Bio-Rad ProteinChip Data Manager Software User Manual
ProteinChip®SELDI System:
Reader Guide
Personal Edition and
Enterprise Editon
Page i
Bio-Rad Laboratories, Inc.
Notice to Purchaser: Limited License
Surface Enhanced Laser Desorption/Ionization (“SELDI”) is a patented process. To use the SELDI
process an end user must obtain a two-part license, including an up-front fee component and a
running-royalty component, under U.S. Patent 5,719,060 or its foreign counterparts, from Bio-Rad
Laboratories, Inc. (“Bio-Rad”). The purchase price of your ProteinChip® SELDI system (the “Reader”)
includes limited, nontransferable rights under the up-front fee component to use this Reader to
practice SELDI and related processes described in said patents for the research and development
activities of the purchaser when this product is used in conjunction with Bio-Rad ProteinChip products
whose use is covered by the running-royalty component. The rights under the running-royalty
component may be purchased only from Bio-Rad or one of its authorized distributors as part of the
purchase of SELDI ProteinChip products. No rights of use are granted herein in the field of clinical
diagnostics. Further information on licenses to practice the SELDI process and on assigning your
exclusive clinical diagnostic rights to any intellectual property developed by you using our SELDI
products, if any, may be obtained by contacting the Legal Department at Bio-Rad Laboratories, Inc.,
1000 Alfred Nobel Drive, Hercules, California 94547.
Microsoft, Windows, and Windows XP are trademarks of Microsoft Corporation. ONEAC is a
trademark of ONEAC Corporation.
Page ii
ProteinChip SELDI System: Reader Guide
Table of Contents
Page iii
Introduction 1
Specifications 1
ProteinChip SELDI Reader 1
Mass Analysis Range 1
Sensitivity 1
Mass Resolving Power 2
Mass Accuracy 2
Laser 2
Sample Handling 2
Vacuum System 2
Control System 3
Equipment Ratings 3
Electrical Requirements 3
Identification and Certification
Label 3
Environmental Conditions
During Operation 3
Environmental Conditions
During Storage or Transport 4
Safety Precautions 4
Laser Radiation 5
High Voltage 6
Radio Frequency Energy 6
Set Up
Requirements 6
Packing Case 6
ProteinChip SELDI Reader 6
Ventilation 7
Mounting 7
Network Connection 7
Installing the ProteinChip
SELDI Reader 7
Setup Time 7
Pre-Installation Reader
Inspection 7
Optional Accessories 8
Setting Up the ProteinChip
SELDI System 9
Setting Up the ProteinChip
SELDI System 9
Operating the ProteinChip
SELDI Reader 13
Multicassette Autoloader
(Enterprise Edition) 14
Overview of Operation 14
Shutting Down the ProteinChip
SELDI Reader 18
Page iv
Basic Maintenance 18
Load Lock Door Cleaning for
Enterprise Edition Instruments 18
Load Lock Door Cleaning for
Personal Edition Readers 23
Warranty and Service Agreements 23
Getting Technical Assistance 24
Moving the ProteinChip
SELDI System Reader 24
Appendix A: Networking the
ProteinChip SELDI System 25
Networking the ProteinChip SELDI
System Using DHCP 26
Overview 26
Verify the Reader Software
Version 26
Set the Reader to DHCP 28
Change the Server to DHCP 31
Redirect Client Computers to the
New Server Address 32
Redirect Client Computers to
the New Server Address 42
Obtain a New License File (If
Necessary) 43
Connect to the Reader 44
Edit the Reader Options 47
Troubleshooting 48
How To 48
Questions or Comments? 49
Obtain a New License File (If
Necessary) 34
Connect to the Reader 34
Edit the Reader Options 37
Networking the ProteinChip SELDI
System Using Static IP Addresses 38
Overview 38
Obtain Static IP Address 38
Assign Static IP to the Reader 38
Assign a Static IP to the Server
Computer 41
ProteinChip SELDI System: Reader Guide
Introduction
ProteinChip SELDI System: Reader Guide
Page 1
Introduction
Specifications
The ProteinChip SELDI System, Personal Edition and Enterprise Edition, is
designed to read Bio-Rad’s proprietary ProteinChip arrays in conjunction with
Bio-Rad software. Sample preparation, protocol development, and analysis are
outside the scope of this guide. For information on ProteinChip arrays, sample
preparation, and protocols, please see the
(bulletin 10008221), volumes 1–2. For data analysis, see the ProteinChip
Guide
Data Manager Software Operation Manual.
1
The ProteinChip SELDI reader is a linear laser desorption/ionization time-offlight mass spectrometer.
ProteinChip SELDI System Applications
ProteinChip SELDI Reader
Designed for benchtop operation
Dimensions: 115 cm (H) x 59 cm (W) x 79 cm (D)
Mass: 105 kg
Mass Analysis Range
From less than 0.02 kD to greater than 150 kD
Sensitivity
Lower limit of detection less than 10 fmol 150 kD protein per spot
1. All specifications are for reference only and are subject to change without notice as part of Bio-Rad’s policy of
continuous improvement.
Page 2
Mass Resolving Power
Peptide
Better than 1000 for [Arg8]-vasopressin at 1084 Da, standard operating voltage
Mass Accuracy
Inherent
Measured mass will be within 0.5% of true mass with 95% confidence
(0.25% CV)
External calibration
Measured mass will be within 0.1% of true mass with 95% confidence
(0.05% CV)
Internal calibration
Measured mass will be within 0.01% of true mass with 95% confidence
(0.005% CV)
Laser
Pulsed nitrogen laser (337 nm), 4 ns pulse width
Sample Handling
Personal
Runs one 8-spot array within 20 minutes using 250 transients per spot
Enterprise
Runs a cassette of up to twelve 8-spot ProteinChip arrays within 2 hours using
250 transients per spot
Vacuum System
Operating pressure < 2.7 x 10-4 Pa
Gauges: active inverted magnetron (high vacuum) and active Pirani (low
vacuum) turbomolecular pump
ProteinChip SELDI System: Reader Guide
Equipment Ratings
Page 3
Equipment
Ratings
Personal Edition:
Enterprise Edition:
70 L/s high compression with two-stage rotary-vane
backing pump
250 L/s high compression with two-stage rotary-
vane backing pump
Control System
Network compatible PC with Microsoft Windows 2000 or XP for reader
operation and data storage.
Electrical Requirements
For safety, the ProteinChip SELDI system must be connected with a certified
power cord rated to at least 10 A to a grounded outlet. Power supply voltage
fluctuations must not exceed ±10% of the nominal voltage.
Supply voltage, current ratings, and fuse ratings
Fig. 1:
Supply voltages, current ratings, and fuse ratings for the ProteinChip SELDI
system Personal Edition (left) and Enterprise Edition (right).
Identification and Certification Label
Fig. 2:
ProteinChip SELDI system identification and certification label.
Environmental Conditions During Operation
Intended for indoor use
Temperature 18°C to 27°C
Page 4
20–80% relative humidity, noncondensing
Mains supply voltage fluctuations not to exceed ±10% of the nominal voltage
Environmental Conditions During Storage or Transport
Temperature -20°C to 60°C (-4°F to 140°F)
Maximum relative humidity 93% non-condensing at 35°C
Maximum operational altitude 2,000 meters
Safety Precautions
Safety symbols are present on the user-accessible parts of the system, on the
top rear of the tower. These labels are shown in Fig. 4. Internal symbols used
are:
ISO 3864, No. B.3.6 Caution, risk of electric shock
ISO 3864, No. B.3.1 Caution (refer to accompanying documents)
The indicator light, which shows when high-voltage power and laser power are
enabled, is labeled with the “caution” (refer to accompanying documents)
symbol (symbol 14, Table 1 of EN61010-1) and a label worded “CAUTION:
high-voltage power supplies and laser are enabled when yellow LED is
illuminated”. Documentation needs to be consulted in all cases where symbol
14, Table 1 of EN61010-1 is used in order to find out the nature of the potential
hazard and any actions which have to be taken.
Fig. 3:
Safety symbols associated with the indicator LED.
There is a risk of electric shock from the high-voltage cables and connections.
Caution is required when working with the components that require periodic
maintenance. In all cases, the instrument should be shut down and power
any
removed from the instrument before performing
maintenance.
All high-voltage connections are labeled with the “Caution, risk of electric
shock” symbol (symbol 12, table 1 of EN 61010-1) and the words “Danger”
and “High Voltage.”
service, including periodic
ProteinChip SELDI System: Reader Guide
Safety Precautions
Page 5
DANGER
HIGH VOLTAGE
Fig. 4:
Safety symbols indicating high voltage inside the ProteinChip SELDI system
cabinet. These labels are located on the exterior of the instrument, near the screws
retaining the side covers.
Warning:
If the equipment is used in a manner other than specified, the
protection provided by the equipment may be impaired. No contact with
hazardous parts or emissions is possible if the instrument panels are kept in
place. It is the user’s responsibility to ensure that untrained persons do not
access the interior. Serious injury or death may result from contact with
components inside the cabinet under single-fault conditions.
The enclosure is an integral part of the safety of this unit. In all cases, the
instrument should be shut down and power removed from the instrument
any
before removing
external cover.
Only personnel aware of the hazards of high voltage and Class 3B laser
radiation should service the reader. The following label should be present near
the safety interlock defeat port and near the safety interlock switches associated
with panels protecting the user from laser radiation:
Fig. 5:
Laser safety warning label inside the system cabinet. This label is visible from
the front when the side panels are removed.
Laser Radiation
Warning:
laser (337 nm, 250 µJ maximum energy/4 ns pulse, 20 Hz maximum pulse
rate). The mass analyzer is a CLASS 1 LASER PRODUCT according to EN 60825:
1993. This means it is safe under reasonably foreseeable conditions of
operation. However, normal operation does not include maintenance or
service. When the enclosure panels and any of the optics covers inside the
instrument are removed, human access to Class 3B laser radiation becomes
possible. Laser safety glasses must be worn when servicing the instrument. The
The system contains an ultraviolet (UV)-emitting pulsed nitrogen
Page 6
glasses must have an optical density of >5 at 337 nm. Care should be taken to
avoid specular reflection of the beam. Laser energy levels up to 250 µJ at
337 nm could be accessible in the interior if the inner cover is removed.
High Voltage
Warning:
are fully insulated under normal conditions, electrostatic charge can accumulate
on wires and feedthroughs carrying high voltage as well as nearby components.
Contact with these components should be avoided when high voltage may be
present.
The unit contains high-voltage power supplies. While the components
Radio Frequency Energy
Note:
This equipment has been tested and found to comply with the limits for
a Class A digital device, pursuant to part 15 of the Federal Communications
Commission (FCC) rules and regulations. These limits are designed to provide
reasonable protection against harmful interference when the 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 the instruction manual, may cause harmful interference to radio
communications. Operation of this equipment in a residential area is likely to
cause harmful interference, in which case the user will be required to correct
the interference at his expense.
Set Up Requirements
The ProteinChip SELDI reader (Fig. 6) is approximately 115 cm high, 59 cm
wide, and 79 cm deep. The reader will fit on a normal height laboratory
bench. The reader will be delivered in a packing case and weighs about
105 kg. The packing case must be unloaded and moved with a forklift or
pallet jack.
Packing Case
143 cm (H) x 84 cm (W) x 89 cm (D)
ProteinChip SELDI Reader
115 cm (H) x 59 cm (W) x 79 cm (D)
Weight 105 Kg
4 x 120 V in US
2 x 13 A in EU
2 m bench space
ProteinChip SELDI System: Reader Guide
Installing the ProteinChip SELDI Reader
Page 7
Ventilation
The ProteinChip SELDI reader requires 3.0 cm of space at the rear and 3.0 cm
above the vents on the top of the main enclosure and at the top of the tower
for adequate ventilation. The air on all sides of the enclosure must meet the
environmental conditions specified above during operation. The region around
the system should be kept free of dust.
Mounting
The ProteinChip SELDI reader has no special mounting requirements. If your
location is subject to earthquakes, adequate restraints should be used to
prevent the reader from moving.
Network Connection
A network connection can be made to the computer according to the
computer manufacturers’ instructions.
Installing the
ProteinChip
SELDI Reader
Setup Time
It takes approximately one day to get the ProteinChip SELDI reader ready for
operation, including unpacking and moving the reader to the laboratory,
connecting it to the power supply, connecting a computer to the reader, and
allowing the unit to reach operating pressure. Installation is generally
performed by a Bio-Rad engineer.
Pre-Installation Reader Inspection
1. Position the reader’s shipping case on a level surface.
2. Release the straps at the bottom of the case, then remove the upper part of
the case. The reader is secured to the bottom part of case with four bolts
which can now be released.
Page 8
Fig. 6:
The ProteinChip SELDI reader, Personal Edition, on its shipping pallet.
3. Inspect the reader for physical damage. If the reader appears to be
damaged, contact Bio-Rad customer service.
4. Check the voltage label on the rear of instrument to verify that the
operating voltage is correct for your line voltage.
If the selected voltage is incorrect, change it by removing and reinserting
the fuse assembly with the arrows aligned to the proper operating voltage.
Optional Accessories
Uninterrupted power supply
An uninterrupted power supply (UPS) is recommended to ensure continuous
operation and to guard against data loss.
We recommend the following UPS for North American systems:
Model:
ProteinChip SELDI System: Reader Guide
S1000XA-1 from ONEAC (available from Bio-Rad)
Setting Up the ProteinChip SELDI System
Page 9
Setting Up the ProteinChip SELDI System
Description:
Ordering: Uninterruptible Power Supply, 120 V
We recommend the following UPS for countries utilizing 230 V AC,
50 Hz power:
Model:
Description:
Ordering: Uninterruptible Power Supply, 230 V
Sinergy 1KVA UPS, 120 V AC input/output, 60 Hz line
frequency. 5-minute backup time.
(catalog # A30-10010)
One kVA UPS provides clean and uninterruptible power
for the US and countries utilizing 120 V AC, 60 Hz power.
This unit will provide 5–8 minutes of backup time in the
event of a utility power loss.
S1000XA-2 from ONEAC (available from Bio-Rad)
Sinergy 21KVA UPS, 230 V AC input/output, 50 Hz
line frequency. 5-minute backup time.
(catalog # A30-10020)
One kVA UPS provides clean and uninterruptible
power for countries utilizing 230 V AC, 50 Hz power.
This unit will provide 5–8 minutes of backup time in
the event of a power loss.
Setting Up the ProteinChip SELDI System
If you are planning to put the reader onto your network please refer to
Appendix A
Required materials
• ProteinChip SELDI reader
• Workstation computer and associated peripherals
• Crossover cable (included)
Connect the reader and the workstation
1. After the ProteinChip SELDI system reader has been powered up, allow up
to 2 hours for the vacuum pump to reach optimum pressure.
2. Plug the crossover cable into the network slots on the reader, and into the
computer. The crossover cable is clearly labeled (on the cable itself).
3. Power up the computer.
Page 10
Launch the software
1. Locate the ProteinChip data manager client software shortcut on the
desktop and double-click it to launch the client (please refer to the
ProteinChip Data Manager Installation and Setup guide Bulletin#
10008270 for software installation instructions).
1.
Login
2. In the
for the
Fig. 7:
The
dialog box (Fig. 7), enter
Password
Login
. Leave the
dialog box.
Server
3. Log in to the ProteinChip data manager client software by pressing the
Logon
button.
admin
set to
for the
Local host
User name
.
, and
admin
New
Instrument
button
Create the instrument profile using ProteinChip data manager
client software
1. Click the
2. Click the New Instrument button on the toolbar or select File | New |
Instrument. The New Instrument dialog box will open.
ProteinChip SELDI System: Reader Guide
Instruments node in the Explorer pane.
Setting Up the ProteinChip SELDI System Page 11
Fig. 8: The New Instrument dialog box.
3. Enter a name for the reader into the Name field. This can be any name of
your choosing. This is a required field.
4. Enter the reader’s Serial Number. This is a required field. See Fig. 8, below,
for the location of the serial number.
Fig. 9: The serial number plate.
5. Enter the IP address of the instrument in the Host Name/IP field. The IP
address is preconfigured to be “192.168.1.200”. This is a required field.
6. Click the Create button to complete the instrument profile.
Page 12
Connect to the reader using ProteinChip data manager client
software
1. After the reader profile has been created, connect to the reader by
highlighting the reader name in the Explorer pane.
2. Once the connection is made, the Home tab will be displayed. You may
receive a “Server mismatch” error message on connecting. You must now
configure the reader to communicate with the ProteinChip data manager
server software.
Set up communication between the reader and ProteinChip data
manager server software
In order for the reader to save data to the server, you must specify the name of
the computer running the ProteinChip data manager server software.
1. On the ProteinChip data manager client computer, open the Control Panel,
then click System. In the System Properties dialog box, click the Computer
Name tab.
2. To determine the computer name, locate the field called Full computer
name and copy down the text up to the first decimal point (Fig. 10). Once
recorded, you can click Cancel to close the dialog box.
Fig. 10: The System Properties dialog box.
ProteinChip SELDI System: Reader Guide
Server computer name
Operating the ProteinChip SELDI Reader Page 13
3. In ProteinChip data manager client software, connect to the reader by
clicking its name in the Explorer pane.
4. Once connected, select Instrument | Instrument Options. Allow a few
moments for the dialog box to retrieve the current settings from the
ProteinChip SELDI reader.
Fig. 11: The Instrument Options dialog box.
5. Enter the computer name recorded in step 2 into the ProteinChip Data
Manager Name field and click the Update button to update the
instrument. Click the Close button to exit.
6. You are now ready to begin using the ProteinChip SELDI system. Please
refer to the ProteinChip data manager software manual for details.
Operating the ProteinChip SELDI Reader
Except for the power switch (located at the back of the reader), there are no
operating controls on the ProteinChip SELDI reader. For the Personal Edition, the
only movable part is the door, which is opened to insert or remove an array. For
the Enterprise Edition, the only movable parts are the cassette dust cover lids,
which are opened to insert or remove cassettes. The reader is controlled through
the software. See the ProteinChip data manager software manual for more
information. Please note that if the reader is used in a manner not specified by
Bio-Rad, the safety protection system provided by the reader may be impaired.
CAUTION
Use of controls and adjustments or performance of procedures other than
those specified herein may result in hazardous radiation exposure.
Loading...