nmrML Example Instances
We here introduce six example nmrML data sets that were selected to show the expressivity of the nmrML format along different application settings such as Example 1: minimal raw data capture,Example 2: processed 1R spectrum inclusion, Example 3: single reference compound capture with complete compound peak annotations using NMR Assign, Example 4: representing a complex biosample spectrum with quantification information added to many identified molecules with Bayesil, Example 5: capturing a dataset that was drawn from the Metabolights repository, and Example 6: an example to illustrate 2D NMR spectrum capture for a HSQC experiment. With these diverse use cases we hope to illustrate the versatileness of the nmrML data standard.
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Example 1: A hop metabolite profiling experiment (Varian/Agilent), raw FID data
This spectrum is from a metabolomic profiling experiment Humulus lupulus L.It shows how a minimal nmrML file as generated by the Vendor to nmrML converter looks like. It just contains the raw data (FID) and no processed data/spectrum. The spectrum was recorded on a Varian VNMRS 600 NMR spectrometer operating at a proton NMR frequency of 599.83 MHz using a 5 mm inverse detection cryoprobe. 1H NMR spectra were recorded with the following parameters: digital resolution 0.367 Hz/point (32 K complex data points); pulse width (pw) = 3 ls (4°C); relaxation delay = 23.7 s; acquisition time = 2.7 s; number of transients = 160. Find more in the paper at http://link.springer.com/article/10.1007%2Fs11306-013-0547-4
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Example 2: Metabolic profiling of the Tomato plant, PhenoTom 2013 (Bruker), including a processed spectrum
This spectrum is from a metabolomic profiling experiment onLycopersicon esculentum. Besides the FID it contains the Bruker 1R spectrum (real part data points) after FT processing. This example illustrates how nmrML can include processed data beyond the raw FID data. We here store a 1R NMR spectrum (as another binary blob) and including its metadata. The FT transformed spectrum is stored in the spectrumList/spectrum1D/spectrumDataArrayelement and its processingParameterSets. The spectrum was recorded at 500.162 MHz on a Bruker Avance III spectrometer using a 5 mm probe flushed with nitrogen gas and an electronic reference for quantification (ERETIC2).
View example | Download nmrML file | Download original Raw Data
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Example 3: An HMDB reference spectrum for a single identified molecule, created with nmrML-Assign
This spectrum is a reference spectrum for a single substance, 2-Ketobutyric acid (HMDB00005). Here, for each atom environment in the molecule, detailed atom assignments have been made for the spectral peaks using nmrML-Assign, which is an interactive tool for creating reference spectra and generating nmrML-formatted files. It is an example that illustrates how identification metadata can be stored along a spectrum in nmrML.
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Example 4: A complex biosample spectrum (Varian) quantified with Bayesil
This biosample spectrum of a compound mixture (analytical metabolomics setting) was processed with Bayesil. The nmrML format of results from Bayesil contains a list of compounds and peak assignments from the quantification process and exemplifies how nmrML can be used to store quantification metadata alongside a complex spectrum.
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Example 5: Human urine sample spectra from the MTBLS1 study
These spectra of human urine samples are part of the MTBLS1 study archived in the MetaboLights database. It serves as an example to illustrate the case of an autoconverted file taken from a database.
View example | Download nmrML files | Download original Raw Data
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Example 6: A example of a 2D nmrML formatted file representing a heteronuclear (HSQC) experiment
nmrML file for a heteronuclear experiment. The data represents the bmse00400-exp06 (HSQC) data set from PDBj-BMRB. The substance under investigation is ethanesulfonate (http://bmrbdep.pdbj.org/bms/bmse000400) (exp06: 2D [1H,13C]-HSQC)
View more examples in the GitHub repository and on the documentation pages.
