Bruker ImagePrep User Manual
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Bruker ImagePrep User Manual

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ImagePrep
User Manual
(for Software Version 2.0)
Revision 4 (April 2013)

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  • Page 1 ImagePrep User Manual (for Software Version 2.0) Revision 4 (April 2013)

  • Page 2: Copyright

    It is only permitted to use wires equipment that is not furnished and cables provided by the by Bruker Daltonik GmbH. manufacturer. ImagePrep User Manual, Revision 4 (April 2013) Copyright: Bruker Daltonik GmbH Fahrenheitstr. 4 D-28359 Bremen Germany...

  • Page 3: Safety Symbols

    To do so can contaminate and pollute the environment. To dispose of the equipment responsibly, contact your community waste disposal authority. The details are regulated in national law. ImagePrep User Manual Revision 4 Page 3 of 77...

  • Page 4: Technical Support

    Changes Remarks Aug 2007 First edition Oct 2007 Editorial update Aug 2009 Updated hardware and ImagePrep software Version 2.2 Jun 2010 Procedural changes Apr 2013 WEEE, SAP renumbering and web address update, added figure and table numbering Page 4 of 77...

  • Page 5: Getting Started

    • Simplified Spray Head Adjustment procedure section 6.2 • Improved sample loading procedure section 3.3 • New Test Spray buttons section 3.5.3 • Improved clean method section 3.5.5 • Diverse bug fixes ImagePrep User Manual Revision 4 Page 5 of 77...

  • Page 6: Table Of Contents

    3.5.3 Test Spray and Start Automatic Preparation ........... 21 3.5.4 Mounting the Glass Slide into the Adapter ..........22 3.5.5 Cleaning the Spray Chamber and the Spray Head ......... 23 Manual Sample Preparation with ImagePrep ..........25 Page 6 of 77 ImagePrep User Manual Revision 4...
  • Page 7 Date / Time Setting ..................69 Touch Panel Stylus ..................69 Filter Replacement ..................69 6.10 Fuse Replacement ..................69 6.11 List of Spare Parts ..................70 Appendix 1: ......................71 Appendix 2: ......................73 ImagePrep User Manual Revision 4 Page 7 of 77...

  • Page 8: Safety And Site Requirement Issues

    Figure 1 Instrument in ventilated fume hood NOTE Only use manufacturer’s approved chemicals! See list in section 1.3 NOTE Never disable or bypass any of the safety features. Page 8 of 77 ImagePrep User Manual Revision 4...

  • Page 9: Installation And Site Requirements

    The matrix concentration should be at least 20% below saturation. Figure 3 List • Optionally you can acidify the solution with up to solvents 0.5% TFA. NOTE Other solvents or chemicals can be used with manufacturer’s agreement. ImagePrep User Manual Revision 4 Page 9 of 77...

  • Page 10: General Introduction

    (typical >200 µm) and perfect alignment with the mass spectrometer is critical. ImagePrep is a new preparation device for MALDI Imaging that reproducibly provides high resolution images at high speed and high spectra quality at the same time.
  • Page 11 ImagePrep is a push-button system: The user just selects a method, adapts it to the respective tissue to be coated with three intuitive parameters (matrix thickness, incubation time and wetness) and starts the sample preparation. The tissue section is coated automatically without further user intervention.

  • Page 12: Sample Preparation Workflow Description

    Please wait until you see the ImagePrep main menu. Figure 5 Main switch NOTE Make sure that no USB device is plugged into the instrument when starting the boot process. Page 12 of 77 ImagePrep User Manual Revision 4...

  • Page 13: Preparing The Tissue Sections

    2. Mount tissue sections on ITO coated microscope glass slides (75x25 mm, Bruker # 8237001). These transparent slides are perfectly suited to light microscopy and for the optical sensor of ImagePrep. Furthermore their electrical conductivity fulfills a prerequisite for successful MALDI TOF analysis.

  • Page 14: Loading The Sample

    Sample Preparation Workflow Description Bruker Daltonik GmbH Loading the Sample Position slide on the elevated rectangular area on the bottom of the ImagePrep spray chamber. Do not position the tissue on the sensor window (see Figure 7). The scattering behavior of the sample is unpredictable.

  • Page 15: Loading The Matrix Solution

    Sample Preparation Workflow Description Loading the Matrix Solution 1. Prepare the matrix solution. Note: If you use ImagePrep standard methods, you will find the matrix recipe in the information window which appears when you open this method. If you want to spray other matrix solutions with ImagePrep,...

  • Page 16: Automatic Sample Preparation

    5. Start preparation right after matrix loading. Long delays lead to spray head clogging. In order to ensure high quality sample preparations, Bruker recommends that the spray generator (# 8261614) is replaced after every 30 preparations. An internal counter will inform you when the replacement is necessary.

  • Page 17: Select Method

    Switch on the ImagePrep device with the main switch (see section 3.1). Select AutoPrep in the main menu once the software has opened (see Figure 12). Depending on the matrix used and on the analyte molecules under scrutiny, different preparation methods have to be used.
  • Page 18 Sample Preparation Workflow Description Bruker Daltonik GmbH Table 1 Preinstalled methods on ImagePrep; * xy is the version number, e.g. SA_nsh01 or DHB_nsh05 Methods for Methods for Scope Matrix Recipe old spray head new spray head (nsh) Figure 16 Figure 15...

  • Page 19: Customize Method

    In the Default customization all three sliders are set to the middle position (see Figure 17). This instrument setting was tested by Bruker on rat brain tissue and is also widely applicable to other tissues.
  • Page 20 2 s / 10 s / 18 s in the first phase and of 10 s / 20 s / 30 s in the second phase. If a customization is not allowed in any of the phases, then the slider for the respective parameter is grayed-out and inactive. Page 20 of 77 ImagePrep User Manual Revision 4...

  • Page 21: Test Spray And Start Automatic Preparation

    After checking the spray power, tap the Start button to start the sample preparation (see Figure 21). First, the system will be flushed with nitrogen in order to achieve ImagePrep User Manual Revision 4 Page 21 of 77...

  • Page 22: Mounting The Glass Slide Into The Adapter

    Wipe off the matrix at the edges of the slides (see red stripes in Figure 24) before inserting the slides into the adapter target (Bruker # 8235380). These regions on the slide ensure electrical contact with the MALDI adapter target.

  • Page 23: Cleaning The Spray Chamber And The Spray Head

    2). Blow air into the two openings next to the clamp for at least 30 seconds each in order to dry the interior parts of the spray head. Figure 26 Spray head cleaning procedure ImagePrep User Manual Revision 4 Page 23 of 77...
  • Page 24 Note: Never try to clean the spray cap when it is mounted on the spray head. The wetness inside would immediately decrease the spray power! Page 24 of 77 ImagePrep User Manual Revision 4...

  • Page 25: Manual Sample Preparation With Imageprep

    Bruker Daltonik GmbH Sample Preparation Workflow Description Manual Sample Preparation with ImagePrep Figure 27 Manual Operation mode window sensor control Figure 28 Manual Figure 29 Preparation preparation Progress workflow window The Manual Operation mode allows operating the instrument for a defined number of cycles at a given spray power with a fixed time scheme (spray time ...

  • Page 26: Method Development

    An ADC (National Instruments NI USB-6008) is included with the instrument. Connect the ADC to your computer (USB) and to ImagePrep (Signal Out, BNC connector on the rear of the instrument). A detailed description of ADC software (Data Logger) installation is given in Appendix 2.

  • Page 27: Interpretation Of The Scattered Light Curves

    Note: If the sensor signal first drops and then increases during the spray period, the sample is too wet and too much liquid has been applied. In this case ImagePrep will apply additional drying time to ensure that the sample is completely dry before the next spray is applied.
  • Page 28 Cycle No. Cycle No. Time [min] Time [min] Figure 32 Scattered light intensity of a complex workflow Page 28 of 77 ImagePrep User Manual Revision 4...

  • Page 29: The Method Development Gui

    To open the method development GUI, tap Other… in the main menu and then Method Editor Open… (see Figure 33). An instrument specific password is needed to enable method development on the ImagePrep. Bruker provides customers with this password on request: Send the controller ID (see menu Other  About) to maldi.sw.support@bdal.de password must be re-entered with every reboot.
  • Page 30 1. Tap Select… to open the file system. 2. Press on the method you want to delete for more than 2s to open context menu (equivalent to right mouse button) 3. Tap Delete and confirm. Page 30 of 77 ImagePrep User Manual Revision 4...

  • Page 31: Starting Methods For Test Purposes

    Note: It is recommended that the preparation is dried completely before proceeding with the run. This is, in general, a good practice but critical for proper operation in sensor control mode. ImagePrep User Manual Revision 4 Page 31 of 77...

  • Page 32: Method Editor: Phase Overview Level

    Methods consist of one or more phases each with individual spraying, incubating and drying conditions (see Figure 38). Different phases allow you to adapt the parameters of the ImagePrep during a matrix preparation, i.e. at the beginning of a preparation it may be desirable to choose more gentle spray conditions than towards the end of the matrix coating process.
  • Page 33 Bruker Daltonik GmbH Method Development Select a method and tap Edit…, the Phases overview window opens (see Figure 39): Figure 39 Edit phases in Phases overview window ImagePrep User Manual Revision 4 Page 33 of 77...
  • Page 34 Edit a phase name by selecting a phase from list and then tapping Name… Note: There is no “new phase” button! To create a new phase: duplicate an existing phase, rename this phase and edit it. Page 34 of 77 ImagePrep User Manual Revision 4...

  • Page 35: Editing A Phase

    Actions of the Phase editor The phase editor consists of four windows (see Figure 41) which are described in detail below. At the bottom of all four windows you will find: ImagePrep User Manual Revision 4 Page 35 of 77...

  • Page 36: The Matrix Thickness Window

    Difference, provided that the number of spray cycles is in the defined range. The phase will also end if the maximum number of spray cycles is reached even if the Final Voltage Difference criterion is not met. Page 36 of 77 ImagePrep User Manual Revision 4...
  • Page 37 SA_Proteins SA_Proteins SA_Proteins SA_Proteins Default Default Default Default Default Default Figure 44 Influence of the customize values in a special phase on the matrix thickness slider in the general customization window ImagePrep User Manual Revision 4 Page 37 of 77...
  • Page 38 When the slider position is set to e.g. Thick, ImagePrep applies the individual maximum amount of matrix in every phase of the preparation. If the customize value for any phase is set to zero, the slider position will not influence the matrix thickness of these phases.

  • Page 39: The Nebulize Window

    Nebulize window (see Figure 45). How strong? How strong? Test the spray. Switches on the spray for 3 seconds How long? How long? Figure 45 Nebulize window parameters ImagePrep User Manual Revision 4 Page 39 of 77...
  • Page 40 The underlying physical effect is that scattered light intensity decreases with increasing wetness. Sensor control can therefore measure actively the wetness of the preparation and control the strength of Page 40 of 77 ImagePrep User Manual Revision 4...
  • Page 41 As the spray process is stopped, remaining aerosol settles onto the preparation resulting in the observed signal fluctuation (“overspray phenomenon”). Figure 47 Illustration of different workflows in sensor controlled mode ImagePrep User Manual Revision 4 Page 41 of 77...
  • Page 42 In the event where the end of the list is reached and the selected on-time criterion is not met, the spray will be stopped. • Break Time: This is the interruption period between two on-times. Page 42 of 77 ImagePrep User Manual Revision 4...
  • Page 43 Spray Sequence: Note: Short times (<0.1 s) are usually Spray on-time table correlated with shorter spray distance! Of no importance if spray on-time table Break Time 0.1-0.2 s contains one entry only. ImagePrep User Manual Revision 4 Page 43 of 77...
  • Page 44 Method Development Bruker Daltonik GmbH Note: If ImagePrep detects that the spray is too weak, it automatically increases the spray power. The spray power boost is shown in the Preparation in Progress window. Page 44 of 77 ImagePrep User Manual Revision 4...

  • Page 45: The Incubation Window

    Thus the slider in the Automatic Matrix Preparation window affects all phases according to their specific Customize values. If the slider position is set to e.g. Long, ImagePrep applies the individual maximum incubation time in every phase of the preparation with exception of the phases where the customize value is set to zero.
  • Page 46 Influence of the customize values in a special phase on the incubation time slider of the general customization window Table 5 Typical values in the Incubation window Parameter Typical values Incubation Time 0 – 60 s Customize < Incubation Time Page 46 of 77 ImagePrep User Manual Revision 4...

  • Page 47: The Dry Window

    Method Development 4.3.4.4 The Dry Window The ImagePrep permits active drying of samples using dry Nitrogen. In this step, remaining liquid present on the surface of the preparation is evaporated. An on- board pressure regulator supplies a constant gas flow of about 3L/min into the spray chamber.
  • Page 48 Please keep in mind that customization can be specified for every phase in a method. The slider affects all phases, therefore if the slider position is set to Wet, ImagePrep applies the maximum wetness grade in every phase of the preparation that the customize value is set to a value other than zero.
  • Page 49 We recommend drying the sample to complete dryness at least every 10-15 Complete drying 2-15 cycles. This allows easy monitoring of the every n cycle matrix thickness. Safe Dry 20-40 s ImagePrep User Manual Revision 4 Page 49 of 77...

  • Page 50: General Method Development Rules

    Time [min] Figure 56 Inverted signal during the initialization phase Figure 57 Inverted signal problem is prevented by using a cover slip (see section 3.3) Page 50 of 77 ImagePrep User Manual Revision 4...
  • Page 51 After having optimized all phases, check MS results for spectra quality (many peaks?) and analyte dislocation (look at the tissue border). Spectra quality can simply be judged by comparing the ImagePrep preparation with manual dried droplet preparation, which usually gives the best results (but, of course, very poor spatial resolution).

  • Page 52: Troubleshooting

    The nitrogen inlet is not connected properly. b) The nitrogen pressure is below 2 bar (29 PSI). Remedy Check both options. If this does not help, please contact Bruker service. Page 52 of 77 ImagePrep User Manual Revision 4...
  • Page 53 The nitrogen pressure is higher than 8 bar (116 PSI). Remedy Set pressure between 2-8 bar (29-116 PSI). If this does not help, please contact Bruker service. Message Could not prepare a sufficient amount of matrix in phase xy. Cause...
  • Page 54 Not all folders and files can be written during the creation of a status report because the USB device has insufficient free space left. Remedy Make sure that there is enough space on the USB device and repeat the status report generation. Page 54 of 77 ImagePrep User Manual Revision 4...

  • Page 55: Other Problems

    Table 8 Other Problems The system does not boot. • Ensure that no USB device is connected to the instrument; otherwise the ImagePrep software will not start automatically. • Check the fuse and replace it, if necessary (see section 6.10).
  • Page 56 • Cause: The sample is too wet errors (see section 5.1) occur. • Make sure that the spray head is not clogged. If this does not help, please contact Bruker service. The sample looks too wet / shows wet sub areas.
  • Page 57 (see section 3.2). Wrong timestamp for the log files. • Adjust date and time as described in section 6.7. • In rare cases the internal battery might be dead. In this case, please contact the Bruker service. ImagePrep User Manual Revision 4...
  • Page 58 In this case the drying phase will be skipped automatically. It can be caused by incompatible sensor controlled drying with fixed spray on-time workflow (see section 4.3.4.2 and section 4.3.4.4). Page 58 of 77 ImagePrep User Manual Revision 4...

  • Page 59: Faq (Frequently Asked Questions)

    • Yes. To access detailed instructions and a dedicated method, see Appendix 3. What has to be considered if I do not use my ImagePrep for a long period of time? • Switch off the instrument. • Dismount the matrix bottle and remove the collecting pan from the spray chamber.
  • Page 60 How can I ensure that my ImagePrep works well? • Coat a blank ITO glass slide on its conductive side (Bruker # 8237001) with sinapinic acid using the ‘Instrument_Test’ method (included in the delivery). Use the matrix recipe given in the Information window of that method.
  • Page 61 Can I save/archive the scattered light curves and all relevant parameters of my matrix preparations? • Yes. • If you connect the ImagePrep to a PC (see section 4.1) and display the scattered light curves using the Data Logger software included in delivery, the curves can be archived with this software.

  • Page 62: Maintenance

    Spray Head Upgrade Kit (# 8261619) In order to ensure high quality sample preparations, Bruker recommends that the spray generator (# 8261614) is replaced after every 30 preparations. This thin perforated metal sheet wears mechanically and chemically, resulting in larger pinhole diameters and uneven spray.
  • Page 63 5. Finished! C) Remount the spray cap 1. Press cap fully onto spray head. No further adjustment is necessary! 2. Lock cap position with thumbscrew. Figure 61 Remounting the spray cap ImagePrep User Manual Revision 4 Page 63 of 77...

  • Page 64: Global Spray Power Adjustment

    A global spray power offset can be defined in the spray head adjustment window (see Figure 62). Open the window by tapping Other… in the main menu and then Spray Head Adjust…. Figure 62 Spray Head Adjustment window Follow the instructions given below. Page 64 of 77 ImagePrep User Manual Revision 4...
  • Page 65 The spray should look roughly the same as shown in the 10% picture above. If the spray is stronger or weaker shift the offset until the spray looks ok (Figure 64). If 25% offset is not enough, contact Bruker service. Reset the counter after mounting a new spray generator.

  • Page 66: Dismount The Spray Head

    Software updates can be performed by copying the relevant files to a USB device (follow the instructions provided with the update), connecting the device to ImagePrep and starting the update from the Updates window. Open that window by selecting Other… in the main menu and then Updates Install… (see Figure 66).

  • Page 67: Generate A Status Report

    Error log files (*.erl) … contain error events which did not happen during matrix preparations and as a result will not appear in the log files (*.log). Methods Contains all methods currently installed on the ImagePrep. directory Settings Contains non user-accessible instrument settings.
  • Page 68 Bruker Daltonik GmbH Status reports can be saved on a USB device connected to the instrument by starting Status Report… from the Other Functions menu (see Figure 67). Figure 67 Status Report window Page 68 of 77 ImagePrep User Manual Revision 4...

  • Page 69: System Reboot (See Section 3.1)

    The AC power inlet at the back of the instrument is equipped with a fuse for customer and instrument safety. If you have to exchange the fuse it is forbidden to use fuse types other than Littelfuse, type 215, rated 3.15 A, 250 VAC. ImagePrep User Manual Revision 4 Page 69 of 77...

  • Page 70: List Of Spare Parts

    Spray Generator II 10 x # 8249088 Filter Pad # 8246375 Matrix Bottle (10 mL, glass) # 8237001 Glass Slides for MALDI Imaging 100 x # 8267942 Coverslips for ImagePrep 200 x Page 70 of 77 ImagePrep User Manual Revision 4...

  • Page 71: Appendix 1

    Interruption period (‘break time’) between two spray on-times (see section 4.3.4.2). Spray and gas flow are switched off. Paused Matrix preparation is paused either manually by user or automatically by software due to detected error. ImagePrep User Manual Revision 4 Page 71 of 77...
  • Page 72 ‘Sample too wet (detected during spraying)‘ detected for the second time. TooWetDrying ‘Sample too wet (detected during drying)‘ detected. CouldNotDry ‘Sample too wet (detected during drying)‘ detected. Even 5 x 2min additional drying time was not sufficient. Page 72 of 77 ImagePrep User Manual Revision 4...

  • Page 73: Appendix 2

    6008 device from VI Logger Lite to Signal Express. Nevertheless, we recommend using VI Logger Lite in order to display the ImagePrep sensor signal. The ImagePrep user manual refers to VI Logger Lite. If your CDs are labeled “NI-DAQmx … Also includes: LabView Signal Express”...
  • Page 74 Maintenance Bruker Daltonik GmbH Figure 72 Software installation procedure Page 74 of 77 ImagePrep User Manual Revision 4...
  • Page 75 Bruker Daltonik GmbH Maintenance Software Configuration: Creating a task Figure 73 Software configuration procedure ImagePrep User Manual Revision 4 Page 75 of 77...
  • Page 76 Starting VI Logger software: StartAll ProgramsNational InstrumentsVI LoggerVI Logger (NI-DAQmx) Help Start / Stop New measurement can be started at this level only! Archive Figure 74 Overview of VI Logger Software interface Page 76 of 77 ImagePrep User Manual Revision 4...
  • Page 77 Service > Support & Upgrades > Software Downloads. 3. On the Software Downloads page, click Mass Spectrometry. 4. On the Mass Spectrometry Software Support page, click ImagePrep. Alternatively use this link; http://www.bruker.com/service/support-upgrades/software- downloads/mass-spectrometry/imageprep.html. ImagePrep User Manual Revision 4...

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