (toward or away from
the MS ion transfer tube)
Fine-adjustment for the Z axis
CAUTION Be aware of accessible high voltage components. Although the ion source
is shielded, you can easily access its head. Always make sure that the mass spectrometer is
in off mode before you touch the ion source head. Do not leave the source unattended
while the spray voltage is on.
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Nanospray Flex Series Ion Source User Guide
19
3
Installing the Nanospray Flex Series Ion Source
Adjusting the Video Picture
Adjusting the Video Picture
Follow this procedure to focus the video picture. For additional information, refer to the
manuals for the monitor and camera.
 To adjust the video picture
1. Turn on the monitor by pressing its POWER button.
2. If the picture is too dark, press the light button at the top of each camera.
3. If the picture is out of focus, adjust each camera’s focusing wheel, and then optionally
place the provided O-rings around each wheel.
4. To display the other camera input, press the SOURCE button.
The monitor displays the selected video input channel (AV1 or AV2) for a few seconds.
Removing the Nanospray Flex Series Ion Source
Follow this procedure if you must remove the ion source from the MS.
 To remove the ion source from the mass spectrometer
1. Turn off the LC liquid flow and instrument.
2. Disconnect the LC plumbing.
3. Disconnect the camera and monitor connections, including their power supplies.
4. After the system has cooled to room temperature, unlock the source’s locking levers.
5. Grasp the source housing with both hands and slowly pull it away from the MS.
The MS automatically switches to off mode after a few seconds.
You can store the source in its original shipping box after you remove the cameras. The
Nanospray Flex Series ion source does not require cleaning.
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Nanospray Flex Series Ion Source User Guide
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4
Configuring the Mass Spectrometer for NSI Mode
Follow the applicable procedure in this chapter to configure the Thermo Scientific MS for
nanoelectrospray ionization (nanoESI or NSI) mode.
IMPORTANT Before you begin NSI analysis, check that the source’s bottom is pushed
completely toward the instrument; otherwise, an error message appears.
Contents
• Configuring the NSI Parameters for the Nanospray Flex NG Source
• Configuring the NSI Parameters for the Nanospray Flex Source
• Selecting the Source for the LCQ Deca XP Max Mass Spectrometer
Configuring the NSI Parameters for the Nanospray Flex NG Source
After you complete the instrument configuration, use the Thermo Tune application to
configure the NSI source parameters. For additional information, refer to the Tune Help.
 To set the NSI source parameters in Tune
1. Open the Tune window from the Windows taskbar: choose Start > All Programs >
Thermo Instruments > model > model Tune.
2. Click Ion Source, and then click the Ion Source tab to view the Ion Source page.
The MS automatically detects and enters the source type (NSI) in the Ion Source Type
box.
3. In the Pos Ion Spray Voltage (V) box, enter 1900.
Use 1900 V as the start value for the spray voltage. If the intensity of the full-scan
spectrum is low, gradually increase the spray voltage to improve the spectrum. The
recommended range for the spray voltage is 1500–2200 V.
4. In the Sweep Gas (Arb) box, enter 0.
5. Click Apply.
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Nanospray Flex Series Ion Source User Guide
21
4 Configuring the Mass Spectrometer for NSI Mode
Configuring the NSI Parameters for the Nanospray Flex Source
Configuring the NSI Parameters for the Nanospray Flex Source
After you complete the instrument configuration, use the Thermo Tune Plus application to
configure the NSI source parameters. For additional information, refer to the Tune Plus Help.
 To set the NSI source parameters in Tune Plus
1. Open the Tune window from the Windows taskbar: choose Start > All Programs >
Thermo Instruments > model > model Tune Plus.
2. Choose Setup > NSI Source to open the NSI Source dialog box.
3. In the Spray Voltage (kV) box, enter 1.90.
Use 1.90 kV as the start value for the spray voltage. If the intensity of the full-scan
spectrum is low, gradually increase the spray voltage to improve the spectrum. The
recommended range for the spray voltage is 1.50–2.20 kV.
4. Click OK.
Selecting the Source for the LCQ Deca XP Max Mass Spectrometer
Note This section is for the LCQ Deca XP Max MS, which uses the Xcalibur™ data
system version 2.0.7 or earlier.
After you install the Nanospray Flex ion source, use the Instrument Configuration window to
configure the MS for NSI mode.
 To configure the mass spectrometer for NSI mode
1. On the Windows taskbar, choose Start > All Programs > Xcalibur > Instrument
Configuration to open the Instrument Configuration window.
2. Select the devices to control from the Xcalibur data system if they are not already selected:
a. In the Device Types list, select All.
b. Under Available Devices, double-click the icons for the mass spectrometer and
nanoelectrospray LC instrument to add them to the Configured Devices list.
3. Double-click the instrument icon to open the Model Configuration dialog box.
4. In the left pane, select Ion Source to display the ion source configuration page, and then
select Nanospray in the Default Source list.
5. Click OK, and then click OK again to close the message box.
6. Configure the LC device if you have not done so.
For instructions, refer to the LC instrument documentation.
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4 Configuring the Mass Spectrometer for NSI Mode
Selecting the Source for the LCQ Deca XP Max Mass Spectrometer
7. In the Instrument Configuration window, click Done.
8. Restart the data system computer and the mass spectrometer.
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Nanospray Flex Series Ion Source User Guide
23
4 Configuring the Mass Spectrometer for NSI Mode
Selecting the Source for the LCQ Deca XP Max Mass Spectrometer
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5
Troubleshooting
Table 3 lists common problems with the Nanospray Flex Series ion source, their causes, and
their possible solutions. If you need further troubleshooting assistance, contact your local
Thermo Fisher Scientific service engineer. See “Contacting Us.”
Contents
• Camera issues
• Signal issues
Table 3. Nanospray Flex Series ion source problems, causes, and possible solutions (Sheet 1 of 3)
Problem
Cause
Solution
One or both camera lights are
off.
Turn on one or both cameras by pressing their light
buttons (Figure 3).
There is a leak somewhere in
the liquid path.
Check all of the LC connections.
Camera issues
Camera issues:
The light is not on.
–or–
The video output is too
dark.
Signal issues
The signal intensity is
weak.
The parameters for the LC, MS, Try these solutions:
or both might need adjusting.
• Verify that the emitter is correctly positioned.
• Check the LC method and MS tune method
parameters.
• Run a known standard to check the sensitivity.
The MS’s spray cone and ion
transfer tube are dirty.
Thermo Scientific
Clean both the spray cone and ion transfer tube. For
instructions, refer to the instrument documentation.
Nanospray Flex Series Ion Source User Guide
25
5
Troubleshooting
Table 3. Nanospray Flex Series ion source problems, causes, and possible solutions (Sheet 2 of 3)
Problem
Cause
Solution
The spray is unstable.
–or–
There is no spray.
There is a leak somewhere in
the liquid path.
Check all of the LC connections.
Air bubbles in the emitter
might cause the spray to “spit.”
Try degassing the mobile phase or purging the line, and
then recheck the line for air bubbles.
There is an emitter blockage
from particles in the sample,
other small particles from the
flow lines or valves, and so on.
Try adjusting the spray voltage. If that does not resolve
the blockage problem, replace the emitter or column.
The cleaning solvent is not
LC/MS grade, which can
negatively affect the spray
stability.
Use an LC/MS-grade solvent to clean the emitter tip.
The emitter is out of alignment, Follow the procedure“To adjust the emitter tip position.”
which might occur if you
bumped the source or moved
the source from one MS to
another MS.
The HV connection to the
stainless steel emitter might be
loose or dirty.
26
Nanospray Flex Series Ion Source User Guide
After you place the MS in off mode, check the HV cable
connection on the DirectJunction adapter.
Thermo Scientific
5
Troubleshooting
Table 3. Nanospray Flex Series ion source problems, causes, and possible solutions (Sheet 3 of 3)
Problem
Cause
Solution
The spray is unstable.
–or–
There is no spray.
(continued)
The source’s HV connection
might be unstable.
Check the high voltage contact on the back of the source
(Figure 11) and the front of the MS.
If the problem continues for the Nanospray Flex NG
source, do the following:
1. Open Tune and view the Ion Source – Ion Source
page.
2. Compare the setting for the spray voltage to the
adjacent readback value.
A green box ( ) indicates that the parameter is
functioning properly.
If the problem continues for the Nanospray Flex source,
do the following:
1. Open Tune Plus, choose View > Display Status
View, and then click the All tab.
2. Choose Setup > NSI Source to open the NSI Source
dialog box.
3. Compare the setting in the dialog box to the
readback value for the NSI source’s absolute spray
voltage.
A green check mark (
) indicates
that the parameter is functioning properly.
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Nanospray Flex Series Ion Source User Guide
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28
Troubleshooting
Nanospray Flex Series Ion Source User Guide
Thermo Scientific
6
Replaceable Parts
To order any of these parts for the Nanospray Flex Series ion source, go to
www.proxeon.com/productrange/nano_ES_ion_sources or contact your local Thermo Fisher
Scientific service engineer.
Spare Parts
LCD monitor and power supply unit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ES217
Video camera and power supply unit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ES216
Conductive Emitter Configurations
DirectJunction adapter (includes ZDV union SC600) . . . . . . . . . . . . . . . . . . . . . . .
Liquid junction Tee 1/32. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Offline Nano ES ion source head . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Offline Nano ES Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
ES256
ES258
ES260
ES259
Nonconductive Emitter Configurations
HPLC liquid junction cross 1/32 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ES257
HPLC micro union kit 1/32, PEEK, red . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . G10-0035
UHPLC Liquid Junction Kit (360 μm OD tubing) . . . . . . . . . . . . . . . . . . . . . . . . ES269
Tightening tool. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-278 (IDEX™)
Tubing, column-out . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6041.5290
Tubing, waste-in . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6041.5289
UHPLC blind ferrule plugs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-116 (IDEX)
UHPLC cross, 360 μm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . UH-752 (IDEX)
UHPLC fused-silica union (use with ES269) . . . . . . . . . . . . . . . . . . . . . . . . . . . ES272
UHPLC microferrules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . PK-152 (IDEX)
Consumables
Emitters, SilicaTip™, uncoated . . . . . . . . . . . FS360-20-10-N-5-105CT (New Objective™)
For other consumables, visit www.proxeon.com/productrange/nano_ES_emitters,
www.fishersci.com, and www.unitylabservices.com.
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Nanospray Flex Series Ion Source User Guide
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6
Replaceable Parts
Consumables
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A
Contents of the Installation Kits
Table 4 lists the parts supplied in the Nanospray Flex NG Ion Source Kit (P/N ES072) and
the Nanospray Flex Ion Source Kit (P/N ES071), which are identical except for the source
housing. For a list of replaceable parts, see Chapter 6, “Replaceable Parts.”
Table 4. Contents of the Nanospray Flex Series ion source kits (Sheet 1 of 2)
Image
Part
Quantity
Part number
Provided in the Nanospray Flex NG Ion Source Kit (P/N ES072)
See Figure 2.
1
–a
1
–b
Dino-Lite™ digital video camera and
power supply (not shown)
2
ES216
LCD monitor, power supply
1
ES217
DirectJunction
1
ES256
UHPLC Liquid Junction Kitc
1
ES269
Emitter, stainless steel, 150 μm OD,
30 μm ID, 40 mm long (4 pieces)
1
ES542
Emitter sleeves, PEEK, 1/32 in. OD,
280 μm (10 pieces)
1
SC903
Nanospray Flex NG housing
Provided in the Nanospray Flex Ion Source Kit (P/N ES071)
See Figure 3.
Nanospray Flex housing
Provided in both ion source kits
–
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Nanospray Flex Series Ion Source User Guide
31
A
Contents of the Installation Kits
Table 4. Contents of the Nanospray Flex Series ion source kits (Sheet 2 of 2)
32
Image
Part
–
BNC adapters
–
Hex keys, 1.5 mm and 3 mm
–
Spare parts (blind plug, O-rings,
screws, sleeves)
Quantity
Part number
2
–
1 each
–
–
–
a
To order just the Nanospray Flex NG source housing, you must order the Nanospray Flex NG Ion Source Kit
(P/N ES072).
b
To order just the Nanospray Flex source housing, you must order the Nanospray Flex Ion Source Kit
(P/N ES071).
c
Older versions of the ES071 installation kit contained the Liquid Junction Cross 1/32 (P/N ES257) instead of
this UHPLC kit.
Nanospray Flex Series Ion Source User Guide
Thermo Scientific
B
Mounting the UHPLC Liquid Junction Cross
The UHPLC liquid junction cross, which is included in the UHPLC Liquid Junction Kit
(ES269), is for use with glass-emitter LC configurations. Using the tools and equipment listed
in Table 5, follow the procedures in this appendix to assemble and mount the cross onto the
DirectJunction adapter.
Table 5. Tools and equipment
Item
Part number
Gloves, lint-free and powder-free
Fisher Scientific™ 19-120-2947a
Unity Lab Services:
• 23827-0008 (size medium)
• 23827-0009 (size large)
a
Screwdriver, slotted, small
–
UHPLC Liquid Junction Kit, includes a tightening tool
ES269
Multiple sizes are available.
Contents
• Configuration Overview
• Connecting the Plumbing to the UHPLC Liquid Junction Cross
• Mounting the UHPLC Liquid Junction Cross
Thermo Scientific
Nanospray Flex Series Ion Source User Guide
33
B
Mounting the UHPLC Liquid Junction Cross
Configuration Overview
Configuration Overview
Figure 18 shows a two-column setup with modified Column Out and Waste In lines and an
analytical column with an external emitter. Both the precolumn and analytical column have
bare fused-silica ends. For a one-column configuration, exclude the precolumn and the
fused-silica union.
Figure 18. Two-column setup example (modified Column Out and Waste In lines and an analytical
column with an external emitter)
Column Out line
with bare fused-silica
tubing at one end
UHPLC fused-silica
union (ES272)
UHPLC liquid junction
assembly
Precolumn
PEEK union
PEEK sleeve for 360 μm OD
tubing
Waste In line with bare fused-silica
tubing at one end
The UHPLC fused-silica union (Figure 19) connects the Column Out line to the precolumn’s
inlet and is designed for a two-column configuration that includes nanoflow columns with
fused-silica ends. The ends of the externally threaded PEEK holder have different internal
depths. The internal stainless steel cartridge sits within the deeper end of the PEEK holder.
The microferrule ends are for use with sleeveless, 360 μm OD fused-silica tubing, which are
secured by the two internally threaded knurled nuts.
Figure 19. UHPLC fused-silica union (cross section, P/N ES272)
Microferrule fitting (IDEX™, PK-152)
Internally threaded knurled nut
Deeper end of the PEEK holder
Stainless steel cartridge (coned ports, 280 μm thru-hole)
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Nanospray Flex Series Ion Source User Guide
Thermo Scientific
B Mounting the UHPLC Liquid Junction Cross
Connecting the Plumbing to the UHPLC Liquid Junction Cross
Connecting the Plumbing to the UHPLC Liquid Junction Cross
Follow these procedures for a two-column configuration with the UHPLC liquid junction
cross. For a one-column configuration, exclude the precolumn and the fused-silica union.
CAUTION Wear protective gloves and safety glasses when handling the solvent lines. To
prevent contamination, wear lint-free and powder-free gloves.
 To assemble the UHPLC fused-silica union
1. Slip an internally threaded knurled nut and a microferrule onto both the Column Out
line and the inlet end of a precolumn.
2. Insert the stainless steel cartridge into the deeper end of the PEEK holder (Figure 19).
3. Insert both microferrules into the holder and hand-tighten the knurled nuts (Figure 20).
Figure 20. Column Out line and precolumn connected to the PEEK holder
Column Out line
4. Using the tightening tool, tighten both knurled nuts an additional 1/4–turn (Figure 21).
Figure 21. Using the tightening tool on a knurled nut
Tightening tool
PEEK holder
Knurled nuts
Thermo Scientific
Nanospray Flex Series Ion Source User Guide
35
B
Mounting the UHPLC Liquid Junction Cross
Mounting the UHPLC Liquid Junction Cross
 To assemble the UHPLC liquid junction cross
CAUTION Avoid contact with high voltage. Before you start, make sure that the
cable from the UHPLC liquid junction cross is disconnected.
1. Follow the procedure “To assemble the UHPLC fused-silica union.”
2. Remove the knurled nuts and the microferrules from the UHPLC liquid junction cross.
3. Use these nuts and ferrules to connect the precolumn, analytical column, and Waste In
lines to the UHPLC liquid junction cross as shown in Figure 22.
Figure 22. Connections to the UHPLC liquid junction cross (two-column setup)
Waste In line, as applicable
Analytical column
UHPLC liquid junction cross
(without protective cover)
HV cable
4. Using the tightening tool, tighten the three nuts an additional 1/4–turn.
Mounting the UHPLC Liquid Junction Cross
Follow this procedure to mount the assembled UHPLC liquid junction cross to the
DirectJunction adapter.
CAUTION Avoid contact with high voltage. The UHPLC liquid junction cross operates
at high voltage. Make sure that you securely mount the cross to the DirectJunction
adapter inside its two-piece protective cover.
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Nanospray Flex Series Ion Source User Guide
Thermo Scientific
B
Mounting the UHPLC Liquid Junction Cross
Mounting the UHPLC Liquid Junction Cross
 To mount the UHPLC liquid junction cross onto the DirectJunction
1. Using the slotted screwdriver, remove the screws from the top protective cover.
Figure 23 shows a side view of the two-piece protective cover.
Figure 23. Protective cover (side view)
Top piece
Disconnect before opening
Mounting hole (slides onto the
DirectJunction’s metal rod)
Compression screw
2. Place the bottom cover under the DirectJunction’s metal rod. If necessary, loosen the
compression screw to adjust the hole size, and then tighten the screw.
3. Place the UHPLC liquid junction cross into the bottom protective cover, and then attach
the top cover by using the slotted screwdriver.
Figure 24. UHPLC liquid junction cross with the bottom protective cover
Waste In line
Analytical column shown in front of the
DirectJunction metal rod (gray)
360µm
360
Precolumn (two-column setup) or
Column Out line (one-column setup)
360µm
360
Top cover
4. After you complete the plumbing connections, connect the HV cable to the source
bottom.
Thermo Scientific
Nanospray Flex Series Ion Source User Guide
37
B
Mounting the UHPLC Liquid Junction Cross
Mounting the UHPLC Liquid Junction Cross
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Nanospray Flex Series Ion Source User Guide
Thermo Scientific
I
Index
A
DirectJunction cable 18
troubleshooting 26
analysis, offline 2
C
cameras
adjusting the picture 20
focusing wheel 16
installing 15
troubleshooting 25
contacting us xii
D
directive, WEEE iii
DirectJunction adapter
column configuration 5
installing 17
DirectJunction, attaching 17
documentation, accessing x
E
emitter
setup angle and distance 18
tip position, adjusting 19
F
figures, list of vii
G
gas connection, optional 16
H
high voltage
caution statement 19
connector, source back 15
Thermo Scientific
I
ion sources
attaching to the MS 14
installation procedures 13
locking levers, positions 14
optional gas connection 16
removing 20
L
Liquid Junction Cross 1/32 32
M
mass spectrometer
ion sweep cone, types 14
NSI mode manually, LCQ Deca XP Max 22
preparing before installing the source 13
preparing for the source 13
spray cone attached to MS 15
monitor, installing 15
N
nanoViper fitting, using 7
NSI Mode, configuring the MS 21
O
offline analysis 2
R
replaceable parts 29
Nanospray Flex Series Ion Source User Guide
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Index: S
S
safety
high voltage 19
symbol descriptions xi
signal issues, troubleshooting 25
spray voltage, setting the value 22
symbols, meaning xi
T
Thermo Fisher Scientific website, user documents x
troubleshooting 25
Tune
application, opening 21
legacy application, opening 22
U
UHPLC fused-silica union, assembling 35
UHPLC liquid junction cross
assembling 36
mounting 37
V
viewing documents x
W
WEEE directive iii
X
XYZ manipulator control knobs 19
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Nanospray Flex Series Ion Source User Guide
Thermo Scientific
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