OptiMS Thermo MS Adapter
For Nanospray II, Nanospray Flex, and Nanospray Flex NG Ion
Sources
Installation Guide

RUO-IDV-05-3313-B | 5302405

December 2023

This document is provided to customers who have purchased SCIEX equipment to use in the operation ofsuch SCIEX equipment. This document is copyright protected and any reproduction of this document or
any part of this document is strictly prohibited, except as SCIEX may authorize in writing.
Software that may be described in this document is furnished under a license agreement. It is against thelaw to copy, modify, or distribute the software on any medium, except as specifically allowed in the license
agreement. Furthermore, the license agreement may prohibit the software from being disassembled,
reverse engineered, or decompiled for any purpose. Warranties are as stated therein.
Portions of this document may make reference to other manufacturers and/or their products, which may
contain parts whose names are registered as trademarks and/or function as trademarks of their respective
owners. Any such use is intended only to designate such products as those manufacturers' products anddoes not imply any right and/or license to use or permit others to use such manufacturers' and/or theirproduct names as trademarks.
SCIEX warranties are limited to those express warranties provided at the time of sale or license of its
products and are the sole and exclusive representations, warranties, and obligations of SCIEX. SCIEX
makes no other warranty of any kind whatsoever, expressed or implied, including without limitation,
warranties of merchantability or fitness for a particular purpose, whether arising from a statute orotherwise in law or from a course of dealing or usage of trade, all of which are expressly disclaimed,
and assumes no responsibility or contingent liability, including indirect or consequential damages, for any
use by the purchaser or for any adverse circumstances arising therefrom.
(GEN-IDV-09-10816-E)

For Research Use Only. Not for use in Diagnostic Procedures.
Trademarks and/or registered trademarks mentioned herein, including associated logos, are the propertyof AB Sciex Pte. Ltd., or their respective owners, in the United States and/or certain other countries (seesciex.com/trademarks).
AB Sciex™ is being used under license.
© 2023 DH Tech. Dev. Pte. Ltd.

EC Authorized
Person

AB Sciex Netherlands B.V.
1e Tochtweg 11,2913LN Nieuwerkerk aan den Ijssel
Netherlands

AB Sciex Pte. Ltd.
Blk33, #04-06 Marsiling Industrial Estate Road 3
Woodlands Central Industrial Estate, Singapore 739256

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
2/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Contents

1 Overview.................................................................................................................................... 5
Bill of Materials..........................................................................................................................5
Regulatory Compliance.............................................................................................................5International Standards........................................................................................................ 5
Decommissioning and Disposal................................................................................................ 6
Hazard Symbols........................................................................................................................6
Occupational Health and Safety Symbols............................................................................6
Symbols, Indicators, and Labels.......................................................................................... 7
Documentation Symbols and Conventions.......................................................................... 7
2 Install the Adapter.....................................................................................................................9
Install the Adapter (Nanospray Flex and Nanospray Flex NG)................................................. 9Connect the Cables............................................................................................................14
Install the Adapter (Nanospray II)........................................................................................... 18
Connect the Cables............................................................................................................24
3 Change the Mass Spectrometer Type................................................................................... 27
4 Align the System with the Mass Spectrometer.................................................................... 29
Align the System with the Mass Spectrometer (Nanospray II)................................................29
Align the System with the Mass Spectrometer (Nanospray Flex and Nanospray Flex NG)... 34
5 Prepare the Reagents............................................................................................................. 39
Prepare the 10% HAc Solution............................................................................................... 39
Prepare the 20% HAc Solution............................................................................................... 39
Prepare the 200 mM LE Buffer, pH 4.0................................................................................... 40
Prepare the Beta-Galactosidase Stock Solution..................................................................... 40
Prepare the Beta-Galactosidase Test Sample........................................................................ 41
Prepare the Peptide Test Sample........................................................................................... 41
6 Prepare the Buffer Trays........................................................................................................ 42
7 Prepare the System................................................................................................................ 43
Install the Cartridge................................................................................................................. 43
Remove and Install the Interface Plate.............................................................................. 48

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
3/83

Contents
Condition the Capillaries......................................................................................................... 50
Establish a Stable Spray.........................................................................................................52
Optimize the ESI Voltage........................................................................................................ 55
About Tune Files..................................................................................................................... 59
Fine-Tune the Position of the Sprayer Tip...............................................................................60
8 Do a Test Separation...............................................................................................................62
Create the Mass Spectrometer Method.................................................................................. 62
Create and Start a Sequence with the Xcalibur Software....................................................... 65
Manually Create the CESI-MS Separation Method.................................................................67
Create a Sequence in the 32 Karat Software..........................................................................69
Load the Sample.....................................................................................................................73
Start the Sequence in the 32 Karat Software..........................................................................74
Analyze the Data.....................................................................................................................75
9 Shut Down and Disconnect................................................................................................... 78
Remove the Cartridge.............................................................................................................78
Store the Cartridge..................................................................................................................82
Disconnect the CESI 8000 Plus System from the Mass Spectrometer...................................82

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
4/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Overview

1

Overview

This document includes instructions to install an adapter for the mass spectrometer, connect
the CESI 8000 Plus system to the mass spectrometer, and perform a a test separation to verify
correct system operation.
Note: For instructions about how to use the system safely, refer to the document: User Guide.

Bill of Materials
Part Number Description

Quantity

B10249Adapter

1

B83710Adapter mounting bracket

1

B83380High-voltage cable

1

B86096

OptiMS Thermo MS Adapter for NanoSpray II, NanoSpray
Flex, and NanoSpray Flex NG Ion Sources Installation Guide(this document)

1

B83383

Relay cable

1

B82395Thumbscrews

2

Regulatory ComplianceThis system complies with the regulations and standards listed in this section. For dated
references, refer to the declaration of conformity included with the system and the individual
system components. Applicable labels have been affixed to the system.

International Standards
The OptiMS Thermo MS Adapter for NanoSpray II, NanoSpray Flex, and NanoSpray Flex NG
Ion Sources has been evaluated as part of the CESI 8000 Plus High Performance SeparationESI Module and found to be in compliance with the International Electrotechnical Commission
standard IEC 61010-1, 2nd edition: 2010 Safety requirements for electrical equipment formeasurement, control, and laboratory use - Part 1: General requirements.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
5/83

Overview

Decommissioning and Disposal
WARNING! Environmental Hazard. Obey established procedures for disposalof biohazardous, toxic, radioactive, and electronic waste. The customer is
responsible for the disposal of hazardous substances, including chemicals,
waste oils, and electrical components, in accordance with local laws andregulations.
Before decommissioning, obey local regulations to decontaminate the entire system.
When the system is removed from service, obey national and local environmental regulations todivide and recycle different materials.
Note: SCIEX will not accept any system returns without a completed Decontamination Form.
Contact an FSE to get a copy of the form.
Do not discard system components or subassemblies, including computer parts, as unsorted
municipal waste.

Hazard Symbols
This section lists the hazard symbols and conventions used in the laboratory environment, on
the system, and in the documentation.

Occupational Health and Safety Symbols
This section describes some occupational health and safety symbols found in the documentationand laboratory environment.
Table 1-1 General Hazard Symbols
Safety Symbol

Description
Personal Injury Hazard

Table 1-2 Chemical Hazard Symbols
Safety Symbol

Definition
Biohazard

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
6/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Overview

Table 1-2 Chemical Hazard Symbols (continued)
Safety Symbol

Definition
Explosion Hazard

Toxic Chemical Hazard

Fire Hazard

Table 1-3 Electrical Hazard Warning Symbols
Safety Symbol

Definition
Electrical Shock Hazard

Table 1-4 Mechanical Hazard Symbols
Safety Symbol

Definition
Hot Surface Hazard

Symbols, Indicators, and Labels
Note: If any of the labels used to identify a component become detached, then contact a SCIEX
service representative.

Documentation Symbols and Conventions
The following symbols and conventions are used throughout the guide.
DANGER! Danger identifies an action that can cause severe injury or death.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
7/83

Overview

WARNING! Warning identifies an action that can cause personal injury if
precautions are not obeyed.
CAUTION: Caution identifies an operation that can cause damage to the system or
corruption or loss of data if precautions are not obeyed.
Note: Notes supply important information in a procedure or description.
Tip! Tips supply information that helps to apply the techniques in a procedure or gives ashortcut, but that is not essential to the completion of a procedure.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
8/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Install the Adapter

2

Install the Adapter
Install the Adapter (Nanospray Flex andNanospray Flex NG)

WARNING! Electrical Shock Hazard. Before the adapter is installed, make sure that
the ESI voltage is zero, the mass spectrometer is idle, and the separation voltage
from the CESI 8000 Plus system is off.
WARNING! Hot Surface Hazard. Beware of burns. The ion sweep cone becomes
hot during system operation. Do not touch the part until it has had sufficient time
to cool.
1.

Use the manufacturer's instructions to remove the ion sweep cone from the mass
spectrometer.

2.

Use the manufacturer's instructions to install the ion source on the mass spectrometer.

3.

Pull the ion source drawer fully out, away from the inlet on the mass spectrometer.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
9/83

Install the Adapter
Figure 2-1 Ion Source Drawer Components Without Mounting Bracket

Item

Description

1

Ion source2

Ion source drawer

3

XYZ manipulator

4

Mounting bracket

5

Thumbscrews

4.

If applicable, then remove the direct junction adapter from the mass spectrometer.

5.

Use the thumbscrews to attach the mounting bracket to the ion source.
The top of the arm on the mounting bracket should be parallel with the horizontal plane of
the XYZ manipulator.

6.

Use the alignment knobs on the XYZ manipulator to do an initial alignment:

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
10/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Install the Adapter
Figure 2-2 Alignment Knobs on the XYZ Manipulator

a.

Item

Description

A

Moves toward the inlet on the mass spectrometer (coarse)

B

Moves horizontallyC

Moves verticallyD

Moves toward the inlet on the mass spectrometer (fine)Use knob A to move the stage as far as possible away from the inlet on the mass
spectrometer. Make sure that the 0 marks are aligned.
Figure 2-3 Alignment of Rulers: Knob Ab.

Use knob B to align 14 on the moveable ruler with 0 on the static ruler.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
11/83

Install the Adapter
Figure 2-4 Alignment of Rulers: Knob B

c.

Use knob C to align 12 on the moveable ruler with 0 on the static ruler.
Figure 2-5 Alignment of Rulers: Knob Cd.

Use knob D to align 0 on the rotating ring with 5 on the static ruler.
Figure 2-6 Alignment of Rulers: Knob D

7.

Install the adapter in the mounting bracket until the adapter is tight against the bracket.
Make sure that the high-voltage cable hangs freely from the adapter. If required, then turnthe adapter.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
12/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Install the Adapter
Figure 2-7 Adapter and Mounting Bracket

Item

Description

1

Mounting bracket

2

Adapter

3

High-voltage cable

Figure 2-8 Adapter Installed in the Mounting Bracket

8.

Push the ion source drawer toward the inlet on the mass spectrometer.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
13/83

Install the Adapter

Connect the Cables
1.

Put the CESI 8000 Plus system approximately 18 cm to 20 cm (7.1 inches to 7.9 inches)away from the ion source.

2.

Connect the single connector on the end of the relay cable (Figure 2-10, item 4) to the relay
port on the CESI 8000 Plus system (labeled I/O in the following figure).
Figure 2-9 Relay Cable Connection

3.

Connect the other end of the relay cable (Figure 2-10, item 1) to the mass spectrometer.
Figure 2-10 Relay Cable

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
14/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Install the Adapter

Item1

Description
To Peripheral Control port on mass spectrometer
Connector for:• LCQ Deca XP MAX, LTQ-series, and Velos-series ion trap
• LTQ Orbitrap-series and Orbitrap Velos-series hybrid ion trap-Orbitrap

2

To leftmost ports of Input section of Peripheral Control area on mass
spectrometer (labeled Digital Start In)
Connector for:• Exactive-series Orbitrap• Q Exactive-series hybrid quadrupole-Orbitrap• TSQ Quantum-series and TSQ Vantage triple-stage quadrupole

3

Connects to Peripheral Control connector on mass spectrometer
Connector for:• Orbitrap Fusion Tribrid• TSQ Endura triple-stage quadrupole

4

To CESI 8000 Plus system

WARNING! Personal Injury Hazard. Route the relay cable where users cannot
trip on it.
4.

Connect the input cable between the ion source and the CESI 8000 Plus system.
a.

Connect the high-voltage input cable to the port on the ion source.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
15/83

Install the Adapter
Figure 2-11 High-Voltage Input Cable for the Adapter

Item

Description

1

Ion source port

2

High-voltage input cableb.

On the right side panel of the CESI 8000 Plus system, open the door to the high-voltage
connections panel (Figure 2-12).

c.

Connect the white high-voltage cable to the Input port on the connections panel, andthen turn the cable clockwise to lock it in position.

d.

Connect the red banana plug to the red port on the connections panel.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
16/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Install the Adapter
Figure 2-12 High-Voltage Connections Panel

Item

5.

Description

1

Input (red) port on connections panel

2

Red banana plug3

Output (black) port on connections panel

4Black banana plug

5

High-voltage input cable from mass spectrometer

6

High-voltage output cable to adapter

Connect the high-voltage output cable (attached to the adapter) to the CESI 8000 Plus
system.
a.

Connect the white high-voltage cable to the Output port on the connections panel, andthen turn the cable clockwise to lock it in position.

b.

Connect the black banana plug to the black port on the connections panel.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
17/83

Install the Adapter

Install the Adapter (Nanospray II)WARNING! Electrical Shock Hazard. Make sure that the mass spectrometeris idle, the ESI voltage is zero, and the separation voltage on the CESI 8000
Plus system is off.
WARNING! Hot Surface Hazard. Beware of burns. The ion sweep cone becomes
hot during system operation. Do not touch the part until it has had sufficient time
to cool.
1.

Make sure that the 1-inch adapter ring is not installed.
Figure 2-13 Adapter Ring

Item

Description

1

Socket head screws

2

Ion max adapter

3

1-inch (deep) adapter ring

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
18/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Install the Adapter
If necessary, then use the manufacturer's instructions to remove 1-inch adapter ring.
2.

Use the manufacturer's instructions to remove the ion sweep cone from the mass
spectrometer.
Figure 2-14 Ion Sweep Cone

Item
1

Description
Gas inlet

3.

Use the manufacturer's instructions to install the ion source on the mass spectrometer.

4.

Use the alignment knob to move the ion source stage as far away as possible from the inlet
on the mass spectrometer.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
19/83

Install the Adapter
Figure 2-15 Alignment Knob

CAUTION: Potential System Damage. Move the stage before the adapter is installedon the mass spectrometer. During the installation of the sprayer assembly, the glass
tip of the sprayer is exposed. If the ion source stage is too close to the inlet on themass spectrometer, then damage to the sprayer tip can occur.
5.

Install the adapter in the holder on the ion source.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
20/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Install the Adapter
Figure 2-16 Orientation of the Adapter Before Installation

Item

Description

1

High-voltage output cable2

Adapter3

Ion source

6.

If the ion source has a metal set screw on the right side of the holder, then replace the metal
set screw with the plastic thumbscrew supplied in the adapter kit.

7.

Make sure that the position of the adapter is tight, and then tighten the thumbscrew.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
21/83

Install the Adapter
Figure 2-17 Tighten the Thumbscrew

8.

Item

Description

1

Thumbscrew

2

Adapter installed in the ion source

Remove the protective sleeve from the sprayer tip.
Figure 2-18 Protective Sleeve and Sprayer Tip

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
22/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Install the Adapter

Note: Keep the protective sleeve for later use.
CAUTION: Potential System Damage. When the protective sleeve is removed, theprotective guard on the tip can retract. During the installation of the sprayer
assembly, if the ion source stage is too close to the inlet on the mass spectrometer,
then damage to the sprayer tip can occur.
9.

To install the sprayer assembly, carefully align the arrow with the Unlock position on theadapter. Do not let the sprayer tip touch any surfaces.

10. Turn the sprayer assembly counterclockwise to lock it in the adapter.
Figure 2-19 Lock the Sprayer Assembly in the Adapter

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
23/83

Install the Adapter

Item

Description

1

Sprayer assembly in the Unlock position

2

Sprayer assembly in the Lock position

Connect the Cables
WARNING! Electrical Shock Hazard. Make sure that the mass spectrometeris idle, the ESI voltage is zero, and the separation voltage on the CESI 8000
Plus system is off.
WARNING! Electrical Shock Hazard. Before turning on and operating the
CESI 8000 Plus system, make sure that the high-voltage input and output
cables are fully connected at both ends.
The high-voltage cables connect the mass spectrometer adapter to the power supply on the
CESI 8000 Plus system.
1.

To connect the input cable for the adapter to the input cable for the mass spectrometer,push the connectors together and then twist to lock them in position.
Figure 2-20 High-Voltage Input Cable-to-Cable Connection

2.

Put the CESI 8000 Plus system approximately 4 inches (10 cm) away from the ion sourcestage.

3.

On the right side of the CESI 8000 Plus system, open the access door to show the highvoltage connections panel.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
24/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Install the Adapter
Figure 2-21 High-Voltage Connections Panel

Item

4.

Description

1

Input (red) port on connections panel

2

Red banana plug3

Output (black) port on connections panel

4Black banana plug

5

High-voltage input cable from mass spectrometer to Input (red)6High-voltage output cable to adapter to Output (black)Connect the black banana plug to the black port on the connections panel.
Note: If the black banana plug is not installed, then EMI from the high-voltage cables canoccur.

5.

Connect the high-voltage output cable from the adapter to the Output port on theconnections panel, and then turn the cable 90 degrees clockwise to lock it in position.

6.

Connect the red banana plug to the red port on the connections panel.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
25/83

Install the Adapter

Note: If the red banana plug is not installed, then EMI from the high-voltage cables canoccur.
7.

Connect the high-voltage input cable from the mass spectrometer to the Input port on theconnections panel, and then turn the cable 90 degrees clockwise to lock it in position.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
26/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Change the Mass Spectrometer Type

Change the Mass Spectrometer Type 3
1.

Turn on power to the CESI 8000 Plus system.

2.

Click Start > CESI 8000 Software, and then click Change MS Type.
Figure 3-1 Change MS Type Option

3.

Make sure that the Connect to AB SCIEX MS check box is cleared.
Figure 3-2 Change MS Type Dialog

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
27/83

Change the Mass Spectrometer Type

Note: The IP address in the dialog should be the one that was preconfigured for the mass
spectrometer. Do not change the IP address unless it is known that the IP address is in
use by another network connection. If the IP address that shows needs to be changed, thencontact sciex.com/request-support.
4.

Click Change.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
28/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Align the System with the Mass Spectrometer

Align the System with the Mass
Spectrometer4

To prevent hydrodynamic (siphoning) flow in the capillaries and to let the coolant drain from the
cartridge before the cartridge assembly is removed, align the sprayer tip installed in the mass
spectrometer adapter with the height indicator on the CESI 8000 Plus system.

Align the System with the Mass Spectrometer(Nanospray II)
1.

If required, then use the alignment knob to move the ion source stage and adapter fully
away from the curtain gas plate. Make sure that the capillary will not touch the mass
spectrometer when the stage moves forward.
Figure 4-1 Nanospray II Alignment Knob

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
29/83

Align the System with the Mass Spectrometer

Item

Description

1

Alignment knob

2

Screw for the holder screw

3

Screw for the holder with the stage

4

Holder5

Screw that tightens the stage

6

Screw that tightens the stage

7

Thumbscrews for the faceplate

Note: The stage and stage holder become loose with use. Frequently tighten all of thescrews.
CAUTION: Potential System Damage. Move the stage before the adapter is installedon the mass spectrometer. During the installation of the sprayer assembly, the glass
tip of the sprayer is exposed. If the ion source stage is too close to the inlet on themass spectrometer, then damage to the sprayer tip can occur.
2.

Make sure that the CESI 8000 Plus system is approximately 4 inches (10 cm) away from theion source stage so that the coolant tubes can be extended fully.
Figure 4-2 System Near the Ion Source Stage

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
30/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Align the System with the Mass Spectrometer

Item

3.

Description

1

CESI 8000 Plus system

2

Ion source stage

3

Mobile cart

At the same time, align the sprayer tip with the height indicator on the CESI 8000 Plus
system and the center of the inlet on the mass spectrometer.
Figure 4-3 Alignment of the Sprayer Tip, Height Indicator, and Inlet on the Mass
Spectrometer

Item

4.

Description

1

Height indicator on the CESI 8000 Plus system

2

Sprayer tip

3

Inlet on the mass spectrometer

Use the Up and Down buttons on the front of the mobile cart to adjust the height of the cart
until the height indicator on the CESI 8000 Plus system aligns with the sprayer tip.
WARNING! Personal Injury Hazard. Remove consumables from the mobile cart
before the height is adjusted.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
31/83

Align the System with the Mass Spectrometer

Note: Do not press both the Up and Down buttons at the same time.
Figure 4-4 Buttons for Height Adjustment on the Mobile Cart

Item

Description

1

Up button

2

Down button

Note: If the cart cannot move to its lowest height or if it becomes locked in position, then the
cart must be programmed again. To set the home position for the mobile cart, refer to the
document: CESI 8000 Plus High Performance Separation-ESI Module User Guide.
5.

When the CESI 8000 Plus system is in visual alignment with the mass spectrometer, stepon the locking lever of each caster to lock each wheel of the mobile cart in position.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
32/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Align the System with the Mass Spectrometer
Figure 4-5 Lock the Wheels of the Mobile Cart

Note: When the alignment is correct, the tubing from the sprayer assembly will not havedips or pockets.
6.

Use the other adjustment knobs on the mass spectrometer to fine-tune the alignment of thesprayer tip with the center of the inlet on the mass spectrometer.
CAUTION: Potential System Damage. Keep the sprayer tip at least 2 mm away fromthe inlet on the mass spectrometer. If the sprayer tip is too close to the inlet, then theaccidental suction of rinse solution into the mass spectrometer can occur and cause
damage.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
33/83

Align the System with the Mass Spectrometer
Figure 4-6 Alignment Knobs on the Nanospray II Ion Source

Item

Description

1

Y-axis (movement up and down)

2

X-axis (movement toward and away from the inlet on the mass
spectrometer)

3Z-axis (movement side to side)4

Height indicator

Align the System with the Mass Spectrometer(Nanospray Flex and Nanospray Flex NG)
CAUTION: Potential System Damage. Before the adapter is installed and aligned, push
the ion source drawer fully toward the inlet on the mass spectrometer. If the sprayer is
too close to the inlet on the mass spectrometer, then damage can occur.
1.

Make sure that the CESI 8000 Plus system is approximately 18 cm to 20 cm (7.1 inches to
7.9 inches) away from the ion source so that the coolant tubes can be extended fully.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
34/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Align the System with the Mass Spectrometer2.

To adjust the height of the cart, press the buttons on the front of the cart until the indicatorline on the CESI 8000 Plus system is aligned with the inlet on the mass spectrometer.
WARNING! Personal Injury Hazard. Remove consumables from the mobile cart
before the height is adjusted.
Note: Do not press both the Up and Down buttons at the same time.
Figure 4-7 Alignment of the CESI 8000 Plus System and the Ion Source Inlet

Note: If the cart cannot move to its lowest height or if it becomes locked in position, then the
cart must be programmed again. To set the home position for the mobile cart, refer to the
document: CESI 8000 Plus High Performance Separation-ESI Module User Guide.
3.

When the CESI 8000 Plus system is in visual alignment with the mass spectrometer, stepon the locking lever of each caster to lock each wheel of the mobile cart in position.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
35/83

Align the System with the Mass Spectrometer
Figure 4-8 Lock the Wheels of the Mobile Cart

Note: When the alignment is correct, the tubing from the sprayer assembly will not havedips or pockets.
4.

Install the sprayer tip in the adapter.
CAUTION: Potential System Damage. Do not move the sprayer tip too close to theinlet on the mass spectrometer. If the sprayer tip is < 2 mm from the inlet, then theaccidental suction of rinse solution into the mass spectrometer can occur and cause
damage.
a.

Remove the protective sleeve from the sprayer tip.
Figure 4-9 Protective Sleeve and Sprayer Tipb.

While holding the body of the adapter to prevent it from moving towards the inlet, install
the sprayer in the adapter, aligning the arrow on the cartridge with the unlock positionon the adapter.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
36/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Align the System with the Mass Spectrometer
Figure 4-10 Sprayer Tip Approaching the Adapterc.

Push the sprayer into the adapter and turn it counterclockwise to lock it in position. The
triangle on the sprayer should line up with the lock icon on the adapter.
Figure 4-11 Sprayer in the Locked Position in the Adapter

5.

Put the sprayer tip in position relative to the ion source inlet.
CAUTION: Potential System Damage. Do not move the sprayer tip too close to theinlet on the mass spectrometer. If the sprayer tip is < 2 mm from the inlet, then theaccidental suction of rinse solution into the mass spectrometer can occur and cause
damage.
a.

While watching the position of the sprayer tip on the monitor, slowly turn knob A
clockwise to move the sprayer tip forward. Refer to the figure: Figure 2-2.

b.

Move the sprayer tip until it is approximately 2 mm to 4 mm away from the ion source
inlet.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
37/83

Align the System with the Mass Spectrometer
Figure 4-12 Sprayer Tip at the Ion Source Inlet

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
38/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Prepare the Reagents

Prepare the Reagents

5

The following reagents are used with the silica surface OptiMS cartridge. The sample typecontrols which reagents are required to do a separation.
Note: The examples in this guide use beta-galactosidase stock solution. For information about
how to prepare and use PepCalMix, refer to the document: CESI 8000 Plus High Performance
Separation-ESI Module User Guide.
Table 5-1 Required Reagents for the Silica Surface OptiMS Cartridge
Reagent

Purpose

10% Acetic acid (HAc)

Background electrolyte (BGE) and conductive
liquid

20% HAc

pH adjustment of leading electrolyte (LE)LE buffer, 200 mM ionic strength in ammonium Sample and system suitability preparation
acetate (AmAc), pH 4.0
Beta-galactosidase stock solution, 1 μM

Test sample(Optional) PepCalMix

Test sample

Peptide test sample

Optimize electrospray ionization (ESI) voltage

Prepare the 10% HAc Solution
Use this solution as the background electrolyte (BGE). Prepare new 10% HAc solution everyday.
1.

In a clean 20 mL glass vial, add 18 mL of CE Grade Water.

2.

Inside a fume hood, add 2 mL of HAc to the vial.

3.

Invert the vial three times to mix the contents.

4.

Keep the 10% HAc solution at room temperature.

5.

At the end of the day, discard the solution that was not used.

Prepare the 20% HAc Solution
Only prepare new 20% HAc solution when the 200 mM LE buffer, pH 4.0 is prepared.
1.

In a 100 mL glass bottle, add 80 mL of CE Grade Water.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
39/83

Prepare the Reagents
2.

Inside a fume hood, add 20 mL of HAc to the bottle.

3.

Invert the bottle three times to mix the contents.

4.

Attach a label with the name 20% HAc solution and the preparation date to the bottle.

5.

Keep the 20% HAc solution at room temperature.

6.

At the end of the day, discard the solution that was not used.

Prepare the 200 mM LE Buffer, pH 4.0
1.

To prepare 50 mL of 400 mM LE buffer, pH 4.0, do this:a.

In a 50 mL glass volumetric flask, add 20 mL of CE Grade Water.

b.

Inside a fume hood, add 2.7 mL of 7.5 M AmAc to the flask.

c.

To increase the volume to 50 mL, add CE Grade Water.

d.

Invert the flask three times to mix the contents.

2.

Pour the 50 mL of 400 mM AmAc solution into a 100 mL beaker.

3.

Use a calibrated pH meter to measure the initial pH of the solution.

4.

Add aliquots of newly prepared 20% HAc solution until the pH of the solution is 4.0.

5.

Transfer the solution to a 100 mL volumetric flask.

6.

To increase the volume to 100 mL, add CE Grade Water.

7.

Invert the flask three times to mix the contents.

8.

Attach a label with the name 200 mM LE buffer, pH 4.0 and the preparation date to
the flask.

9.

When it is not in use, keep the buffer at 2 °C to 8 °C for as long as 2 years after preparation.

Prepare the Beta-Galactosidase Stock Solution
WARNING! Toxic Chemical Hazard. When handling, storing, and disposing ofchemicals, refer to the chemical product safety data sheets. Obey all of therecommended safety procedures . For health and safety precautions, refer to the
document: Overview Guide.
1.

Add 625 µL of CE Grade Water to the vial with beta-galactosidase stock solution.

2.

Mix the solution in a vortex mixer for at least 30 seconds.

3.

Use a centrifuge to spin the vial and move the liquid to the bottom.

4.

Divide the beta-galactosidase stock solution into aliquots of 50 µL.

5.

Keep the beta-galactosidase stock solution at –35 °C to –15 °C for as long as 1 year.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
40/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Prepare the Reagents

Prepare the Beta-Galactosidase Test Sample
1.

If required, then remove 50 µL of beta-galactosidase stock solution from the freezer and let
it thaw at room temperature.

2.

In a 0.5 mL centrifuge tube, add 50 µL of beta-galactosidase stock solution and 50 µL of
1 μM 200 mM LE buffer, pH 4.0 to make a 1:1 solution.

3.

Mix the solution in a vortex mixer for at least 30 seconds.

4.

To remove any precipitant, use a centrifuge to spin the solution at 12,000 g for 5 minutes.

5.

Use a pipette to put 90 µL of the supernatant in a sample vial.
Keep the sample at 2 °C to 8 °C for as many as 3 days.

Prepare the Peptide Test Sample
1.

In a centrifuge tube, add 100 μL of BGE.

2.

Add 5 μL of a peptide marker, such as pI 9.5.

3.

Put the cap on the tube.

4.

Mix the solution in a vortex mixer for 3 seconds.

5.

Keep the sample at 2 °C to 8 °C.

6.

At the end of the day, discard the solution that was not used.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
41/83

Prepare the Buffer Trays

6

Prepare the Buffer Trays
1.

Use the following table to prepare the required reagents.
Table 6-1 Required Reagents2.

Content

Quantity

VolumeBGE (such as 10% HAc solution or 50 mM AmAc
buffer, pH 3.0)

3 vials

1.5 mL

Peptide test sample

1 vial

1.5 mLCE Grade Water

4 vials

1.5 mL

0.1 M NaOH

1 vial

1.5 mL

0.1 M HCl

1 vial

1.5 mLUse the following figure to put each reagent vial in the correct position in the buffer inlet andoutlet trays.
Note: This layout is the same for all five methods in the CESI 8000 Plus software.
Figure 6-1 Buffer Tray Layout

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
42/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Prepare the System

7

Prepare the System

This section describes how to verify that the CESI 8000 Plus system and the mass spectrometercan communicate.
WARNING! Electrical Shock Hazard. Do not touch the adapter when it is connectedto the CESI 8000 Plus system and the separation voltage is on.

Install the Cartridge
Before a cartridge can be installed, the interface plate must be installed on the CESI 8000 Plus
system. Refer to the section: Remove and Install the Interface Plate.
1.

Open the cartridge cover.
Figure 7-1 Cartridge Cover

2.

Loosen the thumbscrews on the insertion bar, and then lift the insertion bar.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
43/83

Prepare the System
Figure 7-2 Insertion Bar

3.

Open the access panel.
Figure 7-3 Access Panel4.

Put the sprayer housing through the side panel, and then put the sprayer in the holster.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
44/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Prepare the System
Figure 7-4 Sprayer in the Holster

Note: To prevent damage, make sure that the protective sleeve stays on the sprayer tip. Do
not let the sprayer tip touch any surfaces.
5.

To install the cartridge body, put the ends of the cartridge on the aligning blocks of theinterface plate at a 45-degree angle, and lightly push the cartridge in.
Figure 7-5 Aligning Blocks

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
45/83

Prepare the System

Item

Description

1

Aligning blocks

2

T slider6.

Turn the cartridge up until it is parallel with the interface plate.

7.

Put the upper handles in the position shown in the figures: Figure 7-6 and Figure 7-7.

8.

Align the T slider in the groove of the interface plate and move the cartridge down. As the
cartridge moves down, the covers on the inlet and outlet sides retract and the capillaries canbe seen below the interface block within the ejectors.
Figure 7-6 T Slider

Item1

Description
Align the T slider in the groove

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
46/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Prepare the System
Figure 7-7 Capillaries Below the Interface Block

Item
1
9.

Description
Capillaries can be seen below the interface block within the ejectors

Put the coolant and capillary tubing through the notched arm.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
47/83

Prepare the System
Figure 7-8 Coolant and Capillary Tubing

10. Lower the insertion bar, and then tighten the thumbscrews.
Figure 7-9 Thumbscrews on the Insertion Bar

Remove and Install the Interface Plate
1.

To remove the interface plate, do this:a.

Remove the cartridge. Refer to the section: Remove the Cartridge.

b.

Turn off the power to the CESI 8000 Plus system.

c.

Loosen the thumbscrews on the sides of the interface plate.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
48/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Prepare the System
Figure 7-10 Thumbscrews on the Interface Plate

2.

Item

Description

1

Thumbscrewsd.

Hold the handle on the top of the interface plate and pull it out.

e.

Keep the interface plate in a safe place.

To install the interface plate, do this:a.

Hold the handle on the top of the interface plate and install it. Make sure that theinterface plate is flush with the mounting surface of the CESI 8000 Plus system.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
49/83

Prepare the System
Figure 7-11 Install the Interface Plateb.

Tighten both thumbscrews.
Figure 7-12 Tighten the Thumbscrews

Condition the Capillaries
Condition the capillaries before a new cartridge is used for the first time and before a cartridgethat has been in storage is used again.
Use the CESI-MS conditioning method to rehydrate the coating of the bare fused-silica
capillaries and to establish the electrical connection in the sprayer tip.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
50/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Prepare the System
1.

Remove the protective sleeve from the sprayer tip.

2.

To make sure that the flow of liquid through the separation capillary is sufficient, do this:3.

a.

Do a forward rinse with CE Grade Water at 100 psi for 3 minutes.

b.

When a liquid droplet shows at the end of the sprayer tip, stop the application ofpressure.

To make sure that the flow of liquid through the conductive liquid capillary is sufficient, do
this:
a.

Do a reverse rinse with CE Grade Water at 100 psi for 5 minutes.

b.

When a liquid droplet shows at the end of the stainless steel needle, stop theapplication of pressure.

4.

Install the protective sleeve on the sprayer.

5.

Put 10 mL of MeOH in a 50 mL Falcon tube, and then put the Falcon tube in the holster on
the side of the system.
CAUTION: Potential System Damage. Do not put more than 10 mL of MeOH in the
Falcon tube. If there is more than 10 mL in the tube, then the liquid can splash onto
the metal components of the sprayer and cause damage.

6.

Carefully immerse the sprayer tip in the Falcon tube.
Figure 7-13 Sprayer Immersed in Liquid

7.

Run the CESI-MS conditioning method.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
51/83

Prepare the System
8.

When the method is complete, remove the sprayer from the Falcon tube.

9.

Use lint-free wipes to dry the sprayer carefully.
Figure 7-14 Dry the Sprayer

CAUTION: Potential System Damage. To prevent the sprayer tip from breaking, do not
move the retractable protective guard during drying.
10. Make sure that the ESI voltage on the mass spectrometer is off.
11. Install the sprayer in the adapter on the mass spectrometer.
The cartridge is ready to set a stable spray.
12. Remove the Falcon tube from the holster, and discard the contents.

Establish a Stable Spray
1.

Make sure that the sprayer tip is in the correct position for the inlet on the mass
spectrometer.

2.

In the Xcalibur software, make sure that the ESI voltage is zero.

3.

To fill the conductive liquid capillary with BGE, do this:a.

In the 32 Karat software, go to the Direct Control window.

b.

Click the Pressure field.
Figure 7-15 Pressure Settings Dialog to Fill the Conductive Liquid Capillary

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
52/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Prepare the Systemc.

In the Pressure field, type 100.

d.

In the Duration field, type 2.

e.

Click Reverse.

f.

Click Pressure.

g.

Click OK.
To identify the direction of the pressure being applied, in the Direct Control window, lookat the Rinse Direction icon (a blowing face identified by a red arrow in the following
figure). The reverse direction refers to rinsing the conductive liquid capillary, and theblowing face shows on the right side of the window.
Figure 7-16 Rinse Direction (Blowing Face) Icon

When the conductive liquid capillary is filled with BGE, a droplet will show at the end of
the stainless steel needle.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
53/83

Prepare the System
Figure 7-17 Droplet at the End of the Stainless Steel Needle

4.

When the rinse is complete, to fill the separation capillary with BGE, do this:a.

Go to the Direct Control window.

b.

Click the Rinse field.
Figure 7-18 Pressure Settings Dialog to Fill the Separation Capillaryc.

In the Pressure field, type 100.

d.

In the Duration field, type 2.

e.

Click Forward.

f.

Click Pressure.

g.

Click OK.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
54/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Prepare the System
When the separation capillary is filled with BGE, a droplet will show at the end of thesprayer tip.
Figure 7-19 Droplet at the End of the Sprayer Tip

Note: If the separation capillary is empty, then the first droplet of solution might notshow at the sprayer tip for as long as 7 minutes.
5.

To find the minimum ESI voltage, refer to the section: Optimize the ESI Voltage.

Optimize the ESI Voltage
1.

Make sure that the separation capillary and conductive liquid capillary are filled with BGE.

2.

To set the values for voltage in the 32 Karat software, do this:a.

Go to the Direct Control window, and then double-click the Voltage field.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
55/83

Prepare the System
Figure 7-20 Voltage Settings Dialogb.

In the Voltage field, do this:• For the silica surface OptiMS cartridge, type 20.
• For the neutral OptiMS cartridge, type 30.

c.

In the Duration field, type 60.

d.

In the Ramp time field, type 1.

e.

Click Normal.

f.

Click OK.

Note: If the BGE used is 10% HAc solution, then the electrical current should be 2 μA to
3 μA. If the BGE used is 50 mM AmAc buffer, pH 3.0, then the electrical current should be
0.5 µA to 1 µA.
3.

In the Analyst TF software, in the Navigation bar, under Tune and Calibrate, double-click
Manual Tuning.

4.

On the Source/Gas tab, do this:a.

In the Curtain Gas (CUR) field, type 10.
Note: In the Analyst TF software, the minimum value for curtain gas is 10. CESI-MS
runs use a value of 5 for curtain gas. If the mass spectrometer is connected to the CESI
8000 Plus system, then the factory setting of 5 for curtain gas is applied.

b.

In the IonSpray Voltage Floating (ISVF) field, type 1.0.
The IonSpray Voltage Floating (ISVF) parameter sets the ESI voltage.

c.
5.

In the Interface Heater Temperature (IHT) field, type 50.0.

On the MS tab, do this:a.

In the Scan type field, select TOF MS.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
56/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Prepare the Systemb.

In the Accumulation time field, type 500.

c.

In the TOF Masses (Da) Min field, type 200.

d.

In the TOF Masses (Da) Max field, type 2000.

e.

In the Period Duration field, type 10.

6.

Click Start.

7.

If a non-SCIEX mass spectrometer is in use, then do this on the mass spectrometer
acquisition computer:8.

a.

Set the ESI voltage to zero.

b.

Set the scan range from 200 m/z to 2000 m/z.

c.

Click Start.

Increase the value in the IonSpray Voltage Floating (ISVF) field in increments of 0.1 kV
until a continuous signal shows in the mass spectrum window.
Note: This is the minimum ESI voltage.
Figure 7-21 Typical Spray Profile of a Cartridge that Uses 10% HAc Solution as the
BGE

9.

In the Direct Control window, click Stop.

10. On the Source/Gas tab, in the IonSpray Voltage Floating (ISVF) field, type 0.0, and thenclick OK.
Make sure that there is no spray or background mass spectrum.
Note: If there is still spray when IonSpray Voltage Floating (ISVF) is 0.0, then there might
be an issue with the connection. Refer to the section: Fine-Tune the Position of the Sprayer
Tip.
11. In the IonSpray Voltage Floating (ISVF) field, type the minimum ESI voltage, and thenclick OK.
Make sure that electrospray starts again.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
57/83

Prepare the System
12. In the IonSpray Voltage Floating (ISVF) field, increase the value by 100 V.
13. To find the best position for the sprayer in relation to the inlet on the mass spectrometer, use
the XYZ-axes adjustment knobs to get a maximum total ion current signal.
Note: Keep the sprayer tip at least 2 mm away from the curtain gas plate.
14. To check the stability of the spray, continue to apply 20 kV (normal polarity) for 20 minutes.
15. In the Analyst TF software, do this:a.

Open the Advanced MS tab, and then click MCA.

b.

Open the MS tab.

c.

In the Scan type field, select TOF MS.

d.

In the Accumulation time field, type 1.

e.

In the TOF Masses (Da) Min field, type 70.

f.

In the TOF Masses (Da) Max field, type 2000.

g.

In the Period Duration field, type 5.

16. Click Acquire, and then type a file name (for example, Baseline).
17. If a non-SCIEX mass spectrometer is in use, then do this on the mass spectrometer
acquisition computer:a.

Set the ESI voltage to 1.0 kV and continue to acquire data.

b.

Increase the ESI voltage in increments of 0.1 kV until there is a continuous signal in themass spectrum window.

c.

To find the best position for the sprayer in relation to the inlet on the mass spectrometer,maximize the XIC (eXtracted Ion Electropherogram) signal for the pI 7.0 or pl 10 marker
in use while minimizing its fluctuations.

d.

When the position of the sprayer is optimized, decrease the ESI voltage in incrementsof 0.1 kV until the spray stops.

e.

Increase the ESI voltage in increments of 0.1 kV until continuous spray is detected.

f.

Record this value as the minimum ESI voltage.

g.

Increase the minimum ESI voltage by 0.2 kV.

18. Use the Y-axis alignment knob to maximize the baseline fluctuations.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
58/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Prepare the System
Figure 7-22 Find the Baseline Fluctuationa.

If the baseline fluctuation is < 40% within 2 minutes to 5 minutes, then make a noteof the ESI voltage for the mass spectrometer methods (ion collection ESI voltage):
Baseline fluctuation (%) = [(highest value - average value)/average value] x 100.

b.

If the baseline fluctuation is > 40%, then do this procedure again until a good baseline isset. If a good baseline cannot be set, then refer to the section: Fine-Tune the Position of
the Sprayer Tip.

19. If a non-SCIEX mass spectrometer is in use, then do this:a.

Monitor the spray stability for 20 minutes to 30 minutes to make sure that the baseline
fluctuation is ≤ 40%.
If the baseline fluctuation is > 40%, then condition the capillaries. Refer to the section:
Condition the Capillaries.

b.

Turn off the electrospray voltage on the mass spectrometer.

About Tune Files
Make sure that the mass spectrometer system is calibrated correctly before a test separation isdone.
Note: The customer must calibrate the mass spectrometer. Refer to the manufacturer’s
documentation for calibration procedures and the recommended performance frequency.
As a general guideline, any known peptide can be used as a tuning mix. For metabolomic
applications, use a metabolite-type compound to generate the tuning. Make sure that the tune
mix buffer is in 10% acetic acid.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
59/83

Prepare the System
Two tune files must be created. The first tune file is set with a spray voltage of 0 kV. The second
tune file is set with a spray voltage that has been found to supply a stable spray. Refer to thesections: Establish a Stable Spray and Optimize the ESI Voltage.
Both tune files are used to do the test separation. The tune file with 0 kV is used for 1 minute,which relates to the interval when the CE voltage gradually increases to 20 kV. When theseparation voltage gets to the applicable magnitude of 20 kV, the second tune file with the
optimal spray voltage is applied. This is to make sure that the correct voltage is applied during
the sample separation.
When the tune files have been acquired and saved successfully, continue with the section: Do a
Test Separation.

Fine-Tune the Position of the Sprayer Tip
CAUTION: Potential System Damage. Do not move the sprayer tip too close to the inlet
on the mass spectrometer. If the sprayer tip is < 2 mm from the inlet, then the accidental
suction of rinse solution into the mass spectrometer can occur and cause damage.
Before a separation is run, it is critical to optimize the position of the sprayer tip in front of
the inlet on the mass spectrometer to get the correct ESI voltage. If the sprayer tip is too far
away from the inlet on the mass spectrometer, then a high ESI voltage can be required, whichcauses analyte fragmentation. For intact proteins, electrochemical reactions such as oxidation
can occur. The green area in the following figure shows the recommended distance of thesprayer tip and the recommended ESI voltage values. Avoid the red area.
Figure 7-23 Sprayer Tip Distance and ESI Voltage Correlation

Use this procedure to adjust the position of the sprayer tip and find the required ESI voltage formass spectrometer acquisition:• After installing a cartridge

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
60/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Prepare the System• If the signal separation voltage is changed• If a different BGE is used
For troubleshooting information, refer to the document: CESI 8000 Plus High Performance
Separation-ESI Module User Guide.
1.

Fill the separation capillary and the conductive liquid capillary with BGE.

2.

Put the sprayer tip 2 mm to 5 mm from the inlet on the mass spectrometer.

3.

In the 32 Karat software, use the Direct Control window to apply 20 kV voltage.
• Make sure that the cartridge does not spray when the ESI voltage is 0 V during mass
spectrometer scanning.
• Monitor the Direct Control window to make sure that the electrical current is stable.

4.

Set the ESI voltage to 0.5 kV, and then increase the value in increments of 0.1 kV until
electrospray is detected.

5.

Increase the ESI voltage by 0.2 kV.

6.

Use the XYZ-axes adjustment knobs to move the sprayer tip and maximize the signal
intensity of the mass spectrometer while minimizing the ion trap time.
Make sure that the sprayer tip is approximately 3 mm from the inlet on the mass
spectrometer.

7.

When the position of the sprayer is optimized, set the ESI voltage to zero.

8.

Set the ESI voltage to 0.5 kV, and then increase the value in increments of 0.1 kV until
electrospray is detected.
Note: This is the minimum ESI voltage. This voltage is not high enough to maintain an
effective spray during separation.

9.

Increase the minimum ESI voltage by 0.2 kV.
Note: This is the optimal ESI voltage. Use this voltage with the mass spectrometer method
to supply a stable electrospray during separation.

10. Set the ESI voltage to zero.
11. Turn off the separation voltage.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
61/83

Do a Test Separation

8

Do a Test Separation

This section gives the instructions to do a test separation with beta-galactosidase test sample to
make sure that the CESI 8000 Plus system and the mass spectrometer operate correctly.
As an alternative, PepCalMix can be used as the test sample. PepCalMix has 20 different
stable isotope-labeled peptides and is available from SCIEX. For instructions about how to use
PepCalMix, refer to the document: CESI 8000 Plus High Performance Separation-ESI Module
User Guide.
Note: Before a test separation is run, make sure that a stable spray has been establishedand the optimum ESI voltage has been set. Refer to the section: Fine-Tune the Position of theSprayer Tip.

Create the Mass Spectrometer Method
Use the Xcalibur software to create an MS method with two segments.
1.

Create one method with two segments.
• The following figure shows the first segment of the tune method that was created whenthe mass spectrometer was tuned, with a duration of 1 minute and an ESI voltage set tozero.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
62/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Do a Test Separation
Figure 8-1 First Segment of a Method Used to Run Beta-Galactosidase Test Sample• The following figure shows the second segment of the tune method, with a duration of
44 minutes and an the optimum ESI voltage set for a stable spray.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
63/83

Do a Test Separation
Figure 8-2 Second Segment of the Method Used to Run Beta-Galactosidase Test
Sample2.

In the Scan Description section, from the Data type list, select Profile.

3.

In the Scan Ranges section, in the First Mass (m/z) field, type 300.00, and in the Last
Mass (m/z) field, type 1500.00.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
64/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Do a Test Separation
Figure 8-3 Scan Event Settings

4.

Save the method.
Note: We recommend that the temperature of the ion transfer capillary be set to 200 °C for
the analysis of the beta-galactosidase stock solution test sample. If the sample is different,
then the temperature might be different.

Create and Start a Sequence with the Xcalibur
SoftwareUse the Xcalibur software to include the MS method in a sequence.
Note: Make sure that the system will go into standby mode when the sequence completes.
1.

In the Xcalibur software, open the New Sequence Template window.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
65/83

Do a Test Separation
Figure 8-4 New Sequence Template Window

2.

Click OK.

3.

On the Sequence Setup-Home Page, highlight the row for the sample to run, and then click
the Sequence Run icon.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
66/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Do a Test Separation
Figure 8-5 Sequence Setup-Home Page

4.

When the sequence finishes, in the Run Sequence dialog, set the instrument to standby,and then click OK. Otherwise, the spray voltage will stay on.
The Acquisition Queue tab shows the sequence that is running and the sequence row
being acquired. The Status tab shows the status of the sequence. As the sequence isdownloaded and queued, the status will change from Ready to Downloading to Waiting
for contact closure.

5.

Load the sample and buffer trays in the CESI 8000 Plus system.
Note: Before starting a sequence on the CESI 8000 Plus system, make sure that the statuson the Xcalibur software is Waiting for contact closure.

Manually Create the CESI-MS Separation Method
The CESI-MS Separation for Thermo MS.met method file is installed with the 32 Karatsoftware 10.3 or later in the folder C:\32Karat\projects\CE MS\Method. If the method is
missing, then use this procedure to create it manually.
1.

In the 32 Karat software, click File > Method > New.

2.

Use the initial conditions in the following figure.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
67/83

Do a Test Separation
Figure 8-6 Initial Conditions for the CESI-MS Separation Method

3.

Use the time program in the following figure.
Figure 8-7 Time Program for the CESI-MS Separation Method

Note: For a new method, make sure that the value for the duration of the Relay On event is
at least 0.05 minutes.
4.

In row 10 of the sequence table, click the Event cell, then select Separate.

5.

Set the parameters that show in the following figure, and then click OK.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
68/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Do a Test Separation
Figure 8-8 Voltage Ramp Down

6.

Click File > Method > Save As, and then save the method as CESI-MS Separation
for Thermo MS.met.

Create a Sequence in the 32 Karat Software1.

In the 32 Karat software, click File > Sequence > Sequence Wizard.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
69/83

Do a Test Separation
Figure 8-9 Sequence Wizard - Method Page

2.

To the right of the Method field, click

3.

Click Next.

, and then select the CESI-MS separation method.

Figure 8-10 Sequence Wizard - Unknowns Page

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
70/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Do a Test Separation
4.

In the Sample ID field, type a text string, and then click the blue arrow icon to the right of the
Sample ID field.
Figure 8-11 Sample ID Options Menu

If an option is selected from this menu, then a related parameter symbol is included in
the Sample ID field. When the sequence is run, the parameter is added to the sample ID
automatically. Any combination of parameters can be used.
5.

Select the options to include in the sample ID automatically when the sequence is run.
A symbol shows in the Sample ID field for the parameters selected.

6.

To the right of the Data path field, click the green folder icon, and then select the file path tothe data files.

7.

In the Data file field, type a text string, and then click the blue arrow icon to the right of theData file field.
Figure 8-12 Data File Options Menu

If an option is selected from this menu, then a related parameter code is included in the
Sample ID field. When the sequence is run, the parameter is added to the data file nameautomatically.
Note: The Open File option is used to reprocess data files, not to acquire data.
8.

Select the applicable options.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
71/83

Do a Test Separation
A symbol shows in the Data file field for the parameters selected.
9.

In the Number of unknown runs in sequence field, type the number of sample runs.
This number does not include autocalibration runs.

10. In the Repetitions per Run field, type the number of times to run each line in the sequence.
When this option is used, an identifier is added to the file name for each repetition
automatically.
11. Click Next.
Figure 8-13 Sequence Wizard - Vials Page

12. If the Allow Override check box has been selected for the method, then, in the Inlet andOutlet fields, type the vials positions to use in the sequence table.
The Allow Override option is set in the Inject event. For more information, refer to the
document: CESI 8000 Plus High Performance Separation-ESI Module User Guide.
13. To set the advance direction for the sequence, click Advance direction.
Note: The advance direction is different than vial incrementing. The advance direction helps
to simplify the planning and organization of the sequence table. The values for the vial
positions can be changed in the sequence table, and the values are not saved with any
method. The values are saved in the sequence.
Note: If the Advance check box is selected for the inlet, outlet, or both vials, then the values
for the vial positions are filled down automatically in the Sample Inject Inlet/Outlet columns
in the sequence table.
OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
72/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Do a Test Separation• To fill down vial positions automatically and increase them by rows in the same tray (forexample, A1, A2, A3, A4, A5, A6, B1, B2, B3, B4 for buffer tray configuration), click Row
major.
• To fill down vial positions automatically and increase them by columns in the same tray
(for example, A1, B1, C1, D1, E1, F1, A2, B2, C2, D2 for buffer tray configuration), click
Column major.
A set of calibration vials can also be identified. For information about calibration through thesequence table, refer to the document: CESI 8000 Software Online Help.
14. Click Next.
15. Keep all of the check boxes on the Sequence Wizard - Reports page cleared.
None of the settings apply to CESI-MS.
16. Click Finish.
Figure 8-14 Sequence Table: Part A

Load the Sample
1.

Put the reagents in the following table in CESI-MS vials.
Table 8-1 Reagent Requirements

2.

Content

Quantity

VolumeBGE

3 vials

1.5 mLCE Grade Water

1 vial

1.5 mL

0.1 N NaOH

1 vial

1.5 mL

0.1 N HCl

1 vial

1.5 mLPut the reagents in the following positions in the buffer tray.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
73/83

Do a Test Separation
Figure 8-15 Buffer Inlet and Outlet Tray Layout for Sample Separation Method3.

Put the beta-galactosidase stock solution test sample in a microvial.

4.

Put the microvial inside a CESI-MS vial, and then attach a cap.

5.

Put the CESI-MS vial in position SI:A1 of the sample inlet tray.

6.

In the 32 Karat software, go to the Direct Control window, and then click Load.

7.

When the carriers have moved forward, open the front cover of the CESI 8000 Plus systemand put the inlet and outlet buffer trays in the correct carrier.

8.

Put the sample inlet tray in the back of the inlet carrier (left).

Start the Sequence in the 32 Karat Software.

1.

On the toolbar, click the Sequence Run icon

2.

Make sure that the value in the Sequence name field is correct, or click the yellow folder
icon to browse to the correct file.

3.

Click Start to start the sequence.
When the method starts, the status in the Queue Server on the mass spectrometer changes
from Ready to PreRun.
When the signal is sent from the 32 Karat software to the mass spectrometer, the status in
the Queue Server changes from PreRun to Acquiring.
As the batch run continues, a green check mark shows for each run that is acquired
successfully and the run status changes to Acquired.

4.

To see the status of the first autocalibration run, monitor the Bgal_Installation sequence. The
first autocalibration run in the following figure is being acquired.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
74/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Do a Test Separation
Figure 8-16 Monitor the Sequence Run

Analyze the Data
Use the Xcalibur software to analyze the data from the test run.
Efficient system performance can be gauged by the identification and clear separation of thebeta-galactosidase peaks 714.8469 m/z and 729.3652 m/z. The following table shows the mass
assignment for the two fragments of interest.
Table 8-2 Beta-Galactosidase 729 m/z and 714 m/z Mass Assignmentm/z

Peptide Sequence

Monoisotopic Molecular
Weight (Da)Charge State714

DWENPGVTQLNR

1427.6793

2

729

APLDNDIGVSEATR

1456.7158

2

1.

Click File > Open, and then browse to the location where the beta-galactosidase data file
was saved.

2.

Click Open.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
75/83

Do a Test Separation
Figure 8-17 Example of a Typical Beta-Galactosidase TIC

3.

Change the view to Base Peak Chromatogram.

4.

Configure the base peak chromatogram to see peaks 714 and 729.

5.

Apply the following settings to the base peak chromatogram:• Set the peak ranges to 714.5 to 714.7 and 729.2 to 729.4.
Note: If required, then use the mass spectrometer mass calibration to adjust the peak
ranges 714.5 to 714.7 and 729.2 to 729.4.
• Set automatic processing to include smoothing with a smoothing value of 5.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
76/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Do a Test Separation
Figure 8-18 Identification and Clear Separation of the Beta-Galactosidase 714 and 729
m/z Fragments

6.

Calculate the migration time of each peak.

7.

Make sure that the two peaks are separated by at least 0.05 minutes.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
77/83

Shut Down and Disconnect

9

Shut Down and Disconnect
Remove the Cartridge

If the CESI 8000 Plus system will be shut down and the power turned off, then remove thecartridge.
1.

Make sure that the ESI voltage on the mass spectrometer is off.

2.

Do the applicable procedure in the section: Store the Cartridge.

3.

In the 32 Karat software, go to the Direct Control window, and then click Load.

4.

Open the cartridge cover.
Figure 9-1 Cartridge CoverThe coolant pump for the CESI 8000 Plus system turns on and releases the coolant fromthe cartridge coolant lines. Approximately 30 seconds are required. Wait for the pump toturn off.
5.

Loosen the thumbscrews on the insertion bar.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
78/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Shut Down and Disconnect
Figure 9-2 Thumbscrews on the Insertion Bar

6.

Lift the insertion bar fully.

7.

To prevent damage to the sprayer tip, retract the stage as far away from the inlet on themass spectrometer as possible.

8.

To loosen the end of the sprayer from the adapter, turn the arrow on the sprayer to the
Unlock position.
WARNING! Hot Surface Hazard. The surfaces of the ion source become hot
during operation. Let the ion source cool for at least 30 minutes before thesprayer is removed from the adapter on the mass spectrometer.
Figure 9-3 Unlock the Sprayer from the Cartridge

Item1

Description
Sprayer in the Unlock position

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
79/83

Shut Down and Disconnect

Item
2
9.

Description
Turn to lock the sprayer from the adapter

Remove the sprayer from the adapter.
Figure 9-4 Sprayer Removal

10. Install the protective sleeve on the sprayer tip.
11. Put the tubing with the sprayer end through the access panel.
Figure 9-5 Sprayer and Tubing Through the Access Panel

12. Remove the coolant tubing from the notched arm.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
80/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Shut Down and Disconnect
Figure 9-6 Coolant and Capillary Tubing

13. Hold the cartridge sprayer with one hand and the midsection of the cartridge in the other,
then lift the cartridge up and pull it out.
Figure 9-7 Remove the Cartridge

Note: As the cartridge is moved up, the sheaths on the inlet and outlet sides go down overthe capillary ends.
Note: Drops of liquid coolant that might fall from the cartridge ends are normal and do notcause damage to the hardware.
14. Refer to the section: Store the Cartridge.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
81/83

Shut Down and Disconnect

Store the Cartridge
WARNING! Puncture Hazard. Be careful when handling the cartridge. The tips ofthe capillaries are extremely sharp.
CAUTION: Potential System Damage. To prevent contamination of the internal surface ofthe separation capillary, do not use the pressure rinse function to blow air through thecapillaries. Use the vacuum function to dry the capillaries.
1.

2.

To prepare the cartridge to be stored for less than 3 days, do this:a.

Run the CESI-MS cleaning method.

b.

Store the cartridge in the system for as long as 3 days.

To prepare the cartridge to be stored for more than 3 days, do this:a.

Run the CESI-MS storage method.
Note: The CESI-MS storage method cannot be run as part of a sequence because
methanol is volatile and can evaporate before the sequence is complete. Vials filledwith methanol must be used immediately. The ESI needle can stay in air but not inliquid. The ESI needle can be dried by vacuum.

b.

Disconnect the sprayer from the ion source.

c.

Remove the cartridge from the system.

d.

Install the protective sleeve on the sprayer tip.

e.

Put the sprayer tip in a 2 mL microcentrifuge tube of water.

f.

Loosely seal the tube with Parafilm.

g.

Keep the cartridge in a safe place at room temperature.

Disconnect the CESI 8000 Plus System from theMass Spectrometer
Disconnect the CESI 8000 Plus system from the mass spectrometer when:• The mass spectrometer will be used without the CESI 8000 Plus system.
• The mass spectrometer or the CESI 8000 Plus system will be moved.
1.

Make sure that the cartridge has been removed.
Refer to the section: Remove the Cartridge.

2.

Turn off the CESI 8000 Plus system.

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
82/83

Installation Guide
RUO-IDV-05-3313-B | 5302405

Shut Down and Disconnect
3.

On the CESI 8000 Plus system high-voltage connections panel, disconnect the input andoutput cables and the black and red banana plugs.
Refer to the figure: Figure 2-21.

4.

Disconnect the relay cable from the CESI 8000 Plus system and the mass spectrometer.

5.

Disconnect the high-voltage input cable from the mass spectrometer.

6.

Adjust the height of the mobile cart to the lowest position.

7.

Disconnect the power cables from the CESI 8000 Plus system and the mobile cart.

8.

To unlock the wheels on the mobile cart, lift the lever at each caster.
Figure 9-8 Unlock the Wheels of the Mobile Cart

9.

Carefully move the CESI 8000 Plus system away from the mass spectrometer.

10. Loosen the thumbscrew on the adapter, and then move the adapter fully off the stage.
11. Remove the adapter from the ion source. If required, then remove the adapter mounting
bracket.
12. Keep the adapter, adapter mounting bracket and thumbscrews, and cables in a safe place.

Installation Guide
RUO-IDV-05-3313-B | 5302405

OptiMS Thermo MS Adapter For Nanospray II,
Nanospray Flex, and Nanospray Flex NG Ion Sources
83/83