bigbio / bigbio/proteomics-sample-metadata

Support of SDRF for SRM/PRM (targeted) experiments

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#769 3 comments 0 reactions 0 assignees View on GitHub
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Description

Hi all,

I have been working with targeted proteomics for a little while, and I think metadata for targeted experiments would be useful for the proteomics field. Based on the latest versions of SDRF that I have used, I think the additional information should contain spiked-in standard system including **target ids, protein/peptide sequence, and definitely spiked-in concentration**.

For analysis software, please see https://github.com/bigbio/quantms/issues/648.

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Research direction

Start by reviewing the SDRF versions referenced in the issue and the related quantms issue 648. Compare how targeted SRM/PRM experiments are currently represented and document an agreed specification for target IDs, protein or peptide sequences, and spiked-in concentrations; completion requires community agreement on the metadata scope.

Written by the indexing model from the issue text.

Assessment

Domain
bioinformatics
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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