Fixing record of carmine red

[tilfischer]

While working on the NFDI4Chem Lead-by-Example dataset of carminic acid and its MS(/MS) data, I found the MassBank records for "carmine red" (e.g. ACCESSION: MSBNK-RIKEN_NPDepo-NGA00405). This records link to PubChem_CID https://pubchem.ncbi.nlm.nih.gov/compound/14950, which does not give any information whether it is the α-C-glycoside or β-C-glycoside with the anthraquinone type aglycon. The α-C-glycoside does not exist in nature, while the record provides "Animal, Organic chemicals, Polycyclic compounds, Carmines" for the origin of the measured substance and provides the SMILES, InChI and InChIKey for the α-C-glycoside, while PubChem_CID 14950 does not provide stereo info in SMILES, InChI and InChIKey DGQLVPJVXFOQEV-UHFFFAOYSA-N (UHFFFAOY -> no existing data on stereo).

Moreover, the exact mass provided in this records is wrong, while the peak table gives, as expected, m/z 493.1 as the most abundant signal, while with the exact mass given in the record m/z 493.4 would be expected to be the most abundant signal.

Initially, I thought that someone mixed up the carminic acid with its mixed aluminium/calcium salt, which is a lack pigment of carminic acid. However, the CAS provided [1260-17-9] is the CAS_RN of β-C-glycoside which is carminic acid, while [1343-78-8] is probably the CAS_RN of the α-C-glycoside. Moreover, the metal ions should form stable chelates, which might not dissociate in the MS spectrometer at low collision energies. Finally, the lack pigment is very insoluble and is is unlikely, that someone was able to obtain MS data from the lack pigment with the LC-MS methods provided in the MassBank records of carmine red or carminic acid. In other words: The underlying MS data must be obtained with carminic acid and not with the mixed aluminum/calcium lack pigment of carminic acid. Hence, I also updated the name and also included the IUPAC name with absolute stereo.

[tsufz]

Hi @tilfischer, thanks a lot for your request and contribution. However, open an issue to discuss problems in advance of pull requests, please. I assigned the PR to @schymane to discuss the issue before merging.

Best Tobias

[tilfischer]

Hello Tobias! I tried to find information on how to discuss my observations in the MassBank contributors documentation and found some info on the very bottom of that page https://massbank.github.io/MassBank-documentation/contributor_documentation.html . Best, Tillmann

[meier-rene]

I rebased the PR to dev, because our main branch is protected and only accepts PR from the dev branch. So we need to merge the PR to dev and later we release a new version of MassBank with the changes included.

[meier-rene]

OK, we can not do it like that, because I can not resolve merge conflicts that way. We can have the discussion here but finally we would need to close that PR open the PR from dev to dev.

[schymane]

I am not sure why I was assigned this - these are RIKEN spectra and thus this should be discussed with them?

[meier-rene]

@schymane right, thats not your issue. Please just ignore that.