Setting experiment types

Introduction

When loading spectra into Analysis (or editing the experiment information), the user specifies the type of NMR experiment that was run. This can be done by particularly selecting options in the |Category|, |Type Synonym| and |Full Type| columns in the {Experiment Types}/{Specify Experiment Types} tab in the Experiments: Experiments popup:

Note that the Full Type (also called experiment prototype) is the most important one to set, but selection can be difficult because of the abstract syntax that is used (which is based on the CCPN Data Model).

Category and Type Synonym

If the full name of the experiment type is known we can simply select the Full Type from the pull down menu:

In case the full type is not known we can start by setting the Category and/or Type Synonym, which will reduce the number of available Full Types dramatically. Without setting Category and Type Synonym, all possible experiment types that have matching isotopes will be shown. Setting the Category for the NMR experiment gives a sub division between through-bond, through-space, quantification and other types. An experiment may belong to more than one Category, but in this system it is only listed in the least populous. For example a 15N HSQC-NOESY has both through-bond and though-space transfers but is categorised as through-space. If the Category for an experiment is unknown, or not particularly helpful, it may be wise to set the Type Synonym in the first instance. The Type Synonym of an experimental type in Analysis is usually a common “human-readable” name, for example “HNCA” or “15N HSQC NOESY”. However, as mentioned above, the exact specification of an NMR experiment is done only through the Full Type.

Full Type

The Full Type (also called experiment prototype) for an experiment uses a special nomenclature that is described in the CCPN experiment nomenclature paper. The idea is that the user can distinguish between different magnetisation transfer pathways. For example a 15N HSQC-TOCSY could have either the HSQC step or the TOCSY step first. In this instance the system offers a choice between H[N]_H.TOCSY (HSQC first) and H_H[H].TOCSY (TOCSY first). The experiment naming system for the Full Type is fairly complex, and is designed to give a precise specification of the magnetisation steps, which atom sites they visit and what measurements are made; giving rise to an experimental dimension. It should be noted however, that this system does not describe the precise NMR pulse sequence that was used. For example no distinction is made between HSQC and HMQC. 

The essential features of the nomenclature for Full Type are as follows:

• • Capital letters indicate atom sites that were recorded and result in an experimental dimension.

  • Lower case letters are atom sites that are part of the pathway but not recorded, e.g. carbonyl in H[N[co[CA]]].

  • Square brackets represent out-and-back transfers.

  • Curly brackets with “|” sub-divisions represent alternative pathways.

  • Underscores represent transfers that are not one-bond (the transfer type is listed after at the end after a dot).

The following examples should get you started on the Full Type nomenclature:

• • HNCAHA: 4D HNCAHA prototype, starting on HN and ending on HA. The prototype includes HNcaHA (3D), HACAnH (3D, note reversed direction), HncaHA (2D) etc.

  • H[N[CA[HA]]]: 4D HNCAHA prototype with out-and-back magnetisation transfer.

  • H[N]_H.NOESY: 3D HSQC-NOESY. Prototype includes NOESY-HSQC (H_H[N])

  • H{CA|Cca}NH: 4D HCBCANNH

  • C[h(0)]: 1D carbon, selecting quaternary carbons only.

More detailed explanations about the naming system can be found here, or at http://www.springerlink.com/content/h57q76k245r14558/.

Next: Setting reference dimensions