llms.txt

# SDRF-Proteomics

> SDRF-Proteomics is a HUPO-PSI community standard defining a tab-delimited file format for capturing sample-to-data-file relationships in proteomics experiments. It standardizes sample metadata (organism, disease, tissue), technical metadata (instrument, labels, enzymes), and experimental design (factor values) to enable automated reprocessing and reuse of public proteomics datasets. Compatible with MAGE-TAB SDRF from transcriptomics.

## Specification

- sdrf-proteomics/README.adoc - Core specification: format rules, column headers, cell values, templates, factor values, ontologies
  - sdrf-proteomics/quickstart.adoc - Quick Start Tutorial (10-15 min)
  - sdrf-proteomics/metadata-guidelines/sample-metadata.adoc - Sample Metadata Guidelines: age, sex, disease, organism part, cell type
  - sdrf-proteomics/TEMPLATES.adoc - Templates Guide: template selection, YAML schema, validators, and developer reference
  - sdrf-proteomics/metadata-guidelines/sdrf-terms.tsv - SDRF Terms Reference: all column terms with ontology mappings

- sdrf-proteomics/VERSIONING.adoc - Versioning and Deprecation Policy: version tracks, template compatibility, deprecation lifecycle, transition timelines
- sdrf-proteomics/open-issues.adoc - Open Issues and Future Decisions: community discussions for post-v1.1.0 changes
- psi-document/v1.0.0/SDRF_Proteomics_Specification_v1.0.0.pdf - Official HUPO-PSI specification (PDF, v1.0.0)
- psi-document/v1.1.0-dev/sdrf-proteomics-specification-v1.1.0-dev.pdf - Development specification (PDF, v1.1.0-dev)

## Templates

- sdrf-proteomics/templates/ms-proteomics/README.adoc - MS-Proteomics: labels, instruments, modifications, cleavage agents
- sdrf-proteomics/templates/affinity-proteomics/README.adoc - Affinity Proteomics: Olink and SomaScan
- sdrf-proteomics/templates/human/README.adoc - Human: disease, age, sex, ancestry, disease staging
- sdrf-proteomics/templates/vertebrates/README.adoc - Vertebrates: mouse, rat, zebrafish
- sdrf-proteomics/templates/invertebrates/README.adoc - Invertebrates: Drosophila, C. elegans
- sdrf-proteomics/templates/plants/README.adoc - Plants: Arabidopsis, crops
- sdrf-proteomics/templates/cell-lines/README.adoc - Cell Lines: Cellosaurus integration
- sdrf-proteomics/templates/dia-acquisition/README.adoc - DIA Acquisition: scan windows, isolation width
- sdrf-proteomics/templates/single-cell/README.adoc - Single-Cell Proteomics: cell isolation, carrier proteome
- sdrf-proteomics/templates/immunopeptidomics/README.adoc - Immunopeptidomics: MHC protein complex, MHC typing
- sdrf-proteomics/templates/crosslinking/README.adoc - Crosslinking MS: crosslinker reagents
- sdrf-proteomics/templates/metaproteomics/README.adoc - Metaproteomics: environmental and microbiome samples
- sdrf-proteomics/templates/olink/README.adoc - Olink: proximity extension assays
- sdrf-proteomics/templates/somascan/README.adoc - SomaScan: aptamer-based proteomics

## Template YAML Schemas (sdrf-templates submodule)

Machine-readable YAML definitions used by sdrf-pipelines for validation. Each template has a `.yaml` schema and an optional `.sdrf.tsv` example file. Templates follow a layered hierarchy: base → sample-metadata → technology/sample/experiment.

- sdrf-proteomics/sdrf-templates/templates.yaml - Template manifest: all templates with latest versions, inheritance, and layer metadata
- sdrf-proteomics/sdrf-templates/base/1.1.0/base.yaml - Base template (internal, not user-facing): infrastructure columns (source name, assay name, technology type, etc.)
  - sdrf-proteomics/sdrf-templates/base/1.1.0/base.sdrf.tsv - Base example
- sdrf-proteomics/sdrf-templates/sample-metadata/1.1.0/sample-metadata.yaml - Sample-metadata template (intermediate, not user-facing): sample columns (organism, organism part, cell type, biological replicate, pooled sample, disease, biosample accession). Extends base.
  - sdrf-proteomics/sdrf-templates/sample-metadata/1.1.0/sample-metadata.sdrf.tsv - Sample-metadata example
- sdrf-proteomics/sdrf-templates/ms-proteomics/1.1.0/ms-proteomics.yaml - MS-Proteomics (technology layer): minimum valid template for any MS experiment. Extends sample-metadata.
  - sdrf-proteomics/sdrf-templates/ms-proteomics/1.1.0/ms-proteomics.sdrf.tsv - MS-Proteomics example
- sdrf-proteomics/sdrf-templates/affinity-proteomics/1.1.0/affinity-proteomics.yaml - Affinity Proteomics (technology layer): Olink, SomaScan base. Extends sample-metadata.
  - sdrf-proteomics/sdrf-templates/affinity-proteomics/1.1.0/affinity-proteomics.sdrf.tsv - Affinity Proteomics example
- sdrf-proteomics/sdrf-templates/human/1.1.0/human.yaml - Human (sample layer): disease, age, sex, ancestry. Extends sample-metadata.
  - sdrf-proteomics/sdrf-templates/human/1.1.0/human.sdrf.tsv - Human example
- sdrf-proteomics/sdrf-templates/vertebrates/1.1.0/vertebrates.yaml - Vertebrates (sample layer): mouse, rat, zebrafish, etc. Extends sample-metadata.
  - sdrf-proteomics/sdrf-templates/vertebrates/1.1.0/vertebrates.sdrf.tsv - Vertebrates example
- sdrf-proteomics/sdrf-templates/invertebrates/1.1.0/invertebrates.yaml - Invertebrates (sample layer): Drosophila, C. elegans. Extends sample-metadata.
  - sdrf-proteomics/sdrf-templates/invertebrates/1.1.0/invertebrates.sdrf.tsv - Invertebrates example
- sdrf-proteomics/sdrf-templates/plants/1.1.0/plants.yaml - Plants (sample layer): Arabidopsis, crops. Extends sample-metadata.
  - sdrf-proteomics/sdrf-templates/plants/1.1.0/plants.sdrf.tsv - Plants example
- sdrf-proteomics/sdrf-templates/cell-lines/1.1.0/cell-lines.yaml - Cell Lines (experiment layer): Cellosaurus integration
  - sdrf-proteomics/sdrf-templates/cell-lines/1.1.0/cell-lines.sdrf.tsv - Cell Lines example
- sdrf-proteomics/sdrf-templates/dia-acquisition/1.1.0/dia-acquisition.yaml - DIA Acquisition (experiment layer): scan windows, isolation width
  - sdrf-proteomics/sdrf-templates/dia-acquisition/1.1.0/dia-acquisition.sdrf.tsv - DIA example
- sdrf-proteomics/sdrf-templates/crosslinking/1.1.0/crosslinking.yaml - Crosslinking MS (experiment layer): crosslinker reagents
  - sdrf-proteomics/sdrf-templates/crosslinking/1.1.0/crosslinking.sdrf.tsv - Crosslinking example
- sdrf-proteomics/sdrf-templates/single-cell/1.0.0/single-cell.yaml - Single-Cell (experiment layer): cell isolation, carrier proteome
  - sdrf-proteomics/sdrf-templates/single-cell/1.0.0/single-cell.sdrf.tsv - Single-Cell example
- sdrf-proteomics/sdrf-templates/immunopeptidomics/1.0.0-dev/immunopeptidomics.yaml - Immunopeptidomics (experiment layer): MHC protein complex, MHC typing
- sdrf-proteomics/sdrf-templates/metaproteomics/1.0.0-dev/metaproteomics.yaml - Metaproteomics (experiment layer): environmental and microbiome samples
  - sdrf-proteomics/sdrf-templates/metaproteomics/1.0.0-dev/metaproteomics.sdrf.tsv - Metaproteomics example
- sdrf-proteomics/sdrf-templates/olink/1.0.0/olink.yaml - Olink (experiment layer): proximity extension assays
  - sdrf-proteomics/sdrf-templates/olink/1.0.0/olink.sdrf.tsv - Olink example
- sdrf-proteomics/sdrf-templates/somascan/1.0.0/somascan.yaml - SomaScan (experiment layer): aptamer-based proteomics
  - sdrf-proteomics/sdrf-templates/somascan/1.0.0/somascan.sdrf.tsv - SomaScan example

## Tools

- sdrf-proteomics/tool-support.adoc - Tool Support Overview: annotators, validators, analysis tools
  - https://github.com/bigbio/sdrf-pipelines - sdrf-pipelines: official Python CLI/library for SDRF validation
  - https://lessdrf.streamlit.app/ - lesSDRF: web-based SDRF creation tool
  - https://cupcake-vanilla-demo.proteo.nexus/ - CupCAKE: web annotation platform with ontology integration
  - https://quantms.org/ - quantms: Nextflow pipeline for quantitative proteomics
  - https://www.maxquant.org/ - MaxQuant: desktop proteomics software with SDRF export
  - https://github.com/wombat-p - Wombat-P: benchmarking platform for proteomics workflows

## Examples

- examples/PXD004684/ - Label-free, DDA, human
- examples/PXD008934/ - Label-free, human proteome
- examples/PXD002137/ - Label-free, clinical, human
- examples/PXD006482/ - Label-free, renal carcinoma, human
- examples/PXD003772/ - TMT labeling, mouse
- examples/PDC000126/ - TMT labeling, large cohort, human
- examples/PXD013923/ - SILAC, phosphoproteomics, human
- examples/PXD012667/ - DIA acquisition, human
- examples/PXD019515/ - Single-cell proteomics, human
- examples/PXD003791/ - Metaproteomics, gut
- examples/PXD005969/ - Metaproteomics, human gut extraction methods
- examples/PXD003572/ - Metaproteomics, soil (Mediterranean dryland)
- examples/PXD009712/ - Metaproteomics, ocean (Pacific depth profiles)
- examples/PXD006439/ - Label-free, mouse
- examples/PXD013868/ - Label-free, plant (Arabidopsis)

## Annotated Projects

- annotated-projects/ - 250+ public proteomics datasets annotated in SDRF format
  - annotated-projects/PXD008934/PXD008934.sdrf.tsv - Label-free quantification
  - annotated-projects/PXD017710/PXD017710.sdrf.tsv - TMT-labeled quantitative proteomics
  - annotated-projects/PXD000612/PXD000612.sdrf.tsv - SILAC-based quantification
  - annotated-projects/PXD018830/PXD018830-DIA.sdrf.tsv - Data-independent acquisition
  - annotated-projects/PXD000759/PXD000759.sdrf.tsv - Phosphoproteomics
  - annotated-projects/PXD001819/PXD001819.sdrf.tsv - Cell line proteomics

## Publications

- https://www.nature.com/articles/s41467-021-26111-3 - Dai et al. (2021) Nat Commun: A proteomics sample metadata representation for multiomics integration
- https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.0c00376 - Perez-Riverol et al. (2020) J Proteome Res: Towards a sample metadata standard in public proteomics repositories

## Project

- README.md - Project overview and contributor list
- CHANGELOG.md - Version history and changes
- CITATION.cff - Citation metadata
- LICENSE - GNU General Public License
- DEVELOPMENT.md - Building the documentation website locally

## Optional

- https://github.com/bigbio/proteomics-metadata-standard/wiki - 30-Minute Guide to SDRF-Proteomics
- https://www.youtube.com/watch?v=TMDu_yTzYQM - Introduction to SDRF-Proteomics (video)
- https://www.psidev.info/sdrf-sample-data-relationship-format - HUPO-PSI official page