Nmr Experiment Nomenclature - Obsolete

This is version one of the nomenclature. It has been superseded by version 2 as of February 2011.

CCPN has proposed a nomenclature for NMR experiments. Experiments are organised in NmrExpPrototypes, that describe a magnetisation transfer pathway. In turn these contain RefExperiments, that describe a specific experiment using the pathway. The systematuic names are used as the names of the corresponding objects in the NmrExpPrototypes that are distributed as reference information with the CcpNmr releases. The nomenclature has been published in an older form. The description here is the current and official version.

There are so many experiments that it is hard for any systematic naming scheme to cover all possibilities. These rules give a systematic name for most of them, and we recommend sticking to them whenever possible. There may be cases where a partially free-form text name is unavoidable. Even though we do not cover all possibilites the system is still quite complicated. Hopefully it will be easier to interpret existing names than to make new ones.

The rules are as follows:

• 1. The names are global reference information. It is strongly recommended to stick with existing names for existing reference desriptions, and not to make duplicate records. New descriptions should be submitted to the CCPN for inclusion in the reference distribution.

  2. There is only one ExpPrototype for every magnetisation transfer path, which may correspond to a 5D or 6D experiment. The various 2D, 3D, 4D, projections, reversed direction, reduced dimensionality or coupled/decoupled variants etc. are RefExperiments under the same ExpPrototype. E.g. the 5D HCACONH ExpPrototype would cover 4D HCAcoNH, 3D HncoCAH, etc.

  3. Experiments are normally named by concatenating the names of the AtomSiteTypes that describe the magnetisation transfer path ( e.g. HCACONH). You are free to use atom names that do not correspond to existing AtomSiteTypes where this is easier to understand, e.g. HNCAHA instead of HNCAH or HBCBCGCDHD, instead of HCaliCaroCaroH. Note that HN means 'H then N', and *not* 'peptide backbone proton'.

  4. By default transfer is by J coupling or one-bond transfer. Other transfer types are indicated by putting an underline in the transfer path, and appending the transfer type to the end of the name. E.g. H_H.TOCSY, H_H_H.TOCSY,NOESY, HC_CH.TOCSY. TROSY transfer is not distinguished from other kinsd of one-bond transfer.

  5. Out-and-back segments are indicated by putting the out-and-back trace in square brackets. E.g. H[N]_H.NOESY is the normal HSQC-NOESY, H[C]_H[C].NOESY the 4D carbon-carbon NOESY. In HNCAHA magnetisation starts on backbone H and ends on HA, whereas the out-and-back version is called H[N[CA[HA]]].

  6. The transfer types are a minimum set. They describe only the relationship between the atoms on either side, and do not distinguish between different transfer types. Precise transfer types can be stored in the CCPN data model, but are not reflected in the names (or, currently, supported in the NmrExpPrototype editor). Allowed transfer types are:

     1. 'NOESY': Solution state dipolar interaction. Includes ROESY

     2. 'TOCSY': Multiply relayed J coupling transfer

     3. 'onebond': Transfer over a single bond, by any mechanism.

     4. 'Jcoupling': J coupling transfer by a single coupling over one or more bonds

     5. 'Jmultibond' J coupling transfer by a single coupling over more than one bond

     6.  'Jnonlocal' J coupling transfer over a coupling that does not follow the covalent molecular structure, e.g. through hydrogen bonds, metal coorcination bonds, or through-space J coupling.

     7. 'DipDip': Solid state equivalent of NOESY

     8. 'SpinDiff': Solid state transfer through multiply relayed dipole-dipole coupoling

     9. 'CP': Transfer through cross-polarisation.

     10. TROESY is strictly speaking a combination of a shift and a coupling and could be described as such. However this would require that TROESY and non-TROESY versions were described by separate NmrExpPrototypes, and would give horribly complex names. Instead TROESY is considered as a subtype of onebond and is not considred in the experiment prototype description at all. If desired it can be added as a '.TROESY' suffix.

  7. Some experiments may have several possible nuclei for a given axis, or several alternative magnetisation transfer paths. These are shown by putting the alternatives in curly braces. If the possibilities are mutually exclusive, they are separated by a vertical line. Examples would be e.g. H[{N|C}]_H.NOESY, an HSQC-NOESY with both C and N in parallel on the second axis, or H{CA|Cca}CONH, the protein backbone experiment more commonly known as HBCB/HACACONNH. Separate transfer paths that are both followed in parallel are also put in curly braces, but separated by a plus sign. Examples would be H{[N]+[HA]}, the HNHA experiment, or H_H{[n(0)]+[c(0)]}.NOESY, a NOESY with protons bound to no labelled heavy atoms selected in the second dimension.

  8. AtomSites that are part of the coupling network but are not actually being measured are given in lower case. This is used for experiments that filter on coupling partners without necessarily transferring magnetisation to them, such as the H[C[co]] CO-filtered HSQC. It is also used for atoms in the transfer path that cannot be sensibly measured, as in the H{CA|Cca}CONH (HBCB/HACACONNH) experiment. The latter usage is the same as used for lower-dimensionality RefExperiments (see below).

  9. If you want to indicate the number of atoms of a given type that serve as coupling partners you simply affix the number, in parentheses. A 3D HSQC-NOESY set up to suppress signals starting on CH2 groups would be HC[h(2n+1)]_H.NOESY. An HCC-3D set up to select quaternary carbons in the third dimension would be H[C[C[h(0)]]]

  10. The most complex names are probably those for double-half filtered NOESYs - fortunately there are not that many of them. A double-half-filtered 15N/13C NOESY, which serves to select intermolecular NOEs between doubly labeled molecules and unlabeled molecules is be written { H[{n|c}]_H{[n(0)]+[c(0)]} | H{[n(0)]+[c(0)]}_H[{n|c}] }.NOESY.

  11. Non-shift dimensions are given as their type followed by the AtomSites in parentheses. E.g. J(HH) (proton-proton coupling), DQ(CN) (carbon-nitrogen double quantum magnetisation).

  12. RefExperiments are specific variants of their ExpPrototypes. While it is not possible to cover all possibilities it is recommended to follow these rules. Extra information can always be added as a dot-separated suffix.:

• • 1. Lower-dimensional experiments: The most common RefExperiments are simply cases where not all possible dimensiopns are measured. These are named by putting the dimensions that are not measured in lower case. E.g. the 5D HCACONH ExpPrototype would give 4D HCAcoNH, 3D HncoCAH, etc

    2. Reversed experiments: The ExpPrototype describes the magnetisation transfer network, which may be traversed in wither direction. This measn that e.g. HNCAH and HCANH will be described in the same ExpPrototype. The recommended naming style is simply to reverse the name (as shown here). RefExperiments have an 'isReversed' attribute that indicate that the order of traversal is the opposite of the one specified for the ExpPrototype.

    3. Couplings: Couplings will often be unresolved, and will rarely be of interest in the analysis. It is possible to specify that e.g. J(CH) is active for a given dimension, but generally this is only done if there are couplings that need to be measured and assigned. The recommended naming style for these cases is e.g. 'HC.C coupled to CO', or 'HNCAH.H1,H2 coupled to C'. 

    4. Reduced-dimensionality and projection experiments: Here several measurements from the ExpPrototype are measured in the same dimension, as a linear combination. The total dimension of the experiment is added as a suffix, followed by a curly brace describing the AtomSites that may appear on the combined axis. Projection experiments are generally acquired as sets with different linear combinations appearing on the combined axis. The coefficients of the linear combinations are not considered to be parts of the RefExperiment description, but are stored in the description of the experiment itself. In experiment naming it is assumed that alla vailable AtomSites are used on the combined axis; dimensions that are not used in a given set of projections are simply given coefficients of zero. Examples are:

       • HNCOCA 2D projection: H[N[CO[CA]]].2D.{N;CO;CA}

       • HNCOCA, CA as splitting on CO axis: H[N[CO[CA]]].3D.{CO;CA}

       • In the unlikely case that more than one dimension is acquired as a combination, it is possible to add more than one curly brace suffix.