Guide to Generating International Chemical Identifier (InChI) Label for Isotopically Labelled Compounds
Roland C. Wilhelm
stable isotope probing
minimum information for any sequence
MIxS
amplicon
metagenome
metatranscriptome
MIMARKS
MIMS
microbial ecology.
Abstract
This protocol was written to support the article by Simpson et al. , 2024 entitled: MISIP: A data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment. The same guide, with additional screen shots illustrating each step, is provided in Supplementary Information. This guide can be used to generate the MISIP standard field: ‘ isotopolog_atom_pos ’
Steps
Generating International Chemical Identifier (InChI) Label
The InChI label is a machine-readable format that specifies the exact position of all atoms in a molecule, including the isotope number (at the end of the label). The label is a stable identifier supported by the IUPAC. The InChI label is the required format to specify the isotopomer of the isotopolog supplied in the isotoplog_atom_pos field. At the time of publication, the following freely available software tools could be used to generate an InChI label using visualizations to guide the appropriate designation of isotopic labeling. The same tools can be used to visualize an InChI label as a molecular structure. We will demonstrate how to obtain an InChI for the commercially available 13C-labeled L-DOPA (IUPAC: (S)-2-Amino-3-(3,4-dihydroxyphenyl)propanoic acid).
Install the Marvin Sketch software developed by Chemaxon https://chemaxon.com/marvin.
The software is available for non-commercial use under an academic license.
In Marvin Sketch, select ‘Import Name’ and specify the IUPAC name for your isotopolog compound. The IUPAC name can be obtained from a PubChem search: <https://pubchem.ncbi.nlm.nih.gov/>.
The molecular structure will be displayed. For each isotopically-labeled atom in your isotopomer, select the atom with your cursor, then select from the ‘Atom’ menu find the ‘Isotope’ panel and chose the correct isotope.
Repeat until all atoms are labeled, then select ‘File’ and ‘Save As’ from the menu bar. Save the file as either an MDL SDfile (.sdf) or Tripos SYBYL Molfile (.mol).
Either (1) use the software ‘OpenBabel’, available online HERE to convert the .sdf or .mol to the InChI format, or (2) download the InChI software binaries from the InChI Trust (available for Linux or Windows OS). Start the InChI software using the executable file, then select ‘Open’ and navigate and select the .sdf or .mol file created in Marvin Sketch. The InChI label for your isotopolog will be displayed in the dialogue box beneath the molecular structure.
Double check that all isotopically labeled atoms are correctly assigned in your structure, then copy and paste the InChI into your MISIP data standard spreadsheet.
