Standardization workflow for Mass Spectrometry chemical structures pretreatment.

Performs required structure standardization tasks (related to salts/solvents, tautomers/mesomers, mixtures, inorganics, metals, aromaticity, 2D/3D...) prior to MS related data analysis. Starts from structures in SDF or SMILES format and produces standardized structures in different formats based on the selected parameters.

It also provides the list of failed structures and a summary file with initial and MS-ready smiles as well as InChI and InChIKeys.

All configuration required is available in the input component. The workflow will then adapt and run autonomously.

The workflow can also be executed in batch mode using the command line:
<knime path>\knime.exe -reset -nosplash -nosave -application org.knime.product.KNIME_BATCH_APPLICATION -workflowDir="knime-workspace/QSAR-ready_2.5.8" -workflow.varaiable=cmd_input,"<input path>\inputfile",String

Reference:
McEachran, A.D., Mansouri, K., Grulke, C. et al. “MS-Ready” structures for non-targeted high-resolution mass spectrometry screening studies. J Cheminform 10, 45 (2018). https://doi.org/10.1186/s13321-018-0299-2

External resources

• KNIME Hub
• GitHub repository