1D Acquisition and Processing

Bruker DPX200 / Topspin 1.3
print version: pocketmod (1 page) or full size (5 pages)

  1. Sign the Logbook that you are sitting at the spectrometer
    1. Sign the logbook (name and phone number)
    2. IF Topspin is not open, then open Topspin
      • topspin icon
  2. new window
    Create a new file the "experiment number"
    each expno file can contain one fid file called "fid" calls a set of standard parameters for acquisition (eda) and processing (edp)

  3. Insert the sample(sample preparation)
    tube in spinner
    1. Place the spinner into the depth measure
      Slide the tube down to the bottom (liquid level c.a. ≥ 3 fingers)
    2. Hold the tube above the spinner
      Wipe the outside of the tube and the spinner
    3. BSMS keypad (full picture on page 2):
      press the “lift on/off” (green = on)
    4. WAIT until you hear the air flow then set the spinner on the air cushion
    5. Press the “lift on/off” button (no light = off)
    6. Wait for the green "down" to light.

  4. bsms top row
    Spin (optional)
    • Use the BSMS keypad:
    1. Press “spin on/off” (green = on)
    2. To check the spin rate:
      press the orange 2nd button and then the
      "spin rate/spin measure" button
    3. To deselect spin rate, press: stand-by

  5. Lock
    the lock display
    1. Click lock display menu icon or type: lockdisp

    2. Read a shim file by typing: rsh qnp
      (or add a button to your menu bar)
      qnp stands for the type of probe used (1H, 19F,31P, 13C,2H probe.

    3. Click lock icon or type: lock
      select your deuterated solvent
      this sets the chemical shift scale

  6. Shim
    the bsms keypad

    1. Adjust the lock phase to maximize the locked signal amplitude

    2. Adjust the axial shims
      Z, Z2, Z, Z2 . . .
      until no further changes

      lock signal off the screen?
      reduce lock power
      or lock gain
      or lock DC

      pressing a lit button
      will undo changes

      pressing an unlit button
      (example: std-by)
      will save changes

    3. Done?
      press STD BY

  7. acquisition parameters
    Parameter setup
    1. Click the AcquPars tab or
      type: ased

    2. Type: rga
    3. click play icon or type: zg
      for a preliminary acquisition

      The pulse program “zg” is a
      single-pulse experiment. Type: showpp to see it graphically.

      The command zg starts acquisition.

      Click the PulseProg tab
      to see the Bruker code
      defining pulses, delays,
      power levels, channels, and phase

    4. Tailor the parameters
      FID, time domain
      aim: avoid clipping of the free induction decay
      x-axis: estimate the final acquisition time (FID takes up ~ the screen)
      y-axis: if rga gave rg = 1, then reduce your pulse width (p1)

      Spectrum, frequency domain
      type: proc (this macro runs ft, apk, abs, ppf, .vr)
      how is the shimming?
      zoom in and check . . . do more shimming if needed (for example: Z, Z2,Z3, turn off the spinning and check X and Y; go into go-setup mode with d1 0s, gs)
      OPTIMIZE the region of interest:
      center the signals (o1p)
      reduce sw to avoid measuring excess noise and increase digital resolution
      (or expand the region on the screen and click set sw-o1p icon or type: .setsw
      OPTIMIZE the acquisition time:
      adjust td to get the desired aq(aq = td*dw = td/(2swh))
      adjust si=2*td to get optimal zero filling
      (note:, the smaller (Hz/pt), or (sw/si), the higher the digital resolution)
      set ns (8 for a full phase cycle)
      set ds (common value = 2)
      set d1 (depending on T1's)
      check the experimental time by clicking clock iconor typing: expt

  8. Acquire a FID
    1. play icon or type: zg
    2. Options during FID acquisition:
      • tr - saves the data and continues acquiring
      • h halt icon - HALTs the acquisition and SAVEs your FID
        • the FID is automatically saved once ns is reached
      • go - acquires more ns without deleting the stored FID
        • adds the new transients (ns) to the stored FID
      • stop - terminates the experiment – data will be lost
      • kill - terminates the experiment – data will be lost

  9. Processing
    1. ft (Fourier transform)
      automatically applies the bc_mod and me_mod specifications
      window functions can optionally be applied to the FID
      • sensitivity-enhancement (lb > 0), type: ef
      • resolution-enhancement (lb < 0, gb > 0), type: gf
      right-click to alter the display properties

    2. apk (automatic phase correction)
      Manual phase correction: type: .ph or click:
      phase icon and menu
      “0” for zero-order phase correction
      (on the largest peak; red line)
      “1” for first-order phase correction
      (on the furthest peak)
      to change the red line's position: right-mouse click (“set pivot point”)
      save and exit: .sret save and return icon

    3. chemical shift calibration icon
      chemical shift calibration
      type: .cal or click:
      place the cursor at a known position (e.g. CDCl3 = 7.26 ppm)
      click the left-mouse button to define its position

    4. Baseline correction
      Type: abs (automatic baseline correction)
      automatic integration is also performed if the parameter intbc is set to yes
      baseline correction icon
      Manual correction: .basl or click:
      click the triangle to view changes
      save and exit

    5. Peak picking
      Type: ppf (automatic peak picking)
      to toggle display units to relative: click y-axis icon or type .y
      peak pick icon
      to change parameters for peak picking, type: pp
      or type the values in the command line for mi, maxy, cy
      Manual/interactive peak picking, type: .pp
      define the peak picking range (green box)
      draw a box around the peaks to pick
      the symbol with the "m" allows you to change the box dimensions
      the peak picking icon allows you to select a single peak with the mouse
      save and exit

    6. Integration
      Type: abs (automatic integration and baseline correction)
      for automatic integration without baseline correction, absg 0 then abs
      integration mode icon

      Manual correction: .int or click:
      to delete all: “select all” with select all integrals icon and delete delete integrals icon
      to define new integrals, highlight:define integrals icon
      to select or calibrate an integrand, with the cursor on the peak, right-click: integrals sub-menu
      save and exit

    7. 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)

  10. Save your data onto another computer
    1. Open the nmr200 file icon on the desktop (double-click)
    2. Click the “start” icon to get to the nmrlab4 network shortcut
    3. Drag and drop files from nmr200 to nmrlab4 and preserve the hierarchy: directory/data/user/nmr/name/expno

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

  12. Log off

  13. 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

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