bigbio/proteomics-sample-metadata

Any possiblity to require users to upload correction factors for TMT data in PRIDE?

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#723 opened on Sep 11, 2024

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Specificationenhancementhelp wanted

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Description

Hi everyone,

Our group is recently working with TMT datasets from published data. When we search for the dataset, we found that very few research provide the imputrity correction factors for the TMT dataset in the article, which made it impossible to reanalyze the data properly.

We're wondering if in the future, it would be possible to require users to provide the impurity correction factors, or the Lot # of the TMT reagent kit, when they upload the TMT dataset to PRIDE? We believe it'll help a lot to improve the reproducibility and reanalysis of the TMT datasets.

Best, Jinqiu

Contributor guide

Research direction
Investigate the PRIDE submission metadata schema and identify where TMT correction factors could be added. Review existing examples in the repository to understand the standard format.
Tech stack
None
Domain
database
Issue type
Feature
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
2
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
1-3 hours
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
Active
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Clear
Prerequisites
GitProteomics
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
60