1d Nmr Processor

Posted on by

Nuclear Magnetic Resonance Data Processing and Analysis with Spectrus Processor

  • Import 1D NMR data (1H, 13C, DEPT, etc.) and 2D NMR data (COSY, TOCSY, HMQC/HSQC/HMBC, NOESY, HETCOR etc.) from Bruker, Agilent/Varian, JEOL, and more
  • Perform manual and/or automatic data processing: Fourier transformation, calibration, peak picking, integration, multiplet analysis etc.
  • Assistance with spectral analysis and interpretation:
    • Attach chemical structures to a spectrum for real-time visual feedback on peak/atom assignments
    • Easily evaluate spectrum/structure consistency using quantitative NMR Match Factor values
    • Search commercial spectral libraries or use the Known Structure Add-on for fast and efficient compound identification
  • Conveniently generate formatted multiplet reports on the fly

On the Edit menu of ACD/1D NMR Processor, point to Export to PDF, and then choose Standard. On the Edit menu of ACD/1D NMR Processor, point to Create Report, and then choose Standard. On the Edit menu of ACD/ChemSketch, point to Export to PDF, and then choose Standard. Practice Task Create a PDF report. It is designed for the processing, the display and the analysis of 1D, 2D & 3D NMR data-sets.' M.A.Delsuc, CBS, France. NMR Desk - 1D and 2D data processing and simulation (MS Windows). CROSREL - 'a program for the analysis of ROESY and NOESY NMR data' - Bas R. Leeflang, Utrecht, The Netherlands. 1D 1 H NMR is a common technique applied to metabolomic studies, being well suited to untargeted analysis of complex biofluids. It has been successfully applied to the classification and diagnosis of a number of diseases including ref.

Add NMR Predictors to your installation to compare the experimental and predicted spectrum for a given structure, and more. Read more about NMR Predictors.

Mass Spectrometry Data Processing and Analysis with Spectrus Processor

  • Import LC/MS, LC/UV/MS and GC/MS data from AB SCIEX, Agilent, Bruker, LECO, PerkinElmer, Shimadzu, Thermo, Waters, and more
  • Perform manual and/or automatic data processing: peak detection, generate extracted ion chromatograms (XICs), total ion chromatograms (TICs), and total absorbance chromatograms (TACs)
  • Assistance with spectral analysis and interpretation:
    • Automatic extraction of relevant chromatogram from structure/formula/mass
    • Automatic confirmation of mass/molecular formula
    • Attach chemical structures to chromatographic peaks to evaluate consistency through color-coded 'MS Match'
    • Screen peaks/total spectra against spectral libraries to accelerate compound identification
  • Comprehensive one-click reports, including annotated chromatograms and spectra

Chromatography Data Processing and Analysis with Spectrus Processor

  • Import chromatographic data from Agilent, AB Sciex, Bruker, Shimadzu, Thermo Scientific, Perkin Elmer, Waters, and more
  • Perform manual/automatic data processing: peak detection, smoothing, baseline correction, and integration
  • Conveniently visualize chromatograms in a series
  • Conveniently visualize chromatograms in a series:
    • Automatically calculate peak areas
    • Assign chemical structures to chromatographic peaks
    • Search the available Applications Database (1444 HPLC/UHPLC applications, and 275 GC applications with structure assignments)
  • Create reports with structure assignments, method parameters, peak tables, annotations, and chromatograms

Optical Data Processing and Analysis with Spectrus Processor

  • Process and interpret data from a variety of optical techniques including:
    • Infra-red spectroscopy (IR, NIR, FIR, MIR UV-Vis)
    • Absorption
    • Raman
    • Reflectance
    • Fluorescence
    • Phosphorescence
    • Circular dichroism (CD)
    • Spectroscopic ellipsometry
  • Import data from Bruker, JASCO, Perkin Elmer, Shimadzu, Thermo Scientific (Nicolet, Galactic), and more
  • Perform manual/automatic data processing on single and multiple spectra: baseline correction, peak picking, smoothing
  • Conveniently visualize spectral series
  • Assistance with spectral analysis and interpretation
    • Attach chemical structures to spectra and assign peaks to structural fragments
    • Verify chemical structures using the knowlegebase of spectra-structure correlations or available content databases
      • IR Assigned Polymers
      • Raman Assigned Amino Acids
  • One-click reports display key elements of your analysis

Acd 1d Nmr Processor Download

Processing and Analysis for additional techniques with Spectrus Processor

  • Handle a wide range of analytical data, including:
    • EELS (Electron Energy Loss Spectra)
    • Thermal analysis (DSC, DTA, TGA)
    • DMA
    • Calorimetry
    • Titrimetric methods
    • Voltametric methods
    • X-ray methods (powder diffraction, fluorescence, and photoelectron)
    • ESR spectroscopy
    • Kinetics
  • Perform various X- and Y-axis conversions and data manipulation manually or automatically
  • Attach chemical structures to curves
  • Conveniently visualize and compare series of related spectra
  • Perform spectral based database searches
  • Report your analysis with a single click
Handle a wide array of x,y data including thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC)

1D 1H NMR is a common technique applied to metabolomic studies, being well suitedto untargeted analysis of complex biofluids. It has been successfully applied tothe classification and diagnosis of a number of diseases including [ref].

There are a number of important steps that must be applied prior 1D 1H NMR datato statistical analysis, all gearded towards ensuring that the variation observedin the data is representative of real biological variation and not a artifact ofsample handling, metabolite extraction or NMR acquisition. These steps aredescribed briefly below and approached in turn in the following method. It isimportant to familiarise yourself with both the purpose of these steps, andany associated caveats or limits, so that you can correctly apply them to yourown data.

Setting up

To process raw NMR data we will be making use of of the nmrglue library. Inaddition we will make use of features from the numpy, scipy and matplotliblibraries, which you should already have installed.To make sure you can run the following command on the terminal:

The demo data for this example is available for download.

Download and unzip the file into your data folder.

Loading Bruker FID spectra

Create a new Jupyter notebook using the Python 3 kernel, and in the first cellenter and run the following. This will import all the neccessary libraries, aswell as using the %matplotlib magic to display output figures in the notebook.

Bruker-format data is processed using a digital filter before saving as FID, thisfilter must be removed for subsequent analysis to work. To open a given spectra,pass the parent folder of the fid file.

We can plot the spectra using matplotlib.

  1. We don't have the x-axis ppm scale yet, so we generate a linear scale of the same size as the data. Here .shape[0] is the length of the fid along the first (and only) axis of the 1D spectra.

Fourier transform (FT)

A fourier transform is a signal transformation that decomposes a signalinto it's constituent frequencies. In the case of NMR data, this decompositionis to a series of peaks, that represent the resonance of chemical subgroups. Thesepeaks contain both our identification (frequency) and quantification (amplitude)information.

The nmrglue package provides a fast fourier transform (FFT) for this purpose

You'll notice that the spectra is out of phase, i.e. the peaks are notsymmetrical and well defined. We will fix this shortly, but first lets loada complete set of spectra so we can view them all at once.

Batch loading + FFT for multiple spectra

  1. We build as a list, then transform to an array for speed.
  2. Zero-filling to a power of 2 speeds up FFT.
  3. Reverse the data to match common representation (for convenience only).

The data is output in a 2D array, with samples along the first axis.

We want to be able to plot multiple spectra on the same plot, so we'll writea simple function to do this.

  1. This block allows us to select regions of the spectra to view by filtering on the supplied ppms.

1d Nmr Processor Download Free

We can use this function to look at all spectra following fourier transform:

We can take a close up view of the TMSP peak, which is currently on the lefthand side of the spectra in the region 28000-30000.

Clearly the spectra are all out of phase and poorly aligned. We will fix thephasing problem first, but lets start off by getting the correct ppm values forthe spectra.

Processor

Calculating ppm values

The method for calculating ppm values is rather complicted for Bruker formatfiles. However, the following will give the correct output:

We can now plot the spectra with the correct ppms.

Phase correction

Acd Labs 1d Nmr Processor

The next step is to phase correct all the spectra. The package nmrglue providesa few automated algorithms that do a reasonable job with most normal, good qualityspectra. Thankfully, that's what we have here.