Processing non-uniformly sampled spectra with Multidimensional Decomposition

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Processing with MDD

This section gives a step-by-step manual to processing with the MDDGUI program, developed in the Arrowsmith lab (University Health Network and University of Toronto). It is designed for processing 3D spectra collected with non-uniform or non-linear sampling (NUS). The spectra can be collected either on Varian spectrometers with later versions of BioPack installed (click here for the relevant guide for Varian spectrometers) or on Bruker spectrometers running TopSpin (click here for the Arrowsmith protocol for NUS data collection on Bruker instruments).

The GUI package uses the software developed by Vladislav Orekhov (Swedish NMR Centre, University of Gothenburg, http://www.nmr.gu.se/~mdd)

Before the Multi-dimensional decomposition can be started, the raw data has to be converted through a number of steps to an appropriate format. The steps below are accompanied by the GUI screen shots. To move between the different stages of the processing, use "Next" and "Back" buttons. Refer to README files for more specific instructions.

  • Rearrange the FIDs in the "ser" file so that they are in correct positions for an imaginary case as if the data set was sampled regularly. The missing FIDs are replaced by zeros. Click "Insert Zeros" before proceeding.


  • Convert to NMRPipe format. In this step there are a few parameters that the GUI might read wrong, especially with later versions of TopSpin.You can edit it as a simple bruk2pipe script. Pay extra attention to carrier and spectrometer frequencies, matrix sizes and acquisition modes. In TopSpin2.1 we discovered that sweep width is sometimes not recorded in the acqu* files, therefore check that as well. Click "Save", then "Run".
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  • Process the first plane (it is regularly sampled!) and adjust phasing, apodisation, region of interest and other parameters for the acquisition dimension. The better the phasing, the better the convergence and the fewer the artefacts. It will be difficult to change the acquisition dimension parameters afterwards without redoing the calculation, so spend a few rounds with NMRDraw until you are happy and the phases are set properly. As usual, click "Save", then "Run". Button "nmrDraw" simply calls that program.

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  • Using the same parameters, Fourier transform (FT) the acquisition dimension for the whole data set and extract the region of interest. Now that the acquisition dimension is apodized and phased properly, one can apply the same parameter values to the whole spectrum.

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  • Divide the the partially FT'ed and still sparse spectrum into a number of regions overlapping by their acquisition dimension and convert them to MDD format. This is the step before proceeding to calculations themselves. Make sure you select "Multiregion" radiobutton. Parallel computation is slowly becoming obsolete, although is supported for now.

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  • Run MDD. As simple as that. Check README for more detailed instructions. You might need to do some editing of the "runmdd.sh" script depending on cluster availability. In Toronto, we usually open a separate terminal window, login to cluster and start the claculation from there. Don't close the GUI in the meantime. If you do, it is a bit tricky to restart from where you are.

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  • Using the output of MDD, replace the zeros ( i.e. missing FIDs) by the reconstructed values. Here, if you had the GUI open through the previous step, the values will be filled automatically. If you did close it, go to step 5, choose "Multiregion" radiobutton, proceed to step 7 and fill out the values. That was the tricky part.

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  • FT of the two indirect dimensions. Here the task is purely NMRPipe. Do to your indirect dimensions what you need to do. You may need to play around with "FT -auto" if your peaks are not making sense. That is mainly because the GUI can't easily distiguish between "Complex", "States-TPPI" and related modes. So you may need to change the FT flags to rectify. Plus, you don't need the GUI anymore, that is the final step and you can edit the script to your liking.

<img alt="s8.jpg" src="%ATTACHURL%/s8.jpg" />

  1. -- Main.AleksGutmanas - 21 Aug 2007
    • README.pdf: PDF of the README for the processing package </li>
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