Experimental Assignment Strategies

    There are many different NMR experiments that a spectroscopist can collect.  However, certain combinations of experiments are better than others for determining protein NMR resonance assignments.  The better strategies typically use more experiments.  However, more experiments means more time spent collection, processing, and peak picking these experiments.  However, certain datasets are harder than others and require a more rigorous approach. Below are listed the major types of experimental strategies that AutoAssign can handle. They are broken down into categories based on the number of resonances or rungs used to linked nearest neighbor spin systems together.   Typically a 5-rung strategy is better than a 4-rung strategy from an assignment robustness perspective.  However, some experiments are simply better than others depending on their implementation and on the sample analyzed.  For example,  an HNcaCO experiment is typically horrible for any decent-sized protein, unless the sample is significantly deuterated.  Collecting an HNcaCO will probably not improve the assignment results for a 30kDa protein that is not deuterated. 
    Also, the experiment names below refer to a family of related experiments that provide the given type of resonance information.  For example, "HNCACB" refers to the family of straight-through and out-and-back experiments that provide amide H, amide N, and intra/sequential CA/CB resonances.
    AutoAssign also needs a "ROOT" spectrum for creating spin systems.  This is typically an NH-HSQC, but it could also be an HNCO or HNcoCA peak list.  These 3 experiments are usable because only one peak exists for each spin system.  An "alternate root" spectrum can be specified as well.  The HNCO is the alternate root by default, but the HNcoCA could be the alternate root as well.  An alternate root spectrum is used to help detect HN-overlapped spin systems.

5-Rung Matching

4-Rung Matching

3-Rung Matching

2-Rung Matching


Experiments in "[]" are optional to the strategy.
Experiments in "{}" represent equivalent sets of experiments that provide the same information for the strategy.
Experiments with a "-phased" suffix refers to a type of experiment where the resonances in its 3rd dimension are distinguishable by the sign of their intensity.
Resonances in lower case are not detected.