Metabolomnics technology type

bigbio / proteomics-sample-metadata

The Proteomics Experimental Design file format: Standard for experimental design annotation

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Metabolomnics technology type #702

Open ypriverol opened 2 months ago

ypriverol commented 2 months ago

We have two technology types for metabolomics:

LC-MS-based metabolomics: @mmattano used (https://github.com/bigbio/proteomics-sample-metadata/pull/680) in the PR the EDAM ontology NT=LC-MS-based metabolomics;AC=EDAM:3172 we should move this term to PSI-MS or PRIDE ontologies.
NMR metabolomics: Similar to the previous term, we should move it into PSI-MS or PRIDE ontologies. The main reason is because we use these two ontologies to handle data properties (comment).

To be discussed.

nilshoffmann commented 2 months ago

We also frequently use direct infusion mass spectrometry (DI-MS), which uses no separation. Also, there are quite many different specializations of LC-MS-based metabolomics (nanoLC, HILIC, SFC, ...): do we list them as children or are they already classified and organized into a hierarchy somewhere else?

mmattano commented 2 months ago

Hi Nils, we currently have a column for comment[chromatography type] in there where for example nanoLC, HILIC, SFC, ... can be specified. Also direct infusion etc could be specified there. Do you think this is sufficient or do you think more information is needed?

nilshoffmann commented 2 months ago

Hi Matthias, that sounds sufficient. Although direct infusion is not really a chromatography type, but since I suspect that chromatographic separation is much more frequently being used, I would be ok with having direct infusion below that column. Looking at the possible child terms of the PRIDE CV (https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000565?lang=en) and HUPO-PSI MS CV (https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1002270?lang=en) we probably should add some CV terms, too. I could not find terms for nano-LC (exists in CHMO), SFC or direct infusion/shotgun MS.

omicsdev commented 1 month ago

Hi, for Metabolomnics technology type, GC-MS and CE-MS is essential, thought both system can not use to detect protein (CE-MS can use for di- or tri-peptide). I can not imagine how to implement these terms to PRIDE CV.