Bruker ultraflex III User manual

ultraflex III
User Manual
Version 1.0 (September 2006)

Bruker Daltonik GmbH
© Copyright 2006
Bruker Daltonik GmbH
All Rights Reserved.
Reproduction, adaptation,
or translation without prior
written permission is
prohibited, except as
allowed under the
copyright laws.
Document History
First edition: March 2004
Printed in Germany.
Warranty
The information contained
in this document is
subject to change without
notice.
Bruker Daltonik GmbH
makes no warranty of any
kind with regard to this
material, including, but not
limited to, the implied
warranties of
merchantability and
fitness for a particular
purpose.
Bruker Daltonik GmbH is
not liable for errors
contained herein or for
incidental or
consequential damages in
connection with the
furnishing, performance or
use of this material.
Bruker Daltonik GmbH
assumes no responsibility
for the use or reliability of
its software on equipment
that is not furnished by
Bruker Daltonik GmbH.
The names of actual
companies and products
mentioned herein may be
the trademarks of their
respective owners.
Safety Information
Safety Class
The ultraflex III with the
closed safety cover is a
Class I Laser product.
It has been designed and
tested in accordance with
IEC Publication 1010-1
Safety Requirements for
Electrical Equipment for
Measurement, Control,
and Laboratory Use.
WARNING
Connecting an instrument
to a power source that is
not equipped with a
protective earth contact
creates a shock hazard
for the operator and can
damage the instrument.
Likewise, interrupting the
protective conductor
inside or outside the
instrument or
disconnecting the
protective earth terminal
creates a shock hazard
for the operator and can
damage the instrument.
WARNING
The instrument must be
disconnected from its
power source before any
cover is removed or it is
opened!
WARNING
All connections of the
instrument must be used
in correct way. The
instrument should only
be used with the wires
and cables delivered
with the system or
otherwise provided by
the manufacturer.
Instrument
Identification
Each instrument is
identified by a serial
number. This number is
located on the rear of
the instrument.
When corresponding
with Bruker Daltonik
GmbH about your
instrument, be sure to
include the model name
and the full serial
number. Write the serial
number of the
instrument here for
reference:
Serial #
Part Numbers
In this manual, Bruker
Daltonik GmbH part
numbers are generally
listed in parentheses
after the name of the
part. A few tools and
supplies listed have no
part numbers and are
not available from
Bruker Daltonik GmbH.
Most of these can be
obtained from
laboratory supply
companies.
Manual part number:
PN # 245596
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Bruker Daltonik GmbH
Technical Support
If you encounter problems with your system please contact a Bruker representative in
your area, or:
Bruker Daltonik GmbH Bruker Daltonik GmbH
Fahrenheitstr. 4 Permoserstr. 15
D-28359 Bremen D-04318 Leipzig
Germany Germany
Phone: [phone] Phone: [phone]
Fax: [phone] Fax: [phone]
E-mail: [email protected]
E-mail (software support):
[email protected]
Internet: www.bdal.de
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Bruker Daltonik GmbH
Table of Changes
Version Date Changes Remarks
1.0 2006-09-25 ultraflex III User Manual First edition
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Bruker Daltonik GmbH
Contents
1ULTRAFLEX III MASS SPECTROMETER........................................................... 9
1.1 Weights and Measures of the ultraflex III ...................................................................... 9
1.2 Site Preparation Specification...................................................................................... 10
1.3 Safety ........................................................................................................................... 10
1.3.1 Safety Symbols.................................................................................................. 10
1.3.2 Manual Conventions and Symbols .................................................................... 11
1.3.3 Operating Precautions ....................................................................................... 12
1.3.4 Electrical Safety ................................................................................................. 13
1.3.5 Environmental Conditions.................................................................................. 14
2INSTALLATION AND SETUP ............................................................................ 15
2.1 Facility and Electrical Requirements............................................................................ 15
2.2 Unpacking .................................................................................................................... 16
2.3 Setup............................................................................................................................ 17
3INSTRUMENT LAYOUT ..................................................................................... 19
3.1 Schematic of the Mass Spectrometer.......................................................................... 19
3.1.1 Instrument Controller ......................................................................................... 20
3.1.2 Rear Panel......................................................................................................... 21
3.1.3 Vacuum System................................................................................................. 24
3.1.4 Scout MTP Ion Source....................................................................................... 25
3.1.4.1 Pulsed Ion Extraction.................................................................................... 26
3.1.4.2 Target Plates ................................................................................................ 27
3.1.4.3 AnchorChip Target.................................................................................... 28
3.1.4.4 Transponder ................................................................................................. 28
3.1.5 TOF/TOF Analyzer ............................................................................................ 29
3.1.5.1 Precursor Ion Selector.................................................................................. 29
3.1.5.2 LIFT 31
3.1.5.3 How Does LIFT Work? ................................................................................. 33
3.1.5.4 Reflector ....................................................................................................... 35
3.1.5.5 Detector ........................................................................................................ 36
3.1.5.6 Digitizer37
3.1.5.7 Laser System................................................................................................ 37
3.1.5.8 Camera 37
3.2 PC Configuration.......................................................................................................... 38
3.3 Remote Service Capability........................................................................................... 38
3.4 Twister (optional) ......................................................................................................... 41
3.5 Example of the Structure of a Bruker ID ...................................................................... 42
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4OPERATION ....................................................................................................... 43
4.1 Locating the Instrument Functions - Turning the Instrument ON or OFF .................... 43
4.1.1 Rear Panel......................................................................................................... 43
4.1.2 Front Panel ........................................................................................................ 45
4.2 Manual Cartridge ......................................................................................................... 47
4.2.1 Checking for Instrument Operational Readiness............................................... 47
4.2.2 Moving Targets In and Out with the Manual Cartridge...................................... 47
4.3 Using the Twister (optional) ......................................................................................... 51
4.3.1 Turning the Instrument On or OFF .................................................................... 51
4.3.2 Checking for Instrument Operational Readiness............................................... 52
4.3.3 Moving Targets In .............................................................................................. 52
4.3.4 Moving Targets Out ........................................................................................... 52
4.3.5 Instrument Control in Analytical Operations ...................................................... 52
5INSTRUMENT MAINTENANCE ......................................................................... 53
6INDEX ................................................................................................................. 54
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Bruker Daltonik GmbH
Safety Instructions
The following symbols may be found on or near various components.
Before starting the installation, pay attention to these important safety instructions!
Warning
Warning attracts attention to procedures that could result in personal injury, if protocols
are not followed.
This symbol is placed on the product in the area where a hazardous voltage is present.
Only trained service personnel should perform work in this area.
When the instrument is operating high DC voltages are present, in addition to the 230V
AC mains supply. All panels must be fitted prior to operation. Only under these
circumstances does the instrument comply with the electromagnetic radiation
guidelines (EC certificate).
Laser radiation
Indicates that laser light may be present.
The autoflex with the closed safety cover is a Class I Laser product.
With safety cover opened it turns to a Class IV Laser product.
Caution
Caution attracts attention to procedures that could result in damage to
the instrument, if protocols are not followed.
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Bruker Daltonik GmbH
Instrument Classification
The autoflex III is an electrical equipment for measurement, control, and laboratory use
where the electromagnetic environment is kept under control. That means in such an
environment transmitting devices such as mobile phones should not be used in
immediate vicinity.
EN 61326/A1:1998,
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Bruker Daltonik GmbH ultraflex III Mass Spectrometer
1 ULTRAFLEX III MASS SPECTROMETER
The ultraflex III is a MALDI (Matrix Assisted Laser Desorption/Ionization) tandem
mass spectrometer specially designed for automated MS and MS/MS high throughput
identification of proteins and peptides. Tandem Mass Spectrometry is a technique that
utilizes more than one mass selective stage in a mass spectrometer.
The most common form in practice is a two stage arrangement to record MS/ MS or
(MS)2 spectra.
The incorporated LIFT device allows acquiring full fragment ion spectra within one
single scan and replaces traditional measurements of segmented spectra with
stepwise-reduced reflector potentials.
1.1 Weights and Measures of the ultraflex III
Figure 1-1 Weights and measures of an ultraflex III instrument
(L x W x H = 230 cm x 133,2 cm x 87,4 cm; Weight 550 kg)
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Bruker Daltonik GmbH ultraflex III Mass Spectrometer
1.2 Site Preparation Specification
Before starting the installation of the instrument the site must be properly prepared.
Please refer to the Site Preparation Specification document that is sent to any
customer prior to the shipment of the instrument.
It contains information regarding the device requirements, such as operating
environment, gas supply, power, exhaust, venting, grounding, etc.
This document has to be verified and returned with your signature to Bruker before a
service representative will start the installation.
1.3 Safety
Safety considerations for the ultraflex III spectrometer include:
ultraflex III Safety Symbols (chapter 1.3.1)•
•
•
•
Manual Conventions and Symbols (chapter 1.3.2)
Operating Precautions (chapter 1.3.3)
Electrical Safety (chapter 1.3.4)
1.3.1 Safety Symbols
The following symbols may be found on or near various components of the mass
spectrometer:
Table 1-1 Safety Symbols
Symbol Description
Indicates that an operation or condition on
the instrument could cause instrument
damage if precautions are not followed.
This can be any type of hazard. When this
symbol is observed, refer to the safety
pages in the manual for further
information.
Indicates the danger of electric shock due
to the presence of high voltage, if
precautions are not followed.
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Bruker Daltonik GmbH ultraflex III Mass Spectrometer
Symbol Description
Indicates that laser light may be present.
The ultraflex III with the closed safety
cover is a Class I Laser product.
With safety cover opened it turns to a
Class IV B Laser product.
Indicates that a terminal either receives or
delivers alternating current or voltage.
Indicates that a protective grounding
terminal must be connected to earth
ground before any other electrical
connections are made to the instrument.
Indicates the OFF position of the main
power switch.
Indicates the ON position of the main
power switch.
1.3.2 Manual Conventions and Symbols
The following graphic text formats and symbols are used to set apart important safety
information:
Note: Indicates important information in a procedure or description.
Caution: Indicates an operation that could cause instrument damage if
precautions are not followed.
Warning:
Indicates that an operation could cause personal injury if precautions
are not followed.
High Voltage:
Indicates that an operation could cause personal injury if precautions
are not followed.
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Bruker Daltonik GmbH ultraflex III Mass Spectrometer
1.3.3 Operating Precautions
To protect yourself from harm and prevent system malfunction, observe the following
guidelines:
Before using the instrument, read all warnings presented in the beginning of this
manual.
•
•
•
•
•
•
Wear appropriate protective clothing, including safety glasses and gloves, when
preparing samples and solutions for use with this instrument.
Follow the correct safety procedure and the manufacturer's recommendations
when using solvents.
Clean the exterior surfaces of the instrument with a soft cloth dampened with a
mild detergent and water solution. Do not use abrasive cleaners or solvents.
Exercise caution when moving as the ultraflex III mass spectrometer weighs
550 kg / 1212 lb. Wear appropriate clothing and use appropriate tools when
carrying or moving the instrument.
The ultraflex III mass spectrometer contains a Class IV B pulsed ultraviolet
laser (100 µJ at 337 nm). Wear appropriate eye protection and never look
directly into the laser when any of the protective covers are removed. In
operation, laser light is directed onto the analysis chamber sample target. The
same interlocks that assure the analysis chamber vacuum integrity, also assure
that no laser light escapes through the target loading port. If the vacuum
system fails and system allows the load port to be opened, the laser cannot be
fired.
Caution: When shipping or transporting the instrument it is critical that the target is in
the OUT position. Failure to do so will result in damage to the instrument.
Caution: Do not restrict ventilation air intake at the rear of the machine or the exhaust
at the back of the machine.
To ensure proper operation check the ventilation air filter at the instrument
rear every three months and replace, if necessary, as explained in
chapter 5 Instrument Maintenance.
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Bruker Daltonik GmbH ultraflex III Mass Spectrometer
1.3.4 Electrical Safety
Electrical safety considerations consist of the following chapters:
General Safety: Before installing or operating the ultraflex III mass
spectrometer, read the following information concerning hazards and potential
hazards. Ensure that anyone involved with installation and operation of the
instrument is knowledgeable in both general safety practices for the laboratory
and safety practices for the ultraflex III mass spectrometer. Seek advice from
your safety engineer, industrial hygienist, environmental engineer, or safety
manager before installing and using the instrument.
•
•
•
•
Position the ultraflex III mass spectrometer in a clean area that is free of dust,
smoke, vibration, and corrosive fumes, out of direct sunlight, and away from
heating units, cooling units, and ducts.
Verify that there is an adequate and stable power source for all system
components.
Verify that the power cord is the correct one for your laboratory and that it
meets the national safety agency guidelines for the particular country of use.
Warning:
DO NOT attempt to make adjustments, replacements or repairs to this
instrument. Only a Bruker Daltonics Service Representative or similarly
trained and authorized person should be permitted to service the
instrument.
Warning:
When it is likely that the electrical protection of the ultraflex III mass
spectrometer has been impaired:
1. Power off the ultraflex III mass spectrometer.
2. Disconnect the line cord from the electrical outlet.
3. Secure the instrument against any unauthorized operation.
Warning:
The ultraflex III mass spectrometer and MALDI-TOF analyses use very
high voltages. Under normal operation, the instrument requires NO user
access to the inner components of the instrument. NEVER OPERATE
the ultraflex III mass spectrometer with the protective cover removed as
this exposes the user to risk of severe electrical shock and harmful,
invisible, ultraviolet laser radiation.
Caution: Use only fuses with the required current and voltage ratings and of the
specified type for replacement.
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Bruker Daltonik GmbH ultraflex III Mass Spectrometer
Caution: Use the instrument according to the instructions provided in this manual.
If used otherwise, the instrument-provided protection can be impaired.
Caution: Connect the instrument to an AC line power outlet that has a protective
ground connection. To ensure satisfactory and safe operation of the
instrument, it is essential that the protective ground conductor (the green
/ yellow lead) of the line power cord is connected to true electrical
ground. Any interruption of the protective ground conductor, inside or
outside the instrument, or disconnection of the protective ground
terminal, can impair the instrument-provided protection.
1.3.5 Environmental Conditions
The ultraflex III mass spectrometer is designed for indoor use and functions correctly
under the following ambient conditions:
Table 1-2 Environmental Conditions
Operating Conditions
Temperature 10 - 30 °C (50 to 86 °F)
Relative Humidity 15-95% non-condensing 35 °C
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Bruker Daltonik GmbH Installation and Setup
2 INSTALLATION AND SETUP
Please refer to the Bruker Site Preparation Specification document for your mass
spectrometer.
Installation and setup consists of:
Facility and Electrical Requirements (chapter 2.1).•
•
•
•
•
•
Unpacking (chapter 2.2).
Setup (chapter 2.3).
2.1 Facility and Electrical Requirements
The facility must provide:
100 to 230 V/ 3-1.5 A / 50–60 Hz. The instrument back panel is fitted with an
IEC320–C14 mains inlet (Figure 3-3). The instrument comes with a 3 m long
IEC320 line cord and a mains plug, suitable for use in your country.
The ultraflex III mass spectrometer requires approximately 2 m2of space on a
surface that can safely support the full 550 kg instrument weight.
To ensure proper ventilation, and access to the connections and main switch,
maintain at least 80 cm of clearance behind the instrument.
Warning:
The main supply must provide adequate grounding.
The system has an exhaust port to accommodate venting. This port is located on the
rear of the instrument. Individual facilities may have safety guidelines, which require
ventilation. It is the responsibility of the user to adhere to the requirements of their
respective facility.
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Bruker Daltonik GmbH Installation and Setup
2.2 Unpacking
The packing list is created for each order and placed in the crate with the machine.
Note: The warranty does NOT cover damage resulting from customer mishandling.
Do not open the shipping container unless a BRUKER representative is
present. Opening of the container without authorized persons will void the
warranty of the instrument. Our service engineers will set up the instrument in
customer’s laboratory.
The surface on which the instrument is placed must be able to safely
support the full 550 kg weight, and computer, monitor and printer as well.
Let the machine on the palette and wait for the Bruker representative to move
the instrument to its desired location!
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Bruker Daltonik GmbH Installation and Setup
2.3 Setup
To setup the instrument:
1. At the rear of the instrument, plug in the following cord and cables into the
corresponding connections (Figure 3-3.
a. Line cord.
b. Remote cable.
c. Signal cables.
2. Plug the other end of the AC line cord into a suitable AC outlet.
Caution: Read and follow all electrical and safety precautions described in
chapter 1.3 Safety or chapter 1.3 Safety.
3. Plug the data system end of the signal cable connections into the appropriate
connections (Figure 2-1).
4. Plug the data system end of the Remote cable into the COM-1 port on the PC.
5. Turn on the AC mains switch.
6. Ensure that the POWER LED is illuminated (Figure 3-2).
After initial power-up it may be as long as 12 hours before the instrument is ready for
operation, at which time the Ready LED illuminates (Figure 3-2).
Note: If any faults occur within the system the Error LED (Figure 3-2) illuminates and
the system goes into standby. Contact your authorized service personnel for
help.
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Bruker Daltonik GmbH Installation and Setup
Trigger input digitizer
Signal from the linear
detector
Signal from the
reflector detector
Figure 2-1 Connection at the rear of the PC
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Bruker Daltonik GmbH Instrument Layout
3 INSTRUMENT LAYOUT
Bruker flex systems, such as the ultraflex III are always composed of only two main
components:
1. Mass spectrometer (twister optional).
2. Data system (chapter 3.2).
3.1 Schematic of the Mass Spectrometer
Figure 3-1 shows the principle the ultraflex III mass spectrometer works.
P2
+
Target Reflector Reflector
plate detector
Linear detector
Driftregion
PLMS
P1
+
PCIS
/ IS2
Ground
potential
P1
+
P1
+
LIFT
IS1
IS1
Figure 3-1 Schematic of the instrument
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Bruker Daltonik GmbH Instrument Layout
3.1.1 Instrument Controller
When the instrument is ready for operation the three green LED’s Mains,Ready, and
Access illuminate green light as shown in Figure 3-2.
Figure 3-2 Control panel at the front of the instrument
1. Load / Eject: Moves the target in or out.
2. Access:
a) Permanently lit: When either the tray is inside or outside the instrument in the
end position.
b) OFF: During the target moves in or out.
3. In Progress: Permanently lit as long as the docking procedure is in progress
(Target In/ Out).
4. Error:
a) Permanently lit: Malfunction, requires intervention of the user or a service
technician details are shown on the PC (flexControl).
b) Flashing (combined with system error): Service mode or firmware update.
5. Automode: Permanent lit as long as AutoXecute is in progress. During this run
applying the related button cannot retract the target plate.
6. Ready:
a) Permanently lit: Ready for acquiring spectra, i.e. any interlock is closed; N2
pressure is correct, sufficient vacuum, HV present, etc.
b) OFF: During the docking procedure.
7. Warm up:
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