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Curate Experiment Parameters
This popup window is used to control parameters that relate to the NMR experiment entities within a CCPN project. It should be noted that an experiment is specifically a record of what was done, not a reference to the data that was obtained; this is what Analysis refers to as a spectrum. Also, an experiment doesn’t just refer to what kind of NMR experiment was performed, but rather to something that was done on a particular occasion to a particular sample. The kinds of information that are stored at the experiment level describe how the experiment was performed and how certain data that derives from the experiment should be interpreted. Several tabs are used to sub-divide the popup window into several sections to control different aspects of the experiments.
Main “Experiments” Tab
This table is the main display of all if the NMR experiments described within the CCPN project. Each experiment may refer to one or more spectra (and even an FID) that resulted from the experimental operation; the names of these are listed in the “Data Sources” column. Several experimental parameters may be adjusted in this table and, as far as resonance assignment is concerned, the most important of these are the “Shift List” and “Mol Systems”. It should be noted that the “Shift Ref” column can only be configured if chemical shift reference details have been entered at the “Shift References” tab.
The shift list of an experiment states how chemical shift measurements should be grouped. An experiment’s assignments, on the peak of its spectra, only contribute to the chemical shift measurenemts in one shift list. In normal operation each shift list corresponds to a given set of conditions, where resonance positions in spectra a fairly static. Different experiments may use different shift lists if their sample conditions are different enough to cause peaks to move. Accordingly, a resonance derived from a given atom may have several different recorded chemical shift values, each of which resides in a different chemical shift list. Because each experiment is associated with a single shift list it is thus known which chemical shift average the assignments in its spectra contribute to and which chemical shift values to look at when suggesting assignments for peaks. The shift list that an experiment is linked to may be changed at any time, and when an experiment is moved from one shift list to another (which may be new and empty) the contributions that its spectrum peaks make to the calculation of average chemical shift values will automatically be adjusted; the experiments that are linked to a given shift list dictate which peaks to average chemical shift values over.
The “Mol Systems” for an experiment specify which molecular systems were present in the sample. In essence this means which group of molecular chains the spectrum peaks, that come from the experiment, could be assigned to (caused by). In normal operation the molecular information need not specifically be set in this table, because the connection is made automatically when a peak is assigned to a resonance that is known to be from a specific atom in a specific residue. Once an experiment is associated with a particular molecular system, subsequent attempts to assign its peaks to atoms in a different molecular system will trigger a warning. The molecular system for an experiment may nonetheless be set via this table. Sometimes this is to preemptively associate particular experiments, and hence spectra, with specific molecular systems so that there is less chance of accidentally assigning a peak to the wrong thing. The molecular system, and hence residues, that an experiment is linked to is used to facilitate several operations in Analysis. For example, when operating on a peak to associate one of its assigned resonances with an atom, the molecular system link allows the correct group of chains to be displayed automatically.
Experiment Types
This table is used to specify what kind of NMR experiment was done for each of the experiment records within the project. The general idea is that the basic magnetisation transfer pathway is given and how this relates to the experimental dimensions. Setting such information helps facilitate several operations in Analysis. For example when making NMR derived distance restraints only peaks from “through-space” experiments like NOESY are listed. Also, and perhaps most importantly, the linking of experimental dimensions to references, which correspond to particular points of the magnetisation transfer pathway, enables the assignment system to have knowledge of experimental dimensions that are linked together via covalent “one-bond” connectivity. Thus, if an experiment is set to be of 15N HSQC type, then it is known that any spectrum peaks represent one-bond correlations between hydrogen and nitrogen. This dictates what the isotope type of any assignments must be, and if a peak dimension is assigned to a specific atom then the assignment on the other peak dimension must be to the covalently bound atom.
Setting the experiment type means setting the ‘Full Type’ column. The many possibilities and difficult names makes this hard to do directly, and we have tried to help with the process. The ‘Type Synonym’ column also sets the ‘Full Type’ column but gives alternative and more human-readable names like ‘HNCA’ instead of ‘H[N[CA]]’ or ‘15N HSQC-NOESY’ instead of ‘H[N]_H.NOESY’. Some ‘Type Synonyms’ correspond to more than one Full Type; anything in the ‘Alt Types’ is an alternative Full Type. The possibilities given for these columns are filtered, so that experiments that do not fit the nuclei on the axes are not shown. The most common experiments are shown at the top of the selection menu, the rest can be found in one or more of the categories lower down. The ‘Categories’ column divides experiments into a few rough groups and are used to filter the possibilities in the other columns. Experiments that could belong to more than one group are listed only in the most ‘interesting’ one. The ‘use external’ category is a special case; it means that the program should use the information in the ‘External Source’ and ‘External Name’ columns to set the Full Type. This option is selected automatically when you are loading a spectrum that contains information about the Full Type. At the moment the program understands only Bruker pulse program names, and only if they follow the standard naming conventions used by the Bruker Applications department.
In normal operation the user specifies the type of NMR experiment that was run by selecting options in the “Category”, “Type Synonym” and “Full Type” columns. If the full CCPN name of the experiment type is known then the user can go straight for the “Full Type”, but selecting the category and/or synonym first allows the number available options to be reduced dramatically; without this all possible experiment types that have matching isotopes are shown. Setting the category for the NMR experiment gives a rough sub division between through-bond, through-space, quantification and other types. Strictly speaking 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, the user may set the synonym in the first instance. The “synonym” of an experimental type in Analysis is a common human-readable name, for example “HNCA” or “15N HSQC NOESY”, but this may still not be sufficient to fully specify the exact NMR experiment that was run. To do this the full CCPN type should be considered. The External Source and corresponding name columns are only used in situations where the loading of a spectrum specifies what kind of experiment was run. At present this only occurs for data loaded from Bruker files, and then only if the pulse sequence name in the parameters is known to the system. Nevertheless, if this data is present the experiment type information can be automatically be filled in.
The full CCPN type for an experiment uses a special nomenclature that is described in the CCPN experiment nomenclature paper (slightly out of date now). In essence the user can distinguish between different magnetisation transfer pathways, some of which may have the same common name (synonym). 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[N].TOCSY (TOCSY first). The experiment naming system for the full CCPN 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 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 or J-coupling (the transfer type is listed after at the end after a dot).
The lower tables are used to show how the dimensions of the actual experiment relate to the reference dimensions that described in the experiment type. Even when an experiment type is set it will not always be possible to automatically determine which of the experimental dimensions relates to which part of the magnetisation transfer pathway. For example a 3D HCCH TOCSY experiment (full type HC_cH.TOCSY) has two hydrogen dimensions; one dimension is the hydrogen bound to the measured carbon, and one dimension is the hydrogen in the acquisition dimension. Deciding which is which is crucial for the correct assignment and interpretation of spectra. The problem only arises when there are two or more dimensions with the same nucleus. Sometimes Analysis guesses wrong and the user has to check. Changing the dimension mapping is a matter of looking in the lower left table and seeing how one dimension relates to another. Each dimension that has a direct transfer to another recorded dimension is listed. For example, in an HCCH TOCSY dimension 1 (hydrogen) might be ‘onebond’ to dimension 3 (carbon), but the user may know that it is actually dimension 2 that is really ‘onebond’ to the carbon. This problem may be fixed by double-clicking either the “First Dim” or the “Second Dim to to change the transfer pathways so that dimension 3 (carbon) is listed as ‘onebond’ to dimension 2 (hydrogen) (the other rows in the table will adjust automatically). The Numbering of dimensions in this table is the same as that presented when assigning a peak, i.e. in the Assignment Panel. It helps to know that dimension ‘1’ is usually (but not always) the acquisition dimension.
The lower right “Reference Dimension Mapping” is an alternative way of looking at the same information and shows how the experimental dimensions have been mapped to their reference counterpart in the experiment type database. Here, the “Ref Measurement” column can be used to follow the steps in the magnetisation transfer pathway by following increasing measurement numbers. Changing the “Ref Exp Dim” column in this table is equivalent to making changes in the lower left table, but is perhaps more difficult to understand.
Experimental Details, Instruments and Shift References
The “Experimental Details” table is used to list and edit details about the recorded experiments in terms of its physical setup. The user may specify which instruments were used and information about the sample and NMR tube. It should be noted that in order to specify a spectrometer or probe the specification for the instrument must first be entered in the “NMR Instruments” tab. Currently, none of the NMR details given in this table have any influence on resonance assignment or NMR data analysis, although spinning information may be used for solid-state spectra at some point. However, any experimental details entered into the CCPN project will be present when submissions to the BioMagResBank database are made; initially using the CcpNmr ECI.
The “Shift References” table is use to enter chemical shift reference information into the CCPN project. This may them be linked to experiments via the first “Experiments” tab, and such information is required for database deposition. To add a chemical shift reference specification the user first clicks on either “Add Internal Reference” (internal to the sample) or “Add External Reference” as appropriate. Then for the rows that appear in the table the user double-clicks to edit the columns to specify: which atom in which kind of molecule was used, what the reference value and unit is, and whether the reference is direct or indirect. A reference atom allows the direct referencing of resonances that have the same kind of isotope, but other isotopes may be referenced indirectly by using a shift ratio to relate to a direct reference.
The “NMR Instruments” section contains two table that allows the user to add descriptions of the NMR probe and spectrometer that were used during the experiments. To achieve this the user adds a new specification for the appropriate kind of instrument then double-clicks to fill in the details for each of the rows that appears in the table.
Caveats & Tips
An experiment may be linked temporarily with a new shift list; selecting “<New>” in the Shift List column of the first tab then reseting the shift list back to the original one, in order to make a shift list that contains only chemical shift value for that experiment at that time. Without any experiment links these chemical shift values will not alter as peaks and assignments change.
References
A nomenclature and data model to describe NMR experiments. Fogh RH, Vranken WF, Boucher W, Stevens TJ, Laue ED. J Biomol NMR. 2006 Nov;36(3):147-55 (link)
A table listing the NMR experiments available within the current project including details of which shift lists they use
Table 1 | |
# | The serial number of the experiment |
Name | A short identifying name for the experiment, for graphical display (Editable) |
Num. Dim | The number or independent dimensions recorded in the experiment |
Exp. Type | The name of the reference type for the experiment; to indicate what kind of experiment was run |
Acquisition Dim | Which of the recorded experimental dimensions was the final acquisition dimension (Editable) |
Shift List | Which shift list the experiment uses to record the chemical shifts for it’s assigned peaks (Editable) |
Data Sources | The names of the spectra (or other data sources) that are derived form the experiment |
Mol Systems | The molecular systems (groups of chains) that assignments in the experiment are made to (Editable) |
Shift Ref | The chemical shift reference records used by the experiment (Editable) |
Num. Spectra | The number of fully processed spectra resulting from the experiment |
Raw Data | Whether there is an unprocessed data source (spectrum) associated with the experiment |
Details | A user-editable textual comment for the experiment (Editable) |
Measurement Lists: Show a table of NMR measurement lists (chemical shifts, T1, J-coupling etc) that relate to the selected experiment
New Experiment: Make a new blank experiment record; you will be prompted for the number of dimensions
Delete: Delete the selected experiments from the project; any spectrum data on disk is preserved
The experiment type definitions that are associated with the current NMR experiments
Table 2 | |
# | The serial number of the experiment |
Experiment Name | The name of the experiment used in graphical displays |
External Source | Whether the experiment type information comes from an external source, e.g. Bruker pulse programs (Editable) |
External Name | The name of the experiment type as specified fom an external source, e.g. from the Bruker pulse program (Editable) |
Category | A loose, mutually exclusive classification of the experiment to help simplify subsequent setting of experiment type (Editable) |
Type Synonym | A common human readable name for the type of experiment (Editable) |
Full Type | The precise CCPN name for the reference experiment type; indicating what experiment was performed (Editable) |
Alt Types | Alternative reference experiment names which share the same human readable synonym |
Propagate Experiment Type: Spread the experiment type specification, where possible, from the last selected experiment to all highlighted experiments
Edit Experiment Prototypes: Open a popup to view and administer the reference experiment type specifications; can be use to describe new experiment types
Table 3 | |
First Dim | The first recorded experimental dimension involved in a magnetisation transfer (Editable) |
Transfer Type Between Dims | The type of magnetisation transfer (e.g. NOSY, TOCY, J-coupling, one-bond) between the experimental dimensions |
Second Dim | The second recorded experimental dimension involved in a magnetisation transfer (Editable) |
Table 4 | |
Exp Dim | The number of the experimental dimension |
Ref Exp Dim(.Ref) | Which dimension in the reference experiment (prototype) specification the real experimental dimension corresponds to (Editable) |
Isotope | The isotope involved with the reference experimental dimension |
Ref Measurement | What is recorded on the experimental dimension, and which steps of the magnetisation transfer pathway it applies to |
A table of ancillary experimental details, relating to samples and instrumentation
Table 5 | |
# | The serial number of the experiment |
Name | The textual name for the experiment, for graphical displays |
Spectrometer | The specification of the spectrometer used to record the NMR experiment (Editable) |
Probe | The specification of the NMR probe which was used in the experiment (Editable) |
Num. Scans | The number of repeated scans made during the experiment (Editable) |
Sample State | The state that best describes the sample and any molecular ordering; liquid (solution), solid, powder, ordered or crystalline (Editable) |
Sample Volume | The total volume of sample used the experiment (Editable) |
Volume Unit | The physical units used to describe the sample volume (Editable) |
NMR Tube Type | A description of the type of NMR tube used in the experiment (Editable) |
Spinning Angle | If the experiment involved a spinning sample, what the angle of spin was (Editable) |
Spinning Rate (Hz) | If the experiment involved a spinning sample, what the rate of spin was, in Hz (Editable) |
Edit NMR Instruments: Display a table to view and administer NMR spectrometer and probe specifications
Propagate Experimental Details: Spread the experimental details in the table from the last selected experiment to all highlighted experiments
A table of chemical shift reference information that is used by th experiments of the project
Table 6 | |
# | The serial number of the chemical shift reference specification |
Class | Whether the chemical shift reference is internal or external to the sample |
Isotope | The kind of nuclear isotope to which the reference applies (Editable) |
Experiments | The number of experiments in the project which use the shift reference specification (Editable) |
Mol. Name | The name of the molecule used to give a reference value to chemical shifts (Editable) |
Atom | Which atom of the reference molecule provides the reference chemical shift value (Editable) |
Value | The reference value of the chemical shift for the specified atom (Editable) |
Unit | Which measurement unit the chemical shift reference value is in; ppm, ppb or ppt (Editable) |
Ref Type | Whether the chemical shift referencing is direct or indirect (and thus uses a shift ratio) (Editable) |
Indirect Shift Ratio | The precise numeric ratio used to indirectly get the reference shift value of an isotope, given the direct measurement of a different isotope (Editable) |
Sample Geometry | For external references, a description of the geometry of the container used to hold the reference compound, e.g. cylindrical or spherical (Editable) |
Location | For external references, a description of the location of the reference (Editable) |
Axis | For external references, orientation of the reference container with respect to external magnetic field, e.g. parallel or perpendicular (Editable) |
Add Internal Reference: Add a new record for a chemical shift reference that is internal to the sample
Add External Reference: Add a new record for a chemical shift reference that is external to the sample
Delete Selected: Delete the selected chemical shift reference records
Descriptions of NMR spectrometers and probes used in the experiments
Table 7 | |
# | Serial number of NMR probe specification |
Name | The name of the probe for graphical representation (Editable) |
Type | A classification for the kind of probe used, e.g. liquid, solid, nano, flow or MAS (Editable) |
Model | The manufacturer’s definition of the probe model (Editable) |
Serial # | The manufacturer’s serial number for the specific NMR probe (Editable) |
Diameter (cm) | The probe diameter in cm (Editable) |
Details | A user-specified textual comment about the probe (Editable) |
New Probe Specification: Add a new NMR probe specification to the CCPN project
Delete Probe Specification: Delete the selected NMR probe specification
Table 8 | |
# | Serial number of the NMR spectrometer specification |
Name | A name for the spectrometer, for graphical displays (Editable) |
Nominal Freq. | The rounded spectrometer frequency, from the 1H resonance frequency in MHz, used in textual description, e.g. “500”, “900” |
Proton Freq. (MHz) | The actual numeric magnetic field strength expressed as a 1H resonance frequency in MHz, e.g. “500.013” (Editable) |
Model | The manufacturer’s definition of the spectrometer model (Editable) |
Serial # | The manufacturer’s serial number for the specific NMR spectrometer (Editable) |
Details | A user-specified textual comment about the NMR spectrometer (Editable) |
New Spectrometer Specification: Add a new NMR spectrometer specification to the CCPN project
Delete Spectrometer Specification: Delete the selected NMR spectrometer specification