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Official repository of open data MassBank records
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Add new UFZ WANA ESI posititve spectra of 2018 mixes #237

Closed tsufz closed 1 year ago

tsufz commented 1 year ago

Interesting, that I committed 3 weeks ago :-/

tsufz commented 1 year ago

Handling of empty COMMENT line to be checked in RMassBank (issue 348)

tsufz commented 1 year ago

@meier-rene, the formula is valid, because, we have a M+ ion. The validator is too restrictive in this case. I suggest to check the inner formula only.

Formula from CH$IUPAC:   [C27H42NO2]+
Formula from CH$FORMULA: C27H42NO2

I remove the M+ spectra until this is fixed in the validator.

Added an issue

tsufz commented 1 year ago

I analysed the situation with the brackets. The validator writes the brackets which is misleading. The underlying issue is that RMassBank does not calculate the charged formula, but the uncharged (and the curator did not check the infolist for this issue). Causing the error in the validation. Will add issue in RMassBank.

meier-rene commented 1 year ago

Just a little bit of background: The validator uses the cdk to process formulas, inchi, smiles... If there is a charged molecule in the SMILES or InChI field and no charge in the formula field the validator will produce an error. The syntax for charged molecules in cdk is [Formula]Charge. This is a non ambiguous notation and I like it. Just consider a sulfate ion: [SO4]2- compared to SO42-. Can you produce that with R somehow?

tsufz commented 1 year ago

@meier-rene thanks for your comment. I will add the link to the new issue in RMassBank.