RMassBank Workshop on 29 August 2023 by NORMAN Association ‐ community notes

RMassBank workshop 29 August 2023 - community notes

Introduction to RMassBank

Stravs et al., DOI: 10.1002/jms.3131

Oberacher et al., DOI: 10.1186/s12302-020-00314-9

Using RMassBank

.ini settings file

The settings file contains the annotations which are added to the record. There is a standard format for the annotations. Documentation can be found in the document MassBankRecordFormat.

My settings.ini does not contain the presented information. Solution: The reason is maybe the outdated BioConductor version. You can check the version by running BiocManager::version() in R. The latest version is 3.18. To update run BiocManager::install(version = "3.18") The Bioc Version is dependent on the R version.

Settings file: spectraList

• The order of the scans listed must match the order in the data.
• In the mzML file, some instruments label the spectra with the collision type and energy

The accession number (after the entry_prefix) can be arbitrary and you can using a running number for your spectra if you wish. It is recommended to use an accession number builder as above to avoid any duplicates.

Contribution through Github

If you have only a few spectra for upload, contact Tobias directly, the Github process can be done for you.

Things to keep in mind

• Fork the MassBank-Data repository into your own account
• Use the "dev" branch for contributing new records
• New accession numbers can be up to 256 characters long
• Do not reuse accession numbers
• Records are deprecated, not deleted
• Spectra for newer or less-known compounds would be more valuable
• For recommended CEs, check Oberacher et al.

Steps for contributing

• Add data into your local copy of the "dev" branch of your MassBank-data fork
• Commit and Push changes
• Create a "Pull Request" so that the changes are moved to the upstream "dev" branch

Exporting from MassBank

Different formats of the MassBank database are available through the Release page on Github.

Contribution of GC-Orbitrap spectra

This needs to be discussed with Michele.

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List of new contributors

If you want to submit records to MassBank in future, create a user entry. You can find existing contributors in this table. Add the following information by copying the example.

Example: Database: UFZ Research Group: Helmholtz Centre for Environmental Research Prefix: UF

Database: NILU Research Group: The Climate and Environmental Research Institute NILU Prefix: NILU