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2D Acquisition and Processing

Bruker Avance AV 500 / Topspin 2.1

  1. Preliminaries
    1. Sign the logbook (name and phone number)
    2. Login to the computer
        user name
        password
    3. Open Topspin (double-click the icon)
        topspin icon
  2. Acquire a 1H spectrum
    1. Is the shimming okay?
    2. Does the sample appear as expected?
    3. What is the region of interest for the 2D spectrum?
      (note the relevent region in ppm)
    4. Calibrate the 1D spectrum, what is SR (ProcPars)?
    5. You can use this high resolution spectrum as a projection
      when you print your 2D spectrum

  3. Create a new experiment number
    new window
  4. Tune and match (for each nucleus and each sample)
    type: atma
    performs automatic tuning and matching - automatically

    which nuclei depends on the expno open when you typed atma
    choose an expno with both H and X defined

    for manual mode,
    type: atmm

    the wobble curve is displayed in the acquisition window
    to just view the wobble curve without adjusting the tune or match,
    type: wobb

  5. Modify parameters
    1. Set the region(s) of interest
      (sw = total range; o1p = center of range) Note: to zoom in on a select region (subset of all shifts), you should run the experiment with selective excitation using a shaped pulse. Instructions can be found under the Topspin Help Menu: “1D and 2D experiments step-by-step tutorial” Advanced Experiments

        COSY and TOCSY:
        set sw the same for both axes (F1=y-axis; F2=x-axis)
        set o1p

        JRES:
        set sw (F2=x-axis)
        set o1p
        the default swh (Hz) on F1 should be okay

        HMQC and HMBC:
        for 1H set sw (F2=x-axis) and o1p
        for X (for example, 13C) set sw (F1=y-axis) and o2p

    2. Set ns
      with gradients (most experiments), ns = 1 or 2, etc.
      without gradients (JRES), ns = 8, 16 or 32, etc.
    3. Set the y-axis resolution (F1) td = 128 or 256

    4. Check the experimental time (expt)
      2D experiments should acquired until the end

  6. Acquisition
    1. To minimize “t1 noise” use the same rg value
      determined from the 1D 1H experiment
      otherwise type: rga
    2. or type: zg


  7. Processing
    1. Type: xfb
      (eXecute a Fourier transform in Both dimensions)
    2. Additional processing tools:
        COSY and JRES: tilt
        the dialog box allows for symmetrizing of COSY data
        (to undo the operation, type: xfb)
        and for tilting JRES data
    3. will change the levels
      If the projections are selected (blue boxes), the same icons will adjust the intensities of the projections
      To save the current levels of the 2D spectrum, click (or type: .ls)
    4. To attach an “external projection” to the 2D plot
      (a separately measured high-resolution 1D spectrum):
        right-click on the 1D experiment in the Topspin browser
        and choose “display as 2D” (F2 = x-axis; F1 = y-axis)
    5. To save an internal projection, type: proj
    6. To expand a region: use the left-mouse to drag a box over a region
    7. To calibrate the 2D plot, use the same SR as the calibrated 1D spectrum

  8. Plotting
    For a simple printout of the screen, type: prnt
    To export pdf files of your plot, or have control of colors, fonts, sizes
    enter the topspin plot editor by typing: plot
    In brief, a description of the plotting elements:
    “Data” contains the list of expno's listed in the plot editor's portfolio
    The green squares icon allows data window selection
    “Edit” to change colors, fonts, displayed regions, etc.
    “1D/2D Edit” to interactively change intensity and plot region
    File, Print to get a hardcopy (control p)
    File, Export to save a picture (formats include: pdf, jpg, emf, and bmp)
    DO NOT SAVE (this changes the file called by “layout” in topspin)

  9. Save your data onto another computer
    DATA MAY BE DELETED at any time WITHOUT WARNING
    1. Open the my computer file icon on the desktop (double-click nmr500)
    2. Click the “start” icon to get to the nmrlab4 network shortcut
    3. Drag and drop files to nmrlab4.
      Preserve the hierarchy:
      directory/data/user/nmr/name/ expno

  10. Remove your sample
    1. on the BSMS keyboard:
    2. TURN OFF: spin and lock (no light = off)
    3. press “lift on/off” (green = on)
    4. gently remove your sample from the magnet – lift it up to clear the magnet
    5. press “lift on/off” (no light = off)

  11. Log off

  12. Open your files on another computer
    To open Topspin files on the other computer:
    Topspin icon
    1. Open the program Topspin
    2. Navigate to your data using the Browser
    3. Drag you data file into the display window

  13. Report problems and bugs to Yael or Shifi - 3748