Bruker ultraflex III User Manual
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Bruker ultraflex III User Manual

Mass spectrometer
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ultraflex III
User Manual
Version 1.0 (September 2006)

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Summary of Contents for Bruker ultraflex III

  • Page 1 III User Manual Version 1.0 (September 2006)
  • Page 2 Bruker Daltonik GmbH. names actual companies and products mentioned herein may be the trademarks of their respective owners. ultraflex III User Manual, Version 1.0...

  • Page 3: Technical Support

    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: +49 (421) 2205 430...
  • Page 4 Bruker Daltonik GmbH Table of Changes Version Date Changes Remarks 2006-09-25 ultraflex III User Manual First edition ultraflex III User Manual, Version 1.0...

  • Page 5: Table Of Contents

    Bruker Daltonik GmbH Contents ULTRAFLEX III MASS SPECTROMETER............9 Weights and Measures of the ultraflex III ..............9 Site Preparation Specification..................10 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...
  • Page 6 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 INSTRUMENT MAINTENANCE ................. 53 INDEX ......................... 54 ultraflex III User Manual, Version 1.0...

  • Page 7: Safety Instructions

    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. ultraflex III User Manual, Version 1.0...
  • Page 8 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, ultraflex III User Manual, Version 1.0 viii...

  • Page 9: Ultraflex Iii Mass Spectrometer

    III Mass Spectrometer 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.

  • Page 10: Site Preparation Specification

    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: •...

  • Page 11: Manual Conventions And Symbols

    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.

  • Page 12: Operating Precautions

    • 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.

  • Page 13: Electrical Safety

    • 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.

  • Page 14: Environmental Conditions

    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...

  • Page 15: Installation And Setup

    Bruker Daltonik GmbH Installation and Setup 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).

  • Page 16: Unpacking

    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!

  • Page 17: Setup

    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. ultraflex III User Manual, Version 1.0...
  • Page 18 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 ultraflex III User Manual, Version 1.0...

  • Page 19: Instrument Layout

    Bruker Daltonik GmbH Instrument Layout 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.

  • Page 20: Instrument Controller

    6. Ready: a) Permanently lit: Ready for acquiring spectra, i.e. any interlock is closed; N pressure is correct, sufficient vacuum, HV present, etc. b) OFF: During the docking procedure. 7. Warm up: ultraflex III User Manual, Version 1.0...

  • Page 21: Rear Panel

    • Nitrogen inlet to operate a N -laser (Class IV Laser Product). • Gas inlet to vent the instrument. ultraflex III User Manual, Version 1.0...
  • Page 22 • The instrument is fitted with an IEC320-C14 mains inlet. At the rear of the machine behind the cover there is the air intake with a filter. Replace the air filter every three month. ultraflex III User Manual, Version 1.0...
  • Page 23 Bruker Daltonik GmbH Instrument Layout Figure 3-3 Schematic of the connections at the rear ultraflex III User Manual, Version 1.0...

  • Page 24: Vacuum System

    The instrument operates at a high vacuum pressure of about 8*10-7 mbar or better. The rough vacuum pressure ranges from atmosphere to about 1*10 mbar. ultraflex III User Manual, Version 1.0...

  • Page 25: Scout Mtp Ion Source

    Ar. CID has proved to be useful to enhance intensities of fragments in the low fragment mass range. ultraflex III User Manual, Version 1.0...

  • Page 26: Pulsed Ion Extraction

    During the next few hundred nanoseconds the analyte moves further towards P2. ultraflex III User Manual, Version 1.0...

  • Page 27: Target Plates

    The standard target plate is a SCOUT-MTP plate (MicroTiter Plate) with 384 defined sample positions (Figure 3-5). A video CCD camera and a video capture card inside the PC provide high resolved sample images. Figure 3-5 Illustration of an microwell plate and a Scout MTP plate ultraflex III User Manual, Version 1.0...

  • Page 28: Anchorchip Target

    3.1.4.4 Transponder All the Scout MTP targets are equipped with a programmable semiconductor chip, called transponder. The transponder contains information from Bruker, such as the geometry, the part number, and the serial number (Read only data). Further on the chip contains a ”Use Counter”, which identifies the target and counts on ejection how often this one has been used.

  • Page 29: Tof/Tof Analyzer

    Bruker Daltonik GmbH Instrument Layout 3.1.5 TOF/TOF Analyzer The peculiarity of the ultraflex III analyzer is the LIFT device located in the flight tube, which allows acquiring a full fragment ion spectrum with one single scan. 3.1.5.1 Precursor Ion Selector...
  • Page 30 Bruker Daltonik GmbH Instrument Layout PCIS alternating polarity Stray field Stray field position Figure 3-6 Operation principle of the precursor ion selector ultraflex III User Manual, Version 1.0...

  • Page 31: Lift

    (chapter 3.1.5.1), as fragments that are produced before arriving at the PCIS assembly pass the unit together with the parent because of their same velocity. . ultraflex III User Manual, Version 1.0...
  • Page 32 It can be switched off to allow the detection of the parent, e.g., for calibration purposes. PCIS PLMS LIFT Target Reflector Reflector plate detector ion lenses Ground potential Ion source LIFT Two stage field (PIE) Figure 3-8 Working principle of the TOF/TOF analyzer ultraflex III User Manual, Version 1.0...

  • Page 33: How Does Lift Work

    19 keV). A fragment with a molecular weight of of the parent ion has got energy of 8keV 19,4 keV ( + 19 keV). This is only about 28% less energy and allows the ultraflex III User Manual, Version 1.0...
  • Page 34 + 19 kV Phase 1 Ground + 19 kV Phase 2 Ground + 19 kV Phase 3 Ground + 19 kV Phase 4 Ground Figure 3-9 Potentials during a LIFT process on the related electrodes ultraflex III User Manual, Version 1.0...

  • Page 35: Reflector

    The ultraflex III and other TOF mass spectrometers from the “flex”-series use a gridless reflector with ion lenses (Figure 3-10). Fragments that would arise inside the reflector instead of during their flight in the drift region form an undesired high chemical background.

  • Page 36: Detector

    The multiplication process that takes place in a channel is illustrated beneath. Glass channel wall Semiconducting layer Secondary electrons Output electrons Figure 3-11 Principle of a micro channel ultraflex III User Manual, Version 1.0...

  • Page 37: Digitizer

    (< 1ns) up to ten times faster than other detector configurations, such as channeltrons or discrete dynode multipliers. Each detector of the ultraflex III contains two MCPs coupled in series. The linear detector is equipped with the gating option to be used to avoid saturation effects, which may be caused by the matrix material.

  • Page 38: Pc Configuration

    Figure 3-12 Operating principle of the remote service To obtain a maximum operating time the ultraflex III is equipped with a remote service capability (Figure 3-12). This feature allows for troubleshooting via the internet. Thus problems can often be solved efficiently with the customer PC being fully controlled by the Daltonics Service Board.
  • Page 39 2. Select Join on the web page. Figure 3-14 appears. Figure 3-13 Webpage of Bruker Enterprise Note: The “http”-connection changes to a “https”-connection, coded with 128-bit to provide the highest possible level of security! ultraflex III User Manual, Version 1.0...
  • Page 40 Figure 3-14 Enter the required information Please, enter the required information. A call to Bruker Service on +49 421 2205 430, will provide you with the Support Session Number. Press the “Submit” button and follow the instructions to successfully connect the remote service to your ultraflex III.

  • Page 41: Twister (Optional)

    Bruker MAPII. Both instruments the Twister and the spectrometer are controlled by the controls of the AutoXecute page in flexControl software as shown in Figure 3-16. ultraflex III User Manual, Version 1.0...

  • Page 42: Example Of The Structure Of A Bruker Id

    Target plates without barcodes are identified by the IDs stored in their transponders. 3.5 Example of the Structure of a Bruker ID The ID’s are normally the Bruker Transponder ID. This ID consists of PartNumber.SerialNumber, e.g. 209515.240. This code corresponds to a...

  • Page 43: Operation

    Bruker Daltonik GmbH Operation OPERATION 4.1 Locating the Instrument Functions - Turning the Instrument ON or OFF 4.1.1 Rear Panel Figure 4-1 Schematic of the connections at the rear ultraflex III User Manual, Version 1.0...
  • Page 44 Key field for the service to lift the cover. Mains: • The instrument is fitted with an IEC320-C14 mains inlet. Instrument power is controlled with the mains switch, where: • 0 = OFF (vents the instrument) • I = ON ultraflex III User Manual, Version 1.0...

  • Page 45: Front Panel

    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. ultraflex III User Manual, Version 1.0...
  • Page 46 Permanent lit: malfunction, requires intervention of the user or a service technician; the tool tips feature on the PC shows details (flexControl). d) Flashing: (combined with Target Error): Service mode or firmware update. 9 MAINS: Permanent lit, when the main circuit breaker is on. ultraflex III User Manual, Version 1.0...

  • Page 47: Manual Cartridge

    To change a target of the manual cartridge follow this procedure: 1. Press the “PUSH” button of the cover lid (Figure 4-3). Figure 4-3 Closed cover lid of the manual cartridge with “PUSH” button ultraflex III User Manual, Version 1.0...
  • Page 48 Bruker Daltonik GmbH Operation 2. Wait until the cover lid has reached the lower position. Pay attention not to squash the fingers! Figure 4-4 Open cover lid and free access to the manual cartridge ultraflex III User Manual, Version 1.0...
  • Page 49 Bruker Daltonik GmbH Operation 3. Open the manual cartridge by pulling the lever with a finger. Figure 4-5 Opening the cover plate of the manual cartridge ultraflex III User Manual, Version 1.0...
  • Page 50 Bruker Daltonik GmbH Operation 4. Pull the lever with its target platform until it reaches the horizontal position. Figure 4-6 Manual cartridge during opening Figure 4-7 Manual cartridge completely opened ultraflex III User Manual, Version 1.0...

  • Page 51: Using The Twister (Optional)

    Instrument power is controlled with the mains switch (Figure 3-3), where: • 0 = Off. • I = On. The front panel Power LED (Figure 3-2) illuminates when the machine is properly powered up. ultraflex III User Manual, Version 1.0...

  • Page 52: Checking For Instrument Operational Readiness

    2. Remove the target, and press the “TARGET IN/OUT” button momentarily a second time. 4.3.5 Instrument Control in Analytical Operations How to control the mass spectrometer in analytical operations is described in the manual flexControl and flexAnalysis. ultraflex III User Manual, Version 1.0...

  • Page 53: Instrument Maintenance

    The filter must be replaced. Replace the filter by lifting the old filter up and out of the holder and slide in a new one. Note: Replace only the genuine Bruker filter, PN 73121! For service contact please refer to chapter Technical Support.

  • Page 54: Index

    Transponder/barcode information Grounding Turning the Instrument On or OFF 45, 51 Twister Installation and Setup Instrument controller 20, 45 Vacuum system Instrument layout Ventilation air filter Instrument Maintenance Venting Laser device Laser system LIFT ultraflex III User Manual, Version 1.0...

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