http://www.metabolomics-msi.org/ http://phenomenal-h2020.eu/home/ http://www.cosmos-fp7.eu/WP2
This CV is to be used by metabolomics researchers, or basically any chenomics or proteomics researchers who apply the nmrML xml to store their NMRraw data in a vendor agnostic manner. But nmrML can also be used to capture experimental results and (limited) basic metadata like molecule to spectral feature assignments.
This artefact is an MSI-approved controlled vocabulary primarily developed under COSMOS EU and PhenoMeNal EU governance. The nmrCV is supporting the nmrML XML format with standardized terms. nmrML is a vendor agnostic open access NMR raw data standard. Its primaly role is analogous to the mzCV for the PSI-approved mzML XML format. It uses BFO2.0 as its Top level. This CV was derived from two predecessors (The NMR CV from the David Wishart Group, developed by Joseph Cruz) and the MSI nmr CV developed by Daniel Schober at the EBI. This simple taxonomy of terms (no DL semantics used) serves the nuclear magnetic resonance markup language (nmrML) with meaningful descriptors to amend the nmrML xml file with CV terms. Metabolomics scientists are encouraged to use this CV to annotrate their raw and experimental context data, i.e. within nmrML. The approach to have an exchange syntax mixed of an xsd and CV stems from the PSI mzML effort. The reason to branch out from an xsd into a CV is, that in areas where the terminology is likely to change faster than the nmrML xsd could be updated and aligned, an externally and decentrallised maintained CV can accompensate for such dynamics in a more flexible way. A second reason for this set-up is that semantic validity of CV terms used in an nmrML XML instance (allowed CV terms, position/relation to each other, cardinality) can be validated by rule-based proprietary validators: By means of cardinality specifications and XPath expressions defined in an XML mapping file (an instances of the CvMappingRules.xsd ), one can define what ontology terms are allowed in a specific location of the data model.
Nuclear magnetic resonance (NMR) data annotation as required by the msi sanctioned open access nmrML XML format developed by the COSMOS EU project.
In case we like to be able to convert this owl CV back into the obo format, we should only use DL/owl constructs that are supported by obo. Hence, editors of this CV should take care not to use any higher descriptrion logics semantics, i.e. cardinality restrictions or defined terms using constructors. We should start to build the taxonomic backbone first and later connect the main axis via relations. If we want to use restrictions, we should only use existential quantifiers as the OBO format does not support universal quantification. List of terms required by current XSD (August 2013): these were bookmarked in CV (annotation property) and are visible in the new nmrTab: CVTerm occurrences: buffer-->buffer solvent-->solvent concentration standard type-->calibration compound , what is chemical shift reference ? What calibration_reference_shift under calibration compound ? concentration standard name we here see a use-mention problem arising for the CV. The xsd should probably change here to avoid this. encoding method (Quadrature detection method) is this the same as encoding method ? sample container-->NMR_sample_holder (spectrum) y axis type-->coordinate system descriptor post acquisition solvent suppression method Two usages in xsd, but with differrent type ? -->solvent suppression method calibration compound Two usages in xsd, but with differrent type ?-->calibration compound data transformation method-->data transformation method (spectral) projection method-->projection method spectral denoising method-->spectral denoising method window function method-->window function method baseline correction method-->baseline correction sample type-->NMR sample CVParam occurrences: file content-->data file content software type-->software source file type-->data file attribute (needs refactoring) instrument configuration type-->instrument configuration processing method type-->data processing method CVParamType occurrences: chemical shift standard-->chemical shift standard solvent suppression method-->solvent suppression method encoding scheme (Quadrature detection method)-->encoding method window function parameter-->window function parameter CVParamWithUnitType occurrences: CVParamWithUnitType is currently not used in the xsd and dangling ! I assume ValueWithUnitType substitutes it ? UserParamType occurrences: No CV terms needed ValueWithUnitType occurrences: These will have to be used from the Unit ontology.
This version (1.1.0) uses the Basic Formal Ontology (BFO) as its top level ontology. We might at some point close the resulting semantic gap by using OBI and IAO as intermediate bridges.
OWL MIME type application/rdf+xml (Rather flat CV in OWL syntax. Taxonomic backbone with few relations used. No OWL DL complexity such as cardinalities, blank nodes, nested class definitions. The Semantic Validator used an OBO converted file format due to historic reasons. The OBO file is auto-generated-by the OWL API (version 3.4.2).)
Since this is a prolonged effort spanning a larger time period, there naturally were many people involved in the creation over the years and during different times. People involved in the term creation from ID >1400000 : This part of the NMR ontology was originally developed by the ontology working group (http://msi-ontology.sourceforge.net/) of the msi-metabolomicssociety (msi-workgroups.sf.net): Daniel Schober (EBI) Chris Taylor (EBI and HUPO-PSI) 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) Philippe Rocca-Serra (EBI and MGED Society) Susanna-Assunta Sansone (EBI) People involved in the term creation from ID<1400000: Joseph Cruz Daniel Schober Michael Wilson Reza Salek Daniel Jacob David Wishart Terms with IDs ID<1400000 that were NOT asserted in the original Wishart obo file were created by Daniel Schober (COSMOS WP2). Its IDs were autogenerated with the Protege ID generator. Other people that substantially helped in revising the latest and Cosmos governed CV additions were: Michael Wilson, Wishart Group, Edmonton, Alberta, Canada Daniel Jacob, INRA, Bordeaux, France Annick Moing, INRA, Bordeaux, France Catherine Deborde, INRA, Bordeaux, France Reza Salek, EBI, Hinxton, UK Philippe Rocca-Serra, University of Oxford, Oxford, UK Andrea Porzel, IPB-Halle, Germany and the COSMOS WP2 team A paper describing the overall nmrML data standard and CV has been accepted by Analytical Chemistry (Manuscript ID: ac-2017-02795f.R1), title `nmrML: a community supported open data standard for the description, storage, and exchange of NMR data`, author(s): Schober, Daniel; Jacob, Daniel; Wilson, Michael; Cruz, Joseph; Marcu, Ana; Grant, Jason; Moing, Annick; Deborde, Catherine; de Figueiredo, Luis; Haug, Kenneth; Rocca-Serra, Philippe; Easton, John; Ebbels, Timothy; Hao, Jie; Ludwig, Christian; Günther, Ulrich; Rosato, Antonio; Klein, Matthias; Lewis, Ian; Luchinat, Claudio; Jones, Andrew; Grauslys, Arturas; Larralde, Martin; Yokochi, Masashi; Kobayashi, Naohiro; Porzel, Andrea; Griffin, Julian; Viant, Mark; Wishart, David; Steinbeck, Christoph; Salek, Reza; Neumann, Steffen
For 1r/1i spectra and for Bruker, this term describe an array of integers (32bits).
integer32
A reference number relevant to the sample under study.
The allowed value-type for this CV term.
For 1r/1i spectra and for Bruker, this term describe an array of longs (64bits).
long64
The chemical phase of a pure sample, or the state of a mixed sample.
Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used.
One of the problems that should be apparent after observing the spectrum and the FID is that it is not possible to determine if the frequency is positive or negative. The instrument uses a spectrometer frequency and all signal frequencies are measured relative to the spectrometer frequency. If a molecule produces two signals, one at 300,000,001 Hz and another at 299,999,999 Hz, and the spectrometer frequency is 300,000,000 Hz, the first signal is at +1 Hz and the second is at -1 Hz. Electronically the lower frequency signals are very easy frequency to detect, transmit, amplify and sample. The complication with this rotating frame of reference is that a single detector can not distinguish positive and negative frequencies. This problem is why quadrature detection is important. Quadrature detection uses two detector channels separated by 90 degrees. These are referred to as the real channel and the imaginary channel. Using these two channels, it is possible to distinguish positive and negative frequencies. This section shows how the quadrature signal is processed to obtain an NMR spectrum. The Fourier transform produces a complex number with a real and an imaginary component. The Re function extracts the real spectrum and the Im function extracts the imaginary spectrum from the complex number.
quadrature detection
contact role
data file attribute
NMR instrument type
1D spectrum coordinate system descriptor
pre-acquisition solvent suppression
peak processing
Hexafluorobenzene
Chloroform-d
heavy water
sample pH
post buffer pH
Apodization is an umbrella term that is used to refer to signal processing covering the manipulation of the FID to either increase signal-to-noise (S/N) or resolution. it is usually possible to gain either S/N or resolution, but not both. Apodization is usually performed by applying a window function to the FID
PRS: rename 'reference' to 'identifier'
metabolomics database identifier
Metabolights identifier
acetonitrile
1,4-Dioxane
1H spectrum reference compound
2,2-Dimethyl-2-silapentane-5-sulfonate
sodium acetate
tetramethylsilane
13C spectrum reference compound
Instrument model name not including the vendor's name.
Free text description of a single customization made to the instrument; for several modifications, use several entries.
Chloroform-d1
tetramethylammonium bromide
15N spectrum reference compound
ammonia (liquid)
ammonium bromide
1,4-morpholine
nitromethane
pyridine
sodium nitrate
post-acquisition solvent suppression
Nuclear magnetic resonance decoupling (NMR decoupling for short) is a special method used in nuclear magnetic resonance (NMR) spectroscopy where a sample to be analyzed is irradiated at a certain frequency or frequency range to eliminate fully or partially the effect of coupling between certain nuclei. NMR coupling refers to the effect of nuclei on each other in atoms within a couple of bonds distance of each other in molecules. This effect causes NMR signals in a spectrum to be split into multiple peaks which are up to several hertz frequency from each other. Decoupling fully or partially eliminates splitting of the signal between the nuclei irradiated and other nuclei such as the nuclei being analyzed in a certain spectrum. NMR spectroscopy and sometimes decoupling can help determine structures of chemical compounds.
decoupling method
homonuclear decoupling
heteronuclear decoupling
State if the sample is in emulsion form.
State if the sample is in solution form.
State if the sample is in suspension form.
broad band decoupling
off resonance decoupling
specific decoupling
angle of sinusoid
31P spectrum reference compound
phosphoric acid
phosphorus
trimethyl phosphate
triphenylphosphine
triphenylphosphine oxide
co-dissolved internal reference
synthetic reference signal
residual solvent signal
FID zero filling
data extrapolation using linear prediction
multiplying FID by window function
FID fourier transformation
The mathematical conversion of time-resolved FID raw data into frequency resolved NMR spectra (frequency-resolved NMR data) by means of fourier transformation of coordinate systems.
phase correction
peak integration
peak alignment
peak shape fitting
spectral referencing
Pohl, L.; Eckle, M. (1969). "Sodium 3-(trimethylsilyl)tetradeuteriopropionate, a new water-soluble standard for 1H.N.M.R.". Angewandte Chemie, International Edition in English 8 (5): 381. doi:10.1002/anie.196903811
sodium trimethylsilyl-propionate
linear scaling
scaling
non-linear scaling
total spectral area scaling
Dieterle F, Ross A, Schlotterbeck G, Senn H: Probabilistic quotient normalization as robust method to account for dilution of complex biological mixtures. Application in 1H NMR metabonomics. Anal Chem 2006, 78(13):4281-90.
probabilistic quotient normalization
scaling by generalized logarithmic transformation
pareto scaling
autoscaling
2D J-resolved spectrum
MetaboLab software
Metaboquant software
rNMR software
open source NMR software
commercial NMR software
Günther U, Ludwig C, Rüterjans H: NMRLAB - advanced NMR data processing in Matlab., J Magn Reson 2000, 145(2):201-208.
NMRLab software
Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A: NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 1995, 6(3):277-293.
NMRPipe software
van Beek JD: matNMR: a flexible toolbox for processing, analyzing and visualizing magnetic resonance data in Matlab. J Magn Reson 2007, 187:19-26.
matNMR software
concentration of chemical compound
manual phase correction
automatic phase correction
DC offset correction
Gibbs multiplication
skyline projection
shifted sine window function
sinc window multiplication of FID (1D)
combined sine-bell–exponential window function
SEM window function
Functional form ( 0:t1 linear increase from 0.0 to 1.0, t1:size-t2 1.0 -t2: linear decrease from 1.0 to 0.0 / Parameters ( * data Array of spectral data., * t1 Left ramp length., * t2 Right ramp length., * inv Set True for inverse apodization.
trapezoid window function
shifted gaussian window function
baseline correction using spline function
heteronuclear single quantum coherence spectrum
Zangger-Sterk pulse sequence
pure shift 1D Zangger-Sterk pulse sequence
oneshot pulse sequence
pure shift oneshot pulse sequence
perfect echo watergate pulse sequence
NMR Star 3.1 file format
NMR Star 2.1 file format
3D spectrum
4D spectrum
NMR spectrum by dimensionality
homonuclear chemical shift spectrum
heteronuclear chemical shift spectrum
homonuclear exchange spectroscopy spectrum
heteronuclear exchange spectroscopy spectrum
homonuclear J-resolved spectrum
heteronuclear J-resolved spectrum
calibration test spectrum
NMR star software
Felix software
PIPP software
TALOS+ software
CYANA software
XPLOR-NIH software
computed concentration
XEASY software
sparky software
CARA software
Wattos software
MADNMR software
Pronto software
TRIAD NMR software
library based computed concentration
Lorenzian (-Integration) (Modeled Area) Estimated Concentration
Lorenzian estimated concentration
Measured Area (Integration) based Concentration
measured area based concentration
time-domain amplitude computed concentration
group time delay compensation
This is independent of the bruker acquisition parameter named "GRPDLY" (Group Delay), but this is a "shift" applied on the fid to calibrate its zero
scaling by forward linear prediction
back calculation of first points by linear-prediction
scaling by mirror image linear prediction
digital filtering
3D strip plot generation
A spectrum vizualization method for 3D nmr spectra, assisting assignments for large sequential molecules, i.e. Proteins. The first two axis in the plot represent the ppms along the two acquisition nuclei, and a third dimension captures the sequential molecule order for the third nucleus.
Batman software
JEOL instrument model
tecmag instrument model
Bao et al. (2013) A new automatic baseline correction method based on iterative method, J. Magn. Res. 218:35-43
Golotvin & Williams (2000), Improved baseline recognition and modeling of FT NMR spectra, J. Magn. Res. 146:122-125
automatic baseline recognition
Trimethylsilyl propionate
TMIC lab pulse sequence
probe gradient strength
NMR acquisition computer operating system
NMR autosampler software
Bruker Biospin ICON-NMR software
buffer pH
field frequency lock
concentration standard
NMR acquisition software
CIMR MI standard
signal line width check
signal line width at five percent intensity check
NMR spectrum descriptor
pulse width
hard pulse width
sweep width
number of data points
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
y-axis type
center of bin on x-axis
spectral quantitation algorithm
The NMRProcFlow open source software provides a complete set of tools for processing (e.g. Bucketing) and visualization of 1D NMR data, the whole within an interactive interface based on a spectra visualization.
NMRProcFlow software
Bayesil is a web system that automatically identifies and quantifies metabolites using 1D 1H NMR spectra of ultra-filtered plasma, serum or cerebrospinal fluid. The NMR spectra must be collected in a standardized fashion for Bayesil to perform optimally. Bayesil first performs all spectral processing steps, including Fourier transformation, phasing, solvent filtering, chemical shift referencing, baseline correction and reference line shape convolution automatically. It then deconvolutes the resulting NMR spectrum using a reference spectral library, which here contains the signatures of more than 60 metabolites. This deconvolution process determines both the identity and quantity of the compounds in the biofluid mixture.
Ravanbakhsh S, Liu P, Bjorndahl TC, Mandal R, Grant JR, Wilson M, Eisner R, Sinelnikov I, Hu X, Luchinat C, Greiner R, Wishart DS. (2015) Accurate, Fully-Automated NMR Spectral Profiling for Metabolomics. PLoS ONE 10(5): e0124219.
Bayesil software
nmrML-Assign is a web server for creating an nmrML file from a FID and a structure. The FID is first automatically processed with Bayesil. The resulting interactive spectrum allows assigning peaks to specific atoms in the structure and the assignments are saved in the nmrML format. For more information about nmrML please visit nmrML.org. nmrML-Assign works with 1H and 13C NMR spectra in Bruker or Agilent/Varian format.
Uses JspectraView Software
nmrML Assign
doublet feature
triplet feature
quatruplet feature
a set of peaks that are highly correlated in a series of samples
a feature request by Daniel Jacob inserted at IBP hackathon
cluster of peaks across samples
simulated spectrum
pulse parameter
JEOL FID format
doublet of doublets feature
ABX multiplet pattern
AMX, ABX and ABC patterns, and various related spin systems are very common in Proton NMR of organic molecules.When two of the protons of an AMX pattern approach each other to form an ABX pattern, the characteristic changes in intensities of a strongly coupled system (leaning) are seen, and, as the size of J approaches the value of νAB more complicated changes arise, so that the pattern can no longer be analyzed correctly by first order methods.
singlet feature
quintet feature
doublet of triplets
triplet of douplets
triplet of triplets
NMR spectrum by pulse sequence
NMR spectrum by processing step
2D spectrum coordinate system descriptor
y-axis value type
the subclasses come from the Rubtsov specification
power value type
magnitude value type
real value type
imaginary value type
complex value types
spectral projection axis
f1 axis
f2 axis
NMR Format converter
BML-NMR identifier
will be further specified via a concentration value
creatinine
2D pulse sequence
used to be labeled 'NMR spectrum simulation'
data simulation
dynamic nuclear polarization enhanced NMR system
dynamic nuclear polarization NMR
Chemical shift is the resonance frequency of a nucleus related to a chemical shift standard. in ppm along x-axis
chemical shift
an information object that describes the strength of the NMR signal
nmr signal intensity
baseline correction using polynomial function
first transient of the tnnoesy-presaturation pulse sequence
Varian acquisition parameter file
procpar
acqus
Bruker acquisition parameter file
global
Varian autosampler
Varian SMS 50
Varian probe
5mm HCN probe
Varian liquid cold probe
reference compound NMR spectrum
Mestrelab software
ACD spectrus software
Mat NMR 3 software
Spinworks NMR software
NMR software vendor
Spinworks
iNMR software
NMR pipe
cule NMR software
Git: nmrML\tools\Parser_and_Converters\Matlab
By Batman/ Tim Ebbels Group
Matlab to nmrML converter
Bruker processing parameter file
procs
Varian processing parameter file
PRS: rename 'identifyer' to 'identifier'
Madison Metabolomics Consortium Database MMCD identifier
Bigg metabolomics database identifier
Functional form: gm(x_i) = exp(e - g*g) Where: e = pi*i*g1 g = 0.6*pi*g2*(g3*(size-1)-i) Parameters: * data Array of spectral data. * g1 Inverse exponential width. * g2 Gaussian broaden width. * g3 Location of gauss maximum. * inv Set True for inverse apodization.
Lorentz Gaussian window function
traf window function
A Window function described by Daniel Traficante in their original paper.
trafs window function
peak fitting
peak assignment
deconvolution
A method of sorting multiple spectra by position of chemical shift peaks. This method is used in Batman and improves the fit for shifted/overlapped peaks.
chemical shift sorting
fid file
Varian FID file
Bruker FID file
Jacob D. et al (2013) Analytical and Bioanalytical Chemistry, 405, 5049-5061
ERVA-based bucketing
Taking advantage of the concentration variability of each compound in a series of samples, buckets are linked together into clusters based on significant correlations.This is done i.g. in ERVA-based bucketing
cluster of peaks
Match NMR tube
shaped tube
Shigemi tube
standard tube
Bruker tube
JEOL magnet
JEOL ECS magnet
JEOL ECA magnet
JEOL ECX magnet
Varian NMR software
VnmrJ software
Wilmad tube
4mm Match tube
2.5mm Match tube
3mm Match tube
5mm Match tube
1mm Match tube
1.7mm Match tube
2mm Match tube
4.25mm Match tube
3mm standard tube
5mm standard tube
1mm standard tube
1.7mm standard tube
Wilmad economy tube
Wilmad precision tube
Norell tube
JEOL FID file
Git: nmrML\tools\Parser_and_Converters\R
R statistics to nmrML. Developed by Steffen Neumann, IPB-Halle.de
nmRIO
Git: nmrML\tools\Parser_and_Converters\R\rNMR-IO
rNMR-IO
Based on both nmrML.xsd (XML Schema Definition) and CV params (such as ontologies nmrCV, UO, CHEBI ...), a converter written in Java was developed that automatically generates nmrML files, from raw files of the major NMR vendors. The choice of Java was guided by i) the JAXB framework (Java Architecture for XML Binding), ii) its OS-platform independence and iii) strengthened by the existence of a useful java library (i.e [nmr-fid-tool](https://github.com/LuisFF/nmr-fid-tool)) for further processing and visualisation of the resulting nmrML data. As nmrML intents to gather and integrate several types of data and corresponding metadata in a single file, it is necessary to process each data source separately. Thus, two command tools were developed. The first one, nmrMLcreate allows to create a new nmrML file, based on available Bruker or Varian/Agilent raw files. The second one, nmrMLproc allows to add and fill in additional sections corresponding to the data processing step.
Git: nmrML\tools\Parser_and_Converters\Java\converter
Developed by Daniel Jacob at INRA Bordeaux. The recommended converter for Bruker and Varian/Agilent vendor format conversion.
Vendor2nmrML_Java
Varian magnet
premium compact narrow bore magnet
premium shielded narrow bore magnet
premium shielded wide bore magnet
Functional form: gmb(x_i) = exp(-a*i - b*i*i) Parameters: * data Array of spectral data. * a Exponential term. * b Gaussian term. * inv Set True for inverse apodization.
modified Gaussian window function
exponentially damped J-modulation apodization
Functional form: jmod(x_i) = exp(-e)*sin( pi*off + pi*(end-off)*i/(size-1)) Parameters: * data Array of spectral data. * e Exponential term. * off Start of modulation in fraction of pi radians. * end End of modulation in fraction of pi radians. * inv Set True for inverse apodization
exponentially damped J-modulation window function
Functional form: sp(x_i) = sin( (pi*off + pi*(end-off)*i/(size-1) )**pow Parameters: * data Array of spectral data. * start Start of Sine-Bell as percent of vector (0.0 -> 1.0) * end End of Sine-Bell as percent of vector (0.0 -> 1.0 ) * pow Power of Sine-Bell * inv Set True for inverse apodization.
shifted sine bell window function
Functional form: 0:loc linear increase/decrease from lHi to 1.0 loc: linear increase/decrease from 1.0 to rHi Parameters: * data Array of spectral data. * loc Location of apex, "auto" sets to middle. * lHi Left side starting height. * rHi Right side starting height. * inv Set True for inverse apodization.
triangle window function
The acquisition log file is a created during an acquisition and could useful for debugging an acquisition that has gone awry.
acquisition log file
Git: nmrML\tools\Parser_and_Converters\python
A Python based vendor to nmrML converter developed by MIchael Wilson at TMIC Edmonton.
PynmrML
A web server designed to permit comprehensive metabolomic data analysis, visualization and interpretation. It supports a wide range of complex statistical calculations and high quality graphical rendering functions that require significant computational resources.
Jianguo Xia, Igor V. Sinelnikov, Beomsoo Han and David S. Wishart, MetaboAnalyst 3.0—making metabolomics more meaningful, Nucl. Acids Res. (1 July 2015) 43 (W1): W251-W257. doi: 10.1093/nar/gkv380
MetaboAnalyst software
acqu2s
acqu3s
proc2s
proc3s
NMR spectrum file
Bruker NMR spectrum file
1R file
title file
A new program package, XEASY, was written for interactive computer support of the analysis of NMR spectra for three-dimensional structure determination of biological macromolecules. XEASY was developed for work with 2D, 3D and 4D NMR data sets. It includes all the functions performed by the precursor program EASY, which was designed for the analysis of 2D NMR spectra, i.e., peak picking and support of sequence-specific resonance assignments, cross-peak assignments, cross-peak integration and rate constant determination for dynamic processes.
Christian Bartels, Tai-he Xia, Martin Billeter, Peter Güntert, Kurt Wüthrich, The program XEASY for computer-supported NMR spectral analysis of biological macromolecules, J Biomol NMR (1995) 6: 1. doi:10.1007/BF00417486
NMR spectrum vizualisation software
Used in NMR Assign tool for Baysil
JspectraView software
cryoprobe
inverse detection NMR probe
5mm inverse detection cryoprobe
Git: nmrML\tools\Visualizers\PMB_NMRviewer
Developed by Daniel Jacob, INRA Bordeaux
NMRViewer software
material processing
AB multiplet pattern
NMR solvent
NMR buffer
presat water suppression
Varian VNMRS 600
data content encoding
data compression scheme
byte format
zlib
complex64
This byte format uses a consecutive array of two 32bit float numbers to represent the real and imaginary part of the complex values.
complex128
This byte format uses a consecutive array of two 64bit double precision values to represent the real and imaginary part of the complex values.
binary data compression type
AB2 multiplet pattern
data encoding parameter
uncompressed data
DSPFVS - DSP (Digital signal processing) firmware version corresponds to the version of the digital filter, a hardware component used by the spectrometer
digital signal processing firmware version
DECIM - decimation factor is a (bruker) acquisition parameter that captures the number of raw analog points that are averaged in order to obtain a digital signal recorded in the fid.
decimation factor
GRPDLY - is the time delay (in number of points?) between acquiring the analog signal and producing the digital signal (i.e. "The group delay is the time necessary for the digital filter function to “walk into” the raw FID and start generating significant intensity.")
group time delay
NMR sampling strategy
a type of data acquisition parameter (when recording the FID) which can be continuous/uniform or sparse/non-uniform signal acquisition.
uniform sampling
With uniform sampling, each sample is separated by the "dwell time".
With uniform sampling we don't need to record the time points because we know the dwell time. We may add named strategies to the CV over time that are more specific than non-uniform
non-uniform sampling
with non-uniform, some samples are skipped, there are different strategies for which to skip, but we can simply record the time point as well as the complex data point in order to represent this type of data.
Non-uniform sampling is something likely to become more important in the future, because it allows you to capture higher dimension spectra much more quickly
Bruker XWIN-NMR software
software attribute
NMR software version
ABX3 multiplet pattern
AA'BB' multiplet pattern
AA'XX' multiplet pattern
variable size bucketing
uniform bucketing
intelligent bucketing
bucket importing
bucket resetting
global baseline correction
local baseline correction
bucket fusioning
JNM-ECX Series FT NMR instrument
JNM-ECZR Series FT NMR instrument
JNM-ECZR series is a new system that fully incorporates the latest digital and high frequency technologies. Improved reliability and a more compact size make possible by incorporating more advanced integrated circuits, it supports even greater expandability options than current models for multi-channel operation, high power amplifiers and other accessories. The bus line for control of attachments has been upgraded to high speed and enables highly accurate and rapid control. 400 MHz - 1 GHz
JNM-ECZS Series FT NMR instrument
The entry model ECZS spectrometer has the same basic functions, performance and capability of high-end model. The main console is amazingly small, less than 1/2 that of the current ECS series spectrometer. Coupling the use of advanced software with highly reliable automation, all routine daily measurements can be automated, while the use of the autotune Supercool probe realizes the world’s highest sensitivity in its class. Whatever your application field ECZS can demonstrate its power. 400 MHz
AVANCE III HD
NanoBay400 MHz
Fourier 300HD
DNP-NMR
LC-NMR instrument
LC-NMR/MS instrument
Food-Screener instrument
AVANCE IVDr
JEOL Resonance 400MHz YH magnet
JEOL Resonance 500MHz magnet
JEOL Resonance 600MHz magnet
JEOL Resonance 700MHz magnet
JEOL Resonance 800MHz magnet
single peak feature
NMR instrument vendor
Any organisation ort person that sells NMR instruments to customers.
Avance I spectrometer
Oxford Instruments
Spinlock SRL
General Electric
Kimble Chase
Phillips
Siemens AG
Varian Inova 500
Varian VNMRS instrument
Varian Mercury plus
Varian UnityInova instrument
Varian 400-MR NMR instrument
Varian DDR2 instrument
Agilent NMR instrument
Agilent 400-MR NMR instrument
Varian Mercury 400
Agilent Au 400 (DDR2 Console)
Agilent DDR 2 w/ HCN cryoprobe
BMRB identifier
left trapezoid limit
trapezoid window function parameter
complex64 Integer
This byte format uses a consecutive array of two 32bit integer numbers to represent the real and imaginary part of the complex values (2x32bits=>2x4bytes=> 2 integers) for the FID datatype.
complex128 Integer
This byte format uses a consecutive array of two 64bit long integer numbers to represent the real and imaginary part of the complex values (2x64bits => 2x8bytes => 2 longs) for the FID datatype.
right trapezoid limit
thirty degree pulse duration
The duration of the excitation pulse needed to rotate the magnetisation vector by 30 degrees.
InChi
inchikey
Wiswesser Line Notation
ROSDAL
SLN-Tripos
smarts
line representation
2D topological molecule representation
2D bond line structure
3D geometrical molecule representation
3D bond line structure
CAS number
fingerprint model
molfile
compound similarity measure
Tanimoto similarity
Gaussian window function parameter
Gaussian maximum position
2H spectrum reference compound
ABX2 multiplet pattern
DRX 600 instrument
plot and graph generation
reference deconvolution
vertical alignment of on and offset of the peak of the reference compound.
spectral smoothing
the process of removing noisy jitters in a spectral curve to get clearer and more meaningful signals and peaks.
NMR database format
M. Yokochi, N. Kobayashi, E. L. Ulrich, A. R. Kinjo, T. Iwata, Y. E. Ioannidis, M. Livny, J. L. Markley, H. Nakamura, C. Kojima, T. Fujiwara, “Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins,” Journal of Biomedical Semantics, 5:7:16 (2016)
BMRB/XML file format
nD spectrum
Terms used to describe types of data processing.
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
Description of the instrument or the mass spectrometer.
Instrument properties that are associated with a value.
Conversion of one file format to another.
Software related to the recording or transformation of spectra.
Sample properties that are associated with a value.
Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data.
MD5 (Message-Digest algorithm 5) is a cryptographic hash function with a 128-bit hash value used to check the integrity of files.
SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity.
Describes the type of file and its content.
Details about a person or organization to contact in case of concern or discussion about the file.
Name of the contact person or organization.
Postal address of the contact person or organization.
Uniform Resource Locator related to the contact person or organization.
Email address of the contact person or organization.
Data processing parameter used in the data processing performed on the data file.
The time that a data processing action was finished.
Describes how the native spectrum identifiers are formated.
The nativeID must be the same as the source file ID.
A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the MSI-NMR working group in order to have another CV term added.
Description of the preparation steps which took place before the measurement was performed.
A molecules is a fundamental component of a chemical compound that is the smallest part of the compound that can participate in a chemical reaction.
A compound of low molecular weight that is composed of two or more amino acids.
A describable property of a chemical compound.
The pH of a solution at which a charged molecule does not migrate in an electric field.
The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm.
A combination of symbols used to express the chemical composition of a compound.
A chemical formula which expresses the proportions of the elements present in a substance.
A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked.
A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other.
The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string.
An identifier/accession number to an external reference database.
A unique identifier for a publication in the PubMed database (MIR:00000015).
A substance formed by chemical union of two or more elements or ingredients in definite proportion by weight.
A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA coding for the protein.
A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN).
An nonphysical attribute describing a specific protein.
Accession number for a specific protein in a database.
A long name describing the function of the protein.
An nonphysical attribute that can be used to describe a peptide.
A sequence of letter symbols denoting the order of amino acids that compose the peptide, without encoding any amino acid mass modifications that might be present.
A sequence of letter symbols denoting the order of amino acids that compose the peptide plus the encoding any amino acid mass modifications that are present using the notation where the total mass of the modified amino acid is specified in square bracketed numbers following the letter (e.g. R[162.10111] indicates an arginine whose final modified mass is 162.10111 amu).
A state description of how a peptide might be isotopically or isobarically labelled.
A peptide that has been created or labeled with some heavier-than-usual isotopes.
A peptide that has not been labeled with heavier-than-usual isotopes. This is often referred to as "light" to distinguish from "heavy".
An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label.
Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence.
A practice or product that has become a standard not because it has been approved by a standards organization but because it is widely used and recognized by the industry as being standard.
A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result.
A file that has two or more columns of tabular data where each column is separated by a TAB character.
Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation.
Name of the gene from which the protein is translated.
Type of the source file, the nmrIdentML was created from.
Source file for this nmrIdentML was a data set in a database.
retire? Consider: "NMR database format" ?
Phone number of the contact person or organization.
Fax number for the contact person or organization.
Toll-free phone number of the contact person or organization.
Free text attribute that can enrich the information about an entity.
Keyword present in a scientific publication.
Parameters used in the NMR spectrometry acquisition.
A unique identifier for a metabolite in the HMDB database (HMDB00001).
Chenomx software for data acquisition and analysis.
The format of the file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format.
Parameter file used to configure the acquisition of raw data on the instrument.
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'. def: A NMR spectrum is a set of chemical shifts representing a chemical analysis. synonym: NMR spectrum
as designated Experiment type on http://www.bmrb.wisc.edu/tools/choose_pulse_info.php
Conversion of a file format to Metabolomics Standards Initiative nmrData file format.
Conversion of a file format to JCAMP-DX file format.
Chemical shift reference is a run attribute to designate the parts-per-million value of the peak used to reference a spectrum. It points to a fix chemical shift number, for examples 0 ppm for DSS or TSP. It can also have a calculated concentration, for examples 0.1 mM.
assigned chemical compound concentration
Hilbert transformation based scaling
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...
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.
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
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.
TODO: has spectral post processing parameter
TODO: has spectral post processing parameter.
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
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.
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.
def: A component of an NMR instrument that controls the activities of the other components.
TODO: same as or part of acquisition computer?
tempdef: The number of data points in a data set.
def: A frequency used during Hadamard encoding.
def: The axis onto which the spectrum was projected.
The duration of the excitation pulse needed to rotate the magnetisation vector by 90 degrees.
def: A digital sampling interval. alsprcls: time interval
def: The temperature of an item of analysis material whilst in an autosampler.
def: The temperature of an NMR sample whilst in the magnet of an NMR instrument.
def: The frequency of the RF radiation used to irradiate an NMR sample.
def: The intensity of an electric, magnetic, or other field.
def: The rate at which an item of analysis material is spun.
def: An indication of whether the nucleus being studied is the acquitsition nucleus.
def: A compound added to a sample to alter its pH value.
def: The compound that produced the peak used to reference a spectrum during data pre-processing.
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.
def: The compound that produced a peak that is measured to assess the quality of a data set.
May later import from http://purl.obolibrary.org/obo/CHMO_0001841
See also http://www.jcamp-dx.org/protocols/NMR%20Pulse%20Sequences%20PAC%2079(11)%20pp1748-1764%202001.pdf
def: Automatic or manual procedures performed upon pre-processed NMR data sets that aim to summarise them or annotate them with speculative values.
frequency domain data processing
def: The post acquisition process of producing or refining a spectrum from raw data. defprov: Daniel Schober
time domain data processing
def: A data transformation that converts an NMR input data set into an output data set in a tracable and useful manner.
tempdef: A non FT based method for converting from the time to the frequency domain.
tempdef: A data processing which alteres a data file for a specific purpose. defprov: Daniel Schober
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
def: A method for quadrature detection. synonym: S-TPPI
states-time proportional phase incrementation
def: An Instrument which is used to carry out a NMR analysis of some sample. synonym: NMR instrument
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
NMR instrument acquisition parameter set
data transformation
http://pubs.acs.org/doi/pdf/10.1021/ac0519312 10.1021/ac0519312 Scaling and Normalization Effects in NMR Spectroscopic Metabonomic Data Sets Andrew Craig , Olivier Cloarec , Elaine Holmes , Jeremy K. Nicholson , and John C. Lindon * Biological Chemistry, Faculty of Natural Sciences, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ U.K.
normalization is a data transformation process which aims at making data seem roughly normally distributied by applying a mathematical function, which is most of time a continuous function. This is a row operation that is applied to the data from each sample and comprises methods to make the data from all samples directly comparable with each other. A common use is to remove or minimize the effects of variable dilution of the samples.
tempdef: A technique used to suppress the water resonance 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
A function applied to a FID to increase the signal-to-noise ratio or the resolution.
The exponential function used to multiply a FID by to produce a desitred amount of line broadening.
Functional form: em(x_i) = exp(-pi*i*lb) Parameters: * data Array of spectral data. * lp Exponential line broadening. * inv Set True for inverse apodization.
exponential multiplication window function
def: A method for eliminating or reducing the noise in a spectrum.
def: A method of flattening the baseline of a spectrum.
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.
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.
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.
def: A feature of a peak that is measured to assess the quality of a data set.
def: The number of repeat scans performed and summed to create the data set for an NMR sample.
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.
def: A scheme for producing a numerical representation of the environment of an atom.
def: The delay between repeat scans to allow nuclei to relax back to their steady state.
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).
def: The unit of measurement of the second dimension of a 2D NMR dataset.
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.
http://www.chem.wisc.edu/areas/reich/nmr/08-tech-01-relax.htm. Hans J. Reich 2015, University of Wisconsin
line broadening is a process resulting in spectral peak signal becoming hard to interpret and analysed. Line broadening is affected by spin-spin relaxation and/or spin-lattice relaxation processes. When relaxation is very fast, NMR lines are broad, J-coupling may not be resolved or the signal may even be difficult or impossible to detect. The maximum repetition rate during acquisition of an NMR signal is governed by T1 - short T1 means the magnetization recovers more rapidly, and a spectrum can be acquired in less time. Line broadening may be caused by: Sample inhomogeneity (poor mixing. solid particles), Temperature gradients across sample, Paramagnetic impurities.
line sharpening is a data transformation process inverse to that of line broadening, which aims to improve the quality of the signal being acquired and being analyzed in order to obtain clear, sharp peaks, in turn making interpretation easier. Line sharpening can be optimized during data acquisition or performed during data analysis by applied digital processing and filtering.
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
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
TODO: altsprcls: process, not clear wether set is plural (list) or process.
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
tempdef: A data processing technique used to suppress the water peak in a spectrum in order to get clearer results. defprov: Daniel Schober
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
def: A computational method that archieves water suppression via wavlet multi resolution analysis.
defneed synonym: NMR data pre-processing parameter set
def: The process of ensuring the quality of the raw data that results from an NMR analysis. synonym: NMR quality check
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.
def: A reference to a file containing the raw FID. synonym: FID file reference
def: A reference to a description of a pulse sequence in the literature.
def: A reference to a file containing a specfication of the shape of an excitation pulse.
def: A reference to a file containing a specification of a pulse sequence.
def: A reference to a file of data pre-processing parameters produced by the machine.
def: A reference to information on the provenance of the NMR sample. synonym: NMR sample reference
def: A result of an NMR quality check. synonym: NMR quality check result
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
tempdef: A sample introduction parameter is a parameter that describes the particular method of introducing the sample under investigation into the NMR instrument.
The sample-tube holds the NMR sample and sits in the NMR probe. It is usually a glass tube of 5-20mm diameter.
sortal dimensions are Vendor, Size (Diameter, length), Material (glass, quarz, pyrex ...), Frequency, Concentricity, OD and ID
def: A software artifact used during data pre-processing.
def: A software artifact used during spectral post-processing.
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.
for bucket parameters see 'binned spectrum descriptor'
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
WET
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
nuclear overhauser and exchange spectroscopy-presat
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 jump and return pulse sequence method is a water suppression method that uses a defined pulse sequence to make fast exchanging protons visible.
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.
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).
defneed synonym: 1D NMR acquisition parameter set
defneed synonym: 2D NMR acquisition parameter set
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
carr purcell meiboom gill pulse sequence
CPMG
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 pulse sequence
total correlation spectroscopy pulse sequence
def: One dimensional (referring to a FID, pre-processed spectrum, or post-processed spectrum). synonym: 1D
tempdef: In 1D 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
hadamard total correlation spectroscopy pulse sequence
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.
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
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
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
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
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
For metabolism studies, and analysis of complex mixtures.
NMR Instruments using hyphenated analytical techniques combining mass spectrometry and chromatograph.
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
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
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
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
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
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
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
def: A NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the NMR sample.
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
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
The JNM-ECX series is an FT NMR spectrometer developed making full use of the latest digital and high frequency technology. This high performance, sophisticated spectrometer designed to take advantage of high field magnet development to include 1GHz. Innovative features to support not only the conventional NMR applications such as structural analysis of molecules and evaluation of materials but also future progress of science and technologies including research for development of new drugs, postgenome research and development of new materials.
The JNM-ECA series is an FT NMR spectrometer developed making full use of the latest digital and high frequency technology. This high performance, sophisticated spectrometer designed to take advantage of high field magnet development to include 1GHz. Innovative features to support not only the conventional NMR applications such as structural analysis of molecules and evaluation of materials but also future progress of science and technologies including research for development of new drugs, postgenome research and development of new materials.
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
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
A manufacturer that produces (and eventually sells) NMR instruments.
TODO: May not need definition due to its instance character.
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.
Any data file as generated by some acquisition computer or console.
This is a class annotation exemplifying skos usage. We assume the rdfs:label to capture the skos:preferedLabel.
In the NMR case a file generated by an NMR acquisition computer, console or NMR processing software.
Includes the connection to a high-resolution TOF-LC-MS system.
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.
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.
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
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