OpenMS - Updating MB2HMDBmapping file to create the MBSpectra.mzML for MetaboliteSpectralMatcher node

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1

So, I have downloaded the files from GitHub - OpenMS/MassBankUpdate and the MassBank-data. The scripts are working perfectly fine. Also, I have already updated my HMDB2StructMapping.tsv and HMDBMapping.tsv files according to https://forum.knime.com/t/openms-update-hmdb-to-version-5-0-for-accuratemasssearch-node/37052/3.

However, I would like to ask how can I update the MB2HMDBmapping.csv file for creating an updated MBSpectra.mzML file and use it for MetaboliteSpectralMatcher? Is there any script for this?

2

Hmm Step 3 in your linked Repository should generate the mzML for you. Have you maybe overlooked that, or did it not generate a file for you?

3

There is no problem at all generating the MBSpectra.mzml file. It is indeed created with step 3. However it uses also the MB2HMDBmapping.csv file (to generate the MBSpectra.mzml) which was updated last time in 2018. So I was wondering if there is a way to update also the MB2HMDBmapping file.