SCIEX PA 800 Plus Installation guide

PA 800 Plus Pharmaceutical Analysis
System
System Overview Guide
RUO-IDV-05-5521-A
January 2018

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© 2018 AB Sciex
PA 800 Plus Pharmaceutical Analysis System System Overview Guide
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AB Sciex LLC
500 Old Connecticut Path
Framingham, Massuchesetts 01701
USA

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Contents
CHAPTER 1: Safety, Notices and Labels, 7
Overview, 7
General Safety Information, 7
Alerts for Warning, Caution, Important, and Note, 8
Instrument Safety Precautions, 8
Moving Parts or Sharp Objects, 8
Chemical Precautions, 9
Safety Symbols and Labels, 9
High Voltage Electric Shock Risk Symbol, 9
Sharp Object Label, 9
General Biohazard Symbol, 10
Caution, Biohazard Label, 10
Class 1 Laser Caution Label, 10
RoHS Notices, 10
China RoHS Caution Label, 10
China RoHS Environmental Label, 11
Other Instrument Labels, 11
Recycling Label (WEEE), 11
Disposal of Devices Containing Mercury Components, 12
CHAPTER 2: System Overview, 13
Instrument, 13
Sample Handling System, 15
Capillary Cartridge, 17
Fluid Delivery, Power Supply, and Interlocks, 18
Syringe Pump, 18
High Voltage Power Supply, 18
LED Indicators, 18
Cartridge and Sample Cover Interlocks, 18
UV Detector Optics, 19

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Contents
The Photodiode Array (PDA) Detector, 20
The Laser Induced Fluorescence (LIF) Detector, 21
Laser Module, 22
488 nm Laser Module, 22
Supported Applications, 23
IgG Purity/Heterogeneity Assay, 23
SDS Molecular Weight Analysis, 23
Capillary Isoelectric Focusing (cIEF) Analysis, 23
Carbohydrate Analysis, 23
CHAPTER 3: System Procedures and Training Guide, 25
Controller and Instrument Start Up, 25
Controller/Network Logon, 25
License Key, 25
PA 800 Plus Software, 26
Enterprise Window, 26
Instrument Start Up, 27
System Administration, 27
Configuration, 29
Online versus Offline, 30
How to Load the Cartridge and Samples, 30
How to Run a Method, 33
Analysis, 36
Area Calculation, 40
Annotations, 41
Peak Identity, 42
Run Multiple Methods with a Sequence, 42
Viewing Reports, 47
Standard Reports, 47
Method Custom Reports, 47
Sequence Custom Report, 47
Advanced Reports, 47
Suitability Reports, 49
Viewing and Printing Reports, 49
Maintenance, 49
APPENDIX A: Specifications, 51
PA 800 System, 51
Computer Requirements, 52
UV Detector, 52
PDA Detector, 53

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Contents
LIF Detector, 53
Sample Cooling, 54
Revision History, 55

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CHAPTER 1
Safety, Notices and Labels
Overview
A description of the symbols and labels that are used on the SCIEX PA 800 Plus Pharmaceutical Analysis System,
or that are shown in this guide, can be found in this section.
Do not attempt to perform any procedure before carefully reading all instructions. If in doubt as to how to
proceed in any situation, contact your SCIEX Representative.
General Safety Information
To prevent personal injury or system damage, read, understand, and obey all of the safety precautions and
warnings in this document and product label information. These labels are shown with internationally
recognized symbols. 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.
The information provided covers system related safety information applicable to the operation of the system. It
does not cover every safety procedure that should be practiced. Ultimately, the user and the organization are
responsible for compliance with federal, state, provincial, and local EHS regulations and for maintaining a safe
laboratory environment.
Refer to the appropriate laboratory reference material and standard operating procedures.
WARNING
If the equipment is used in a manner not specified by SCIEX the protection provided by the
instrument may be impaired.

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Safety, Notices and Labels
Alerts for Warning, Caution, Important, and Note
All warnings and cautions in this document include an exclamation point, framed within a triangle.
The exclamation point symbol is an international symbol which serves as a reminder that all safety instructions
should be read and understood before installation, use, maintenance, and servicing are attempted.
WARNING
WARNING indicates a potentially hazardous situation which, if not avoided, could result in
death or serious injury. It may also be used to indicate the possibility of erroneous data that
could result in an incorrect determination. May be used to indicate the possibility of severe
instrument damage.
CAUTION
CAUTION indicates a potentially hazardous situation, which, if not avoided, may result in minor
or moderate injury. It may also be used to alert against unsafe practices. May be used to
indicate the possibility of erroneous data that could result in an incorrect determination.
IMPORTANT Used for comments that add value to the step or procedure being performed. Following the advice in
the IMPORTANT adds benefit to the performance of a piece of equipment or to a process.
NOTE Used to call attention to notable information that should be followed during installation, use, or servicing of
this equipment.
Instrument Safety Precautions
Moving Parts or Sharp Objects
WARNING
Risk of personal injury. To avoid injury due to moving parts, observe the following:
• Never attempt to exchange labware, reagents, or tools while the instrument is operating.
• Never attempt to physically restrict any of the moving components of the instrument.
• Keep the instrument work area clear to prevent obstruction of the movement.
Moving parts are limited to the sample handling system. Plate movement is safety interlocked through the
sample access cover. To avoid injury due to moving parts, observe the following:
• Keep loose clothing and hair away from the plate area.
• Never attempt to physically restrict movement of the plate assembly.

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Safety, Notices and Labels
Chemical Precautions
• A description of the symbols and labels that are used on the SCIEX PA 800 Plus Pharmaceutical Analysis, or
that are shown in this guide, can be found in this section.
• Work in a well-ventilated area.
• Always wear assigned personal protective equipment, including powder-free neoprene or nitrile gloves,
safety glasses, and a laboratory coat.
• Follow required electrical safe work practices.
• Avoid ignition sources when working with flammable materials, such as isopropanol, methanol, and other
flammable solvents.
• Take care in the use and disposal of any chemicals. Potential risk of personal injury if proper procedures for
handling and disposing of chemicals are not followed.
• Avoid skin contact with chemicals during cleaning and wash hands after use.
• Comply with all of the local regulations for the storage, handling, and disposal of biohazardous, toxic, or
radioactive materials.
Safety Symbols and Labels
High Voltage Electric Shock Risk Symbol
This symbol indicates that there is high voltage and there is a risk of electric shock, and the operator should use
care when accessing this area.
Sharp Object Label
This symbol indicates that there are sharp objects, and the operator should use care when accessing this area.

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Safety, Notices and Labels
General Biohazard Symbol
This symbol indicates a possible biohazard risk from patient specimen contamination.
Caution, Biohazard Label
This symbol indicates a caution to operate only with all covers in position to decrease risk of personal injury or
biohazard.
Class 1 Laser Caution Label
A label reading “THIS PRODUCT CONFORMS TO APPLICABLE REQUIREMENTS OF 21 CFR 1040 AT THE DATE OF
MANUFACTURE” is found near the Name Rating tag. The laser light beam is not visible.
RoHS Notices
These labels and materials declaration table (the Table of Hazardous Substance’s Name and Concentration) are to
meet People’s Republic of China Electronic Industry Standard SJ/T11364-2006 “Marking for Control of Pollution
Caused by Electronic Information Products” requirements.
China RoHS Caution Label
This label indicates that the electronic information product contains 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 be in operation. Upon the expiration of the EFUP, the product must be immediately
CLASS 1 LASER PRODUCT
THIS PRODUCT CONFORMS TO
APPLICABLE REQUIREMENTS OF
21 CFR 1040 AT THE DATE OF
MANUFACTURE.
MANUFACTURED:
726024-C

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Safety, Notices and Labels
recycled. The circling arrows indicate the product is recyclable. The date code on the label or product indicates
the date of manufacture.
China RoHS Environmental Label
This label indicates that the electronic information product does not contain any toxic or hazardous substances.
The center “e” indicates the product is environmentally safe and does not have an Environmentally Friendly Use
Period (EFUP) date. Therefore, it can safely be used indefinitely. The circling arrows indicate the product is
recyclable. The date code on the label or product indicates the date of manufacture.
Other Instrument Labels
This section provides information for some labels and symbols appearing on the PA 800 Plus housing. These labels
and symbols may be associated with user-serviceable procedures. Individual hazards associated with a specific
procedure in this guide may use these labels and symbols, and are included in Warnings or Cautions within the
procedures for that task.
Recycling Label (WEEE)
The symbol of a crossed-out wheeled bin on the product is required in accordance with the Waste Electrical and
Electronic Equipment (WEEE) Directive of the European Union.
The presence of this marking on the product indicates:
• That the device was put on the European Market after August 13, 2005 and
• That the device is not to be disposed via the municipal waste collection system of any member state of the
European Union.

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Safety, Notices and Labels
For products under the requirement of WEEE directive, please contact your dealer or local SCIEX office for the
proper decontamination information and details on the take back program that facilitates proper collection,
treatment, recovery, recycling, and safe disposal of this device.
Disposal of Devices Containing Mercury Components
This product may contain a mercury-added part. Recycle or dispose of according to local, state, or federal laws. It
is very important that you understand and comply with the safe and proper disposal of devices containing
mercury components (switch, lamp, battery, relay, or electrode). The mercury component indicator label can vary
depending on the type of device.

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CHAPTER 2
System Overview
Instrument
The main components of the PA 800 Plus Pharmaceutical Analysis System include trays that hold
vials of sample, buffer, and other solutions, an interface block, a high-voltage power supply and
electrodes, a source optics module and detector, temperature control hardware, and a sample
injection mechanism. Refer to Figure 2.1, Figure 2.2, and Figure 2.3.
Figure 2.1 PA 800 Plus System
1. Outer Door (open position)
2. UV Detector
3. Two-ended Fiber Optic Cable
4. Clamp Bar and Cable Connection
5. Capillary Cartridge
6. Interface Block

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System Overview
Figure 2.2 PA 800 Plus System Side View
The main power switch is on the lower-right side of the front of the instrument. All connections for
external system components are on the upper-left side panel of the instrument, except for the AC
inlet and the fuse holder. Three fans supply cooling air flow for internal system components. Air is
exhausted through the vents at the side and back of the instrument. Keep at least six inches of
clearance at each vent to ensure adequate air flow.
1. Outer Door or Sample Cover (open)
2. Inner Door or Cartridge Cover (open)
3. Indicators
4. Fluid Fill Port
5. Sample Trays
6. Buffer Trays
7. Fluid Bubble Indicator
8. Power Switch

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System Overview
Sample Handling System
The sample handling system holds four trays; two sample trays (inlet and outlet), and two buffer
trays (inlet and outlet). The sample trays are primarily used for samples; the buffer trays hold the
other solutions required for electrophoresis (for example, buffer and rinse solutions). The trays are
on two parallel tracks. Under normal operating conditions, the trays on the left are inlet trays for
sample and buffer; the trays on the right are outlet trays for sample and buffer. Refer to Figure 2.3.
Figure 2.3 PA 800 Plus Trays
Each buffer tray has slots for 36 universal vials. Sample trays hold either 48 universal vials or a 96-
well plate. Each slot is assigned a number from the front to the back, starting with the number 1,
and assigned a letter from left to right, starting with the letter A. Refer to Figure 2.4.
1. Inlet Sample Tray (48) or 96-Well Plate
2. Inlet Buffer Tray (36 Vials)
3. Outlet Sample Tray (48) or 96-Well Plate
4. Outlet Buffer Tray (36 Vials)

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System Overview
Figure 2.4 Sample and Buffer Trays
WARNING
The PA 800 Plus Pharmaceutical Analysis System is not intended to accommodate
volatile materials in 96-well plates. Volatile solvents can release hazardous or
flammable vapors leading to a risk of fire or explosion. The solvent vapors can
damage the instrument. Do not use volatile solvents in 96-well plates.
WARNING
Wear safety glasses when opening the sample cover while the vials are
pressurized.
The universal vials are pressurized during rinse and separation-with-pressure
events. To reduce the risk of breakage and expelled particles, use only SCIEX vials
(PN A62251), and inspect every vial for damage before use. Do not use any vial
that appears cracked or damaged in any way.
1. Buffer Tray
2. 48-Vial Sample Tray for universal vials. Universal
vials can also be used as a holder for micro vials
containing samples.
3. 96-Position Sample Tray

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System Overview
Capillary Cartridge
The separation capillary is installed in a cartridge. The cartridge design protects the capillary,
supplies a path for liquid coolant, simplifies installation into the instrument, and aligns the
detection window in the optics. The components of the cartridge are shown in Figure 2.5.
Figure 2.5 The Capillary Cartridge
The detection window is an area of the capillary where the polyimide coating is removed to show
the transparent fused-silica. This area of the capillary is put in a part of the cartridge that contains
a plug that connects the window to the optical system. One type of plug is used for UV and PDA
detectors, and a second type is used for LIF detectors. The procedures to install a capillary in a
cartridge are included in the Maintenance section of this guide.
1. Coolant tubing with capillary inside
2. Double seal
3. Detector Window and Aperture - LIF Detector
4. Detector Window and Aperture - UV and PDA Detectors

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System Overview
The capillary temperature is controlled with an inert liquid that circulates through the cartridge.
The temperature is controlled in a range from 10 °C below ambient (with a minimum of 15 °C) to
60 °C. Coolant flows through the cartridge through two openings in the bottom of the housing
(found between the ends of the capillary). This fluid removes the heat generated by electrophoresis.
Fluid Delivery, Power Supply, and Interlocks
Syringe Pump
The PA 800 Plus System can generate pressures with an internal pump mechanism. This pump can
supply 0.1 psi to 25 psi to perform pressure injections or low-pressure mobilizations. The pump can
apply a maximum of 100 psi to move the fluids through the capillary. Vacuum injections can be
performed from 0.1 psi to 5.0 psi. The pressure can be applied to both ends of the capillary at the
same time to prevent outgassing of gels.
High Voltage Power Supply
The high-voltage power supply can deliver a maximum of 30 kV with a maximum current of 300 µA.
The voltage range is from 1 kV to 30 kV in 100 V increments. The polarity is configured in the
software. The current range is from 3.0 µA to 300 µA in 0.1 µA increments. The software allows the
user to select current, voltage, or power operation. During operation, the system will ramp the
voltage or current up to the programmed value. Limits for voltage, current and power can be
entered to protect the capillary. For example, if the user programs a voltage setting for 30 kV, but
the setting for current is only 3.0 µA, the system can reach the limit set for current before reaching
the voltage setting, and control voltage to keep that current.
LED Indicators
The front panel of the instrument contains LED indicators for power, UV, and high voltage. Refer to
Figure 2.2.
Cartridge and Sample Cover Interlocks
The hinged doors of the PA 800 Plus system have interlock sensors that prevent unsafe access to the
inside of the instrument. The first door is called the outer door or sample cover; the second is called
the inner door or cartridge cover. Refer to Figure 2.2.
Opening the Sample cover:
• Stops any tray movement immediately.
• Prevents the execution of any programmed events that require tray movement.
• Aborts a method when a step that requires tray movement is encountered.

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System Overview
Opening the Cartridge cover:
• Turns off the high voltage if it is on.
• Turns off the pump that circulates the capillary coolant.
• Moves the detector filter wheel to the closed position.
UV Detector Optics
The UV optics include an ultraviolet light source, wavelength filters, aperture, capillary, and a
photodiode detector, as shown in Figure 2.6.
The UV source is a deuterium lamp with a wavelength range of 190 nm to 600 nm. Two lenses focus
and direct the output of the lamp through one of the wavelength-selecting filters found in a rotating
wheel behind the capillary cartridge. The beam continues through the aperture in the cartridge
plug and through a section of the capillary that has been treated to remove the polyimide coating
(the detection window). The non-absorbed beam then continues through a fiber optic cable to a
photodiode. The light signal is converted to an electrical signal, digitized, and sent to the 32 Karat
workstation for processing by the software. This signal is also available as an analog output through
a connection on the left side of the instrument.
The design of the instrument insures that the optical system stays in alignment. No user alignments
are required.
There are eight positions on the UV filter wheel. UV detector systems are shipped with four
standard filters: 200 nm, 214 nm, 254 nm, and 280 nm (10 nm bandwidth). The filters are installed in
positions 2, 3, 4, and 5, respectively on the filter wheel. The position 1 is opaque and has the function
of a shutter for the detection system.
Additional wavelengths are obtained by placing the appropriate filters in positions 6, 7, and 8.
If desired, the standard filters can be replaced. If the instrument is used with a PDA detector,
position 8 must be left open (no filter). The filter wheel will accommodate ½ inch (12.7 mm)
diameter filters with wavelengths from 190 nm to 600 nm.

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System Overview
Figure 2.6 UV Optics Layout
The Photodiode Array (PDA) Detector
The Photodiode Array detector, like the UV detector, uses the absorbance of light to detect if there
are samples as they go through the detection window. Unlike the UV detector, the PDA detector can
give spectral analysis of samples.
The PDA detector uses the same cartridge configuration as the UV detector. Refer to the
Maintenance section of this guide for a description of the cartridge.
In PDA detection, the full spectrum of light from the deuterium lamp illuminates the capillary. Refer
to Figure 2.7. Light that is not absorbed by samples is delivered by a fiber optic cable to a grating that
breaks the light into a spectrum. This spectrum is projected onto an array of 256 photodiodes. With
this design, the absorbance profile of the sample is measured. The PDA detector also allows the
simultaneous measurement of light at different discrete wavelengths. The photo diode array
converts the light signal into an electrical signal. The electrical signal is digitized and sent to the
32 Karat workstation for processing by the software.
The PDA detector always uses filter wheel position #8. When the PDA is in use, it is essential that no
filter is in position #8.
1. Capillary Aperture
2. Lenses
3. Deuterium Lamp
4. Lamp Power Supply
5. Photodiode
6. Fiber Optic Connection
7. Motor
8. Position Filter Wheel
9. Filter Position (e.g., 214nm)
10. Fiber Optic Cable
11. Fiber Optic Connector
12. Capillary