01
Where it fits—and where it doesn’t
Use these four checks before committing implementation time.
- Use it when
- Proteomics studies that need an explicit, machine-readable mapping from biosamples and factors to raw and processed mass-spectrometry files.
- Do not use it as
- Do not treat SDRF-Proteomics as a complete solution on its own. It does not encode downstream statistical-analysis parameters or results. Working-branch templates and rules can move ahead of the final PSI specification, so release and validator versions must be pinned.
- Best for
- Teams working with Omics and Laboratory data across Plan → Acquire → Harmonize → Exchange → Learn + reuse.
- Maturity
- ScalingUsable today, with adoption or tooling still scaling; pilot the exact stack you plan to run.
02
See it in the workflow
A standard creates value by changing a handoff, not by existing in a catalog.
- InputWhat starts
Omics and Laboratory data, metadata, and the local decisions around them
- SDRF-ProteomicsWhat changes
SDRF-Proteomics applies a shared metadata profile across Plan → Acquire → Harmonize → Exchange → Learn + reuse
- OutputWhat becomes possible
A more consistent, reviewable handoff for the next system or team
03
A concrete example
A quantitative proteomics release validates one SDRF table linking subjects, samples, conditions, replicates, labels, instruments, and every raw or result file.
Why it matters: Makes sample grouping, factor assignment, replicate structure, and file joins explicit for reusable training and evaluation datasets.
04
What it fits with
Compatible with MAGE-TAB SDRF; complements ISA study metadata, mzML spectra, mzIdentML identifications, mzTab results, and ProteomeXchange submissions.
- Metadata vocabularyDPV
Both support Omics work and meet around Plan, Acquire, Harmonize, Exchange, Learn + reuse. Compare their roles before treating them as interchangeable.
Explore relationship - FrameworkFAIR
Both contribute at Plan, Acquire, Harmonize, Exchange, Learn + reuse, with different domains or implementation roles.
Explore relationship - Data model / schemaISA
Both support Laboratory and Omics work and meet around Plan, Acquire, Harmonize. Compare their roles before treating them as interchangeable.
Explore relationship - Ontology ecosystemOBO Foundry
Both support Laboratory and Omics work and meet around Plan, Harmonize, Learn + reuse. Compare their roles before treating them as interchangeable.
Explore relationship
05
Implementation starter
Start with one bounded handoff. Pin, test, and review it before scaling.
Name an accountable owner and the decision SDRF-Proteomics must support.
Pin the exact version and companion artifacts: HUPO-PSI 1.0.0 final · 1.1.0 working changes unreleased.
Map one representative input to the required metadata profile artifacts.
Test the result against the canonical source and record every exception.
Preserve the source data, mappings, and review evidence before scaling.
06
Limitation to test first—and the tests that catch it
It does not encode downstream statistical-analysis parameters or results. Working-branch templates and rules can move ahead of the final PSI specification, so release and validator versions must be pinned.
Run one representative end-to-end pilot and record exactly where SDRF-Proteomics loses context, needs an extension, or depends on another standard.
A structured or machine-readable result can still be unfit for analysis or AI.
Test the output for missing context, provenance, terminology alignment, time leakage, and the intended downstream decision. Makes sample grouping, factor assignment, replicate structure, and file joins explicit for reusable training and evaluation datasets.
07
Why we believe this
Checked against the canonical source plus independent operational evidence from an adopter, regulator, or implementation report.
Evidence notation: E1 + E2. The code is shorthand; the plain-language statement above is the claim.
08
Source shelf
Official diagrams, examples, specifications, and explainers. Nothing external loads until you choose to open it.
SDRF-Proteomics specification repository
The canonical publisher or steward source used to verify this metadata profile profile.
- Publisher
- HUPO Proteomics Standards Initiative · EuBIC / BigBio community
- Rights
- Rights remain with the publisher; this knowledge base links to the source rather than copying it.
- Access
- Opens the publisher's source in a new tab; no external media loads on this page.
- Verified
- 2026-07-13