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Overview

The Chemotion ELN supports the upload of many dataset formats. The file size restriction is set by the admin of the Chemotion ELN instance and can be adjusted to your needs. If open file formats are available, spectra viewers can visualize and edit the data set. At the moment, the Chemotion ELN supports ChemSpectra as data viewer.

1. ChemSpectra

This section offers a brief overview over ChemSpectra and its functions. An in-depth description was published here.

ChemSpectra is a web-based software for the visualization and analysis of spectroscopic data and allows the analysis of data attached to a sample or reaction in the Chemotion ELN. The focus of ChemSpectra is on analytical methods used in synthetic organic chemistry, such as infrared spectroscopy, mass spectrometry and NMR spectroscopy (one dimensional 1H and 13C). The tool supports the open file formats JCAMP-DX (jdx) and mz(X)ML. Furthermore, it can support RAW and FID files. The user interface of ChemSpectra is identically for different analytical methods, while the tools are selected to fit the requirements of the different analytical methods. The user interface of ChemSpectra is shown here:

UI-ChemSpectra

The analysis-tools (peak picking, integration, multiplicity, reference) for the spectra can be accessed through the toolbar in the upper left corner of the user interface (red box). ChemSpectra can obtain the frequency and used solvent of the NMR experiment from the uploaded data. Additionally, ChemSpectra will automatically predict the NMR spectra based on the NMRshiftDB (green box) and pick peaks which are above the user defined threshold. The threshold can be defined, and the solvent corrected in the upper right corner (black box). The analysis of the spectra can be submitted to the Chemotion ELN through the blue arrow (blue box) in the upper right corner. After submission, the peak list (green box) is generated automatically and can be further modified by the user.

2. Analysing data in Chemotion ELN

  1. Open your Sample details and select the Analyses tab. Then click on theAdd analysis button to create a new analysis.

    chemspectra create new analysis
  2. Scroll down and select the + button to add a new dataset.

    chemspectra add new analysis dataset
  3. Click to upload your files or drop down your files.

    chemspectra upload analysis dataset
  4. Click the close button to close the popup view and click Save to save your files.

    chemspectra close popup
chemspectra save dataset upload
  1. After your files were processed, click on the Spectra Editor button to open the analyses viewer.chemspectra button open spectra editor
chemspectra frontend

3. Analysing data with NMRium

Besides Chemspectra, you can use NMRium to analyse NMR data.

Note

In Chemotion ELN version 1.5, we only support opening and viewing NMR data. We will support saving your analyzed data in upcoming versions.

You can only open NMRium after defining your Type (Chemical Methods Ontology) is NMR.

nmrium select type

Click on the icon to open your file with NMRium.

open nmrium

1D spectrum

nmrium modal 1D

2D spectrum

nmrium modal 2D