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mwang87 / ReDU-MS2-GNPS

User interface to reanalyze and explore all public data in Metabolomics Public Data
https://redu.ucsd.edu/
MIT License
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Need more approved terms (SampleExtractionMethod) #242

Open Adafede opened 2 years ago

Adafede commented 2 years ago

Hi,

I am actually trying to add ReDu compliant metadata of previously uploaded MassIVE datasets.

I have samples that were extracted using acidic acetone (1% HCl), could this (or related controlled vocabulary) be added to the list of solvents?

Btw, it looks like the acidity (or basicity) is actually not taken into account within solvents. This might be problematic for many extraction protocols (alkaloids...)

Best,

mwang87 commented 2 years ago

@alan-jarmusch what do you think in representing these additional extractions?

alan-jarmusch commented 1 year ago

'acetone-hydrochloric acid (99:1)' will be added to "SampleExtractionMethod" you are correct we do not capture pH information. The point you raise is correct and understood. Given the difficulty of measuring pH in organic solutions - I have defaulted to listed the composition as above (v/v unless otherwise stated)

Adafede commented 1 year ago

Perfectly understandable, thanks a lot!