Processing time-resolved 2D spectra

NmrPipe shell scripts to batch process consecutively acquired 2D NMR experiments as a time-resolved series.

Description & aim

The use case for these tools is the analysis of NMR data sets from evolving samples. The objective is to process time-ordered 2D experiments identically, and then extract spectral features to be monitored - peak intensities in this case. The series of 2D slices can be thus considered a pseudo-3D.

A master peak list is used to define the peak positions at which signal intensities will be tracked along the time pseudo-dimension.

The processing pipeline is initially based on the relaxation demo example from the NmrPipe documentation. You can download a copy here and find the scripts under demo/relax.

Requirements

• In order to run these scripts you will need a working installation of NmrPipe. You can find the installation files and instructions here.

• The code has only been tested in a Linux system.

• Note that NmrPipe uses the C shell (tcsh/ csh). Shebangs in the script files however allow usage from the Bash shell.

Input format

The code here converts raw spectra acquired with Bruker Topspin (ser format), using NmrPipe's bruker tool. Other input formats can be trivially implemented.

How-to

All C-shell scripts can be run individually, and accept three positional arguments:

script.sh /path_to_expdir first_exp last_exp

0. Clone or download this repository.
1. Create a /data folder and put/link your experiment directory(ies) in it. You
   can use get_explist.sh to inspect the title files of all spectra in the folder(s). Note that this is a Bash script.
2. Adjust the size of the time step (in minutes) in the conversion.sh script.
3. Run all.sh for batch conversion, processing, and peak picking.
4. Tune processing as needed by modifying processing.sh and using nmrDraw for inspecting results - e.g. phasing, window functions, etc . It is recommended to perform this step selecting ~5 slices.
5. Use nmrDraw to curate your peak list of interest (clean up noise, add overlapping or newly appearing peaks) and save it in data/your_experiment/master.tab. The series of processed spectra and the difference slices can help you.
6. Run series.sh to track the intensities at the positions of the peaks defined in your master.tab. Results will be saved under the tab folder.

Four folders are created in total:

• fid_*: converted raw spectra series in nmrPipe format.
• ft_*: processed spectra series in nmrPipe format.
• dif_*: difference spectra series vs reference in nmrPipe format.
• tab_*: Picked peak, master, and time series lists.

clean.sh can be used without any argument to wipe all four folders, but keep master.tab.