01
Where it fits and where it does not
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.
- Limits
- 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
- Omics and Laboratory teams working across Plan → Acquire → Harmonize → Exchange → Learn + reuse.
- Maturity
- ScalingUsable now, but adoption or tooling is still developing. Pilot the exact stack first.
02
See it in the workflow
This view shows the input, the change the standard introduces, and the resulting output.
- InputWhat starts
Omics and Laboratory source data, metadata, and local mappings
- SDRF-ProteomicsWhat changes
Use SDRF-Proteomics as a pinned metadata profile across Plan → Acquire → Harmonize → Exchange → Learn + reuse
- OutputWhat becomes possible
A handoff the next system or team can validate against the same release
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.
- Data model / schemaAIRR · MiAIRR
Both support Omics and Laboratory work and meet around Plan, Acquire, Harmonize, Exchange, Learn + reuse. Compare their roles before treating them as interchangeable.
Explore relationship - Metadata profileExpmeta
Both support Omics and Laboratory work and meet around Plan, Acquire, Harmonize, Exchange, Learn + reuse. Compare their roles before treating them as interchangeable.
Explore relationship - 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 - Metadata profileMIxS
Both support Omics and Laboratory work and meet around Plan, Acquire, Harmonize, Exchange. 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.
Define one handoff, its 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
Test the main limitation
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.
Machine-readable output may still be unfit for analysis or ML.
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
Official resources
Specifications, diagrams, examples, and guides from the organizations that maintain them.
SDRF-Proteomics specification repository
Official publisher or steward guidance for this metadata profile profile.
- Publisher
- HUPO Proteomics Standards Initiative · EuBIC / BigBio community