CESI 8000 Plus High Performance
Separation-ESI Module
User Guide

RUO-IDV-05-3897-E

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
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Woodlands Central Industrial Estate, Singapore 739256

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Contents

1 Operational Precautions and Limitations...............................................................................8
General Safety Information....................................................................................................... 8
Documentation Symbols and Conventions............................................................................... 8
Regulatory Compliance.............................................................................................................9Australia and New Zealand.................................................................................................. 9
Canada.................................................................................................................................9Europe..................................................................................................................................9
United States......................................................................................................................10
International....................................................................................................................... 10
Electrical Precautions..............................................................................................................10
Mains Supply......................................................................................................................10
Protective Earth Conductor................................................................................................ 11
Chemical Precautions............................................................................................................. 11
System Safe Fluids............................................................................................................ 12
Physical Precautions ..............................................................................................................12
Environmental Precautions..................................................................................................... 12
Electromagnetic Environment............................................................................................ 13
Decommissioning and Disposal......................................................................................... 14
UV Radiation Precautions....................................................................................................... 14
Laser Precautions................................................................................................................... 14
Qualified Personnel.................................................................................................................15
Laboratory Conditions............................................................................................................. 15
Safe Environmental Conditions..........................................................................................15
Performance Specifications............................................................................................... 16
Equipment Use and Modification............................................................................................ 16
2 Introduction............................................................................................................................. 17
Description.............................................................................................................................. 17
Hardware Overview.................................................................................................................19
Sample-Handling System...................................................................................................20
Syringe Pump.....................................................................................................................22
High-Voltage Power Supply............................................................................................... 22
LED Indicators....................................................................................................................23
Cartridge and Sample Cover Interlocks............................................................................. 23
OptiMS Cartridge............................................................................................................... 25
Mass Spectrometer Adapters.............................................................................................28
Required Reagents and Materials...........................................................................................28
Customer-Supplied Equipment and Supplies.................................................................... 29
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Contents

3 Set Up the Sytem.................................................................................................................... 30
Install the Cartridge................................................................................................................. 30
Connect the GPIB-USB Cable................................................................................................ 35
Connect an Auxiliary I/O Cable............................................................................................... 37
Change the Mass Spectrometer Type.....................................................................................37
Configure the Hardware Profile...............................................................................................38
Install the Adapter................................................................................................................... 46
Connect the High-Voltage Cables...........................................................................................51
Align the System with the Mass Spectrometer........................................................................52
4 Prepare the Reagents............................................................................................................. 60
Prepare the 10% HAc Solution............................................................................................... 60
Prepare the 20% HAc Solution............................................................................................... 60
Prepare the 200 mM LE Buffer, pH 4.0................................................................................... 61
Prepare the PepCalMix Test Sample...................................................................................... 61
Prepare the PepCalMix Solution for Direct Infusion................................................................61
Prepare the Peptide Test Sample........................................................................................... 62
5 Prepare the Trays....................................................................................................................63
About Vials.............................................................................................................................. 63
Fill a CESI Vial................................................................................................................... 64
Fill a Microvial.................................................................................................................... 65
Fill a nanoVial.....................................................................................................................66
Prepare the Buffer Trays......................................................................................................... 67
Prepare the Sample Tray........................................................................................................ 68
6 Prepare the System................................................................................................................ 70
Condition the Capillaries......................................................................................................... 70
Establish a Stable Spray.........................................................................................................72
Optimize the ESI Voltage........................................................................................................ 75
Fine-Tune the Position of the Sprayer Tip...............................................................................79
Manual Calibration.................................................................................................................. 80
Prepare for Manual Calibration.......................................................................................... 80
Create a Reference Table.................................................................................................. 81
Manually Calibrate in TOF MS Mode................................................................................. 85
Manually Calibrate in Product Ion Mode............................................................................ 89
7 Run Workflow..........................................................................................................................94
Methods for the Silica Surface OptiMS Cartridge................................................................... 94
Initial Conditions Tab.......................................................................................................... 95
Time Program Tab..............................................................................................................95
Do a System Suitability Test....................................................................................................97
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Create a Sequence in the 32 Karat Software........................................................................102
Create a Batch in the Analyst TF Software........................................................................... 106
Start the Batch in the Analyst TF Software............................................................................111
Load the Trays.......................................................................................................................112
Start the Sequence in the 32 Karat Software........................................................................ 113
Analyze the Data from the PepCalMix Test Sample..............................................................115
About Autocalibration............................................................................................................ 117
Create the MS Acquisition Method for Autocalibration.....................................................118
Add Autocalibration to the Sequence...............................................................................123
Analyze the Autocalibration Data..................................................................................... 125
8 Shutdown and Disconnection............................................................................................. 131
Remove the Cartridge...........................................................................................................131
Store the Cartridge................................................................................................................135
Disconnect the CESI 8000 Plus System from the Mass Spectrometer.................................135
9 Maintenance.......................................................................................................................... 138
Remove and Install the Interface Plate................................................................................. 138
Interface Block, Electrodes, and Insertion Levers.................................................................141
Replace the Insertion Levers........................................................................................... 141
Replace the Electrodes.................................................................................................... 142
Clean the Electrodes, Insertion Levers, and Interface Block........................................... 144
Add Capillary Cartridge Coolant............................................................................................145
Replace the Quad Rings.......................................................................................................147
Replace the Fuses................................................................................................................ 148
Set the Home Position for the Mobile Cart............................................................................150
10 Troubleshooting..................................................................................................................151
Clean Blockage from the Sprayer Tip................................................................................... 151
Conductive Liquid Capillary Contamination.......................................................................... 151
Condition the Conductive Liquid Capillary....................................................................... 152
Autocalibration Troubleshooting............................................................................................153
No Electrospray Between CESI 8000 Plus System and Mass Spectrometer....................... 155
Electrospray Is Detected When ESI Voltage Is Zero.............................................................156
Electrospray Is Unstable When Voltage Is Applied............................................................... 157
Droplet at Capillary Tip Disappeared But No Mass Spectrometer Signal Is Detected..........158
TIC Signal Is Lower than Usual and/or Intensity of Background Signal Fluctuates Too
Much.................................................................................................................................159
Electrical Current Is Unstable................................................................................................160
Analyte Signals Are Not Detected by Mass Spectrometer During Separation......................161
Some Analyte Peaks Are Missing or Smaller than Expected................................................162
Current Gradually Decreases During Separation..................................................................163
Iron-Acetate Cluster m/z 537 Is Suppressing Sample Signals..............................................164
High-Voltage System Cannot Deliver Required Electrical Current........................................165
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Contents

11 Order Parts.......................................................................................................................... 166
Cartridges and Parts............................................................................................................. 166
A 32 Karat Software................................................................................................................. 170
System Administration.......................................................................................................... 170
Controller and System Start-Up............................................................................................ 170
Controller and Network Login...........................................................................................170
License Key......................................................................................................................171
Start the CESI 8000 Plus System.................................................................................... 171
Open the 32 Karat Software.............................................................................................171
Systems and Projects...................................................................................................... 173
Online and Offline Modes.................................................................................................173
Open the Direct Control Window...........................................................................................174
Create a Toolbar Icon for the Direct Control Window.......................................................175
32 Karat Software Methods...................................................................................................175
Create or Change a Method.............................................................................................176
Single Run and Sequence Runs...........................................................................................185
32 Karat Software Sequences.............................................................................................. 186
Sequence Table Columns................................................................................................ 186
Sequence Validation........................................................................................................ 188
Sequence Transfer...........................................................................................................188
About the Auto-Increment Feature........................................................................................193
Set Auto-Increment for a Rinse Event..............................................................................193
Set Auto-Increment for an Inject Event............................................................................ 195
Set Auto-Increment for a Separate Event........................................................................ 196
Auto-Increment in a Method.............................................................................................198
Review Vial Positions Before a Sequence Is Run............................................................199
B CESI 8000 Plus Software..................................................................................................... 201
User Roles and Privileges.....................................................................................................201
Open the CESI 8000 Plus Software......................................................................................201
Run an Application................................................................................................................204
Samples/Vials Window..........................................................................................................206
Set Up Samples and Vials for a Method.......................................................................... 206
Set Up Samples and Vials for a Sequence...................................................................... 209
Display Options Menu....................................................................................................219
Acquisition Window...............................................................................................................223
During a Run.................................................................................................................... 224
Stop a Run....................................................................................................................... 225
Complete a Run............................................................................................................... 226
Graph Options..................................................................................................................226
Describe Sequence Window................................................................................................. 227
Describe the Sequence....................................................................................................229
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C Connect an Ethernet Cable................................................................................................. 231
D System Specifications......................................................................................................... 233
CESI 8000 Plus System Specifications.................................................................................233
Supplied Controller Configuration......................................................................................... 234
Mobile Cart Specifications.....................................................................................................234
Capillary Temperature Control Specifications....................................................................... 235
Sample Temperature Control Specifications......................................................................... 235
Pressure and Vacuum System Specifications.......................................................................235
Detector Specifications......................................................................................................... 236
UV Detector Specifications.............................................................................................. 236(Optional) LIF Detector Specifications............................................................................. 237(Optional) PDA Detector Specifications........................................................................... 238
E Glossary of Symbols............................................................................................................239
F Glossary of Warnings...........................................................................................................245
Contact Us................................................................................................................................ 246
Customer Training.................................................................................................................246
Online Learning Center.........................................................................................................246
Purchase Supplies and Reagents.........................................................................................246
SCIEX Support......................................................................................................................246
Cybersecurity........................................................................................................................ 246
Documentation......................................................................................................................246

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Operational Precautions and Limitations

Operational Precautions andLimitations

1

Note: Before operating the system, carefully read all of the sections of this guide.
This section contains information about general safety and regulatory compliance. This section
gives descriptions of possible hazards and the related warnings for the system, and theprecautions that should be obeyed to minimize the hazards.
In addition to this section, for information about the symbols that are used in the laboratoryenvironment, on the system, and in this documentation, refer to the section: Glossary of
Symbols. For site requirements, refer to the document: Site Planning Guide.

General Safety Information
To prevent personal injury or system damage, read, understand, and obey all of the safety
precautions and warnings in this document, the manufacturer chemical safety data sheets(SDSs), and product label information. Labels are shown with internationally recognizedsymbols. Failure to heed these warnings could result in serious injury.
This safety information is intended to supplement federal, state, provincial, and local
environmental health and safety (EHS) regulations. It does not include every safety procedurethat should be practiced. Ultimately, the user and the organization are responsible forcompliance with federal, state, provincial, and local EHS regulations and for maintaining a safe
laboratory environment.
Refer to the correct laboratory reference material and standard operating procedures.

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.

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.

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Operational Precautions and Limitations

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.

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.

Australia and New Zealand• Electromagnetic Compatibility (EMC): Radio Communications Act 1992 as implemented inthese standards:• Electromagnetic Interference—AS/NZS CISPR 11/ EN 55011/ CISPR 11 (Class A). Referto the section: Electromagnetic Interference.

Canada• Electromagnetic Interference (EMI): CAN/CSA CISPR11. This ISM device complies with
Canadian ICES-001. Refer to the section: Electromagnetic Interference.
• Safety:• CAN/CSA C22.2 No. 61010-1

Europe• Electromagnetic Compatibility (EMC): Electromagnetic Compatibility Directive 2014/30/EU
as implemented in these standards:• EN 61326-1• EN 55011 (Class A)
Refer to the section: Electromagnetic Compatibility.
• Safety:• EN 61010-1• Waste Electrical and Electronic Equipment (WEEE): Waste Electrical and Electronic
Equipment Directive 2012/19/EU, as implemented in EN 40519. Refer to the section: Waste
Electrical and Electronic Equipment.
• Packaging and Packaging Waste (PPW): Packaging and Packaging Waste Directive
94/62/EC

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Operational Precautions and Limitations• RoHS Restriction of Hazardous Substances: RoHS Directive 2011/65/EU and2015/863/EU

United States• Radio Emissions Interference Regulations: 47 CFR 15, as implemented in FCC Part 15(Class A)• Safety: Occupational Safety and Health Regulations, 29 CFR 1910, as implemented in thesestandards:• UL 61010-1

International• Electromagnetic Compatibility (EMC):• IEC 61326-1• IEC CISPR 11 (Class A)
Refer to the section: Electromagnetic Compatibility.
• Safety:• IEC 61010-1

Electrical Precautions
WARNING! Electrical Shock Hazard. Do not remove the covers. If thecovers are removed, then injury or incorrect system operation can occur.
Removal of the covers is not required for routine maintenance, inspection, or
adjustment. For repairs that require removal of the covers, contact a SCIEX
field service employee (FSE).
• Obey the required electrical safe work practices.
• Use cable management practices to control electrical cables and decrease the risk of atripping hazard.
For information about system electrical specifications, refer to the document: Site Planning
Guide.

Mains Supply
Connect the system to a compatible mains supply as instructed in this guide.

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WARNING! Electrical Shock Hazard. Use only qualified personnel for the
installation of all of the electrical supplies and fixtures, and make sure that
all of the installations adhere to local regulations and safety standards.
WARNING! Electrical Shock Hazard. Make sure that the system can be
disconnected from the mains supply outlet in an emergency. Do not block
the mains supply outlet.
WARNING! Electrical Shock Hazard. Use only the mains supply cables thatare supplied with the system. Do not use mains supply cables that are notcorrectly rated for the operation of this system.

Protective Earth Conductor
The mains supply must include a correctly installed protective earth conductor. The protective
earth conductor must be installed or examined by a qualified electrician before the system isconnected.
WARNING! Electrical Shock Hazard. Do not intentionally interrupt theprotective earth conductor. Any interruption of the protective earth
conductor causes an electrical shock hazard.

Chemical Precautions
WARNING! Ionizing Radiation Hazard, Biohazard, or Toxic
Chemical Hazard. Before cleaning or maintenance, identify whether
decontamination is required. If radioactive materials, biological agents,
or toxic chemicals have been used with the system, then the customer
must decontaminate the system before cleaning or maintenance.
WARNING! Environmental Hazard. Do not discard system components inmunicipal waste. To discard components correctly, obey local regulations.
• Before servicing and regular maintenance, identify the chemicals that have been used in thesystem. For the health and safety precautions that must be obeyed for a chemical, refer to thesafety data sheet (SDS). For storage information, refer to the certificate of analysis. To find a
SCIEX SDS or certificate of analysis, go to sciex.com/tech-regulatory.
• Always wear assigned personal protective equipment, including powder-free gloves,protective eyewear, and a laboratory coat.
Note: Nitrile or neoprene gloves are recommended.
• Do work in a well-ventilated area or fume hood.

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Operational Precautions and Limitations• When flammable materials such as isopropanol, methanol, and other flammable solvents arein use, do not go near ignition sources.
• Be careful with the use and disposal of any chemicals. If the correct procedures for chemicalhandling and disposal are not obeyed, then personal injury can occur.
• During cleaning, do not let chemicals touch the skin. Wash hands after use.
• Collect all spent liquids and discard them as hazardous waste.
• Obey all of the local regulations for the storage, handling, and disposal of biohazardous,
toxic, and radioactive materials.

System Safe Fluids
CAUTION: Potential System Damage. Do not use any other fluid until confirmation isreceived from SCIEX that it does not cause a hazard. This is not an exhaustive list.
Any substance supplied with the CESI 8000 Plus system, or referenced in the documentation
for the system, can safely be used with the system. In addition, the following fluids can also be
used with the system. To identify compatibility with other chemicals, contact sciex.com/requestsupport.
• Acids and Bases
The pH range is from 2 to 12.
• Acetic acid, maximum 10%• Sodium hydroxide, maximum 1 M• Hydrochloric acid, maximum 1 M• Reagents• CE Grade Water

Physical Precautions
WARNING! Lifting Hazard. Use a mechanical lifting device to lift and move thesystem. If the system must be moved manually, then at least four people are
required to move the system safely. Follow established safe lifting procedures. We
recommend the use of a professional moving service.

Environmental Precautions
Use qualified personnel for the installation of electrical mains, heating, ventilation, and plumbing
supplies and fixtures. Make sure that all of the installations comply with local bylaws andbiohazard regulations. For information about the required environmental conditions for thesystem, refer to the document: Site Planning Guide.
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Operational Precautions and Limitations
When the system is set up, make sure that there is sufficient access space around theequipment.
WARNING! Biohazard. For biohazardous material use, always obey local
regulations for hazard assessment, control, and handling. Neither this system nor
any part is intended to be used as a biological containment.
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.

Electromagnetic Environment
Electromagnetic Compatibility
Basic Electromagnetic Environment: Environment existing at locations characterized by being
supplied directly at low voltage from the public mains network.
The equipment is intended for use in a basic electromagnetic environment.
Make sure that a compatible electromagnetic environment for the equipment can be maintained
so that the device will operate as intended. If the power supply line is subject to high electricalnoise, then install a surge protector.

Electromagnetic InterferenceGroup 1 Equipment: This equipment is classified as industrial, scientific, and medical (ISM)
equipment that might use RF energy for internal operation.
Class A Equipment: Equipment which is suitable for use in all establishments other thandomestic and those directly connected to a low voltage power supply network which supplies
buildings used for domestic purposes. [Derived from CISPR 11:2009, 5.3] Class A equipment
shall meet Class A limits.
CAUTION: Potential Radio Interference. This equipment is not intended for use inresidential environments and may not supply adequate protection to radio reception insuch environments.
This equipment has been tested and found to comply with the limits for a Class A digital device,pursuant to Part 15 of the FCC (Federal Communications Commission) Compliance Rules.
These limits are designed to provide reasonable protection against harmful interference whenthe equipment is operated in a commercial environment. This equipment generates, uses,
and can radiate radio frequency energy and, if not installed and used in accordance with theoperator's manual, can cause harmful interference to radio communications.

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Operational Precautions and Limitations
Operation of this equipment in a residential area is likely to cause harmful interference inwhich case you will be required to correct the interference, at your own expense. Changes ormodifications not expressly approved by the manufacturer could void your authority to operate
the equipment.

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.

Waste Electrical and Electronic Equipment
Obey local municipal waste ordinances for the correct disposal provisions to decrease theenvironmental impact of waste, electrical, and electronic equipment (WEEE). To discard thisequipment safely, contact a local Customer Service office for complimentary equipment pick-up
and recycling.

UV Radiation Precautions
WARNING! Ultraviolet Radiation Hazard. Prevent exposure to direct or reflected UV
radiation. Ultraviolet radiation is harmful to the eyes and skin. Do not operate theUV source without the required system safety interlocks.

Laser Precautions
This section is applicable for systems that have a laser-induced fluorescence (LIF) detection
system.
WARNING! Laser Hazard. Obey all local codes, regulations, and standards, andinternal requirements that are applicable to laser safety.

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Operational Precautions and Limitations

WARNING! Laser Hazard. To prevent exposure to hazardous laser radiation, do notuse different equipment and controls or do procedures differently than what is
documented in this guide.
WARNING! Personal Injury Hazard. Do not look directly into the anticipated path ofthe laser beam or at any specular reflections of the laser beam. Invisible ultraviolet
radiation from the laser can cause injury to the eyes.
The LIF detection system contains a Class I laser system in a sealed module. The module
contains an embedded Class 3B laser component. The 3B classification means that direct
intrabeam viewing of this type of laser is always hazardous to personnel.
The laser assembly contains the laser and several other components in a sealed housing, andhas no user-serviceable parts. Service of the laser assembly is restricted to qualified SCIEX field
service employees (FSEs). Therefore, the overall laser classification of the system is Class 1,
defined as lasers that are safe under reasonably foreseeable conditions of operation.

Qualified Personnel
Only qualified SCIEX personnel are permitted to install, examine, and supply servicing for theequipment. After the system has been installed, the field service employee (FSE) uses the
document: Installation Qualification to help the customer become familiar with system operation,cleaning, and basic maintenance. If a system under warranty is serviced by personnel who are
not authorized by SCIEX, then SCIEX is not responsible to repair any damage caused by theservicing.

Laboratory Conditions
Safe Environmental Conditions
The system is designed to operate safely in these conditions:• Indoors• Altitude: Up to 2,000 m (6,560 ft) above sea level• Ambient temperature: 15 °C (59 °F) to 40 °C (104 °F)• Relative humidity: 20% to 80%, noncondensing• Mains supply voltage fluctuations: ±10% of the nominal voltage• Transient overvoltages: Up to the levels of Overvoltage Category II• Temporary overvoltages on the mains supply• Pollution Degree 2

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Operational Precautions and Limitations

Performance Specifications
The system is designed to meet specifications in these conditions:• An ambient temperature of 15 °C to 30 °C (59 °F to 86 °F).
Over time, the temperature must stay approximately 4 °C (7.2 °F), with the rate of the change
in temperature not more than 2 °C (3.6 °F) per hour. Ambient temperature fluctuations thatare more than the limit might cause shifts in migration time.
• Relative humidity from 30% to 70%, noncondensing.

Equipment Use and Modification
WARNING! Electrical Shock Hazard. Do not remove the covers. If thecovers are removed, then injury or incorrect system operation can occur.
Removal of the covers is not required for routine maintenance, inspection, or
adjustment. For repairs that require removal of the covers, contact a SCIEX
field service employee (FSE).
WARNING! Personal Injury Hazard. Use SCIEX-recommended parts only. The useof parts that are not recommended by SCIEX or the use of parts for any purpose
other than their intended purpose can put the user at risk of harm or have anegative effect on system performance.
WARNING! Lifting Hazard. Use a mechanical lifting device to lift and move thesystem. If the system must be moved manually, then at least four people are
required to move the system safely. Follow established safe lifting procedures. We
recommend the use of a professional moving service.
Use the system indoors in a laboratory that has the environmental conditions recommended in
the document: Site Planning Guide, or contact an FSE.
If the system is used in an environment or with a method that is not approved by the
manufacturer, then the performance and protection that is supplied by the equipment might
be decreased.
Contact an FSE for information about servicing the system. Unauthorized modification oroperation of the system might cause personal injury and equipment damage, and might void
the warranty. If the system is operated outside the recommended environmental conditions orwith unauthorized modifications, then the acquired data might be inaccurate.

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Introduction

Introduction

2This guide describes the basic operation, troubleshooting, and maintenance of the CESI 8000
Plus system. Read this guide thoroughly before the product is used, and operate the product inaccordance with the instructions in this guide.
This guide supplies safety instructions and precautions to make sure that the user operates thesystem safely. Obey all Warning and Caution instructions in this guide.

Description
CESI-MS is the integration of capillary electrophoresis (CE) with electrospray ionization(ESI) in a dynamic process within a single device. It is designed for mass spectrometry
applications analyzing charged and polar molecules. CESI is a front-end separation-andionization technology that combines the high-efficiency characteristics of CE with ESI. This
integration brings together the high-resolution power of CE in an ultra low-flow format, which
enhances the sensitivity of mass spectrometry while reducing ion suppression.
In the CESI 8000 Plus system, sample components are separated by an electrical field thatis applied between the inlet vial and the OptiMS sprayer. Conductive fluid is automaticallydelivered from a system vial to complete the CE circuit. The OptiMS sprayer does not require
any make-up (sheath) liquid. This design makes sure that the intrinsic advantages of CE are
delivered by the sprayer to the mass spectrometry without dilution or disturbance, resulting inultra-low flow.
The OptiMS cartridge assembly consists of a separation capillary composed of the porous
sprayer, conductive liquid capillary (CLC), circulating liquid cooling, and sprayer housing.
The circulating coolant maintains the capillary temperature, maximizing reproducibility bycontrolling Joule heating. The capillary is housed in a protective cartridge that allows for easytransfer and routine use in a rugged and robust manner. The cartridge clicks into positionin the CESI 8000 Plus system, creating an easy-to-use plug-and-spray setup for the mass
spectrometer.

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Introduction
Figure 2-1 CESI 8000 Plus System Conceptual Overview

Item

Description

1

Cartridge

2

Separation capillary3

Conductive liquid capillary

4

Sprayer housing

5

Adapter on the mass spectrometer

6

Power supply for the mass spectrometer

7

Current monitor for the CESI 8000 Plus system

8High-voltage power supply

9

High-voltage input cable

10High-voltage output cable

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Introduction
The following optional detectors are also available from SCIEX for use with the CESI 8000 Plus
High Performance Separation-ESI Module:• An ultraviolet (UV) detector that allows for six different bandpass filters• A photo diode array (PDA) detector that is in the 190 nm to 600 nm range• A laser-induced fluorescence (LIF) detector that permits high-sensitivity analysis of labeledmolecular species
For instructions about how to use the UV, PDA, or LIF detector, refer to the documents: PA 800
Plus Maintenance Guide, PA 800 Plus Overview Guide, and PA 800 Plus Methods Development
Guide.

Hardware Overview
WARNING! Electrical Shock Hazard. Connect the high-voltage input andoutput cables at both ends before the CESI 8000 Plus system is turned on oroperated.
The main components of the CESI 8000 Plus system include a CE platform and an OptiMS
sprayer. The CE platform has:
• Trays that hold sample vials, buffers, and other solutions• An interface block• A high-voltage power supply and electrodes• Temperature control hardware• A sample injection mechanism
The high-voltage input cable connects the mass spectrometer to the current monitor circuit on
the CESI 8000 Plus system. The high-voltage output cable sends the voltage from the outlet
side of the current monitor circuit to the capillary, which is required for electrospray.

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Figure 2-2 CESI 8000 Plus System

Item

Description

1

Cartridge installed

2

Access panel

3

Sprayer

4High-voltage input connection from the mass spectrometer

5

High-voltage output connection to the adapter on the mass spectrometer6

Holster for the sprayer

Sample-Handling System
WARNING! Personal Injury Hazard. When the sample cover is opened, wear
protective eyewear, a lab coat, and gloves.

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CAUTION: Potential System Damage. To decrease the risk of breakage and expelled
particles, use only SCIEX vials that are designed for the CESI 8000 Plus system. Examine
every vial for damage before use. Do not use any vial that shows cracks or other damage.
The sample-handling system holds four trays: two sample trays (inlet and outlet) and two buffer
trays (inlet and outlet). The sample trays are used for samples. The buffer trays hold the othersolutions that are required for electrophoresis. The trays are on two parallel tracks. In usual
conditions of operation, the trays on the left are inlet trays for sample and buffer, and the trays
on the right are outlet trays for sample and buffer.
Figure 2-3 CESI 8000 Plus System Trays

Item

Description

1

Inlet sample tray (48 vials)

2

Inlet buffer tray (36 vials)

3

Outlet sample tray (48 vials)

4

Outlet buffer tray (36 vials)

Each buffer tray has slots for 36 CESI vials. The sample tray holds 48 CESI vials. The trays arenumbered from the front to the back, starting with 1, and a letter from left to right, starting with A.

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Figure 2-4 Sample and Buffer Trays

Item

Description

1

Buffer tray

2

48-vial sample tray

Syringe Pump
The CESI 8000 Plus system uses an internal pump mechanism to supply 0.1 psi to 25 psi to dopressure injections or low-pressure mobilizations. The pump can apply a maximum of 100 psi to
move the fluids through the capillary. Pressure can also be applied to both ends of the cartridge(both capillaries) at the same time, so that both background electrolyte and conductive fluid canbe supplied to the cartridge at the same time.

High-Voltage Power Supply
The high-voltage power supply can deliver a maximum of 30 kV with a maximum current of
300 μA. The user supplies values for current, voltage, or power operation. The voltage range isfrom 1 kV to 30 kV, in increments of 100 V. The polarity is configured in the 32 Karat software.
The current range is from 3.0 μA to 300 μA, in increments of 0.1 μA.
During operation, the current, voltage, or power gradually increases to the value set by the user.
Limits for current, voltage, and power can be set to protect the capillary. For example, if the

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voltage is set to 30 kV,, but the maximum current setting is only 3.0 μA, then the system can getto the maximum current setting before getting to the value set for voltage. The system controls
the voltage to keep the current within the maximum setting.

LED Indicators
The front panel of the system has LED indicators for power, ultraviolet (UV), high voltage (HV+and HV–).
Figure 2-5 LED Indicators on the Front Panel

Item

Description

PWR

Identifies if system power is on or off

UV

For service only

HV+

Identifies that high voltage is set to normal polarity

HV–

Identifies that high voltage is set to reverse polarity

Cartridge and Sample Cover Interlocks
WARNING! Personal Injury Hazard. When the sample cover is opened, wear
protective eyewear, a lab coat, and gloves.
CAUTION: Potential Wrong Result. Do not open the cartridge cover during a run. The run
will stop and the separation will fail.
The hinged doors of the CESI 8000 Plus system have interlock sensors that prevent unsafe
access to the inside of the system. The outer door is the sample cover. The inner door is the
cartridge cover.
When the sample cover is opened, this occurs:

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Introduction• Any tray movement stops immediately.
• Any programmed event that requires tray movement is prevented.
• A method or sequence stops when a step that requires tray movement occurs.
• If a method is running or if high voltage is applied while the tray is not moving, then a system
beep occurs every 5 seconds.
Figure 2-6 Sample Cover (Outer Door)

When the cartridge cover is opened, this occurs:• If high voltage is on, then it turns off.
• The pump that supplies the capillary coolant turns off.
• The detector filter wheel moves to the closed position.

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Figure 2-7 Cartridge Cover (Inner Door)

OptiMS Cartridge
WARNING! Electrical Shock Hazard. To prevent a shock, do not touch anadapter on a mass spectrometer that is connected to the CESI 8000 Plus
system when the separation voltage is on.
CAUTION: Potential System Damage. Use the lowest ESI voltage possible. If the ion
source is exposed to high temperatures, then blockage in the emitter and damage canoccur.
The cartridge assembly has a separation capillary that ends in an ESI sprayer tip and a
conductive liquid capillary. Both capillaries are encased in a liquid-cooling tube. The separation
capillary and the conductive liquid capillary are different capillaries. The contents of theseparation capillary never touch or mix with the contents of the conductive liquid capillary.
The inlet ends of the capillaries are protected by sheaths that retract when the cartridge isinstalled in the CESI 8000 Plus system. When the cartridge is not installed in the system, locking
mechanisms prevent the protective sheaths from retracting.
Condition the capillaries before a new cartridge is used for the first time and before a cartridgethat has been in storage is used again. Refer to the section: Condition the Capillaries.

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Figure 2-8 OptiMS Cartridge

Item

Description

1

Cartridge body

2

Separation capillary in liquid-cooling tube

3

Conductive liquid capillary in liquid-cooling tube

4

Protective sheaths that retract when the cartridge is installed

5

Sprayer housing

6

Sprayer tip

7

Protective sheath shown retracted

8

Exposed capillary when protective sheath is retracted

9

Inlet end of separation capillary

10

Outlet end of cartridge body

The ESI needle, located in the sprayer tip, closes the circuit between the CESI 8000 Plus
system and the mass spectrometer, allowing electrospray to occur.

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Figure 2-9 Conceptual View of Inside the Sprayer Tip

Item

Description

1

ESI needle

2

Conductive liquid3

Separation capillary

4

Etched segment of separation capillary

5

Plume

The sprayer tip is made of polyether ether ketone (PEEK), which is a high-performance plastic
material that has been tested and proven to be inert under CESI-MS conditions. The sprayer
locks into an adapter specifically designed to fit the NanoSpray ion source on the mass
spectrometer.
Figure 2-10 Adapter for the NanoSpray Ion Source

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Item

Description

1

High-voltage input cable2

High-voltage output cable

Mass Spectrometer Adapters
The following mass spectrometer adapters are available from SCIEX:• OptiMS SCIEX MS Adapter for NanoSpray III• OptiMS Waters MS Adapter for NanoLockSpray and NanoFlow Ion Sources• OptiMS Thermo MS Adapter for NanoSpray II, NanoSpray Flex, and NanoSpray Flex NG Ion
Sources• OptiMS Bruker MS Adapter
Instructions for the SCIEX adapter follow. For the others, read the Installation Guide for the mass
spectrometer adapter in use.

Required Reagents and Materials
Table 2-1 Stock Reagents
Reagent

VendorPart Number

Acetic acid, glacial (HAc)

Sigma-Aldrich

A6283

7.5 M Ammonium acetate (AmAc)

Sigma-Aldrich

A2706(For neutral OptiMS cartridge only) Ammoniumhydroxide (NH4OH) (30%)

Sigma-Aldrich

05002

CE Grade Water

SCIEX

C48034cIEF Peptide Marker Kit

SCIEX

A58481

0.1 M Hydrochloric acid (HCl)Sigma-Aldrich

1.09060

Methanol (MeOH)

Sigma-Aldrich

A454

0.1 M Sodium hydroxide (NaOH)

SCIEX

3384241 M Sodium hydroxide (NaOH)

Sigma-Aldrich

1.09137

Table 2-2 Additional Supplies from SCIEX
Material
Silica Surface OptiMS Cartridge
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Table 2-2 Additional Supplies from SCIEX (continued)
Material

Part Number

Auxiliary I/O Cable Assembly

5032115

GPIB Connector Extender with Green I/O Connector Kit

A78960CESI Vial (100 Pack)

B11648CESI Vial Cap (100 Pack)

B24699PCR Microvial (100 Pack)

144709nanoVial (100 Pack)

5043467

MS Synthetic Peptide Calibration Kit

5045759(Optional) Neutral OptiMS Cartridge

B07368(Optional) Protein Test Mix

477436

Customer-Supplied Equipment and Supplies• Powder-free gloves, neoprene or nitrile recommended• Safety glasses• Laboratory coat
• Vortex mixer• Pipettes and appropriate tips
• Analytical balance• Centrifuge tubes, 0.5 mL• Volumetric flasks, 30 mL, 50 mL, and 500 mL• Glass bottles, 20 mL and 100 mL• Glass vials, 20 mL• pH meter• Nalgene bottle, 500 mL

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Set Up the Sytem

3

WARNING! Electrical Shock Hazard. To prevent a shock, do not touch anadapter on a mass spectrometer that is connected to the CESI 8000 Plus
system when 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 3-1 Cartridge Cover

2.

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

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Figure 3-2 Insertion Bar

3.

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

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

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Figure 3-4 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 3-5 Aligning Blocks

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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 3-6 and Figure 3-7.

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 3-6 T Slider

Item
1

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Align the T slider in the groove

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Figure 3-7 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.

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Figure 3-8 Coolant and Capillary Tubing

10. Lower the insertion bar, and then tighten the thumbscrews.
Figure 3-9 Thumbscrews on the Insertion Bar

Connect the GPIB-USB Cable
The GPIB-USB cable connects the controller to the CESI 8000 Plus system.
1.

Make sure that the CESI 8000 Plus system controller (computer, monitor, keyboard, andmouse) is assembled.

2.

Make sure that both the CESI 8000 Plus system and the controller are connected toelectrical power.

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3.

Connect the GPIB-USB cable to the port labeled “Controller” on the CESI 8000 Plus system.
If required, then use a spacer.

4.

Connect the other end of the GPIB-USB cable to a USB port on the CESI 8000 Plus system
controller.
Figure 3-10 GPIB-USB Cable Connection

Item

Description

1(Optional) Spacer connector

2

GPIB-USB cable connection to spacer to controller port

3

GPIB-USB cable connection to USB port on acquisition computer onmass spectrometer

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Connect an Auxiliary I/O Cable
The auxiliary input/output (I/O) cable connects the CESI 8000 Plus system to the mass
spectrometer.
Note: To use an Ethernet cable, refer to the section: Connect an Ethernet Cable.
1.

Install the white/black wire in pin position 9.

2.

Install the green/black wire in pin position 10.

3.

Connect the red/black wire and the orange/black wire together to create a short.
Figure 3-11 Auxiliary I/O Connection

Change the Mass Spectrometer Type
1.

Turn on power to the CESI 8000 Plus system.

2.

Click Start > CESI 8000 Software, and then click Change MS Type.

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Figure 3-12 Change MS Type Option

3.

Make sure that the Connect to AB SCIEX MS check box is cleared.
Figure 3-13 Change MS Type Dialog

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.

Configure the Hardware Profile
Note: This procedure applies only to SCIEX 5600 and 6600 systems.

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Do this procedure to configure a hardware profile that recognizes the following components:• Mass spectrometer• Autosampler• Software application (Curtain Gas Patch)
1.

In the Analyst TF software, in the Navigation bar, under Configure, double-click Hardware
Configuration.
Figure 3-14 Navigation Bar

Note: The acquisition computer on the mass spectrometer uses the Analyst TF software.
For information, refer to the document: Analyst Software Advanced User Guide.
2.

Click New Profile.

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Figure 3-15 Hardware Configuration Editor Dialog

3.

In the Profile Name field, type a name, and then click OK.
Figure 3-16 Create New Hardware Profile Dialog

4.

Click Add Device.

5.

Select Mass Spectrometer TripleTOF 6600, and then click OK.

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Figure 3-17 Available Devices Dialog

6.

Click Add Device again.

7.

In the Device Type list, select Software Application, and then click OK.
Figure 3-18 Device Type: Software Application

8.

Click Add Device again.

9.

In the Device Type list, select Autosampler, and then click OK.

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Figure 3-19 Device Type: Autosampler

The added devices show in the Devices in current profile list in the Create New Hardware
Profile dialog.
10. To set up the mass spectrometer, do this:a.

In the Create New Hardware Profile dialog, select Mass Spectrometer TripleTOF
6600, and then click Setup Device.

b.

Open the Communication tab.

c.

Accept the default settings, and click OK.

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Figure 3-20 Mass Spectrometer Dialog: Communication Tab

11. To set up the software application, do this:a.

In the Create New Hardware Profile dialog, select Software Application, and then click
Setup Device.

b.

Make sure that the Beckman CE Driver is selected, and then click OK.

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Figure 3-21 Software Application Settings Dialog

12. To set up the autosampler, do this:a.

In the Create New Hardware Profile dialog, select AutoSampler Agilent, and then click
Setup Device.

b.

Open the Communication tab, and then click Advanced.

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Figure 3-22 Agilent Autosampler Dialog: Communication Tabc.

Select the Simulation Mode check box, and then click OK.
Figure 3-23 Advanced Settings Dialog

The Agilent Autosampler device setup dialog opens.
d.

Click OK.
The Create New Hardware Profile dialog opens.

13. Click OK.
The Hardware Configuration Editor dialog opens.
14. Select the profile that was just created, and then click Activate Profile.
A green check mark shows next to the activated profile.

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15. At the bottom right of the Analyst TF software window, make sure that all of the icons areyellow (standby).
Figure 3-24 Icons in Standby

16. If the icons are not yellow, then deactivate the hardware profile and activate it again.

Install the Adapter
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.
1.

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

2.

Pull the ion source stage as far away as possible from the inlet on the mass spectrometer.
Figure 3-25 Pull the Ion Source Out

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.

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3.

Install the adapter in the ion source and push the adapter as far forward as possible, so thatthe hook at the end of the adapter goes under the end of the rail.
Figure 3-26 Orientation of the Adapter Before Installation

Item

4.

Description

1

High-voltage output cable

2

Hook

3

Adapter4

Ion source

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

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Figure 3-27 Tighten the Thumbscrew

5.

Item

Description

1

Thumbscrew

Remove the protective sleeve from the sprayer tip.
Figure 3-28 Protective Sleeve and Sprayer Tip

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.

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6.

To install the sprayer assembly, carefully align the arrow with the Unlock position on theadapter. Do not let the sprayer tip touch any surfaces.
Figure 3-29 Install the Sprayer Assembly

Item

7.

Description

1

Sprayer assembly2

Unlock position

Turn the sprayer assembly counterclockwise to lock it in the adapter.

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Figure 3-30 Lock the Sprayer Assembly in the Adapter

Item

Description

1

Sprayer in the Unlock position

2

Sprayer in the Lock position

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Connect the High-Voltage 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.

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

2.

On the right side of the CESI 8000 Plus system, open the access door to show the highvoltage connections panel.
Figure 3-31 High-Voltage Connections Panel

Item
1

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Input (red) port on connections panel

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Item

3.

Description

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.

4.

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.

5.

Connect the red banana plug to the red port on the connections panel.
Note: If the red banana plug is not installed, then EMI from the high-voltage cables canoccur.

6.

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.

Align the System with the Mass Spectrometer
1.

If required, then use the coarse Z-axis adjustment knob to move the ion source stage andadapter fully away from the curtain gas plate. Make sure that the capillary will not touch themass spectrometer when the stage moves forward.

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Figure 3-32 Move the Ion Source Stage

Item

Description

1

Coarse Z-axis adjustment knob

2

Ion source stage

Note: Make sure that there is a cover on the source drain assembly on the mass
spectrometer. The source drain assembly must be covered fully to operate correctly.

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Figure 3-33 Cover on the Source Drain Assembly

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.

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Figure 3-34 System Near the Ion Source Stage

3.

Item

Description

1

Coolant tubes

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.

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Figure 3-35 Alignment of the Sprayer Tip, Height Indicator, and Inlet on the Mass
Spectrometer

Item

Description

1

Height indicator on the CESI 8000 Plus system

2

Sprayer tip

3

Inlet on the mass spectrometer4.

Move the stage toward the inlet on the mass spectrometer until the stage goes into position
with a click on the guide rails.

5.

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.
Note: Do not press both the Up and Down buttons at the same time.

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Figure 3-36 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.
6.

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.

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Figure 3-37 Lock the Wheels of the Mobile Cart

Note: When the alignment is correct, the tubing from the sprayer assembly will not havedips or pockets.
7.

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.

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Figure 3-38 XYZ-Axes Adjustment Knobs

Item

Description

1

Height indicator on the CESI 8000 Plus system

2

Fine Z-axis adjustment knob (movement toward the curtain gas plate)3

Coarse Z-axis adjustment knob (movement toward the curtain gas plate)4

Y-axis adjustment knob (vertical movement)

5

X-axis adjustment knob (horizontal movement)

6

Stage

7

Sprayer tip

8

Inlet on the mass spectrometer

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4

Prepare the ReagentsThe following reagents are used with the silica surface OptiMS cartridge. The sample typecontrols which reagents are required to do a separation.
Table 4-1 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
1:10 solution of PepCalMix and CE Grade
Water

Test sample

1:1 solution of PepCalMix and 10% HAc
solution

Direct infusion

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.

2.

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

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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 PepCalMix Test Sample
1.

In a 0.5 mL centrifuge tube, add 10 µL of PepCalMix and 90 µL of 1 μM 200 mM LE buffer,
pH 4.0.

2.

Mix the solution in a vortex mixer for 10 seconds.

3.

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

Prepare the PepCalMix Solution for Direct
Infusion1.

In a 0.5 mL centrifuge tube, add 50 µL of PepCalMix and 50 µL of 10% HAc solution.

2.

Mix the solution in a vortex mixer for 10 seconds.

3.

Put the sample vial in the inlet sample tray in position A1.

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4.

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

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.

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Prepare the Trays
Use only CESI vials and caps in the CESI 8000 Plus system buffer and sample trays.

It is important for each buffer and sample to be in the location identified in the tray layout. The
buffer and sample locations are related to the method in the 32 Karat software. If a vial is put ina different position, then the position must be identified in the method in the 32 Karat software or
manually in the sequence table.

About Vials
CAUTION: Potential System Damage. Do not overfill the vials. If the vials are too full, thenliquid can go into the pressure system and cause damage.
CAUTION: Potential System Damage. Do not underfill the vials or let the liquid level get
too low. If the liquid level in the vials is too low, then the separation capillary can fill with
air and cause the vials to break if voltage is applied.
Three types of vials are used with the CESI 8000 Plus system:• CESI vials are used for buffer and as holders for microvials and nanoVials.
• Microvials are used for sample volumes from 50 µL to 100 µL. These vials must be put in a
CESI vial and then put in the sample tray.
• nanoVials are used for sample volumes from 5 µL to 50 µL. These vials must be put in a
CESI vial and then put in the sample tray.
Note: Always use a CESI vial cap.
Note: Do not use any vial or cap more than once.

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Fill a CESI Vial
Note: To prevent splashing, put the empty vials in the tray, and then add liquid and attach the
caps.
1.

Fill the CESI vial to the maximum fill line.
Note: Do not put more than 1.4 mL in a CESI vial.
Figure 5-1 CESI Vial

2.

Item

Description

1

CESI Cap

2

Maximum fill line

3

CESI Vial

Attach a CESI cap.
Note: When filling the vials, do not make air bubbles. If there are air bubbles in the vial, thenspin the vial in a centrifuge for a few seconds to remove the bubbles.

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Fill a Microvial
Note: To prevent splashing, put the empty vials in the tray, and then add liquid and attach the
caps.
1.

Fill the microvial with at least 50 μL of sample.
Figure 5-2 Microvial

Item

Description

1

CESI Cap

2

Microvial

3

CESI Vial

4

Microvial inside CESI vial

2.

Put the microvial inside the CESI vial.

3.

Attach a CESI cap.
Note: When filling the vials, do not make air bubbles. If there are air bubbles in the vial, thenspin the vial in a centrifuge for a few seconds to remove the bubbles.

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Fill a nanoVial
For sample volumes between 5 μL and 50 μL, use a nanoVial.
Note: To prevent splashing, put the empty vials in the tray, and then add liquid and attach the
caps.
1.

Use a thin pipette tip to transfer the sample to the deeper well of a nanoVial.
When the tab points to the user, the deeper well is on the left side of the nanoVial.
Figure 5-3 nanoVial

Item

Description

1

nanoVial inside the CESI vial with the thin pipette tip transferring sample

2nanoVial inside the CESI vial with the cap attached2.

Attach a CESI cap.

3.

Put the sample vial in the inlet sample tray at position S1:A1.
Note: Make sure that the tab on the outside of the nanoVial points to the front of the sample
tray.

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Figure 5-4 Orientation of the nanoVial Tab in the Sample Tray

Item

Description

1

Electrode at the left side of the nanoVial

2

Capillary at the right side of the nanoVial (for use in loading sample)3

Tab outside of the nanoVial

4

Sample tray

Note: If the number of sample vials will not fill the tray, then keep every second column inthe sample tray empty. This will make it easier to remove the nanoVials from the tray.
Note: When filling the vials, do not make air bubbles. If there are air bubbles in the vial, thenspin the vial in a centrifuge for a few seconds to remove the bubbles.

Prepare the Buffer Trays
1.

Use the following table to prepare the required reagents.

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Table 5-1 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 5-5 Buffer Tray Layout

Prepare the Sample Tray
Sample can evaporate over time. Use a minimum volume of 50 μL of sample for a sequencewith a duration of approximately 24 hours. If the duration of the sequence is more than 50 hours,
then use a minimum volume of 80 μL.
• Use the following figure to put the sample in the correct position in the tray.

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Figure 5-6 Sample Tray Layout

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6

Prepare the System
To make sure that the system operates correctly, do the following procedures.

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.
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.

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Figure 6-1 Sprayer Immersed in Liquid

7.

Run the CESI-MS conditioning method.

8.

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

9.

Use lint-free wipes to dry the sprayer carefully.
Figure 6-2 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.

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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 Analyst TF 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 6-3 Pressure Settings Dialog to Fill the Conductive Liquid Capillaryc.

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.

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Figure 6-4 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.
Figure 6-5 Droplet at the End of the Stainless Steel Needle

4.

When the rinse is complete, to fill the separation capillary with BGE, do this:User Guide
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Prepare the Systema.

Go to the Direct Control window.

b.

Click the Rinse field.
Figure 6-6 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.
When the separation capillary is filled with BGE, a droplet will show at the end of thesprayer tip.
Figure 6-7 Droplet at the End of the Sprayer Tip

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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.

Fill the capillary with PepCalMix test sample solution.

2.

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

3.

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.
Figure 6-8 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.
4.

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

5.

On the Source/Gas tab, do this:User Guide
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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.
6.

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.

b.

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.

7.

Click Start.

8.

If a non-SCIEX mass spectrometer is in use, then do this on the mass spectrometer
acquisition computer:9.

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 6-9 Typical Spray Profile of a Cartridge that Uses 10% HAc Solution as the
BGE

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10. In the Direct Control window, click Stop.
11. 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.
12. In the IonSpray Voltage Floating (ISVF) field, type the minimum ESI voltage, and thenclick OK.
Make sure that electrospray starts again.
13. In the IonSpray Voltage Floating (ISVF) field, increase the value by 100 V.
14. 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.
15. To check the stability of the spray, continue to apply 20 kV (normal polarity) for 20 minutes.
16. 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.

17. Click Acquire, and then type a file name (for example, Baseline).
18. 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.

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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.

19. Use the Y-axis alignment knob to maximize the baseline fluctuations.
Figure 6-10 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.

20. 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.

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Fine-Tune the Position of the Sprayer Tip
CAUTION: Potential System Damage. Make sure that the sprayer tip is in position outsideof the curtain gas plate. If the sprayer tip is too close, then rinse solution can drip onto
the curtain gas plate and cause damage.
Before a separation is run, it is critical to optimize the position of the sprayer tip in front of thecurtain gas plate to get the correct ESI voltage. If the sprayer tip is too far away from the curtaingas plate, then a high ESI voltage can be required, which causes analyte fragmentation. For
intact proteins, electrochemical reactions such as oxidation can occur. The green area in thefollowing figure shows the recommended distance of the sprayer tip and the recommended ESI
voltage values. Avoid the red area.
Figure 6-11 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• If the signal separation voltage is changed• If a different BGE is used1.

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

2.

Use the XYZ-axes adjustment knobs to move the sprayer tip 3 mm from the curtain gas
plate.

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.

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Prepare the System• Monitor the Direct Control window to make sure that the electrical current is stable.
4.

Set the ESI voltage to 1,000 V and then increase the value in increments of 100 V until
electrospray is detected.

5.

Increase the ESI voltage by 200 V.

6.

Use the XYZ-axes adjustment knobs to move the sprayer tip and maximize the signal
intensity of the mass spectrometer.
Make sure that the sprayer tip is approximately 3 mm from the curtain gas plate.

7.

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

8.

Set the ESI voltage to 1,000 V and then increase the value in increments of 100 V 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 200 V.
Note: This is the optimal ESI voltage. Use this voltage with the mass spectrometer method
to provide a stable electrospray during separation.

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

Manual Calibration
To get the most accurate mass determination, manually calibrate the mass spectrometer.
Note: The following procedures were made for the SCIEX 6600 system. For other SCIEX
mass spectrometers or mass spectrometers from other manufacturers, use the manufacturer's
recommendations.
After the mass spectrometer has been manually calibrated, include autocalibration in thesequence when data is acquired for samples. Refer to the section: About Autocalibration.
For more information about calibration, refer to the document: AB SCIEX Mass Calibration
Tutorial. To open the document, click Start Menu > All Programs > AB SCIEX > Analyst TF
1.7 > Hardware and Software Guides.

Prepare for Manual Calibration
1.

In a sample vial, add 90 μL of PepCalMix and 10% HAc solution to make a 1:1 solution.

2.

Put the vial in position A1 (SI:A1) in the sample tray.

3.

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

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Figure 6-12 Inject Parameters Dialog

4.

Select the injection parameters.
Note: To inject at 100 psi for 180 seconds, make sure that the For Capillary Fill check box
is selected.

5.

When the capillary is filled, go to the Direct Control window, and then click Voltage.
Figure 6-13 Voltage Settings Dialog

6.

In the Voltage field, type 20.

7.

In the Duration field, type 20.

8.

Make sure that the capillary inlet is in position BI:A1 and the outlet is in position BO:A1.

9.

Click OK.

Create a Reference Table
1.

In the Analyst TF software, in the Navigation bar, click Acquire.

2.

Click Tools > Settings > Tuning Options, and then click Reference.

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Figure 6-14 Reference Table Editor Window

3.

To open a new, empty reference table, click New.
Figure 6-15 New Reference Table in the Reference Table Editor Window

4.

In the Name field, type a name that identifies the calibration solution (in this example,
PepCalMix).

5.

Make sure that Positive is clicked.

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6.

In the Reference Ions For TOF MS Calibration table, type the following values.
Table 6-1 Reference Ions for TOF MS Calibration

7.

Use

Compound Name

Precursor m/z (Da)CE forMS/MS

DP for
MS/MS

1

AETSELHTSLK

408.55010

40

80

1

GAYVEVTAK

473.26020

40

80

1

IGNEQGVSR

485.25302

40

80

1

LVGTPAEER

491.26559

40

80

1

LDSTSIPVAK

519.79969

40

80

1

AGLIVAEGVTK

533.32333

40

80

1

LGLDFDSFR

540.27342

40

80

1

GFTAYYIPR

549.28633

40

80

1

SGGLLWQLVR

569.83398

40

80

1

AVGANPEQLTR

583.31360

40

80

1

SAEGLDASASLR

593.80053

40

80

1

VFTPLEVDVAK

613.34955

40

80

1

VGNEIQYVALR

636.35273

40

80

1

YIELAPGVDNSK

657.34499

40

80

1

DGTFAVDGPGVIAK

677.85827

40

80

1

YDSINNTEVSGIR

739.36148

40

80

1

SPYVITGPGVVEYK

758.91050

40

80

1

ALENDIGVPSDATVK

768.90340

40

80

1

AVYFYAPQIPLYANK

883.47380

40

80

1

TVESLFPEEAETPGSAVR

964. 97741

40

80

In the Reference Ions for MS/MS Calibration table, type the following values.
Table 6-2 Reference Ions for MS/MS Calibration
Use

Fragment Name

Fragment m/z (Da)1b2

185.09207

1

b3

348.15540

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Table 6-2 Reference Ions for MS/MS Calibration (continued)
Use

Fragment Name

Fragment m/z (Da)1b4

560.30788

1

b5

661.35555

1

N/A

758.91050

1

y7

799.44398

1

y8

856.46544

1

y9957.513121

y101070.59719

1

y111169.66560

1

y121332.72893

8.

In the Use for MS/MS column, select the check box for the applicable compound in thecalibration solution (in this example, the peptide at 758.91 m/z).

9.

Make sure that the value in the Retention time tolerance +/- field is 30.

10. Click OK.
Figure 6-16 Tuning Options Dialog

11. Make sure that the name of the new reference table (in this example, PepCalMix) shows in
the Positive Reference field.
12. Click OK.
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Manually Calibrate in TOF MS Mode1.

In the Analyst TF software, in the Navigation bar, under Tune and Calibrate, double-click
Manual Tuning.
Figure 6-17 Tune Method Editor Window

2.

3.

4.

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

In the Ion Source Gas1 (GS1) field, type 0 (zero).

b.

In the Ion Source Gas1 (GS2) field, type 0 (zero).

c.

In the Curtain Gas (CUR) field, type 5.

d.

In the Interface Heater Temperature (IHT) field, type 50.

On the MS tab, do this:a.

In the Scan type list, select TOF MS.

b.

In the Accumulation time field, type 1.000.

c.

In the TOF Masses (Da) Min field, type 350.

d.

In the TOF Masses (Da) Max field, type 1000.

e.

In the Period Duration field, type 1000.

Open the Advanced MS tab.

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Figure 6-18 Tune Method Editor Window: Advanced MS Tab

5.

Make sure that the MCA check box is cleared.

6.

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

7.

Adjust the position of the sprayer until the spray is stable.

8.

Click Start.
After approximately 1 minute, windows open to show the total ion chromatogram (TIC) andmass spectrum.
Figure 6-19 TIC and Mass Spectrum Windows

9.

To open windows that show the TIC and mass spectrum for the data file that was acquired,right-click the TIC window, and then click Open File.

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Figure 6-20 TIC and Mass Spectrum Windows from the Acquired Data File

10. To delete the mass spectrum pane, click the pane, and then on the toolbar, click the Delete
icon.
11. To get an average mass spectrum, click and drag the cursor to highlight the TIC window,
and then double-click the TIC window.

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Figure 6-21 Average Mass Spectrum Pane

12. Right-click the mass spectrum pane, and then click Re-Calibrate TOF.
Figure 6-22 TOF Calibration Window

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13. From the Reference Table list, select the reference table that was created for the calibrant(in this example, PepCalMix).
Note: If the correct reference file does not show in the list, then the reference table has notbeen created. Refer to the section: Create a Reference Table.
14. In the Tolerance field, type 0.2.
15. To calculate the average error for this new calibration, click Calculate new calibrations.
16. Make sure that the value for the Average Error is within the routine operating standards forthe mass spectrometer being calibrated.
17. Click Calibrate spectrum.
The new calibration values show.
18. Make sure that the Set As Instrument Default check box is selected.
Note: If an ion is not found during calibration, then right-click the missing ion in thereference table, and then click Delete. Click Calculate new calibrations.
19. To apply this calibration to all samples in the file, click Entire File.
20. Click Save.
21. Click OK twice.
22. To close the TOF Calibration window, click Close.
23. Close the TIC and mass spectrum panes.

Manually Calibrate in Product Ion Mode1.

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

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Figure 6-23 Tune Method Editor Window: Compound Tab

2.

3.

4.

Open the Compound tab, and then do this:a.

In the Collision Energy field, type 42.

b.

In the Collision Energy Speed (CES) field, type 5.

On the MS tab, do this:a.

In the Scan type list, select Product Ion.

b.

In the Product Of field, type 758.91.

c.

In the TOF Masses (Da) Min field, type 100.

d.

In the TOF Masses (Da) Max field, type 1500.

e.

Make sure that High Sensitivity is clicked.

Click Start.
Windows open to show the total ion chromatogram (TIC) and mass spectrum generated
during the product ion calibration.

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Figure 6-24 TIC and Mass Spectrum Windows

5.

Right-click the TIC window, and then click Open File.
Windows open to show the TIC and mass spectrum for the product ion calibration data filethat was acquired.
Figure 6-25 TIC and Mass Spectrum Windows from the Product Ion Calibration Data
File

Note: a) Example data for TOF-MS spectrum, b) example data for TOF-MS/MS spectrum
for peptide m/z 758.91 in high-resolution (HR) and high-sensitivity (HS) mode. Arrows show
the m/z values that relate to the peptides in the mixture and values used for TOF-MS and
MS/MS calibration.
Note: The spectrum that shows cannot be used for calibration.

6.

Click the mass spectrum window, and then the toolbar, click the Delete icon.

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7.

To get an average mass spectrum, click and drag the cursor to highlight the TIC window,
and then double-click the TIC window.
Figure 6-26 Re-Calibrate TOF

8.

Right-click the mass spectrum window, and then click Re-Calibrate TOF.

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Figure 6-27 TOF Calibration Window

9.

From the Reference Table list, select the reference table that was created for the calibrant(in this example, PepCalMix).
Note: If the correct reference file does not show in the list, then the reference table has notbeen created. Refer to the section: Create a Reference Table.

10. In the Tolerance field, type 0.2.
11. To calculate the average error for this new calibration, click Calculate new calibrations.
12. Make sure that the Average Error is within the routine operating standards for the mass
spectrometer being calibrated.
13. Click Calibrate spectrum.
The new calibration values show.
14. Make sure that the Set As Instrument Default check box is selected.
15. To apply this calibration to all samples in the file, click Entire File.
16. Click Save.
17. Click OK twice.
18. To close the TOF Calibration window, click Close.
19. Close the TIC and mass spectrum windows.

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7

Run Workflow

This section gives a tutorial about how to use the CESI 8000 Plus system with the mass
spectrometer. A PepCalMix test sample is used as the sample to analyze the performance of themass spectrometer and capillary separation.
To use the CESI 8000 Plus system with the mass spectrometer, first set up a sequence in the
Analyst TF software and then in the 32 Karat software. The mass spectrometer must be set up
before the CESI 8000 Plus system sends the start signal, so that the mass spectrometer canstart data acquisition.
Before the start of the sample run, make sure that a stable spray and the ESI voltage are set
correctly. Refer to the sections: Establish a Stable Spray and Optimize the ESI Voltage.

Methods for the Silica Surface OptiMS Cartridge
The methods and sequences for the silica surface OptiMS cartridge are installed with the
32 Karat software 10.3 or later in the folder C:\32karat\projects\CEMS\Methods.
Table 7-1 Methods for the Silica Surface OptiMS Cartridge
File Name

Method Description

CESI-MS Autocalibration_ABSciex.met

Used for autocalibration during batch runs to achieve
high mass accuracy. Refer to the section: About
Autocalibration.
Note: We recommend that autocalibration be done at aminimum of every 5 hours.

CESI-MS Cleaning.met

Used to clean the capillary at the end of every
sequence.

CESI-MS Conditioning.met

Used to condition the capillary.

CLC Conditioning.met

Used to condition the conductive line.

CESI-MS Separation for
ABSciex.met

Used to inject and separate a sample to make sure that
the CESI 8000 Plus system and mass spectrometer are
set up correctly.

CESI-MS Storage.met

Used to prepare the cartridge for long-term storage.
Refer to the section: Store the Cartridge.

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If the methods are missing, then use the following parameters on the Initial Conditions andTime Program tabs to create them manually. For more information, refer to the section: 32 Karat
Software Methods.
Note: The CESI-MS Auto-calibration_ABSciex.met method file included with the
32 Karat software is for a beta-galactosidase test sample and uses voltage to do the separation.
The autocalibration method used in this guide is for a PepCalMix test sample and uses pressure
to do the separation. This method is not available in the 32 Karat software and must be createdmanually. Either autocalibration method can be used with either test sample type.

Initial Conditions Tab
All of the methods for the silica surface OptiMS cartridge use the initial conditions in the following
figure.
Figure 7-1 Initial Conditions Tab

Time Program Tab
Each of the methods for the silica surface OptiMS cartridge uses a different time program.

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Figure 7-2 Time Program for the Conditioning Method

Figure 7-3 Time Program for the Separation Method

Note: For the system suitability test, do not use a separation voltage that is > 20 kV.

Figure 7-4 Time Program for the Autocalibration Method

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Figure 7-5 Time Program for the Cleaning Method

Figure 7-6 Time Program for the Conductive Liquid Capillary Conditioning Method

Figure 7-7 Time Program for the Storage Method

Do a System Suitability Test
To monitor the separation performance of the cartridge, optimize the position of the sprayer tip,and calibrate the mass spectrometer at the MS and MS/MS levels, do a system suitability test.
1.

In the Analyst TF software, in the Navigation bar, under Acquire, double-click Build
Acquisition Method.

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Figure 7-8 Acquisition Method Window: Acquisition Method Properties Tab

Note: If a completely new method is created, then make sure that:• In the Acquisition method pane, Beckman CE Driver is selected.
• On the Acquisition Method Properties tab:
• The selection in the Synchronization Mode field is No Sync.
• The value for Duration is at least 1.5 minutes shorter than the duration set in themethod in the 32 Karat software.
2.

In the Acquisition method pane, click TOF MS (+).

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Figure 7-9 TOF MS (+) Acquisition Method Window: MS Tab

3.

Click Edit Parameters.
Figure 7-10 TOF MS(+) Parameter Settings Dialog: Source/Gas Tab

4.

Type the values that show in the example.

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5.

Open the Compound tab, type the values that show in the example, and then click OK.
Figure 7-11 TOF MS(+) Parameter Settings Dialog: Compound Tab

6.

Open the Advanced MS tab, and then type values for the other parameters.
Figure 7-12 TOF MS(+) Acquisition Method Window: Advanced MS Tab

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7.

In the Acquisition method pane, click Product Ion (+).
Figure 7-13 Product Ion Acquisition Method Window: MS Tab

8.

Click Edit Parameters.
Figure 7-14 Product Ion Parameter Settings Dialog: Source/Gas Tab

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9.

Type the values that show in the example.

10. Open the Compound tab, type the values that show in the example, and then click OK.
Figure 7-15 Product Ion Parameter Settings Dialog: Compound Tab

11. Save the method file with the name CESI_MS_Sciex_PepCalMix_45min.

Create a Sequence in the 32 Karat Software1.

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

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Figure 7-16 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 7-17 Sequence Wizard - Unknowns Page

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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 7-18 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 7-19 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.

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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 7-20 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.
For information about the Allow Override option, refer to the section: Inject Event.
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.

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Run Workflow• 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 7-21 Sequence Table: Part A

To add autocalibration to the sequence, refer to the section: Add Autocalibration to theSequence.

Create a Batch in the Analyst TF SoftwareThis section gives the procedure to build a batch of 10 runs of PepCalMix with an autocalibration
run every 5 runs.
1.

In the Analyst TF software, in the Navigation bar, under Acquire, double-click Build
Acquisition batch.
The Batch Editor window opens.

2.

Click Add Set.
A new set called SET1 is added.

3.

Click Add Samples.
The Add Sample dialog opens.

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4.

In the Prefix field, type a prefix for the sample name (in this example, PepCalMix).

5.

Select the Sample number check box.

6.

In the Number of digits field, type 3.

7.

In the Sub Folder field, type the data file name, or click Browse and then find theapplicable data file.

8.

In the New samples Number field, type 10.
Figure 7-22 Add Sample Dialog

9.

Click OK.

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Figure 7-23 Batch Editor Window: Sample Tab

10. In the Vial Position column for each run, type 1.
To use the fill-down function, right-click and then click Fill Down.
11. Click Method Editor, and then find the applicable method file (in this example,
CESI_MS_Sciex_PepCalMix_45min).
12. Click File > Save as, and then type a name.
13. In the Batch Editor window, open the Calibrate tab.

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Figure 7-24 Batch Editor Window: Calibrate Tab

14. Select the Auto Calibration check box.
15. In the Calibrate Every field, type 5 for the number of sample runs between autocalibration.
16. In the Calibration Reference Table list, select the reference table that was created for thecalibrant (in this example, PepCalMix_CE-MS_Calibration Ref).
17. To make sure that the correct reference table is selected, click View.
The reference tables show 9 reference ions used for mass spectrometer calibration. The
peptide at 758.91 m/z is selected for MS/MS calibration. The retention time for all of thereference ions is 2.5 minutes, since all of the reference ions are included at the same time.
The retention time tolerance is ±30 seconds.
Table 7-2 Reference Ions for TOF MS Calibration
Use

Compound Name

Precursor m/z (Da)CE forMS/MS

DP for
MS/MS

1

AETSELHTSLK

408.55010

40

80

1

GAYVEVTAK

473.26020

40

80

1

IGNEQGVSR

485.25302

40

80

1

LVGTPAEER

491.26559

40

80

1

LDSTSIPVAK

519.79969

40

80

1

AGLIVAEGVTK

533.32333

40

80

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Table 7-2 Reference Ions for TOF MS Calibration (continued)
Use

Compound Name

Precursor m/z (Da)CE forMS/MS

DP for
MS/MS

1

LGLDFDSFR

540.27342

40

80

1

GFTAYYIPR

549.28633

40

80

1

SGGLLWQLVR

569.83398

40

80

1

AVGANPEQLTR

583.31360

40

80

1

SAEGLDASASLR

593.80053

40

80

1

VFTPLEVDVAK

613.34955

40

80

1

VGNEIQYVALR

636.35273

40

80

1

YIELAPGVDNSK

657.34499

40

80

1

DGTFAVDGPGVIAK

677.85827

40

80

1

YDSINNTEVSGIR

739.36148

40

80

1

SPYVITGPGVVEYK

758.91050

40

80

1

ALENDIGVPSDATVK

768.90340

40

80

1

AVYFYAPQIPLYANK

883.47380

40

80

1

TVESLFPEEAETPGSAVR

964. 97741

40

80

Table 7-3 Reference Ions for MS/MS Calibration
Use

Fragment Name

Fragment m/z (Da)1b2

185.09207

1

b3

348.15540

1

b4

560.30788

1

b5

661.35555

1

N/A

758.91050

1

y7

799.44398

1

y8

856.46544

1

y9957.513121

y101070.59719

1

y111169.66560

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Table 7-3 Reference Ions for MS/MS Calibration (continued)
Use

Fragment Name

Fragment m/z (Da)1y121332.72893

18. In the Calibration Method list, select the mass spectrometer method to be used forautocalibration (in this example, Autocal_PepCalMix).

Start the Batch in the Analyst TF Software1.

In the Batch Editor window, open the Submit tab, and then click Submit.
Figure 7-25 Batch Editor Window: Submit Tab

2.

To preview the queue, click View > Sample Queue.
The Queue Manager window opens to show that there are 12 runs (10 PepCalMix
separations and 2 autocalibrations) in the queue. The hourglass symbol in column 1 showsthat the queue is in Standby mode.

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Figure 7-26 Queue Manager Window

3.

Make sure that the acquisition computer on the mass spectrometer is in Standby mode.
Note: If the acquisition computer is already in Ready mode, then change it to Standby, andthen change it to Ready. Click Acquire > Standby, and then click Acquire > Ready.

Load the Trays
1.

Put the PepCalMix test sample in two microvials and attach caps.

2.

Put the PepCalMix test sample for autocalibration in position SI:A1 of the sample inlet tray.

3.

Put the PepCalMix test sample for the system suitability test in position SI:A2 of the sample
inlet tray.

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Figure 7-27 Sample Tray Layout

4.

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

5.

Wait for the trays to move to the load position, and then open the front cover of the CESI
8000 Plus system.

6.

Put the inlet tray in the inlet carrier (left) and the outlet tray in the outlet carrier (right), andthen close the front cover.

Start the Sequence in the 32 Karat Software1.

On the toolbar, click the Sequence Run icon

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Figure 7-28 Run Sequence Dialog

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 PepCalMix_Installation
sequence. The first autocalibration run in the following figure is being acquired.

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Figure 7-29 Monitor the Sequence Run

Analyze the Data from the PepCalMix Test
SampleEfficient system performance can be measured by the identification and clear separation of thepeaks in the PepCalMix test sample for the following two pairs of ions.
• 485.25 m/z and 491.25 m/z• 739.35 m/z and 768.90 m/z
1.

In the Analyst TF software, open the PepCalMix wiff file.
The following figure shows the total ion chromatograms (TICs) for the separation of
PepCalMix on three different bare fused-silica (BFS) cartridges.

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Figure 7-30 TICs for Three Separation Runs

Note:
2.

Create the extracted ion chromatogram (XIC) for peaks 485.25 m/z and 491.25 m/z andpeaks 739.35 m/z and 768.90 m/z, all with a width of 0.05.
Note: If required, then use the mass spectrometer mass calibration to adjust the peak
ranges.

3.

Calculate the difference in the migration time between for the two pairs of peaks. Thisdifference must be more than 0.05 minutes.
The following figure shows the XIC and mass spectra for peaks 485.25 m/z and 491.25 m/z
and peaks 739.35 m/z and 768.90 m/z of the PepCalMix test sample run. The differencein migration time for peaks 485.25 m/z and 491.25 m/z is 0.08 minutes. The difference inmigration time for peaks 739.35 m/z and 768.90 m/z is 0.25 minutes.

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Figure 7-31 XIC and Mass Spectra for a PepCalMix Run

About Autocalibration
Small variations in temperature that occur during usual operation can cause incorrect masses tobe reported. To increase the mass accuracy, we recommend that autocalibration be done every
5 hours of data acquisition.
Note: Do manual calibration before autocalibration is done. If the reference ions are outside of
the 100 ppm tolerance for peak identification, then autocalibration will not be successful.
Note: The following procedures are for the SCIEX 5600 and 6600 systems. For other SCIEX
mass spectrometers or mass spectrometers from other manufacturers, use the manufacturer's
recommendations.
The following figure shows the sample tray layout for autocalibration.

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Figure 7-32 Sample Tray Layout for Autocalibration

Autocalibration uses the CESI-MS autocalibration method and the following time program.
Figure 7-33 Time Program for Autocalibration

Analyze the autocalibration data to make sure that the peaks were identified and their calculatedmasses are satisfactory. Refer to the section: Analyze the Autocalibration Data.

Create the MS Acquisition Method for Autocalibration
Use this procedure when PepCalMix is the sample solution.
1.

In the Analyst TF software, in the Navigation bar, under Acquire, double-click Build
Acquisition Method.

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Figure 7-34 Acquisition Method Window: Acquisition Method Properties Tab

2.

In the Acquisition method pane, click TOF MS (+).

3.

On the MS tab, click Edit Parameters.

4.

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

In the Curtain Gas (CUR) field, type 10.

b.

In the IonSpray Voltage Floating (ISVF) field, type 1500.
The ISVF parameter sets the ESI voltage.

c.

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

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Figure 7-35 TOF MS (+) Parameter Settings Dialog: Source/Gas Tab

5.

Open the Compound tab, and then do this:CESI 8000 Plus High Performance Separation-ESI
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Figure 7-36 TOF MS (+) Parameter Settings Dialog: Compound Tab

6.

a.

In the Declustering Potential (DP) field, type 100.

b.

In the Collision Energy (CE) field, type 10.

In the Acquisition method pane, click Product Ion (+) 758.91.
Figure 7-37 Acquisition method Pane: Product Ion

7.

On the MS tab, click Edit Parameters.

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Figure 7-38 Product Ion (+) Parameter Settings Dialog: Source/Gas Tab

8.

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

In the Curtain Gas (CUR) field, type 10.

b.

In the IonSpray Voltage Floating (ISVF) field, type 1600.
The ISVF parameter sets the ESI voltage.

c.
9.

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

Open the Compound tab, and then do this:CESI 8000 Plus High Performance Separation-ESI
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Figure 7-39 Product Ion (+) Parameter Settings Dialog: Compound Taba.

In the Declustering Potential (DP) field, type 100.

b.

In the Collision Energy (CE) field, type 42.

c.

In the Collision Energy Spread (CES) field, type 5.

d.

In the Ion Release Delay (IRD) field, type 67.

e.

In the Ion Release Width (IRW) field, type 25.

Add Autocalibration to the Sequence
Use this procedure to edit the sequence table to include autocalibration.
Note: The sequences in the 32 Karat software and on the mass spectrometer must be the
same.
1.

In the 32 Karat software, open the sequence table.

2.

Click to highlight the first run, right-click the highlighted run, and then click Insert Line.

3.

At the bottom of the Method column, click the green arrow icon and then click CESI-MS
Auto-calibration_ABSciex.met.

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4.

In the Sample ID and File name fields, type the applicable values.

5.

To add another line for autocalibration, click to highlight the run on line 7, right-click thehighlighted run, and then click Insert Line.

6.

Do steps 4 and 5 again.
The following figure shows an example of the sequence.
Figure 7-40 Sample Sequence Example

7.

On the toolbar, click Sequence > Properties.
Figure 7-41 Sequence Properties Dialog

8.

Make sure that the File paths for Method and Data show the correct folder to save the data,
and then click OK.
Note: If required, then create a folder.

9.

Click File > Sequence > Save As.

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In this example, the sequence name is PepCalMix_Installation.

Analyze the Autocalibration Data
For the autocalibration to be successful, the following criteria must be met:
• The intensity of the reference ions is at least 10 counts per second (cps) in the mass
spectrometer data and 3.3 cps in the MS/MS data.
• The reference ions are within a mass tolerance of 100 ppm.
• There are ≥ 80% of the selected ions in the reference table.
If autocalibration is successful, then a green check mark shows. If the sample was acquired but
the calibration failed because one or more of the reference ions did not meet the calibration
criteria, then a red circle with a diagonal line through it shows. To see information about the
failure, double-click the circle icon.
If autocalibration fails, then an error message is shown in the Sample Details dialog. Click OK,
and then refer to the section: Troubleshoot an Autocalibration Failure.
1.

In the Analyst TF software, in the Navigation bar, under Explore, double-click Open Data
File.
If the Keep calibration data file check box was selected in the Queue Options dialog,
then data for each autocalibration is saved as a separate data file in the Cal Data
subfolder. The autocalibration data file names start with Cal and include the time stamp
and calibration sample index. For example, Cal20130910162907040.wiff.

2.

To extract the mass spectra from the TIC, highlight the region and then double-click
the region. Extract one mass spectrum between 2 minutes to 2.5 minutes (MS before
calibration) and another between 4 minutes to 4.5 minutes (MS after calibration).

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Figure 7-42 Data Analysis

Item

3.

Description

1

MS before calibration

2

MS/MS before calibration

3

MS after calibration

4

MS/MS after calibration

To get a list of ions in the mass spectrum, right-click the mass spectrum and then click List
data. Do this for both MS before calibration and MS after calibration.

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Figure 7-43 Obtaining List Data

4.

To show all the reference ions used for calibration, in each data list table, open the
Calibration Peak List tab.
Figure 7-44 Reference Ions

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5.

To make sure that the correct reference table has been selected, right-click the referencetable, click the PepCalMix_CE-MS_Calibration Ref reference table, and then click Use as
reference.
Figure 7-45 Reference Table Verification for MS Before Calibration

Figure 7-46 MS After Calibration Analysis

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The tables show the Target Mass (or theoretical mass) and the Found At mass (orexperimental mass) for all eight reference ions selected for autocalibration. The mass shift
between the Target Mass and the Found At mass is given as Mass Shift (ppm).
The mass shift is higher before calibration and lower after calibration for all ions.
6.

To evaluate the MS/MS mass accuracy, do steps 3 and 4 for MS/MS before and after
calibration.
For the MS/MS experiment, the mass shift after calibration is lower than it was before
calibration.
Figure 7-47 Evaluation of Peak Data in MS/MS Experiment

Troubleshoot an Autocalibration Failure
1.

Do the procedure in the section: Analyze the Autocalibration Data.

2.

Make sure that the intensity of the reference ions is correct.
• Mass spectrometer data, > 10 cps• MS/MS data, > 3.3 cps

3.

In the Calibration peak list table, if the value in the Mass shift (ppm) field is > 100 ppm,
then do manual calibration.
Refer to the section: Manual Calibration.

4.

Make sure that the threshold for peak detection is 1% in the spectrum.

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5.

a.

In the Navigation bar, under Tune and Calibrate, click Tools > Settings > Appearance
Options > Other Graph.

b.

In the Default Threshold for the Spectrum field, type 1.

For more autocalibration troubleshooting, refer to the section: Autocalibration
Troubleshooting.

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Shutdown and Disconnection

8

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 8-1 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.

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Figure 8-2 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 8-3 Unlock the Sprayer from the Cartridge

Item1

Description
Sprayer in the Unlock position

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Item
2
9.

Description
Turn to lock the sprayer from the adapter

Remove the sprayer from the adapter.
Figure 8-4 Sprayer Removal

10. Install the protective sleeve on the sprayer tip.
11. Put the tubing with the sprayer end through the access panel.
Figure 8-5 Sprayer and Tubing Through the Access Panel

12. Remove the coolant tubing from the notched arm.

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Figure 8-6 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 8-7 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.

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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.

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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 3-31.

4.

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

5.

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

6.

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

7.

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

8.

Loosen the thumbscrew on the adapter, and then move the adapter fully off the stage.

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Figure 8-9 Loosen the Thumbscrew

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Maintenance

9

WARNING! Electrical Shock Hazard. Turn off the power to the system before
any system disassembly. Failure to do so can cause electrical shock or otherinjury.
WARNING! Electrical Shock Hazard. To prevent the risk of electrical shock or
injury, do not do maintenance or repair procedures that are not included inthis manual. Contact a SCIEX field service employee (FSE) for maintenanceservice and support.
WARNING! Electrical Shock Hazard. Do not try to disable any of the systeminterlocks or safety mechanisms.
WARNING! Ionizing Radiation Hazard, Biohazard, or Toxic
Chemical Hazard. Before cleaning or maintenance, identify whether
decontamination is required. If radioactive materials, biological agents,
or toxic chemicals have been used with the system, then the customer
must decontaminate the system before cleaning or maintenance.

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.

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Figure 9-1 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.

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Figure 9-2 Install the Interface Plateb.

Tighten both thumbscrews.
Figure 9-3 Tighten the Thumbscrews

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Figure 9-4 Interface Block, Electrodes, and Insertion Levers

Item

Description

1

Interface block2

Electrodes3

Insertion levers

Replace the Insertion Levers
Required Materials• Insertion Lever Interface Parts Kit

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WARNING! Puncture Hazard. Do not put fingers directly below the electrodes
during installation of the insertion levers. The electrode ends are sharp. Handle
them carefully.
1.

2.

To remove an insertion lever, do this:a.

Go to the Direct Control window, and then click Load.

b.

Open the cartridge cover, and then wait for the coolant to drain from the cartridge.

c.

Turn off the power to the system.

d.

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

e.

Remove the cartridge from the interface block.

f.

If the trays prevent access to the insertion levers, then remove the trays.

g.

Hold the insertion lever with both hands and pull down firmly.

To install an insertion lever, do this:a.

Align the O-ring and electrode hole in the insertion lever directly under the electrode.
The short cylinder side of the insertion lever should be under the spring.

b.

With fingers on the sides of the insertion lever, push the insertion lever up into theinterface block until the insertion lever moves into position with a click.

Replace the Electrodes
Required Materials• Electrodes• Electrode tool1.

To remove an electrode from the interface block, do this:a.

Remove the insertion levers.
Refer to the section: Replace the Insertion Levers.

b.

Align the electrode tool so that it is flush with the bottom of the interface block.

c.

Push straight forward under the interface block to catch the electrode with the tool.

d.

Make sure that the nub at the end of the electrode tool handle goes into the notch on
the interface block.

e.

Pry carefully with the electrode tool to remove the electrode from the interface block.

f.

Remove the electrode from the electrode tool.

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Figure 9-5 Remove an Electrode

2.

Item

Description

1

Electrode tool

2

Electrode3

Nub at the end of the electrode tool handle

To install an electrode in the interface block, do this:a.

Put an electrode in the electrode tool so that the electrode key points toward the user.

b.

Align the electrode tool below the notch and parallel to the bottom of the interface block.

c.

Push up to install the electrode in the interface block with a click.

d.

To remove the electrode tool, pull straight back.

e.

Install the insertion levers.
Refer to the section: Replace the Insertion Levers.

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Figure 9-6 Install an Electrode

Item

Description

1

Electrode tool

2

Electrode key

Clean the Electrodes, Insertion Levers, and Interface Block
Required Materials• Beaker• Cotton swabs• Lint-free wipes• 150 mL CE Grade Water• Methanol• Mirror• Pen light

Note: To prevent corrosion of the ion source, frequently clean the dry chemical waste thatcollects below the sprayer.
1.

Remove the insertion levers.
Refer to the section: Replace the Insertion Levers.

2.

Immerse both insertion levers in a beaker with at least 150 mL of CE Grade Water.

3.

Remove the electrodes.

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Refer to the section: Replace the Electrodes.
4.

Immerse both electrodes in the CE Grade Water with the insertion levers for 2 hours.

5.

Remove the parts from the CE Grade Water, and then use lint-free wipes to dry them fully.

6.

Use cotton swabs dampened with CE Grade Water and then cotton swabs dampened withmethanol to clean the interface block.

7.

Use a mirror and pen light to examine the interface block.

8.

Do steps 4 through 7 until the interface block is clean.

9.

Let the interface block surface dry.

10. Install the electrodes.
11. Install the insertion levers.
Refer to the section: Replace the Insertion Levers.
12. Install the cartridge.
13. Lower the insertion bar, and then tighten the two thumbscrews.
14. Close the cartridge cover.
15. Turn on the power to the system.

Add Capillary Cartridge Coolant
Required Materials• Capillary cartridge coolant (PN 359976)• Coolant fill tool (PN 144647)

CAUTION: Potential System Damage. To prevent damage, do not use the plunger inthe coolant fill tool when coolant is added. Gravity supplies sufficient force to pull thecoolant into the system.
1.

Open the sample cover.

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Figure 9-7 Sample Cover (Outer Door)

2.

Connect the coolant fill tool to the coolant fill port.
Figure 9-8 Coolant Fill Tool Connected to the Coolant Fill Port

3.

Fill the syringe with 120 mL of coolant.

4.

Make sure that the CESI 8000 Plus system is on and a cartridge is installed.

5.

Slowly add coolant until the fill indicator is between the yellow lines in the coolant sightglass.

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Figure 9-9 Coolant Sight Glass

6.

Remove the coolant fill tool, and then close the sample cover.

Replace the Quad Rings
Required Materials• New quad rings

The quad rings on the interface block make a seal between the interface block and the cartridge.
If coolant is leaking between the interface block and the cartridge, then replace the quad rings.
1.

Go to the Direct Control window, and then click Load.

2.

Open the cartridge cover.

3.

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

4.

Turn off the power to the CESI 8000 Plus system.

5.

Remove the interface plate. Refer to the section: Remove and Install the Interface Plate.

6.

Use tweezers to remove the quad rings.

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Figure 9-10 Quad Rings

7.

Install the new quad ring in the recess of the interface block.

8.

Install the interface plate. Refer to the section: Remove and Install the Interface Plate.

9.

Lower the insertion bar, and then tighten the two thumbscrews.

10. Close the cartridge cover.

Replace the Fuses
Required Materials• Flat-bladed screwdriver, #2• Replacement fuses (Qty: 2)

WARNING! Fire Hazard. Make sure to replace the fuses with the correct typeand rating for continued protection against the risk of fire and incorrect system
operation.

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CAUTION: Potential System Damage. Before the fuses are replaced, find the cause of
the failure. If the fuses continue to blow after they are replaced, then contact sciex.com/
request-support.
1.

Turn off the power to the system.

2.

Disconnect the power cable from the AC power outlet.

3.

Use a flat-bladed screwdriver to remove the fuse block.
Figure 9-11 Fuse Block

4.

Item

Description

1

Fuse block2

Air conditioning vents

3

External connections panel

Replace the fuses.

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Table 9-1 Fuse Type and RatingLine Voltage
Fuse Type and Rating

100 VAC to 120 VAC

200 VAC to 240 VAC

8.0 A Slow Blow, ¼ inches

6.3 A Time Delay, 20 mm

5.

Install the fuse block.

6.

Connect the power cable for the system to the AC power outlet.

Set the Home Position for the Mobile Cart
The internal firmware sets the lowest height for the mobile cart automatically. This firmware
home position is slightly above the physical lower limit and nominally 27 inches from the floor.
The firmware sets an upper limit that is related to the home position at 44 inches from the floor.
If the power module is replaced, then set the home position again.
Note: Push the height adjustments buttons one at a time. Do not push both buttons at the same
time.
1.

On the front of the mobile cart, push Down until the travel stops.
Refer to the figure: Figure 3-36.

2.

Push Down three times. The third time, hold the button for 5 seconds to 10 seconds until aclick occurs and the table movement goes up-down-up.

3.

If the legs do not operate correctly, then do this:a.

Disconnect the power cable.

b.

Wait 10 seconds.

c.

Connect the power cable.

d.

Do step 2 again.

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10

Troubleshooting
Clean Blockage from the Sprayer Tip

CAUTION: Potential System Damage. Do not put more than 10 mL of CE Grade Water inthe tube. If there is more than 10 mL in the tube, then the liquid can splash onto the metalcomponents of the sprayer and cause damage.
1.

Put 10 mL of CE Grade Water in a 50 mL Falcon tube, and then put the tube in the holster
on the side of the system.

2.

Carefully immerse the sprayer tip in the CE Grade Water.

3.

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

4.

Do a forward rinse with BGE at 100 psi for 5 minutes.

5.

If required, then run the CESI-MS conditioning method to condition the capillaries.

6.

After 5 minutes, remove the sprayer from the CE Grade Water.

7.

Use lint-free wipes to dry the sprayer carefully.
Figure 10-1 Dry the Sprayer

8.

Install the sprayer in the adapter on the mass spectrometer.

9.

Remove the Falcon tube of CE Grade Water from the holster, and discard the contents.

Conductive Liquid Capillary Contamination
If the baseline mass spectrum shows a series of peaks with an m/z difference of 98, thenthe conductive liquid capillary might be contaminated with phosphate. To remove phosphate
contamination, condition the conductive liquid capillary.

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Figure 10-2 Profile of Phosphate Contamination

Condition the Conductive Liquid Capillary1.

Use the time program in the following figure.
Figure 10-3 Time Program for the Conductive Liquid Capillary Conditioning Method2.

Use the following figure to put each vial in the correct position in the buffer inlet and outlet
trays.
Note: This method uses reverse rinses. Only one vial is required in the inlet buffer tray, at
position A1.

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Figure 10-4 Tray Layout for the Conductive Liquid Capillary Conditioning Method

Autocalibration Troubleshooting
Symptom

Possible Cause

Corrective Action

Autocalibration failed in TOF
MS mode.

The intensity of the reference
ions is not correct.

In the autocalibration data file,
if the intensity of the reference
ions is < 10 cps, then:1.

Make sure that the value
for IonSpray Voltage
Floating (ISVF) is correct
and the spray is stable.
Refer to the sections:• Establish a Stable
Spray• Optimize the ESI
Voltage

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2.

Prepare a fresh
PepCalMix sample forautocalibration.

3.

In the TOF MS calibration
data, find the missing ion,and then delete that ion
from the reference table.
Run the sequence again.

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Troubleshooting

Symptom

Autocalibration failed in
product ion mode.

Possible Cause

Corrective Action

The mass shift of thereference ions is not correct.

In the autocalibration data
file, if the mass shift of thereference ions is > 100 ppm,
then do manual calibration.

The intensity of the reference
ions is not correct.

In the autocalibration data file,
if the intensity of the reference
ions is < 10 cps, then:1.

Make sure that the value
for IonSpray Voltage
Floating (ISVF) is correct
and the spray is stable.
Refer to the sections:• Establish a Stable
Spray• Optimize the ESI
Voltage

The mass shift of thereference ions is not correct.

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Prepare a fresh
PepCalMix sample forautocalibration.

3.

Make sure that the value
for Collision Energy(CE) is correct for the758.91 m/z ion. If thevalue is incorrect, thenmake sure that the qualityof the 758.91 m/z MS/MS
spectra is correct, andadjust the value forCollision Energy (CE).

In the autocalibration data
file, if the mass shift of thereference ions is > 100 ppm,
then do manual calibration.

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No Electrospray Between CESI 8000 Plus System
and Mass Spectrometer

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Electrospray Is Detected When ESI Voltage Is
Zero

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Electrospray Is Unstable When Voltage Is
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Droplet at Capillary Tip Disappeared But No
Mass Spectrometer Signal Is Detected

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TIC Signal Is Lower than Usual and/or Intensityof Background Signal Fluctuates Too Much

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Electrical Current Is Unstable

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Analyte Signals Are Not Detected by Mass
Spectrometer During Separation

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Some Analyte Peaks Are Missing or Smaller than
Expected

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Current Gradually Decreases During Separation

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Iron-Acetate Cluster m/z 537 Is Suppressing
Sample Signals

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High-Voltage System Cannot Deliver Required
Electrical Current

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Order Parts

11

Order Parts• Use any of the following options to order parts from SCIEX:• Telephone: (877) 740-2129, Option 1 (toll-free, United States only), or go to sciex.com/
contact-us to find a local office• E-mail: Sales.Americas@sciex.com• Fax: (800) 343-1346• Internet: For customers in the United States, Canada, United Kingdom, Belgium,
Netherlands, France, Germany, and Switzerland, go to store.sciex.com

Cartridges and Parts
Note: Parts that have an asterisk (*) after the part number are available only from a SCIEX sales
representative.
Table 11-1 Cartridges, Capillaries, and Apertures
Part Number

Description

144712

Aperture, 100 µm × 200 µm (3)144711

Aperture, 100 µm × 800 µm (3)338472Capillary, bare fused-silica, 50 µm × 5 m

338473Capillary, bare fused-silica, 75 µm × 5 m

338474

Capillary, bare fused-silica, 75 µm × 5 m

338475

Capillary, bare fused-silica, precut, 20 µm × 67 cm (3)338451

Capillary, bare fused-silica, precut, 50 µm × 67 cm (3)338454

Capillary, bare fused-silica, precut, 75 µm × 50 cm (3)477477

Capillary, DNA, 100 µm × 65 cm

477601

Capillary, N-CHO, 50 µm × 80 cm

477441

Capillary, neutral, 50 µm × 67 cm

359976

Capillary cartridge coolant, 450 mL

144647

Capillary cartridge coolant fill tool

A144738

Cartridge, no capillary

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Table 11-1 Cartridges, Capillaries, and Apertures (continued)
Part Number

Description

144660Cartridge, optical calibration (OPCAL)

B07367

Cartridge, silica surface OptiMS cartridge

B07368Cartridge, neutral OptiMS cartridge

A55625Cartridge, pre-assembled with 30 cm bare fused-silica capillary

A11147

Cartridge, semi-assembled, for 30 cm capillaries (capillary notincluded)

144645Cartridge rebuild kit

144717

Cartridge tubing kit, connectors, and 100 cm tubing

144689Cartridge tubing kit, connectors, and tubing, 1 each: 20 cm,
30 cm, 40 cm, and 50 cm

721125

LIF cartridge aperture plug

721126

LIF cartridge probe guide

Table 11-2 MS Adapters
Part Number

Description

B07363

OptiMS Adapter for SCIEX Nanospray III Source

B07366

OptiMS Adapter for Thermo Nanospray II MS Source

B86099OptiMS Adapter Kit with Stage for Bruker MS

B85397

OptiMS Adapter Kit with Stage for Waters MS

Table 11-3 Trays, Vials, and Caps
Part Number

Description

A94462

Buffer tray, 6 × 6

B24699CESI vial caps, 100 Pack

B11648CESI vials, 100 Pack

5043467

NanoVials, 100 Pack

144709PCR Microvials, 100 Pack

A94461

Sample tray, 6 × 8

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Table 11-3 Trays, Vials, and Caps (continued)
Part Number

Description

C04895

Sample tray holder, for 48-vial sample tray

A62250

Universal vial caps, 100 Pack

A62251

Universal vials, 100 Pack

Table 11-4 Filters
Part Number

Description

144940Band-pass filter, 520 nm

149068Band-pass filter, 560 nm

144942Band-pass filter, 655 nm

144941

LIF notch filter, 488 nm

144430

UV filter, 200 nm

144431

UV filter, 210 nm

144437

UV filter, 214 nm

144432

UV filter, 220 nm

144433

UV filter, 230 nm

144438

UV filter, 254 nm

144434

UV filter, 260 nm

144439UV filter, 280 nm

Table 11-5 Detector Parts
Part Number

Description

144667

Deuterium lamp

144951*

LIF 2-color upgrade kit

A59494*

Packaged laser module upgrade kit, 488 nm, single color

144094

PDA fiber-optic Y-cable

B68372*

Photodiode array detector upgrade

144093

UV/Vis fiber-optic cable

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Table 11-6 Other Parts
Part Number

Description

A47775

Electrode

A59525

Electrode tool

A95348Insertion lever interface parts kit

B78399*Software reprocessing key

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32 Karat SoftwareA

32 Karat Software

The 32 Karat software package provides control of the CESI 8000 Plus system. The software
allows the user to develop methods (the means of creating or editing system runs) and view
data traces, such as voltage and current. The 32 Karat software also provides the mechanism
to develop sequences (a list of methods to be run) and the means to launch either a single
method or sequences. In addition to running methods and sequences, the software provides
direct control, which is a way to get immediate access to many system features and actions.
When the CESI 8000 Plus system is used with an OptiMS cartridge and a mass spectrometer
only, the 32 Karat software collects data about voltage, electrical current, pressure, and power
data traces, but not electrophoretic data. When the CESI 8000 Plus system is used with one of
the standard detector modules (UV, PDA, or LIF detector), electrophoretic data is collected.
The CESI 8000 Plus system also provides software with a workflow-oriented approach torunning methods and sequences that have already been developed by a 32 Karat software
user. Refer to the section: CESI 8000 Plus Software.

System Administration
The system administration feature is used to control access to the 32 Karat software and the
CESI 8000 Plus software. System access can be set for a user, system, or project. When it isenabled, the system administration feature also keeps customized settings for each system.
At installation, system administration is disabled. System administration is enabled when a user
logs in with the default user name cesi and the default password 8000. The user name andpassword are required to make any system changes or get access to any system.
To optimize system security, we recommend that the security features in the 32 Karat software
be enabled and that assigned user names and passwords be used. Refer to the document:
System Administration Guide.

Controller and System Start-Up
Controller and Network Login
The default network identification for the controller is 32 Karat. The work group nameis WORKGROUP. If the CESI 8000 Plus system is installed on a network, then the network
administrator must supply the user name and password.
If more than one CESI 8000 Plus system will be installed on the network, then a unique network
name is required for each workstation. Usually, the network administrator assigns the names.

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License Key
A license key for the 32 Karat software is required to acquire data and to open and analyze data
files. The license key is supplied on a flash drive that must be installed in a USB port on the
CESI 8000 Plus controller. Without the license key, the 32 Karat software can only operate indemo mode.
In demo mode, only the data supplied with the 32 Karat software in the Default project can be
opened and analyzed. Data acquisition is not possible.
If required, the license key can be uninstalled on one controller and installed on another.
CAUTION: Potential Wrong Result. Do not remove the flash drive with the license key
from the CESI 8000 Plus system controller when the 32 Karat software is in operation. If
the flash drive is removed, then the software changes to demo mode.

Start the CESI 8000 Plus System
Before the 32 Karat software can be used with the CESI 8000 Plus system, the system mustcomplete an initialization process.
1.

Make sure that a cartridge is installed.

2.

Look at the the level indicator through the coolant sight glass to make sure that the coolant
level for the capillaries is not low. Refer to the figure: Figure 9-9.

3.

If the coolant level is low, then add coolant.
Refer to the section: Add Capillary Cartridge Coolant.

4.

Push the power button, and then wait approximately 5 minutes for the initialization process
to complete.

Open the 32 Karat Software1.

On the Windows desktop, double-click the CESI 8000 Plus icon.

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Figure A-1 CESI 8000 Plus Ready Window2.

On the side menu, double-click the 32 Karat Software icon.

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Figure A-2 Enterprise Window

3.

Click View > Hierarchy Pane.

4.

To show the available instruments in the right pane, click CESI 8000.
Note: The Service Support option is for use by SCIEX field service employees (FSEs). A
UV detector is required to use the Service Support option.

Systems and Projects
A project is a set of folders for file types that are commonly used. A project can be created foreach method or sequence.
When a system is opened, the user is required to specify a project. When a project is opened, allfolders default to this project.
If the system administration feature is enabled, then a user who is logged on to a system canselect any project to which they have access.

Online and Offline Modes
The 32 Karat software has two modes of operation:
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32 Karat Software• Online mode gives the user full control of the system and the ability to acquire data, open
and analyze existing data files, and create methods and sequences. To open an instrument
online, in the 32 Karat Software Enterprise window, double-click the Instrument icon.
• Offline mode lets the user open and analyze existing data files, and create methods
and sequences, but not control the system. To open any instrument offline, right-click theInstrument icon, and then click Open Offline.
If an instrument is open in online mode, then a second window for the same instrument can be
opened in offline mode.
If the instrument is opened in online mode, then the project name is CE-MS and the project is
Default (because the user logon is disabled).

Open the Direct Control Window
The Direct Control window supplies manual control of the instrument and shows the status of
instrument functions.
1.

To open the Direct Control window, click Control > Direct Control > View.
Figure A-3 Direct Control Window

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2.

To get quick access to the Direct Control window, make a toolbar icon. Refer to the section:
Create a Toolbar Icon for the Direct Control Window.

Create a Toolbar Icon for the Direct Control Window
1.

Click Control > Direct Control > View > Preferences.

2.

On the General tab, in the Toolbar options list, select Direct Control.

3.

Select the Show toolbar check box, and then click OK.
Figure A-4 Preferences Dialog

The Direct Control icon

shows on the toolbar.

32 Karat Software Methods
A method is a collection of steps that are done in a series by the CESI 8000 Plus system. A
method has all of the information required to operate the instrument. Methods are created in theInstrument Setup window. The instrument can be online or offline.

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When a method is created or changed online, the user has access to instrument control anddata such as voltage and current.
When a method is created or changed offline, the user does not have access to instrument
control, and so cannot start or stop runs. The user can open data files and create a complete
method, including instrument configuration, which can be opened at a later time and used tooperate the instrument.
For information about method development, refer to the document: 32 Karat Software Help.

Create or Change a Method
1.

2.

To create or edit a method, open the Instrument Wizard:a.

In the Enterprise window, right-click the icon for the applicable instrument, and thenclick Open Offline.

b.

Click Create or Modify a Method.

To create a new method or run a test sample in online mode, open the Instrument Setup
window:a.

Click File > Method > New.
The name of the method in the title bar of the Instrument Setup window changes tountitled.met.

b.

To get access to the sections of the method for instrument control and data acquisition,
click Method > Instrument Setup.

3.

Open the Initial Conditions tab, and set the initial conditions.
Refer to the section: Initial Conditions Tab.

4.

Open the Time Program tab, and then create a time program.
Refer to the section: Time Program Tab.

5.

Save the method:a.

Click File > Method > Save As.

b.

Type a name with a title and date, such as TestMethod_111522.

c.

Click Save.
The default path at installation is C:\32Karat\Projects\Default\Methods. The
system administrator might have changed the default path.

Instrument Setup Window
Use the Instrument Setup window to create a new method or run an instrument test sample inonline mode. Method parameters are set on the Initial Conditions and Time Program tabs.

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Initial Conditions Tab
Use the Initial Conditions tab to set instrument parameters at the start of a method before theseparation starts.
Figure A-5 Instrument Setup Window: Initial Conditions Tab

OptionDescription

Auxiliary datachannels

Select the channels for data collection.
Use the kV and μA fields to set limits for Voltage and Current. Because
voltage and current are interrelated, the CESI 8000 Plus system limits bothparameters when one limit is reached.
For example, assume that the voltage limit is set to 30 kV and the current
limit is set to 10 μA. If a voltage of 12 kV generates a current of 10 μA,
then the voltage will not exceed 12 kV, because the current limit is thedetermining factor.

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OptionDescription

Temperature

Set the temperature of the cartridge coolant and the sample storage unit.
Note: To prevent the formation of condensation on the surfaces of thetubing and cartridge, make sure that the temperature of the capillary
coolant is above the dew point. If condensation collects and falls into theinterface area, then a current leak can occur.

Trigger settings

Select an option to delay the start of a run until the conditions are met.
These options delay only the start of the time program. The parameters thatare set as initial conditions occur without a wait.

Inlet trays andOutlet trays

Select the types of trays to use when a method is run.
When the method is run, this information is compared with the tray types
that are configured in the instrument. If the tray types are not the same,then the method does not run.

For additional information about the parameters on the Initial Conditions tab, refer to the
document: 32 Karat Software Help.
Time Program Tab
Use the Time Program tab to add the events that make up the method. Each event shows on anumbered line. The events are done in numbered order.

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Figure A-6 Instrument Setup Window: Time Program Tab

ColumnDescription

Time

Point after time zero at which the event occurs

Event

Action that occurs

Value

Different for different actions

Duration

Length of time required for the event to complete

Inlet vial andOutlet vial

Location of the capillary ends during the event

Summary

System-generated description of the event

Comments

User-generated annotation of the event

Time is not a required event. Some events do not have a Time option. Events that do not have aTime option are run in numbered order. Each event is completed before the next event starts.
Timed events must be in a group together. A group of timed events cannot be interrupted by an
untimed event. Untimed events can only occur before a group of timed events.

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Data collection starts with the first timed event and ends when the method ends or a Stop Data
event occurs.
To set the parameters of an event, click Event, and then select from the list.
Figure A-7 Time Program Event List

Common Event Types
Descriptions of the most common event types used for CESI-MS methods are given in thefollowing sections. For information about other event types, refer to the document: 32 Karat
Software Help.
Separate Event
Use the Separate event to set the conditions for the separation.

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Figure A-8 Separate Dialog

Parameter Group

Description

Separation TypeElectrically driven separations can be done at controlled voltage,current, or power. When one option is selected, the other two adjust
to values that are controlled by the resistance of the capillary contents.
The values set for voltage and current cannot be more than the limits
set on the Initial Conditions tab.
Separations can also use pressure or vacuum to move the fluid
through the capillary. Voltage, current, or power can be combined withpressure or vacuum, so that two processes are in operation at thesame time.

Polarity

Set the direction of the current. The icon shows the charge on theelectrodes.

ValuesSet values for the selected Separation Type.
Ramp Time, which is only applicable for electrical separations, sets
the length of time for the voltage, current, or power to get to the valuethat is set.

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Parameter Group

Description

Tray Positions

The types of trays selected on the Initial Conditions tab show here.
To change the vial positions after a specified number of cycles, selectthe Inlet, Outlet, or both check boxes, and then type the number ofcycles to occur between changes.
To see and select the tray positions graphically, click Trays.
Figure A-9 Tray Selection Dialog

Pressure Direction

Set whether pressure is applied to the inlet (Forward) or outlet(Reverse) end of the capillary.

At TimeSelect for a timed event, and then type a time value. The Separate
event is usually timed.

External Adapter

If the external adapter accessory is in use, then select to change theway the instrument manages the power supply.

Rinse Event
Use the Rinse event to clean the capillary and to load fresh buffer or other separation media.
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Figure A-10 Rinse Dialog

Parameter Group

Description

Pressure TypeSet the mechanism to be used to move fluid through the capillaries.

Tray Positions

The types of trays selected on the Initial Conditions tab show here.
To change the vial positions after a specified number of cycles, selectthe Inlet, Outlet, or both check boxes, and then type the number ofcycles to occur between changes.
To see and select the tray positions graphically, click Trays.

ValuesSet the magnitude of pressure to be delivered and the length ofdelivery time.

Pressure Direction

Set whether pressure is applied to the inlet (Forward) or outlet(Reverse) end of the capillary.

At TimeSelect for a timed event, and then type a time value. The Separate
event is usually timed.

Inject Event
Use the Inject event to supply sample to the capillary. Usually, the Inject event is untimed andoccurs before the first Separate event.

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Figure A-11 Inject Dialog

Parameter Group

Description

Injection TypeSet whether sample is injected into the capillary by the application ofpressure or voltage (electrokinetic injection).

Polarity

Set the direction of the current during a voltage injection. The icon
shows the charge on the electrodes.

Pressure Direction

Set whether pressure is applied to the separation (Forward) or
conductive liquid capillary (Reverse).

ValuesSet the magnitude of the pressure or voltage and the length of delivery
time. To inject more sample, increase this value.
For experiments where the Inject event fills the full length of thecapillary with a sample mixture, select the For Capillary Fill checkbox. For low-pressure, high-precision Inject events, clear the checkbox.

Tray Positions

The types of trays selected on the Initial Conditions tab show here.
To change the vial positions after a specified number of cycles, selectthe Inlet, Outlet, or both check boxes, and then type the number ofcycles to occur between changes.
To see and select the tray positions graphically, click Trays.

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Parameter Group

Description

Sequence Table

To use the parameters in the sequence table rather than theparameters in the method, select the Allow Override check box. If the
Allow Override check box is selected, then the position of the sample
injection vials can be changed during repetitions of the same method.
Refer to the section: About the Auto-Increment Feature.

Stop Data Event
Use the Stop Data event to stop the collection of data for voltage and current during steps suchas post-run capillary cleaning. The Stop Data event is always timed.
Figure A-12 Stop Data Dialog

End Event
The End event is optional and always timed. The method does not continue after an End event.
Figure A-13 End Dialog

Single Run and Sequence Runs
For single runs, a method must be manually started before every run. Single runs are useful formethod development. The results of one run can suggest modifications to the method or otherprocedures.

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Sequence runs are used to connect multiple methods together for performance in a specified
order.

32 Karat Software Sequences
After a method is optimized, it can be run again and again on different samples or multiple
times on a single sample as part of a sequence. A sequence is a list of methods that gives theorder in which runs are acquired and processed. A sequence can be used to run a batch ofsamples without user intervention, condition the cartridge, and prepare the cartridge for storage.
A sequence shows in a table like a spreadsheet where each row is a method. A sequence table
is used to apply a sequential order to the contents that have been set for the sequence.
The Sequence Wizard can be used to create a sequence and automate data acquisition. The
Sequence Wizard has five windows. Some sequences do not use every window or every option
in a window.

Sequence Table Columns
To select the columns that show in a sequence table, right-click a empty area of the sequencetable, and then click Properties.
Note: Because a sequence table has more columns than can be shown at one time, thefollowing Properties dialog shows the options selected for the example. Refer to the figure:
Figure 7-21.

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Figure A-14 Sequence Table Properties Dialog

OptionDescription

StatusShows whether a run is processing or complete.

Run Type

Identifies the type of run, such as calibration, system suitability, or
shutdown.
In the Run Type column, click the blue arrow to show the available options.

Reps

Shows the number of times to do the same line. When a number other than
1 is selected, the suffix rep 1, rep 2, etc. is added to the data file names
automatically.

Sample Inject
Inlet

Identifies the vial that supplies the sample for injection if the sample is in
the inlet tray.

Sample Inject
OutletIdentifies the vial that supplies the sample for injection if the sample is in
the outlet tray. In the CESI 8000 Plus system, the sample is always in theinlet sample tray.

Sample ID

Shows the name of the sample to be run.

MethodShows the separation method used to run the line.

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OptionDescription

Filename

Shows the file name supplied in the Sequence Wizard. The symbol <D>
shows because the date and time are unknown until the sequence is run.

Sequence Validation
The 32 Karat software makes sure that the methods in the sequence are applicable for the
instrument configuration. If an issue is found, then an error message is shown and the sequence
does not run. To continue, correct any issues, and then start the sequence again.
After a successful sequence validation, the method in the first line is downloaded to the systemand the run starts. To see real-time data about the instrument status during the acquisition ofvoltage and current data, open the Direct Control window.
At the end of each run, the method for the next run is downloaded before the new run starts. The
version of the method that is most recent at the time of the download (last saved) is the version
that runs.
Changes to the sequence table can be made while the sequence is in progress. Lines that havenot been started can be changed or deleted. More lines can be added. Lines that have alreadycompleted or are in progress cannot be changed.
Note: If a sequence includes a method that uses vial incrementing, then changes to the
autogenerated vial positions cannot be made. If the Allow Override check box is cleared, thenthe related entries in the sequence table cannot be changed. For information about the Allow
Override option, refer to the section: Inject Event.

Sequence Transfer
To make the methods and sequences available to routine users, a method developer withadministrator privileges must transfer the final methods and sequences from the 32 Karatsoftware to the CESI 8000 Plus software.

Create a New Instrument1.

Open the 32 Karat software and log in as an Administrator.

2.

Click File > New > Instrument.

3.

Type a name for the instrument.
Note: The instrument name must be a valid Windows folder name. For routine users to
get access to an application in the CESI 8000 Plus software, the 32 Karat software project
name must be the same as the 32 Karat software instrument name.

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4.

Right-click the new instrument name, and then click Configure > Instrument.

5.

In the Instrument type field, select the instrument, and then click Configure.

6.

From the module list in the left window, select the instrument, and then click

7.

Right-click the instrument, and then click Open.

8.

Select the applicable tray sizes, home positions, and other options.

9.

Click OK.

.

10. Click Options.
11. Click the applicable General Options and Instrument Options, and then click OK.
12. Click OK to close the open dialogs.

Create a Project for the Instrument
1.

Click Tools > System Administration Wizard.

2.

Click Project, and then click Next.

3.

Click Create a new project, and then click Next.
Note: The project name must be the same as the instrument name and must be a 32 Karatsoftware folder name.

4.

Type the name of the instrument.

5.

(Optional) Type a description, and then click Next.

6.

Select the applicable general project settings, and then click Next.

7.

Set the electronic signature roles, and then click Finish.

Add Routine Users and Privileges (Data System)
1.

Click Tools > Options.

2.

Open the Enterprise tab.

3.

Click Add User.

4.

Type a user name and password, and then click Save.

5.

Click OK.

6.

Click Tools > System Administration Wizard.

7.

Click User, and then click Next.

8.

Select the user name, and then click Next.

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32 Karat Software9.

If applicable, then click System administration or Instrument administration, and thenclick Next.
Note: System and instrument administration privileges are not required for routine users.

10. Add instruments for the user, and then click Next.
11. Add projects for the user, and then click Next.
12. Add the Open Method, Open Sequence, Save Sequence, and Lock Instrument
privileges.
Note: Routine users must be given the Open Method, Open Sequence, Save Sequence,and Lock Instrument privileges in the 32 Karat software to get access to the CESI 8000
Plus software.
13. Add any other required privileges, and then click Next.
14. Set the applicable electronic signature roles, and then click Finish.
The sequence is ready to be transferred. Refer to the section: Transfer the Methods.

Add Routine Users and Privileges (Domain Controller)
1.

Click Tools > System Administration Wizard.

2.

Click User, and then click Next.

3.

Select the domain, and then type the user name.

4.

Click Check Names. To add the name to the Selected Users, click

5.

Click Next.

6.

If applicable, then click System administration or Instrument administration, and thenclick Next.

.

Note: System and instrument administration privileges are not required for routine users.
7.

Add instruments for the user, and then click Next.

8.

Add projects for the user, and then click Next.

9.

For each of the projects to which the routine user needs access, add the Open Method,
Open Sequence, Save Sequence, and Lock Instrument privileges.
Note: Routine users must be given these privileges to get access to the CESI 8000 Plus
software.

10. Add any other required privileges, and then click Next.
11. Assign the applicable electronic signature roles, and then click Finish.
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The sequence is ready to be transferred. Refer to the section: Transfer the Methods.

Transfer the Methods• Copy the methods and paste them in the project Method folder.
Note: The approved methods for the application should be in the Method folder for the
32 Karat software project.
Note: If the instrument configuration and the project were already created on the system,
then there might be other methods in the project folder.

Transfer the Sequences• Copy the sequences and paste them in the project Sequence folder.
Note: The approved sequences for the application should be in the Sequence folder for the
32 Karat software project.
Note: If the instrument configuration and the project were already created on the system,
then there might be other methods and sequences in the project folder.

Review the Sequence Properties
1.

In the Enterprise window of the 32 Karat software, right-click the instrument and then click
Open.

2.

Type the user name and password, select the project, and then click Login.

3.

Click File > Sequence > Open.

4.

Click Sequence > Properties.

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Figure A-15 Sequence Properties Dialog

5.

In the Method and Data fields, type the file path names that are used for the instrument
project Method and Data folders.
To navigate to the file path, click the green folder icon.
Note: Make sure that the properties for the transferred sequence are set to the applicable
Method and Data folders for the application.

6.

In the Sequence Run table, make sure that the methods are selected from thecorresponding Method folder for this project and that any file paths in the Method column
are correct.
Figure A-16 Method in the Sequence Run Table

7.

Click File > Sequence > Save.

8.

Do steps 1 through 7 for all transferred sequences.

9.

Close the instrument and the Enterprise windows.

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Verify the Sequence
To make sure that the sequence transfer is correct, do a test run. Refer to the section: Run an
Application.
To make sure that the sequence rows are hidden correctly, refer to the section: Sequence Table
Rows.

About the Auto-Increment Feature
The auto-increment feature can be used when a method will be run again and again for an
extended interval. After a specified number of replicates has been achieved with the same
method, this feature automatically moves to the next row of buffer vials. The auto-increment
feature can be used for the Rinse, Inject, and Separate events.

Set Auto-Increment for a Rinse Event
1.

In the 32 Karat software, go to the Direct Control window, and then double-click the Rinse
field.
Figure A-17 Rinse Dialog: Auto-Increment Option2.

Set the increment.
• To increment only the rinse vial at the inlet buffer tray, click Inlet.
• To increment only the rinse vial at the outlet buffer tray, click Outlet.
• To increment the rinse vials at the inlet and outlet buffer trays, click Inlet and Outlet.

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3.

When the increment has been set, in the Increment Every field, type a value.
In this example, both the inlet and outlet buffer trays will be incremented every 6 cycles,
which is 6 repetitions of the same method.
Figure A-18 Rinse Dialog: Number of Cycles Option

The following table shows which buffer vial positions are used at each cycle during the
Rinse event in this example.
Table A-1 Vial Positions Used During the Rinse Event
Cycles

Inlet Buffer Position (BI)Outlet Buffer Position (BO)

1 through 6E1

A1

7 through 12

E2

A2

13 through 18

E3

A3

19 through 24

E4

A4

25 through 30

E5A531 through 36

E6

A6

Note: There are six rows in the buffer trays. Vials will not be incremented beyond row 6.
Start the auto-increment with vial positions at row 1 to maximize the number of cycles.

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Set Auto-Increment for an Inject Event
1.

In the 32 Karat software, go to the Direct Control window, and then double-click the Inject
field.
Figure A-19 Inject Dialog: Auto-Increment Option2.

Set the increment.
• To increment only the injection vial at the inlet buffer tray, click Inlet.
• To increment only the injection vial at the outlet buffer tray, click Outlet.
• To increment the injection vials at the inlet and outlet buffer trays, click Inlet and Outlet.

3.

When the increment has been set, in the Increment Every field, type a value.
In this example, only the inlet buffer tray will be incremented every 12 cycles, which is 12
repetitions of the same method.

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Figure A-20 Inject Dialog: Number of Cycles Option

The following table shows which buffer vial positions are used at each cycle during the Inject
event in this example.
Table A-2 Vial Positions Used During the Inject Event
Cycles

Inlet Buffer Position (BI)Outlet Buffer Position (BO)

1 through 12

A1

B1

13 through 24

A2

B2

25 through 36

A3

B3

37 through 48

A4

B4

49 through 60

A5B561 through 72

A6

B6

Note: There are six rows in the buffer trays. Vials will not be incremented beyond row 6.
Start the auto-increment with vial positions at row 1 to maximize the number of cycles.

Set Auto-Increment for a Separate Event
1.

In the 32 Karat software, go to the Direct Control window, and then double-click the
Separate field.

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Figure A-21 Separate Dialog: Auto-Increment Option2.

Set the increment.
• To increment only the separation vial at the inlet buffer tray, click Inlet.
• To increment only the separation vial at the outlet buffer tray, click Outlet.
• To increment the separation vials at the inlet and outlet buffer trays, click Inlet andOutlet.

3.

When the increment has been set, in the Increment Every field, type a value.
In this example, both the inlet and outlet buffer trays will be incremented every 12 cycles,
which is 12 repetitions of the same method.

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Figure A-22 Separate Dialog: Number of Cycles Option

The following table shows which buffer vial positions are used at each cycle during the
Separate event in this example.
Table A-3 Vial Positions Used During the Separate Event
Cycles

Inlet Buffer Position (BI)Outlet Buffer Position (BO)

1 through 12

A1

A1

13 through 24

A2

A2

25 through 36

A3

A3

37 through 48

A4

A4

49 through 60

A5A561 through 72

A6

A6

Note: There are six rows in the buffer trays. Vials will not be incremented beyond row 6.
Start the auto-increment with vial positions at row 1 to maximize the number of cycles.

Auto-Increment in a Method
If the auto-increment feature is used in a method, then the Summary column shows in the time
program. In the following example, auto-increment is used in lines 4, 5, 7, and 8. The term In /Out vial inc 12 specifies that both the inlet and outlet vials will be incremented after 12cycles.

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Figure A-23 Time Program in a Method

Review Vial Positions Before a Sequence Is Run
Use the Sequence Vials Report Preview window to make sure that the trays have all of the vials
that are required to run a specified sequence fully.
Note: The CESI 8000 Plus software gives a preview of all trays before the start of a sequence.
The Sequence Vials Report Preview is also used to identify vial collisions. To prevent a vial
collision, change the identified vial position in the method and then save the method.
1.

In the 32 Karat software, click File > Sequence > Open, and then select the sequence topreview.

2.

In the main header, click Sequence > Sequence Vials Preview.
Figure A-24 Sequence Vials Report Preview Window

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Note: If the sequence is stopped and started again, then the next method to run goes backto the initial set of vials. The cycle count starts again at 1.
Note: If the auto-increment feature is in use, then do not use different methods in a single
sequence. If the sequence has different methods, then the CESI 8000 Plus system goesback to the initial set of vials specified at the start of each method.

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CESI 8000 Plus SoftwareB

The CESI 8000 Plus software operates with the 32 Karat software. On the CESI 8000 Plus
system, the CESI 8000 Plus software supplies guidance for the system operator through thetasks of running methods and sequences that have been developed by a 32 Karat software user.
Methods and sequences cannot be created or changed directly in the CESI 8000 Plus software.
The CESI 8000 Plus software gets the electronic controls that are required for 21 CFR part 11
compliance from the 32 Karat software.
The license key used for the 32 Karat software is required to operate the CESI 8000 Plus
software. Refer to the section: License Key.
If required, then the 32 Karat software can be opened from the side menu in the CESI 8000 Plus
software.
For information about the CESI 8000 Plus software, refer to the document: Help System.

User Roles and Privileges
The CESI 8000 Plus software has two types of users: routine users and method developers.
A routine user uses the system to get regular access to methods and sequences. Routine users
do not usually change methods, and they only change the required number of samples in asequence. Routine users can only get access to the methods and sequences to which they havebeen given privileges. A method developer or a system administrator for the 32 Karat software
sets the privileges for routine users.
A method developer uses the system to create methods and sequences, transfer methods andsequences to the CESI 8000 Plus software for routine use, and configure instruments andprojects. Privileges for method developers can be limited to specific instruments and projects.
The system administrator for the32 Karat software sets the privileges for method developers.
A system administrator for the32 Karat software creates and configures user accounts, including
user names and passwords, and sets privileges for user access. An account for a routine user
must be created and configured correctly in the 32 Karat software before the user can run
methods and sequences in the CESI 8000 Plus software.

Open the CESI 8000 Plus SoftwareOn the Windows desktop, double-click the CESI 8000 Plus icon.

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Figure B-1 Ready Window

Icon

Description
Run Application: Run methods and sequences.

Describe Sequence: Prepare sequences.

Help: Get access to system help files.

Desktop: Get access to the desktop.

Login and Logout: Open the 32 Karat software.
Note: If security is enabled for the 32 Karat software and an application andsequence or method are selected, then a login dialog opens.

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Icon

Description
Lock and Unlock: Lock and unlock the CESI 8000 Plus software.
This feature lets a user lock the controls in the CESI 8000 Plus software sothat other users cannot change the controls. When the software is locked,
other users can still get access to the 32 Karat software, and view, print,
and export windows.
To unlock the software, click the icon, and then type the user name andpassword for the user who set the lock.
About: Open a dialog that shows the versions for the CESI 8000 Plus
software, 32 Karat software, and system firmware.
Exit: Close the CESI 8000 Plus software.

To hide the side menu, click .
The CESI 8000 Plus software uses different colors to identify the system status.
Color

StatusBlue• Ready• Idle• Run complete

Green• Running• Scheduled run

Light green

Rinsing capillary

Red• Run aborted• System offline• System error

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Color

StatusYellow• System waiting• Sample cover open
• No cartridge• Connection to mass spectrometer lostRun an Application
Note: Do not start a method or sequence run from the 32 Karat software and the CESI 8000
Plus software at the same time. The CESI 8000 Plus software will not let a user start a method
or sequence run from the same connected system.

1.

In the Ready window, click.

Figure B-2 Application Window

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2.

From the list on the left, click the application, and then click Browse to search for a method
or sequence, or select a method or sequence from the list.
Note: Sequences show in the list before methods.
Note: During sequence selection, the application is highlighted in blue or yellow. If an
application was not selected before, then the application is highlighted in blue. If an
application is selected and the CESI 8000 Plus software is connected to the system, thenthe application is highlighted in yellow.
CAUTION: Potential Wrong Result. If the CESI 8000 Plus software is already open witha method or sequence, then do not open a CE-MS project in the 32 Karat software.
This prevents the properties of the method or sequence from being changed or
saved. Instead, click Show 32 Karat.
Figure B-3 Select a Sequence

Figure B-4 Select a Method

3.

If the security features are enabled in the 32 Karat software, then type the user name andpassword for the application.
When the login is successful, a connection with the system is made and the system statusis updated in the top banner of the CESI 8000 Plus software. Real-time data for voltage andcurrent shows in the Instrument Status and Direct Control pane.
Note: If a system error occurs, then a flashingshow the error message.

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4.

Use the Instrument Status and Direct Control pane to move the trays to the home or load
position.

5.

Click Next or 2. Samples/Vials.

6.

Refer to the section: Samples/Vials Window.

Samples/Vials Window
Use the Samples/Vials window to set the number of samples to run, supply sample information,and load trays for a method or sequence, according to the selection made in the Application
window.
The user name, application, and method or sequence show at the top right corner of the window.

The tray detail view shows by default. To show another view, click Display Options. Refer to thesection: Display Options Menu.
Refer to the sections: Set Up Samples and Vials for a Method and Set Up Samples and Vials fora Sequence.

Set Up Samples and Vials for a Method
If a method was selected in the Application window, then the method Samples/Vials window
opens.

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Figure B-5 Method Samples/Vials Window

1.

To create a sample ID, type a value in the Sample ID field, or click Insert and then selectthe values. Refer to the section: Insert Option.

2.

To change the output data path, click Browse and then select the path.
Note: The data folder for the selected application shows as the default output data path.

3.

To create a data file name, type the name for this run in the Data file field, or click Insert
and then select the values. Refer to the section: Insert Option.
Note: If a data file name is not supplied, then the default name is <Date and Time>.dat.

4.

In the Repetition field, select the number of repetitions for the method.
Note: The CESI 8000 Plus software does a check for duplicate data file names. Data filenames must use unique identifiers, such as the date and time or increment number.

5.

To print the method report, select the Print Method Report check box.

6.

To move the trays to the load position, click Load.

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7.

Put the vials in the positions that show in the tray detail view. Refer to the section: Display
Options Menu.

8.

Close the sample door, and then click Next.

9.

Make sure that the samples are loaded, and then click Yes - run now.

10. Refer to the section: Acquisition Window.

Insert Option
In the Samples/Vials window for a method, the Insert option can be used in the Sample ID and
Data file fields to select the options to add to the file names.
Figure B-6 Insert Sample ID Dialog

Figure B-7 Insert Data File Dialog

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OptionDescription

Increment
Number

A count starting from the specified number.
Use 0 to add placeholders for the number of digits to use in the increment
number. For example, type 010 to use three digits and start the count at 10.
Note: It is possible to change the number of placeholders and the start
number for the increment number. For example, change the increment
number to <00200> to start the increment at 00200.

User Name

The user who is logged into the application.

Sample ID(Data file only) The sample ID for the data file in use.

Method Name

The method name for the data file.

Instrument
Name

The name of the instrument on which the sample was run.

Date and Time

The date and time that the sample run started.

Click the value(s) to add to the sample ID or data file name, and then click OK.

Set Up Samples and Vials for a Sequence
If a sequence was selected in the Application window, then the sequence Samples/Vials window
opens.

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Figure B-8 Sequence Samples/Vials Window

To see the vial configuration for a sequence in the tray view, click a row in the sequence table.
Mandatory fields that are empty in the sequence table are highlighted in yellow.
To undo changes made to the sequence table and go back to the original table, click Reload
Sequence.
If the sequence is changed and saved in the Describe Sequence window, then to load thesequence, in the Samples/Vials window, click Reload Sequence.
1.

From the Number of samples list, select the number of samples.
Note: The default number of samples is the maximum number of samples for the sequence.
If the number of samples is not available, then a description of the sequence must be set.
Refer to the section: Describe the Sequence.

2.

To change the output data path, to the right of the Output data path field, click Browse,
and then select the path.
Note: The data folder for the selected application shows as the default output data path.

3.

In the Output sequence path field, type a path, or click Browse and then select the path.

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Note: The default path for the Output sequence path is {Pre-defined Project
folder}\Data\Sequence.
The path will be available in the instrument until a different instrument is used or theapplication is closed.
4.

In the Reps column in the sequence table, type the number of repetitions for each method
line.

5.

In the Sample ID column, type a value for each method line, or right-click and then click Fill
Down.
Refer to the section: Fill Down Option.

6.

In the Data File column, type a value for each method line, or right-click and then click Fill
Down.
Refer to the section: Fill Down Option.

7.

To print the method report, select the Print Method Report check box.
Note: The method report is printed as it was configured in the method.

8.

To print the sequence report, select the Print Sequence Report check box.
Note: The sequence report is printed as it was configured in the sequence.

9.

To move the trays to the load position, click Load.

10. Put the vials in the positions that show in the tray detail view.
Refer to the section: Display Options Menu.
11. Close the sample door, and then click Next.
The sequence is automatically saved in the sequence folder that was created in the Output
Data Path field.
12. Make sure that the samples are loaded, and then click Yes - run now.
Note: To start a run at a later time, click Sequence Run > Schedule Run. The maximum
schedule delay time is 99 minutes.
Note: If a tray collision is possible, then an error message is shown. To see where thecollision is possible and make the changes required to prevent it, click Display Options,and then click Show Vial Preview.
13. Refer to the section: Acquisition Window.

Sequence Table Rows
When a sequence is run, the number of samples can be changed. Rows in the sequence table
are hidden as the sample quantity decreases. When a description of the sequence is set, theUser Guide
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table rows are assigned one of the following types. When the number of samples is set, the type
is used to hide rows.
Note: Before the number of samples for a sequence can be changed, a description of thesequence must be set. Refer to the section: Describe the Sequence.
Type

Description

SampleThe rows from one row beyond the number of samples are hidden (notincluding Control or Always type rows). Refer to the figures: Figure B-9,
Figure B-10, Figure B-11, and Figure B-12.

Control

The Control type row is hidden when the first Sample type row following it
is hidden. Refer to the figures: Figure B-11, Figure B-12, Figure B-13, andFigure B-14.

AlwaysNever hidden and always run, regardless of the number of samples. Referto the figure: Figure B-10.

Note: When the number of samples is set to 0, all rows are hidden except for rows with theAlways type.
Figure B-9 Sequence with All Nine Samples

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Figure B-10 Sequence with No Samples (All Rows Hidden)

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Figure B-11 Sequence with Five Samples

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Figure B-12 Sequence with Four Samples

Note: Notice how Standard C (Row 13) is hidden when the number of samples changes fromfive (refer to the figure: Figure B-11) to four (refer to the figure: Figure B-12).

To show the hidden rows that are not run, right-click the sequence, and then click Show Hidden
Rows. Refer to the figures: Figure B-13 and Figure B-14.

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Figure B-13 Sequence with Five Samples and Hidden Rows

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Figure B-14 Sequence with Four Samples and Hidden Rows

Fill Down Option
In the Samples/Vials window for a sequence, the Fill Down option can be used to select theoptions to add to the sample ID or data file name. The options selected are added automaticallyto the selected row and all subsequent rows. If a range of rows is selected, then the options areapplied to the selected cells.
Right-click the Sample ID or Data File column, and then click Fill Down.

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Figure B-15 Fill Down Option

Note: When the Fill Down option is selected in the Reps column, the value in the selected cellis copied into the subsequent rows.
Figure B-16 Fill Down Sample ID Dialog

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Figure B-17 Fill Down Data File Dialog

OptionDescription

Line Number

The run number in the sequence.

Increment
Number

A count that starts from the specified number.

Sample ID(Data file only) The sample ID for the data file in use.

User Name

The user who is logged into the application.

Method Name

The method name for the data file.

Instrument
Name

The name of the instrument used for the sample run.

Date and Time

The date and time that the sample run started.

Calibration
Level

The calibration level that is specified in the sequence table and method.

Calibration Set

The calibration set that is specified in the sequence table and method.

Use 0 to add placeholders for the number of digits to use in the increment.
For example, type 010 to use three digits and start the count at 10.

Display Options Menu
The Display Options menu gives the user different ways to see information about the trays. To
open the menu, click Display Options.
The Hide Legend, Show Tray Detail, and Show Vial Preview options are also available fromthe Show/Hide menu to the left of the tray view.

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Figure B-18 Location of the Show/Hide Menu

OptionDescription

Program Event

Shows the event type.

Vial Contents

Shows the contents of the vial.
Note: The method definition supplies the information about the vial
contents. The first five characters of the vial contents show in the tray
view. We recommend that each of the vial content types be given a unique
identifier and used consistently between methods.

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OptionDescription

Show Legend

Shows the vial legend (a list of events or contents) set by the tray view
(Program Event or Vial Contents).
The number of vials for each event type or content type shows next to each
item in the legend.
To change the color for the vial type, click the color next to the description
and then click a new color.
To change the colors in the legend to the default settings, click Reset.

Hide Legend

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Hides the vial legend.

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OptionDescription

Show Tray
DetailShows the full tray detail set by the tray view (Program Event or Vial
Contents).
The vials can be shown as circles or rectangles. The tray detail view can beexported and printed.
Figure B-19 Tray Detail View

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OptionDescription

Show Vial
Preview

Shows the order, cycle number, and vials used for each of the methods inthe sequence. Shows possible tray collisions in red.
Note: The cycle number is the number of times that the method has beenrun.
Figure B-20 Vial Preview

Acquisition Window
The Acquisition window shows information about the active sequence or method.
The tables on the left show different levels of detail about a method or sequence:• The Run Queue table is used to make sure that the run that was started in the CESI 8000
Plus system is in the 32 Karat software Run Queue.
• If a sequence is active, then the Sequence Run table shows which row of the sequence isactive.
• The Current Run table shows which event in the method is active.

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Figure B-21 Sequence Run Acquisition Window

The graph on the right has the following tabs:• The Current Run tab shows real-time data as it is collected.
• The All Runs tab shows all of the data that has been collected for the active sequence or
method.

To expand the graph and show more data, to the left of the graph, click
about the graph settings, refer to the section: Graph Options.

. For more information

When a run is complete, to print or export the settings from the run, right-click one of the threeviews, and then click Print or Export.

During a Run
During a run, the Running Acquisition window is empty. The system state is Scheduled Run. The
countdown until the start of the scheduled run shows below the system state.

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Figure B-22 Scheduled Run Acquisition Window

To end the countdown and start the run now, click Start Now.
To see the settings in the Application and Samples/Vials windows, click 1. Application,
2. Samples/Vials, Back, or Next. After a run has started, the settings cannot be changed.
Only one sequence or method at a time can be started from the CESI 8000 Plus software.

Stop a Run
Note: A method or sequence that has been stopped cannot be started again.
1.

Click Stop.

2.

Select the applicable option:• Stop current run only
• Stop after current run (sequence only)• Stop current run and sequence run (sequence only)• Stop all run queue items (sequence only)3.

Click OK.
The system state changes to Run Aborted.

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Complete a Run
1.

Click Finish.

2.

Do one of these actions:• To close the Run application, select Finished.
• To run the same sequence or method, or to start a new sequence or method, click Run
More.
If Run More is selected, then all of the settings supplied by the user are kept in theapplication configuration and can be changed. If a different application sequence or method
is selected, then all of the settings from the previous run are discarded.

Graph Options
In the Acquisition window, some graph settings are independent for the Current Run and All
Runs tabs. Changes or selections that are made in the Graph Options dialog are applied
automatically to the selected tab.
Figure B-23 Graph Options Dialog

OptionDescription

Absolute Value

Shows the absolute values for current and voltage in the graph.

Label with Run
No.

Adds the run number to the graph. The Current Run tab shows the number
as text on top. The All Runs tab shows the number in the key for the trace.

Label with
Sample ID

Adds the sample ID to the graph. The Current Run tab shows the sample
ID as text on top. The All Runs tab shows the sample ID in the key for the
trace.

Multiple Colors

When selected, opens each trace in a different color.

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OptionDescription

Scale Y Axis

When selected, adjusts the Y-axis labels to show a number. A multipliershows in the Y-axis legend.

Separate Panels When selected, each electropherogram/trace shows in a separate pane on
the tab. Use Max Displayed to set the number of panes to show. The
maximum is 5 panes.
When not selected, each electropherogram/trace shows on the same pane.
To help identify the traces, click Multiple Colors.
Thin Lines

Changes the line thickness of the trace.

Other Options

Expands the Graph Options dialog to show additional graph settings.
Note: The additional graph settings only apply if Separate Panels is notselected and there is more than one trace.

Max Displayed

Sets the number of panes to view if Separate Panels is selected. The
maximum is 5 panes.

Show/Hide
TracesUsed to select the traces to show in the graph.

Spacing
Adjusts how much space shows between each of the traces. If spacing is
Between Traces not set between the traces, then they will overlap.
Height of
Display Region

Changes the Y-axis scale of the display region.

Describe Sequence Window
Use the Describe Sequence window to select the properties for the rows and columns in thesequence table and to change specific sequence data, such as the number of samples used in asequence, without creating a new sequence in the 32 Karat software.
For a routine user to change the number of samples used in a sequence, the sequence must be
described in the CESI 8000 Plus software.
Note: For a routine user to describe a sequence, the user must have the Sequence File Write
privilege in the 32 Karat software.
When a sequence is described, the rows in the sequence table are given one of three types:

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Refer to the section: Sequence Table Rows.
Note: To change the columns that show in the sequence table, refer to the section: Sequence
Table Columns.
If a sequence is not described, then:• All of the sequence runs have the Sample type.
• The Sample ID and Data File Name columns are set to Optional.
• The Reps column is set to Required.
Figure B-24 Describe Sequence Window Without Types

If a sequence is changed in the 32 Karat software after being described in the CESI 8000 Plus
software, then the changes are detected and only the full sequence can be run. To change thesample quantity, the sequence must be described again in the CESI 8000 Plus software.

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Describe the Sequence1.

In the CESI 8000 Plus software main window, click.

Figure B-25 Describe Sequence Window

2.

In the Application field, click the application.

3.

In the Sequence field, click the sequence to describe.

4.

If a prompt is shown, then type the user name and password.

5.

In each row, click the row, and then click Sample, Control, or Always.

6.

To change the column settings, click the Reps, Sample ID, or Data File column, and thenclick:• Optional to let information be typed in the column fields or let them stay empty.
• Required to require information in every column field.
• Fixed to prevent any changes to the column fields. The column fields set by thesequence author in the 32 Karat software will be used when the application is run.

7.

To make sure that the sequence is correct, do this:User Guide
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Select the different sample quantities to make sure that the appropriate sequence rows
will be run for every possible sample quantity.

b.

Monitor the Run Type column to make sure that the sequence operates as expected forall possible sample quantities.

c.

To see which rows are hidden as the number of samples changes, right-click thesequence table, and then click Show hidden rows. Refer to the section: Sequence
Table Rows.
Note: If a user changes the number of samples that are run, then rows with the Sample
or Control type might not be included.

8.

Click Save.
The changes made are saved to the template sequence file that was opened. If audit trails
are enabled for the sequence, then a dialog opens. Type the reason for the change. Thechange made to the sequence is saved in the first row of the sequence table.
Note: If a user tries to change the text in the brackets, then the described sequence will be
invalidated. The sequence must be described and saved again.
Figure B-26 32 Karat Software Sequence Editor

9.

Click Finish.

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Connect an Ethernet Cable

Connect an Ethernet CableCAn Ethernet cable can be used to connect the CESI 8000 Plus system and the mass
spectrometer.
1.

Turn on power to the CESI 8000 Plus system and controller.

2.

Connect one end of the Ethernet cable to the CESI 8000 Plus system controller and theother end to the acquisition computer on the mass spectrometer.
Figure C-1 System Communication Setup

Item

Description

1

End of Ethernet cable connected to CESI 8000 Plus system controller

2

End of Ethernet cable connected to acquisition computer on mass
spectrometer

Note: A 14 ft (4.3 m) Ethernet cable is provided. Make sure that the distance between the
CESI 8000 Plus system controller and the acquisition computer on the mass spectrometer is
not more than 13 ft (4 m).
WARNING! Personal Injury Hazard. Put the relay cable in a position whereusers cannot trip on it.

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Connect an Ethernet Cable

Note: The RS-232 Service Only connector on the CESI 8000 Plus system is to be used by a
SCIEX field service employee (FSE) only.
Figure C-2 RS-232 Service Only Connector

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System Specifications

D

System Specifications
CESI 8000 Plus System Specifications
Table D-1 System Specifications
Dimensions (H × W × D)

99.1 cm (cover open), 73.7 cm (cover closed) × 63.5 cm × 72.4 cm(39 inches (cover open), 29 inches (cover closed) × 25 inches ×28.5 inches)

Weight85.3 kg (188 lb)

ElectricalPower requirement: 100 VAC to 240 VAC, 8.0 A, 50 Hz or 60 Hz
Power consumption: Supply voltage must not exceed 10% of
nominalFuses:• 8.0 A slow blow, 1/4 inches (2 each), 100 VAC to 120 VAC• 6.3 A time delay, 20 mm (2 each), 200 VAC to 240 VAC
Installation (overvoltage) category: Category II

Working environment

Altitude: Maximum

2,000 m (6,562 ft)

Humidity:• < 80% (noncondensing) at 15 °C to 30 °C (59 °F to 86 °F)• < 60% (noncondensing) at 30 °C to 40 °C (86 °F to 104 °F)
Temperature: 15 °C to 40 °C (59 °F to 104 °F), 15 °C to 30 °C(59 °F to 86 °F) recommended
Maximum heat dissipation 400 W (1,024 BTU/hr)
Pollution degree

2

I/O

TTL: 2
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System Specifications

Supplied Controller Configuration
Note: Specifications are subject to change without notice.
Note: SCIEX fully validates and supports the controllers supplied with the system. Only limited
support is available for customer-supplied computers.
Table D-2 Supplied Controller Configuration
Item

Details

Operating system

Windows 10 Enterprise LTSC, language set to English (United States)

CPUIntel Core i7-10700 4.7 GHz processor

Random accessmemory (RAM)16 GB

Hard drive

500 GB

Optical drive

DVD-RW drive

Serial ports

1

Ethernet ports

2

USB ports

8

Monitor24 inch wide-screen monitor with 1920 × 1080 resolution

Mobile Cart Specifications
Table D-3 Mobile Cart Specifications
Dimensions (W × D)

91.4 cm × 73.7 cm (36 inches × 29 inches)

HeightAdjustable from 68.6 cm to 111.8 cm (27 inches to 44 inches)

Weight69.0 kg (152 lb)

Electrical

120 VAC at 60 Hz, optional 230 VAC at 50 Hz

Supports

136.0 kg (300 lb)

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Capillary Temperature Control Specifications
Table D-4 Capillary Temperature Control Specifications
Range

10 °C below the ambient temperature to 60 °C (140 °F)
Minimum setting: 15 °C (59 °F)

Stability±1 °C at 25 °C (77 °F)

Accuracy±1 °C within a range of ±1 °C from the ambient temperature±2 °C outside a range of ±5 °C from the ambient temperature

Sample Temperature Control Specifications
Table D-5 Sample Temperature Control Specifications
Range

20 °C below the ambient temperature to 60 °C (140 °F)
Minimum value: 4 °C (39 °F)

Stability±1 °C at 25 °C (77 °F)±3 °C at 4 °C (39 °F) and 60 °C (140 °F)

Accuracy±2 °C within a range of ±15 °C from the ambient temperature±3 °C outside a range of ±15 °C from the ambient temperature

Pressure and Vacuum System Specifications
Table D-6 Pressure and Vacuum System Specifications
Range

Injection: 0.1 psi to 25 psi (pressure) or 0.1 psi to 5.0 psi (vacuum)
Rinse: 0.1 psi to 100 psi (pressure) or 0.1 psi to 5.0 psi (vacuum)

Stability±0.3 psi at 25 psi±1.0 psi at 100 psi

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Table D-6 Pressure and Vacuum System Specifications (continued)
Direction

Applied at inlet or outlet for all pressure functions, rinses, andinjections
This parameter is set by the user in the software.

Detector Specifications
UV Detector Specifications
Table D-7 UV Detector Specifications
Analog output

Output 1 is Data Channel 1
Output 2 is not used
Output 3 is either:• Current signal when voltage is programmed• Voltage signal when current or power is programmed
Full scale output is 1.0 AU/V. Multipliers of 1.0, 0.5, 0.2, 0.05, 0.02,
and 0.01 to supply lower AU/V values can be set in the software.

Filter selection

214 nmPositions for 7 additional filters

Filter dimensions

Diameter: 12.7 mm (0.5 inches)Thickness: 5 mm (0.2 inches)

UV source

30 W pre-aligned deuterium lamp

Wavelength accuracy±2 nm

Wavelength range

190 nm to 600 nm

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Table D-8 LIF Detector Specifications
Analog outputs

Output 1 is Data Channel 1
Output 2 is Data Channel 2
Output 3 is either:• Current signal when voltage is programmed• Voltage signal when current or power is programmed
Full scale output is 1.0 AU/V. Multipliers of 1.0, 0.5, 0.2, 0.05, 0.02,
and 0.01 to supply lower AU/V values can be set in the software.

Baseline drift< 0.2 RFU/hrBaseline noise< 0.005 RFU peak to peak

Dynamic range (at asetting of 1,000)> 104

Filters (optional)

For 488 nm laser: 488 nm notch filter and 520 nm band-pass filter
For user-supplied lasers, two filters are required: a laser filter
to block stray laser light and an emission filter to select the
wavelength of the emitted light.
Filter dimensions must be:• Outer diameter: 12.7 mm to 0.25 mm (0.5 inches to 0.01 inches)• Thickness:

0.89 mm (0.35 inches)• For multiple filters used in a single channel, total thickness:
0.89 mm (0.35 inches)
RFU range

0 RFU to 1,000 RFU

Sensitivity

Minimum signal/peak-peak noise ratio of 10,000:1 for 50 nM
sodium fluorescein in a 75 μm i.d. capillary

Solid-state laser

Laser output delivered to the capillary: 2.5 mW ±0.5 mW
Laser wavelength: 488 nm nominal

Wavelength range (foroptics)User Guide
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Excitation: 300 nm to 700 nm
Detection: 350 nm to 750 nm

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System Specifications(Optional) PDA Detector Specifications
Table D-9 PDA Detector Specifications
Analog output

Output 1 is Data Channel 1
Output 2 is Data Channel 2
Output 3 is either:• Current signal when voltage is programmed• Voltage signal when current or power is programmed
Full scale output is 1.0 AU/V. Multipliers of 1.0, 0.5, 0.2, 0.05, 0.02,
and 0.01 to provide lower AU/V values can be set in the software.

Bandwidth

6 mm minimum (absorbance averaging)

Detector type

256 element diode array

Scan collection frequency 0.5 Hz to 32 Hz
UV source

30 W pre-aligned deuterium lamp

UV source lifetime

1,000 hours

Wavelength accuracy

2 nm

Wavelength range

190 nm to 600 nm

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Glossary of Symbols

E

Glossary of Symbols
Note: Not all of the symbols in the following table are applicable to every instrument.
SymbolDescription
Australian Regulatory Compliance Mark. Indicates that the
product complies with Australian Communications Media Authority(ACMA) EMC and Electrical Safety Requirements.
Alternating current

A

Amperes (current)
Asphyxiation Hazard

Authorized representative in the European community

Biohazard

CE Marking of Conformity

cCSAus mark. Indicates electrical safety certification for Canada
and USA.

Catalog number

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Glossary of Symbols

SymbolDescription
Caution. Consult the instructions for information about a possible
hazard.
Note: In SCIEX documentation, this symbol identifies a personal
injury hazard.
China RoHS Caution Label. The electronic information productcontains certain toxic or hazardous substances. The center
number is the Environmentally Friendly Use Period (EFUP) date,and indicates the number of calendar years the product can bein operation. Upon the expiration of the EFUP, the product must
be immediately recycled. The circling arrows show the product isrecyclable. The date code on the label or product indicates thedate of manufacture.
China RoHS logo. The device does not contain toxic andhazardous substances or elements above the maximum
concentration values and the device is an environmentally-friendly
product that can be recycled and reused.
Consult instructions for use.

Crushing Hazard

cTUVus mark for TUV Rheinland of North America

Data Matrix symbol that can be scanned by a barcode reader toobtain a unique device identifier (UDI)

Environmental Hazard

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SymbolDescription
Ethernet connection

Explosion Hazard

Eye Injury Hazard

Fire Hazard

Flammable Chemical Hazard

Fragile

Fuse

Hz

Hertz
International safety symbol "Caution, risk of electric shock" (ISO3864), also known as High Voltage symbol
If the main cover must be removed, then contact a SCIEX
representative to prevent electric shock.
Hot Surface Hazard

In Vitro Diagnostic Device

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Glossary of Symbols

SymbolDescription
Ionizing Radiation Hazard

Keep dry.
Do not expose to rain.
Relative humidity must not exceed 99%.
Keep upright.

Lacerate/Sever Hazard

Laser Radiation Hazard

Lifting Hazard

Magnetic Hazard

Manufacturer

Moving Parts Hazard

Pacemaker Hazard. No access to people with pacemakers.

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SymbolDescription
Pinching Hazard

Pressurized Gas Hazard

Protective Earth (ground)
Puncture Hazard

Reactive Chemical Hazard

Serial number

Toxic Chemical Hazard

Transport and store the system within 66 kPa to 103 kPa.

Transport and store the system within 75 kPa to 101 kPa.

Transport and store the system within the specified minimum(min) and maximum (max) levels of relative humidity,
noncondensing.
Transport and store the system within –30 °C to +45 °C.

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Glossary of Symbols

SymbolDescription
Transport and store the system within –30 °C to +60 °C.

USB 2.0 connection

USB 3.0 connection

Ultraviolet Radiation Hazard

United Kingdom Conformity Assessment Mark

UKRP

United Kingdom Responsible Person

VA

Volt Ampere (apparent power)

V

Volts (voltage)
WEEE. Do not dispose of equipment as unsorted municipal
waste. Environmental Hazard

W

Watts (power)
yyyy-mm-dd
Date of manufacture

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F

Glossary of Warnings

Note: If any of the labels used to identify a component become detached, then contact a SCIEX
field service employee (FSE).
Label

Translation (if applicable)

FOR RESEARCH USE ONLY. NOT FOR USE FOR RESEARCH USE ONLY. NOT FOR USE
IN DIAGNOSTIC PROCEDURES.
IN DIAGNOSTIC PROCEDURES.

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Contact Us

Contact Us
Customer Training• In North America: NA.CustomerTraining@sciex.com• In Europe: Europe.CustomerTraining@sciex.com• Outside the EU and North America, visit sciex.com/education for contact information.

Online Learning Center• SCIEX Now Learning Hub

Purchase Supplies and Reagents
Reorder SCIEX supplies and reagents online at store.sciex.com. To set up an order, use theaccount number, found on the quote, order confirmation, or shipping documents. Currently,
customers in the United States, Canada, United Kingdom, Belgium, Netherlands, France,
Germany, and Switzerland have access to the online store, but access will be extended to othercountries in the future. For customers in other countries, contact a local SCIEX representative.

SCIEX Support
SCIEX and its representatives maintain a staff of fully-trained service and technical specialists
located throughout the world. They can answer questions about the system or any technicalissues that might arise. For more information, visit the SCIEX website at sciex.com or contact us
in one of the following ways:• sciex.com/contact-us• sciex.com/request-support

Cybersecurity
For the latest guidance on cybersecurity for SCIEX products, visit sciex.com/productsecurity.

Documentation
This version of the document supercedes all previous versions of this document.
To find software product documentation, refer to the release notes or software installation guidethat comes with the software.

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Contact Us
To find hardware product documentation, refer to the documentation that comes with the systemor component.
The latest versions of the documentation are available on the SCIEX website, at sciex.com/
customer-documents.
Note: To request a free, printed version of this document, contact sciex.com/contact-us.

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