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New use case: Mass spectrometry imaging (MSI) #451
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Copying here from Twitter discussion: Here is our minimal metadata from http://metaspace2020.eu/: https://github.com/metaspace2020/metaspace/tree/master/metaspace/metadata, ironed out through the experience of working with 100+ labs, keeping the balance b/w "the more metadata the better" (it's not) & "minimum needed for processing". Also synced w/ https://www.ebi.ac.uk/metabolights/ |
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Specification issues related with PRIDE formats, API, etc
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Sep 17, 2020
Thanks, @theodev for the comment. |
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Hi all,
I made a pull request with three exemplary annotations for MSI data to start a discussion: #450
Here are some thoughts about the annotation of MSI data with the current sdrf file format. Especially the 'MSI specific things' would benefit from a discussion.
Metadata that applies to MSI as well
Metadata that does not apply to MSI
MSI specific things
File type: The open standard format imzML is a composite file type consisting of two files: imzML + ibd
→ In the current annotation I only used one line and referenced only the imzML subfile but not ibd. This makes it easier to annotate and understand the metadata but might be problematic for some (automated) applications?
Multiple samples per run: Multiple tissues can be placed onto one slide As the technique is label-free and spatially resolved the samples can be distinguished by their position on the slide/plate. This might require an additional graphic that shows an ID of each sample or the center of the sample in x and y coordinates.
All files in PXD011104 have multiple samples, I have picked only one of the files to annotate a first simple example. I just numbered the 4 tissue sections (largest image shown here: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/08/PXD011104/Information-gastricmousemodel-MALDI-TOF.docx) from left to right as “position on slide”: 1,2,3,4. This would require an additional image that shows the position IDs.
(Potential) additional MSI metadata columns
Cheers,
Melanie
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