[Feature] Rework sample_processing into a protocol section #95
Description
Is your feature request related to a problem? Please describe.
At the moment, capturing methods / protocol specific reporting beyond what is possible in sample_processing in mzTab-M is currently not supported. sample_processing could be integrated as part of a new protocol section / prefix, that allows to capture different steps happening before the mass spectrometry acquisition. Additionally, the mztab2mtbls code can at the moment not automatically create the necessary protocol parts in ISA-Tab to proceed with a submission to MetaboLights.
Describe the solution you'd like
MTD protocol[1]-name A name for protocol 1
MTD protocol[1]-sample_collection []|[]
MTD protocol[1]-sample_collection_description description for sample collection
MTD protocol[1]-extraction []|[]
MTD protocol[1]-extraction_description asdasd
MTD protocol[1]-chromatography []|[]
MTD protocol[1]-chromatography_description asdasd
MTD protocol[1]-mass_spectrometry []|[]
MTD protocol[1]-mass_spectrometry_description asdasd
MTD protocol[1]-data_transformation []|[]
MTD protocol[1]-data_transformation_description asdasd
MTD protocol[1]-metabolite_identification []|[]
MTD protocol[1]-metabolite_identification_description asdasd
The previous sample_processing parts would then belong to a specific protocol sample_collection.
E.g. this old example:
MTD sample_processing[1] [MSIO, MSIO:0000107, metabolism quenching using precooled 60 percent methanol ammonium bicarbonate buffer,]
MTD sample_processing[2] [MSIO, MSIO:0000146, centrifugation,]
MTD sample_processing[3] [MSIO, MSIO:0000141, metabolite extraction,]
MTD sample_processing[4] [MSIO, MSIO:0000141, silylation,]
Would become:
MTD protocol[1]-sample_collection [MSIO, MSIO:0000107, metabolism quenching using precooled 60 percent methanol ammonium bicarbonate buffer,]|[MSIO, MSIO:0000146, centrifugation,]|[MSIO, MSIO:0000141, metabolite extraction,]|[MSIO, MSIO:0000141, silylation,]
Describe alternatives you've considered
It would be possible to expand the definition of sample_processing to include every step until mass spectrometry. However, the format at the moment is limited to cv / user parameters. Chromatography could be a step within this, but generally, a renaming would align better with domain-driven design and would make cognitive mapping to MetaboLights and similar resources easier.
Submitter Tasks
- Provide a pull request (Please add the link)
- Schema: Update mzTab_m_openapi.yml (View File)
- Specification: Update mzTab_format_specification_2_1-M.adoc with an example (View File)
- Example files: if possible, modify an existing or add a new example file (Existing example files)
Maintainer & WG Tasks
- Triage: Assign labels and Milestones to this issue.
- Discuss and review and approve PR.
Next Steps, once we reach an agreement on the changes above:
- Create a downstream issue in the jmzTab-m repo (https://github.com/lifs-tools/jmzTab-m/issues)
- Implement and test changes in jmzTab-M
- Implement changes in R & Python implementations