Using Experiment Selector in TopSpin to organize standard experiments.
The Experiment Selector was introduced in TopSpin 3.5 patch level 6 to provide a user friendly tool for organizing both the Bruker standard experiments as well as users own experiment libraries. It also allows to greatly simplify the setup of complex experiments. For instance, previously the setup of multi-receiver experiments (Topics in Curr. Chem., 2013, 335, 71-96) required following a rather extensive description in acquisition manuals. In the Experiment Selector these experiments can be set up with a single click via the action item. Another example of the simplified experiment setup that is available in the Experiment Selector is the Hadamard experiments (Prog. NMR Spectrosc., 2003, 42, 95-122) as introduced in TopSpin 3.5 patch level 7. Once again, previously setting up these experiments required following a rather extensive description involving a sequence of numerous steps that had to be executed in a particular order. An example of the Hadamard experiment setup in TopSpin3.5 patch level 7 and TopSpin4.0.2 is described below.
A basic collection of Hadamard experiments is available in the Small Molecule section of the Experiment Selector (see Fig. 1). The HT_SELEX, HT_SELINV and HT_SELREF experiments demonstrate the three basic Hadamard encoding techniques based on multi-selective excitation, inversion and refocusing pulses. A new experiment is created and the required parameter sets of the Hadamard experiments are loaded by clicking on the corresponding item in the Experiment Selector.
Each item in the Experiment Selector can be expanded to reveal the action item(s) (see Fig. 2). The Hadamard experiment is then started by simply clicking on the action item. Before the acquisition starts the aunm script may prompt the user to provide the experiment number containing the peak list unless the required experiment number is already provided in the aunm parameter. The processing is equally simple and only requires executing the proc_had script instead of the usual xfb command.
The rather complex task of creating the frequency encoding shapes that are required by the Hadamard experiments is accomplished by a simple script involving the wvm (WaveMaker) command. An example of a Hadamard NOESY spectrum recorded as described above is shown in Figure 3.
The WaveMaker and Automation
The WaveMaker command, wvm is available in the TopSpin3.5 PL6 and all TopSpin4 releases. It provides a simple and user friendly way of creating shaped pulses, decoupling waveforms and gradient pulses for all experimental needs and is particularly useful in experiments that require great flexibility with use of shaped pulses and decoupling waveforms. The Hadamard experiments is one such example because each sample requires a set of different multi-site excitation pulses, i.e. Hadamard encoding pulses. When the wvm command is executed all shapes that are required for a particular experiment are automatically generated and the associated experimental parameters are automatically set (the –a option). The wvm output showing the experimental parameters must be suppressed when the experiments are run in automation. In TopSpin 3.6 and 4.0.3 this can be achieved by using the –q (quiet) option. For recording the Hadamard experiments in automation the aunm parameter should be set to ‘had_zg#’ where # is the experiment number containing the required peak list. To users with older releases of TopSpin the WaveMaker and the Hadamard experiments are available from our online User Library.
The Online User Library
The Bruker online User Library, the Resonance Exchange is an online platform that allows Bruker users to share their latest developments. The User Library can be accessed here.
The latest contributions include adiabatic relaxation dispersion experiments (F.-A. Chao and A. Byrd), the NOAH experiments (Ē. Kupče and T. Claridge), the HCNMQC experiments (Ē. Kupče and B. Wrackmeyer), a suite of experiments for drug discovery (A.D. Gossert), FAST COSY (P. J. Sidebottom) and many other experiments from the labs of B. Brutscher, A. Bax, G. Morris, G. Bodenhausen, P. Schanda, G. Martin and many others. The readers are encouraged to share their own latest developments with the vast community of the Bruker users via the Resonance Exchange.
Written by Ēriks Kupče, Bruker UK Ltd. Contact Bruker for more information about TopSpin software.