ChemSpectra

info

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 (described here) and NMRium as data viewer.

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). An in-depth description of ChemSpectra was published here.

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:

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.

Using ChemSpectra

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

2. Scroll down and select the + button to add a new dataset:

3. Click to upload your files or drop down your files:

4. Click the close button to close the popup view and click Save to save your files:

5. After your files were processed, click on the Spectra Editor button to open the analyses viewer: