en
msi-owg, http://msi-ontology.sourceforge.net/
NMR
This controlled vocabular (taxonomy) contains mainly Descriptors relevant to the experimental conditions of the Nuclear Magnetic Resonance (NMR) component in a metabolomics investigation.
Andy Tseng (Human Serum Metabolome Project, Un of Manchester, UK)
Bertram Ludaescher (UCDavis Genome Center, US)
Chris Taylor (EBI and HUPO-PSI)
Daniel Schober (EBI)
Dennis Rubtsov (Un of Cambridge, UK)
Helen Jenkins (Un of Wales, Aberystwyth, UK)
Irena Spasic (Center for Integrative Systems Biology, Manchester, UK)
Larissa Soldatova (University of Wales, Aberystwyth, UK)
Lori Querengasser (Un of Alberta)
Martin Scholz (UCDavis Genome Center, US)
Matej Oresic (VTT Technical Research Centre of Finland)
Oliver Fiehn (UCDavis Genome Center, US), MSI Oversight Committee Chair
Philippe Rocca-Serra (EBI and MGED Society)
Ricardo Pietrobon (Duke University) , MSI OWG co-Chair
Susanna-Assunta Sansone (EBI)
0.1
13.10.2006
Daniel Schober, Susanna-Assunta Sansone
Contact via MSI OWG mailing list (mailto:msi-workgroups-ontology@lists.sourceforge.net)
This is the initial draft of the msi-nmr-ontology binned under 'webimported' OBI and BFO classes. This is a primary discussion- and test-version to encourage nmr term development. As a secondary role this ontology serves as a testbed to evaluate the BFO top level ontology , modularization and the owl-import and referencing mechanism.
The nmr ontology is developed by the ontology working group (http://msi-ontology.sourceforge.net/) of the msi-metabolomicssociety (msi-workgroups.sf.net).
NMR-instrument specific component of metabolomics investigations
JEOL_AL95
defneed
Bruker_NMR_probe
TODO: May need no definition.
def: The compound that produced a peak that is measured to assess the quality of a data set.
quality_check_compound_signal
Felix
sample_temperature_in_autosampler
def: The temperature of an item of analysis material whilst in an autosampler.
def: The unit of measurement of the second dimension of a 2D NMR dataset.
additional_axis_unit
CAT
def: A NMR sample holder is the part of an NMR instrument, which carries the nmr probe,sample tube and the nmr sample.
NMR_sample_holder
micromass
tempdef: A technique used to suppress the water peak in a spectrum. Suppression of the strong solvent signal is necessary in order to obtain high signal to noise for the peaks of the sample under investiogation, e.g. protein peaks.
defprov: Daniel Schober
water_suppression_method
defneed
pre-processing_parameter_set
def: A method for quadrature detection.
synonym: S-TPPI
states-time_proportional_phase incrementation
def: Over the past few years there has been a significantly growing demand for miniaturization in all areas ofmodern research and development. Evoked by many exciting applications, there is a need for analytical methods which require less amounts of sample. Bruker BioSpin meets this challenge with a revolutionary NMR probe design: The 1mm MicroProbe. It operates with disposable 1mm capillary sample tubes and the sample volume of 5 microliters enables the use of lowest amounts of sample to run all high resolution NMR experiments with outstanding sensitivity and up to 16 times faster measurements. Due to the TXI-type probe design, the z-gradient coil and the automatic matching and tuning accessory, the 1mm MicroProbe can be used for a wide variety of NMR experiments. The key advantages of this probe include:
up to 4 times higher mass sensitivity than 5mm conventional probes (with respect to the same sample amount)
excellent solvent suppression properties
virtually no salt effect
discrete samples in tubes that can be sealed and stored
automation accessory for sample preparation and handling available
defprov: Bruker website
1mm_MicroProbe
MR_Resources
defneed
solid_NMR_probe
defneed
synonym: presaturation
presat
OceanOptics
indirect_detection_probe
encoding_method
tempdef: A data processing method which compresses a data file for a specific purpose.
defprov: Daniel Schober
def: The intensity of an electric, magnetic, or other field.
field_strength
??? How to model "hoch 2"?
US_2
ThermoNicolet
Nuts
def: A description of the post-processing strategy used to convert a pre-processed NMR spectrum into a suitable data format for chemometric analysis.
synonym: NMR spectrum post-processing parameter set
NMR_spectrum_post-processing_parameter_set
TODO: altsprcls: process, not clear wether set is plural (list) or process.
x-axis_unit
def: The units of measure for the x-axis of a (1D or 2D) FID, (1D or 2D) pre-processed spectrum, 2D projected spectrum, and (1D or 2D) post-processed spectrum.
altdef: The units used to represent either time domain (for a FID) or the frequency domain (for a spectrum).
flip-back_watergate
defneed
FOSS
NMR_quality_check_result
def: A result of an NMR quality check.
synonym: NMR quality check result
NMR_instrument_parameter_set
defneed
Metabolic_Profiler
For metabolism studies, and analysis of complex mixtures.
file_reference
defneed
def: The exponential function used to multiply a FID by to produce a desitred amount of line broadening.
exponential_multiplication
def: The nucleus of an element or isotope that is being studied during an NMR analysis. Common NMR requirements include direct 1D and 2D proton-only NMR, direct observation of 13C NMR with 1H decoupling, direct observation of other nuclei such as 19F, 31P, 29Si, 31P, 27Al, and 15N (with or without 1H decoupling), triple resonance NMR (especially inverse triple resonance such as 1H observe, 13C and 15N decouple), and inverse 2D and 3D experiments such as HMQC and HMBC.
acquisition_nucleus
GE_Omega
defneed
synonym: sb
shifted_bell
Varian_VNMR
high_resolution_probe_with_ATM
def: The ATM option for AVANCE spectrometers is available for:
Double resonance probes in fixed-frequency and broadband tunable configurations with either direct or indirect detection. Thus, for multinuclear operation, as often required for applications in inorganic chemistry, ATM facilitates the accurate setting of 90° pulsewidths on both observe and decoupling channels for each chosen nucleus and each individual sample - even with full automation. Triple resonance probes in fixed-frequency configurations, as typically used for inverse detection with high-field systems.
defprov: Bruker website
synonym: High Resolution Probes with Automatic Tuning and Matching, HR_probe_with_ATM
Bruker_BEST_NMR
def: The introduction of biological screening and combinatorial chemistry for chemical synthesis has also introduced new requirements for NMR automation, e.g., the use of well plates for sample input, increased demands on throughput, and the need for quick and simple interpretation of the acquired NMR data.
defprov: Bruker website
synonym: Bruker Efficient Sample Transfer NMR
excitation_sculpting
def: A specific technique used to suppress the solvent signal in a spectrum.
altdef:: A type of pulse sequence (or part of it) used to suppress a frequency (most commonly solvent).
Paravision
continuous_wave_NMR_instrument
Continuous wave NMR spectrometers are similar in principle to optical spectrometers. The sample is held in a strong magnetic field, and the frequency of the source is slowly scanned (in some instruments, the source frequency is held constant, and the field is scanned).
Defprov: http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm
def: The Discovery™ is a Windows XP Professional-based, integrated console designed especially for Solid-State NMR. The console includes everything needed to interface to any magnet and solids probe - from computer to cables to duplexing network
defprov: tecmag website
DISCOVERY_console
NMR_data_format
jump_and_return
tempdef: A jump and return pulse sequence method is a water suppression method that uses a defined pulse sequences to make fast exchanging protons visible.
synonym: jump and return pulse sequence
sine
defneed
data_processing_method
def: A method or algorithm that converts an input data set into an output data set in a tracable and useful manner.
def:BRUKER BIOSPIN's experienced Research & Development group not only delivers top-performance probes for the more common experiments, but also a wealth of special probes for almost any application. For high resolution (HR) NMR we offer probes with a variety of important characteristics and features.
defprov: Bruker website
synonym: HR Probe
high_resolution_probe
AMX
tube
tempdef: The sample-tube holds the nmr sample and sits in the nmr probe. It is usually a glass tube of 5-20mm diameter.
tempdef: An immanent important, non-obligatory part of any NMR data set.
defprov: Daniel Schober
synonym: cardinal part of NMR data set
cardinal_part_of_NMR_data_set
JCAMP
sample_introduction_method
def: A method of introduction of an NMR sample to an NMR instrument.
defneed
UltraShield
def: .A projection method that sums the intensities of a pre-processed 2D J-resolved NMR spectrum to obtain a projected spectrum.
altdef: The adding of spectra together to produce a composite avergaed spectrum.
summation_projection
Hyphenated_NMR_instrument
NMR Instruments using hyphenated analytical techniques combining mass spectrometry and chromatograph.
tecmag_console
symmetrise
defneed
Doty_Scientific
defneed
method
altspcls: process ???
Hadamard_encoding
defneed
NMR_instrument_acquisition_parameter_set
def: The list of parameters that describe the instrument settings used for the acquisition of a spectrum.
altdef: The set of variables dependent on a given pulse sequence that will be optimised in order to acquire a spectrum.
synonym: NMR instrument acquisition parameter set
TopSpin_1.3
calibration_compound
def: The compound that produced the peak used to reference a spectrum during data pre-processing.
number_of_scans
def: The number of repeat scans performed and summed to create the data set for an NMR sample.
def: The configuration of an NMR Instrument.
synonym: NMR_instrument_configuration
NMR_instrument_configuration
defneed
NMR_plattform
TODO: What is the differrence to NMR instrument?
17O
TODO: Definition depends on sprcls.
one_dimensional_NMR_configuration
tempdef: The process of configuring an NMR instrument for 1D NMR analysis.
defprov: Daniel Schober
synonym: 1D NMR configuration
MERCURY
def: Bruker BioSpin introduces the SampleJet, a robot for NMR tube automation. The SampleJet has been consciously designed to meet the growing customer demand for simplicity, versatility and higher throughput in NMR sample tube automation.
The SampleJet utilizes the modern-day industry standard for sample arrangements—the 96 well plate array. Therefore, the samples may be handled by standard lab automation devices before or after the NMR measurement.
defprov: Bruker website
SampleJet
acdlabs
Includes the connection to a high-resolution TOF-LC-MS system.
LC-NMR/MS
decoupled_nucleus
def: An indication of whether the nucleus being studied is the acquitsition nucleus.
JEOL_NMR_instrument
tenpdef: A function used to multiply a FID by to produce a desired amount of line broadening and spectral resolution.
defprov: Daniel Schober
synonym: ssb
shifted_sine_bell
def: The analysis of one NMR sample at one time by NMR producing one raw dataset (a FID).
synonym: NMR analysis
NMR_analysis
A method of spectral projection.
projection_method
Nicolet_GE/QE-300
defneed
synonym: 1D diffusion edited
one_dimensional_diffusion_edited_pulse_sequence
def: The process of producing an annotated spectrum from a pre-processed spectrum.
synonym: NMR spectral post processing
NMR_spectral_post-processing
one_dimensional_NMR_acquisition_parameter_set
defneed
synonym: 1D NMR acquisition parameter set
defneed
Bruker_NMR_instrument
Jeol_Delta
NMR_data_pre-processing_parameter_set_by_dimension
def: The set of variables dependent on a given pulse sequence for a given dimension that will be optimised in order to acquire a spectrum.
synonym: NMR data pre-processing parameter set by dimension
def: A post-processed NMR spectrum in which the y-values of the datapoints have been summed based on periodic ranges of the x-axis values.
bucketed_spectrum
TODO: has spectral post processing parameter
UNITY
defneed
clsdel: was under study_report
?result
NMR_quality_check_parameter_set
tempdef: A nuclear magnetic resonance spectroscopy quality check parameter set is a parameter set used for the quality check method for an NMR analysis
synonym: NMR quality check parameter set
defneed
flow_probe
Applied_Biosystems
27Al
def: A reference to a file of data pre-processing parameters produced by the machine.
processing_parameter_set_file_reference
def: A reference to a description of a pulse sequence in the literature.
pulse_sequence_literature_reference
J-coupler
multiplet_analysis
autosampler
def: An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument.
altdef: The autosampler is an automatic sample changer.
JEOL
tempdef: A chemical compound is a small object which reacts chemically and is usually a molecule or composed out of molecules.
defprov: Daniel Schober
chemical_compound
TODO: May be imported from other Ontology.
zero_order_phase_correction
def: A parameter used to mix real and imaginary part of an NMR spectrum that the real part of the spectrum is in pure absorption mode.
altdef: The number of degrees that a central peak must be moved in order to achieve an absorptive mode line width.
flow_high_resolution_probe
def: Hyphenated analytical techniques combining mass spectrometry and chromatography are well-established laboratory tools. The combination of chromatography and NMR has also made its way into the analytical laboratory. Further developments even combine all three techniques into an LC-NMR/NMR-MS system. The use of solid phase extraction provides an efficient interface between chromatography and NMR with demands for special type of flow probes.
defprov: Bruker website
synonym: flow_HR-probe
NMR_probe
def: Part of an NMR instrument that detects the signals emitted from a sample. No single probe can perform the full range of experiments, and probes that are designed to perform more than one type of measurement usually suffer from performance compromises. The probe represents a rather fragile “single point of failure” that can render an NMR system completely unusable if the probe is dropped or otherwise damaged. Probes are usually characterised by Sample diameter and Frequency.
altdef: The instrument that transmits and recieves radiofrequency to and from the NMR sample.
window_function_parameter
def: A parameter to a window function.
irradiation_frequency
def: The frequency of the RF radiation used to irradiate an NMR sample.
11B
tempdef: The data matrix a spectrum consists of can be projected from a higher dimension onto a lower dimension, e.g. a 3D NMR spectrum can be converted (projected) into a 2D NMR spectrum.
defprov: Daniel Schober
projected_spectrum
JEOL_Alpha
Galactic
def: A part of an NMR instrument which is cardinally important and hence obligatory and compulsatory for the proper intended function of the instrument.
synonym: cardinal part of NMR instrument
cardinal_part_of_NMR_instrument
projection_axis
def: The axis onto which the spectrum was projected.
two_dimensional_total_correlation_spectroscopy_pulse_sequence
tempdef: Total Correlation Spectroscopy. A 2D homonuclear correlation experiment used to analyse scalar (J) coupling networks between protons. TOCSY is able to relay magnetisation between spins, A-B-C-D.., and can therefore show correlations amongst spins that are not directly coupled (eg A-C and A-D) but exist within the same spin system.
defprov: Daniel Schober
synonym:2D_TOCSY
defneed
NMR_imaging_probe
defneed
water_suppression_parameter
def: In some cases, it is necessary or advisable to control the temperature of the sample at some value other than ambient. The sample may be only slightly solubility at room temperatures, or it may be desirable to control some aspect of the dynamics of the system. In such cases, a default temperature, or some means of selecting this parameter, can be built into the experiment.
sample_temperature
defneed
parameter_set
tempdef: A jump and return 1-1 pulse sequence method is a jump and return method that uses one 90 degree pulse and one 90 degree return puls to make fast exchanging protons visible, first described by Plateau,P. and Gueron,M. (1982) J. Am. Chem. Soc., 104, 7310–7311. Compared to the 1-3-3-1 method it has a lower receiver gain and the dispersive tail of water interferes with the signals of interest.
jump_and_return_1-1
AC
Net_CDF
UltraShield_Plus
hadamard_frequency
def: A frequency used during Hadamard encoding.
Bruker_UXNMR/XWIN-NMR
tempdef: An instrument configuration is the description for the setting of an instrument or a machine in order to archive a certain intended goal or task.
altdef: An instrument configuration is the process of setting the possible parameters of an instrument in order to archive a certain intended goal.
instrument_configuration
Bruker_DISNMR
tempdef: An improved water-suppression technique called WET (water suppression enhanced through T1 effects), developed from a Bloch equation analysis of the longitudinal magnetization over the T1 and B1 ranges of interest, achieves T1- and B1-insensitive suppression with four RF pulses, each having a numerically optimized flip angle. Once flip angles have been optimized for a given sequence, time-consuming flip-angle adjustments during clinical examinations are eliminated.
defprov: Daniel Schober
synonym: WET
water_suppression_enhanced_through_T1_effects
Bruker_WIN_NMR
spinning_rate
def: The rate at which an item of analysis material is spun.
states
defneed
tempdef: A sample is a role that is played by an object of interest in an investigation used to obtain generalizable information about the sample source.
defprov: Daniel Schober
sample
jump_and_return_1-3-3-1
tempdef:A jump and return 1-3-3-1 pulse sequence method is a jump and return method that uses a 1-3-3-1 pulse sequence to make fast exchanging protons visible. Compared to the 1-1 method it has better water suppression (higher receiver gain) capabilities, but with offset-dependent phase distortion (unsuitable for 2D).
tempdef: A quality check result is the usefull outcome of a quality check.
defprov: Daniel Schober
quality_check_result
TODO: Belongs in Ref Ontol.
defneed
vendor
def: The duration of the excitation pulse needed to rotate the magnetisation vector by 90 degrees.
synonym: 90 degree pulse duration
ninety_degree_pulse_duration
29Si
Delta
complex_datatype
def: A complex datatype (or complex value) is a datatype that is not a primitive one (like string or integer) and that references to more primitive values. Often, these are called reference data types. Complex datatypes can belong to the object data type. Data types that define sets of complex values include Array, Date, Error, Function, and XML and others.
TecMag
JEOL_NMR_software
atom_environment_encoding
def: A scheme for producing a numerical representation of the environment of an atom.
one_dimensional_pulse_sequence
def: One dimensional (referring to a FID, pre-processed spectrum, or post-processed spectrum).
synonym: 1D
Perkin_Elmer
TODO: May need no definition.
defneed
Bruker_NMR_software
defneed
Bruker
TODO: May not need definition due to its instance character.
19F
def: An algorithm for achieving a post-processed spectrum.
post-processing_algorithm
JEOL_NMR_probe
defneed
def: A reference to a file containing the raw FID.
synonym: FID_file_reference
free_induction_decay_file_reference
polynomial_fitting
defneed
literature_reference
defneed
defneed
Frydman_encoding
def: A reference to a file containing a specification of a pulse sequence.
pulse_sequence_file_reference
defneed
convolution
def: A reference is a label which refers to data elsewhere, as opposed to containing the data itself. Accessing the value that a reference refers to is called dereferencing it. References are fundamental in constructing many data structures and in exchanging information between different parts of programs and databases.
reference
post-acquisition_water_suppression_method
tempdef: A data processing technique used to suppress the water peak in a spectrum in order to get clearer results.
defprov: Daniel Schober
tempdef: An integral data transformation that re-expresses a function in terms of sinusoidal basis functions, i.e. as a sum or integral of sinusoidal functions multiplied by some coefficients ("amplitudes").
defprov: Daniel Schober
fourier_transformation
AURELIA
def: The Bruker BioSpin CryoProbe is a high-performance cryogenically cooled probe developed for high-resolution applications. It has improved signal/noise (S/N) ratios obtained by reducing the operating temperature of the coil and the pre-amplifier. As a result, the efficiency of the coil is improved and the noise of the coil and the pre-amplifier are reduced.The dramatic increase in the S/N ratio by a factor of 3-4, as compared to conventional probes, leads to a possible reduction in experiment time of up to 16 or a reduction in required sample concentration by a factor of up to 4. The CryoProbes possess key characteristics for NMR analysis:
Significant S/N gains (with moderately salty samples also)
Short pulse widths
Short ring down times
Linear behavior in power response
Gradient capability
CryoProbes are available as Triple Resonance, Dual, Selective X Detection, MicroImaging, and Quad Nucleus Probes configurations at 400 MHz and higher
All high resolution probes have a lock circuit
All high resolution probes have Z-gradient
defprov: Bruker website
CryoProbe
INOVA
def: A software artifact used during spectral post-processing.
spectrum_post-processing_software
Agilent_Technologies
NMR_quality_check
def: The process of ensuring the quality of the raw data that results from an NMR analysis.
synonym: NMR quality check
chemical_shift_standard
def: A compound that is added to an NMR sample to enable the alignment of spectra. The power of NMR is that for most nuclei the NMR frequency changes very slightly with different molecular environment or chemical bonding. These shifts are very small, on the order of 1 part in 10+9. This is referred to as "Chemical Shift." Tables of chemical shifts are tabulated and used to determine molecular structure. Combining NMR chemical shift information with other NMR information such as peak integration, coupling constants and Nuclear Overhauser Enhancement (NOE) can result in complete three-dimensional molecular structures of molecules in solution without using X-ray crystallography.
NMR_magnet
def: A magnet which induces a certain frequency (MHz) and which has a certain bore diameter.
altdef: The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the nmr acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss.
tempdef: A frequency sorted array of the NMR signal frequency components. Nuclei with different resonance frequencies will show up as peaks at different corresponding frequencies in the spectrum, or 'lines'.
synonym: NMR spectrum
NMR_spectrum
defneed
y-axis_unit
B-ACS
def: The Bruker Automatic Sample Changer (B-ACS 60/120), used in conjunction with Bruker DISNMR, UXNMR or XWIN-NMR software, provides dialog-guided facilities which allow the user to easily and effectively perform automatic (continuous) experiments. Features include a 60 or 120 sample capacity, random accessing of samples, positive sample identification with the optional bar code reader, and temperature control of individual samples with the optional sample heater unit.
defprov: Bruker website
ChemMagnetics
defneed
NMR_software
31P
Jasco
watergate
defneed
line_sharpening
defneed
calibration_reference_shift
def: The parts-per-million value of the peak used to reference a spectrum.
first_order_phase_correction
defneed
direct_detection_probe
def: This Method removes the residual water and its side lobes, thereby reducing the baseline for the metabolites of interest and allowing subsequent data analysis using more sophisticated nonlinear least squares algorithms.
synonym: HSVD
hankel_singular_value_decomposition
ECA
def: Automatic or manual procedures performed upon pre-processed NMR data sets that aim to summarise them or annotate them with speculative values.
data_post-processing
def: A sample that has been prepared for chemical analysis by NMR. NMR samples are usually liquid solutions contained in glass tubes. NMR solution sample volume ranges from 50ul to 5ml depending on the NMR probe. Sample concentrations of solute for 1H NMR are usually in the range of 100ug to 5g, with 10 to 50mg being typical. NMR is not a chemical trace analysis technique. The NMR signal of solids and gases can be recorded but to measure solid-state NMR additional specialized hardware is required.
synonym: NMR sample
NMR_sample
defneed
gaussian_broadening
JEOL_Generic
tempdef: A non FT based method for converting from the time to the frequency domain.
non-fourier_transformation
TODO:Exclusion guided definition.
AUREMOL
two_dimensional_NMR_acquisition_parameter_set
defneed
synonym: 2D NMR acquisition parameter set
VXR
13C
magnetic_field_strength
defneed
def: A reference to information on the provenance of the NMR sample.
synonym: NMR sample reference
NMR_sample_reference
def: The Eagle™ is a 4 mm 1H/X solid-state MAS probe with a top spinning speed of 18 kHz. Its simple design is robust, reliable and easy to spin. Configurations are available for 200 to 600 MHz widebore magnets on Tecmag, Bruker, Chemagnetics, JEOL and Varian spectrometers.
defprov: website
tecmag_EAGLE_probe
data_transformation
def: A method for transforming the time-based acquisition data into frequency-based data.
def: This system automatically prepares an NMR sample, inserts it into an NMR magnet, performs NMR experiments on the sample, and transports it back to the preparation system.
The SampleRail fulfills the transporting tasks from the preparation system into the NMR magnet and back
defprov: website
SampleRail
1H
def: The nucleus of the element Hydrogen, a proton.
rem1: The nucleus most often studied in NMR metabolomics.
Varian_NMR_instrument
quality_control_method
tempdef: A quality control method is a method, which is applied to ensure or to verify for a good quality outcome.
defprov: Daniel Schober
def: The number of scans whose data is not summed to create the data set for an NMR sample, but that are carried out to establish the steady-state of relaxation for the nuclei.
number_of_steady_state_scans
one_dimensional_free_induction_decay
def: Having been excited by the RF pulse, the nuclei turn back ("relax") to their initial state ( the initial equilibrium population) within usually several seconds when the induced magnetization decays. Since the precession of the nuclei is free and due to the decay of the induced magnetization the whole process is termed Free Induction Decay (FID). Usually, several FIDs are co-added in order to improve the signal-to-noise ratio of a spectrum. The summed up FID is then once subjected to a mathematical operation (Fourier transform) which results in an NMR spectrum.
synonym: 1D_FID
tecmag
defneed
maximum_intensity_projection
def: A Computer used for NMR, can be divided into central processing unit (CPU), consisting of instruction, interpretation and arithmetic unit plus fast access memory, and peripheral devices such as bulk data storage and input and output devices (including, via the interface, the spectrometer). Under software control, the computer controls the RF pulses and gradients necessary to acquire data, and process the data to produce spectra or images. Note that devices such as the spectrometer may themselves incorporate small computers.
acquisition_computer
ECX
JEOL_DX
Bruker_AutoClean
def: In today's fast-paced research environment, NMR tubes are often used once and discarded, creating needless waste. With the Bruker BioSpin Autoclean™ system you can now recycle 5mm, 3mm, or 5mm/3mm step-down (Wilmad 520-1B) NMR tubes. AutoClean NMR Tube Washing System is a simple way to recoup the substantial investment your organization makes in quality NMR tubes, and cut back on needless waste material.
defprov: Bruker website
high_resolution_magic_angle_spin_probe
def: Samples that are neither solid nor liquid, being of biological, chemical, and/or pharmaceutical interest, reveal highly resolved spectra when magic angle spinning is applied. The correct solution is a gradient, such that the field varies along the spinner axis. This so-called Magic Angle Gradient is employed in Bruker’s high resolution Magic Angle Spinning (hr-MAS) probes, and is implemented in such a way that it is compatible with the stator and does not interfere with the sample eject/insert. Bruker BioSpin has developed a series of dedicated probes for standard bore magnets to accommodate the rapidly expanding field of hr-MAS. These probes are available in double (e.g. 1H and 13C) and triple resonance (e.g., 1H, 13C, 15N) modes and come equipped with a deuterium lock channel. The probes have automatic sample ejection and insertion capability, with the availability of an optional sample changer, enabling fully automated sample runs. Probes can be equipped with an optional B0 gradient, directed along the magic angle, so that gradient spectroscopy can be done used.
defprov: Bruker website
altdef: High resolution MAS (hr-MAS) provides an easy means of obtaining high resolution spectra for a variety of samples that would otherwise result in poorly resolved spectra. The addition of an hr-MAS probe and a MAS pneumatic unit to a standard high resolution spectrometer is all that is needed to open the gate to the world of hr-MAS spectroscopy and gain access to a vast amount of highly interesting samples.
synonyms: High resolution MAS, hr-MAS
window_function_method
def: A function applied to a FID to increase the signal-to-noise ratio or the resolution.
def: An Instrument which is used to carry out a NMR analysis of some sample.
synonym: NMR instrument
NMR_instrument
tecmag_NMR_instrument
NMR_spectral_projection_parameter_set
def: The data processing parameters that describe a method of translating a 2D NMR pre-processed spectrum into a 1D NMR spectrum.
synonym: NMR spectral projection parameter set
MACNMR
sine_squared
defneed
solid_magic_angle_spinning_probe
def: Magic angle spinning, nowadays a routine technique for solids NMR, still offers the capability of innovation. The high mechanical performance of MAS probes in conjunction with efficient rf pulse techniques open new exciting fields in solids NMR of biological samples and in the field of quadrupolar nuclei.
defprov: Bruker website
synonym: solid_MAS_probe
defneed
synonym: NMR data pre-processing parameter set
NMR_data_pre-processing_parameter_set
Varian
two_dimensional_NMR_configuration
tempdef: The process of configuring an NMR instrument for 2D NMR analysis.
defprov: Daniel Schober
synonym: 2D NMR configuration
TODO: depends on superclass view.
APOLLO_console
defneed
In FT-NMR, all frequencies in a spectrum are irradiated simultaneously with a radio frequency pulse. Following the pulse, the nuclei return to thermal equilibrium. A time domain emission signal is recorded by the instrument as the nuclei relax. A frequency domain spectrum is obtained by Fourier transformation.
Defprov: http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm
fourier_transformation_NMR_instrument
peak_picking
defneed
Waters
def: The delay between repeat scans to allow nuclei to relax back to their steady state.
relaxation_delay
data_pre-processing
defneed
def: The starting value for the x-axis of a (1D or 2D) FID, (1D or 2D) pre-processed spectrum, 2D projected spectrum, and (1D or 2D) post-processed spectrum.
altdef: The initial time or frequency a FID or spectrum is recorded from.
x_start_value
normalisation_strategy
def: A strategy for normalising a data set.
TODO: Discuss "obligatory_part_of".
optional_part_of_NMR_instrument
def: Part of an NMR instrument which is not cardinally important and hence optional / facultative for the proper intended function of the instrument.
synonym: optional part of NMR instrument
clsdel: ontologically there is no such universal which characteristic is a possible (!) state of being a part of something...
micro_imaging_probe
defneed
SampleTrack
two_dimensional_hadamard_total_correlation_spectroscopy_pulse_sequence
defneed
synonym: 2D_hadamard_TOCSY
baseline_correction
def: A method of flattening the baseline of a spectrum.
Capillary_LC-NMR
TODO: May need no definition
defneed
AVANCE_II_spectrometer
JEOL_EX
tempdef: A quality check is a quality control method, which is applied to data after they have been processed. It is applied to get information about the quality of the data processing methods.
defprov: Daniel Schober
quality_check
quality_check_peak_feature
def: A feature of a peak that is measured to assess the quality of a data set.
liquid_NMR_probe
2H
TODO: Do we need definitions here?
sample_introduction_parameter
tempdef: A sample introduction parameter is a parameter that describes the particular method of introducing the sample under investigation into the nmr instrument.
ThermoMattson
data_pre-processing_software
def: A software artifact used during data pre-processing.
analysis
def: An investigation of the component parts of a whole and their relations in making up the whole.
defprov: Google define
altdef: A systematic approach to problem solving. Complex problems are made simpler by separating them into more understandable elements. This involves the identification of purposes and facts, the statement of defensible assumptions, and the formulation of conclusions.
two_dimensional_free_induction_decay
def: Having been excited by the RF pulse, the nuclei turn back ("relax") to their initial state ( the initial equilibrium population) within usually several seconds when the induced magnetization decays. Since the precession of the nuclei is free and due to the decay of the induced magnetization the whole process is termed Free Induction Decay (FID). Usually, several FIDs are co-added in order to improve the signal-to-noise ratio of a spectrum. The summed up FID is then once subjected to a mathematical operation (Fourier transform) which results in an NMR spectrum.
synonym: 2D_FID
defneed
synonym: TPPI
time_proportional_phase incrementation
NMR_Case
def: The NMR Case is an economical NMR sample changer for laboratories with modest automation needs. It expands the maximum number of samples your spectrometer can process during unattended operation to 24. The NMR Case consists of multiple components. The NMR Case exchange module installed atop your cryostat. The two front legs are adjustable, making the NMR Case compatible with many different cryostats.
defprov: Bruker website
TX
def: The list of parameters that describe the settings used to process a 2D J-resolved NMR spectrum. altdeft: The set of variables associated with adjusting the spectrum in the frequency domain to phase, baseline correct and integrate a spectrum.
synonym: NMR 2D J-resolved processing parameter set
NMR_two_dimensional_J-resolved_processing_parameter_set
defneed
NMR_tube_washing_system
AMIX_VIEWER_&_AMIX-TOOLS
TODO: same as or part of acquisition computer?
def: A component of an NMR instrument that controls the activities of the other components.
console
defneed
peak-picked_spectrum
TODO: has spectral post processing parameter.
SPE-NMR
A Solid Phase Extraction (SPE) system provides an interface between liquid chromatography (LC) and NMR. For the process of LC-SPE™ NMR a chromatographic separation is done and the peaks of interest are trapped on an individual SPE cartridge after the column. The peak selection is done either by UV detection or by evaluation of the on-line registered MS or MSn spectra.
ThermoFinnigan
defneed
synonym: 1D spectrum
one_dimensional_spectrum
def: A computational method that archieves water suppression via wavlet multi resolution analysis.
WaveWat
Lybrics
Capillary LC-NMR
Capillary LC-NMR is a hyphenated technique coupling capillary liquid chromatography and NMR, which increases sensitivity dramatically through the use of miniaturization of the chromatographic techniques and NMR detection volume.
bucketing
def: A post-processing method that divides a pre-processed NMR spectrum into a series of buckets (or bins) along the x-axis, and then integrates the spectral intensity within each bucket.
altdef: A type of automated integration which occurs across pre-defined regions for a spectrum.
Bruker_autosampler
defneed
Bruker_MATCH
def: The Bruker Multiple Adjustable Tube Clamp Holder MATCH™ system is a holder for 100 mm long NMR sample tubes with diameters ranging from micro tubes up to 5 mm NMR tubes. The MATCH insert fits into a standard 10 mm Bruker spinner and is suitable for all non-spinning applications.
The MATCH system provides an easy and cost efficient means of optimizing the signal-to-noise ratio of each sample. By matching the NMR tube diameter to the size of the sample, most of the sample can be placed in the active column of the NMR coil. This leads to an enhanced signal detection compared to diluting the same sample quantity in a larger tube.
defprov: Bruker website
synonym: Bruker Multiple Adjustable Tube Clamp Holder
pulse_sequence
def: A sequence of excitation pulses.
spectral_denoising
def: A method for eliminating or reducing the noise in a spectrum.
algorithm
def: An algorithm is a procedure (a finite set of well-defined instructions) for accomplishing some task which, given an initial state, will terminate in a defined end-state.
defprov:wiki
nuclear_overhauser_and_exchange_spectroscopy-presat
tempdef: The presat for an nuclear overhauser and exchange spectroscopy experiment. A 2D method used to map NOE correlations between protons within a molecule. The nuclear Overhauser effect (NOE) causes changes in peak areas, as a secondary effect of decoupling.
defprov: Daniel Schober
synonym: NOESY-presat
quantum_momentum_field_gradient
tempdef: Quantum Moment/Field Gradient interaction or relaxation mechanism.
defprov: Daniel Schober
synonym: QF
acquisition_parameter_set_file_reference
def: A reference to the file of acquisition parameters produced by a machine.
def: A reference to a file containing a specfication of the shape of an excitation pulse.
shaped_pulse_file_reference
def: A compound added to a sample to alter its pH value.
buffer
def: The ratio of the mass or volume of a solute to the mass or volume of the solution or solvent.
concentration
defneed
synonym: 2D spectrum
two_dimensional_spectrum
defneed
NMR_vendor
JS_Research
defneed
tilt
NMR_data_set
def: A data set that was generated within, from or for an NMR experiment.
synonym: NMR data set
coherence_pathway_rejection
tempdef: A water suppression method which is used to suppress the natural water signal in a gradient selection experiment (e.g. echo/antiecho), where the water coherence is not "refocused" by the refocus gradient (therefore, is not selected).
defprov: Daniel Schober
tempdef: A modification of Carr-Purcell RF pulse sequence with 90° phase shift in the rotating frame of reference between the 90° pulse and the subsequent 180° pulses to reduce accumulating effects of imperfections in the 180° pulses. Suppression of effects of pulse error accumulation can alternatively be achieved by alternating phases of the 180° pulses by 180°.
defprov: Daniel Schober
synonym: 1D_CPMG
one_dimensional_carr_purcell_meiboom_gill_pulse_sequence
LC-NMR
Wilmad
tempdef: The end value for the x-axis of a (1D or 2D) FID, (1D or 2D) pre-processed spectrum, 2D projected spectrum, and (1D or 2D) post-processed spectrum.
x_end_value
def: A digital sampling interval.
alsprcls: time_interval
dwell_time
Acorn_NMR_Inc
CapNMR_Probe
defneed
synonym: MAS_rotor
magic_angle_spinning_rotor
NMR_solvent
def: A compound added to a sample to an NMR sample to align the spectrometer frequency.
synonym: NMR solvent
TODO: Def not aristotelian.
tempdef: The number of data points in a data set.
number_of_data_points
tempdef: In one dimensional NMR, as the multiplets from different chemically shifted nuclei overlap, spectral assignments become too difficult. In order to resolve the chemical shift and spin-spin coupling parameters along the different axis, 2D and 3D J-resolved NMR spectroscopies are used.
defprov: Daniel Schober
synonym: 2D J-resolved
two_dimensional_J-resolved_pulse_sequence
radon_encoding
defneed
sample_temperature_in_magnet
def: The temperature of an NMR sample whilst in the magnet of an NMR instrument.
tempdef:GFT NMR allows for rapid multidimensional FT NMR spectral information gathering, avoiding sampling limitations without compromising on the precision of chemicalshift.
defprov: ttp://www.nsm.buffalo.edu/Research/GFT/szyperski_publications_1st_page/Szyperski%2067.pdf
synonym: GFT-projection
G_matrix_fourier_transform_projection
GEMINI
Bruker_NMR_magnet
defneed
defneed
echo_anti-echo
line_broadening
defneed
NMR_Suite
spectrum_post-processing
defneed
def: The process of producing a spectrum from raw data.
synonym: NMR data pre-processing
NMR_data_pre-processing
Ultrastabilized
JEOL_Lambda