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Standardizing Proteomics Sample Metadata

SDRF-Proteomics is a community-driven standard for describing sample metadata and its relationship to data files in proteomics experiments. It enables data sharing, reproducibility, and integration across studies.

Read the Specification Open Editor Get the Validator

Prefer reading offline? Download the PDF specification (v1.0.0) or the development version (v1.1.0-dev).

What does an SDRF file look like?

source name characteristics[organism] characteristics[disease] assay name comment[instrument] comment[data file] factor value[disease]
sample_1 homo sapiens normal run_1 Q Exactive HF sample_1.raw normal
sample_2 homo sapiens liver cancer run_2 Q Exactive HF sample_2.raw liver cancer
Sample metadata Data file metadata Experimental factors

Quick Start

New to SDRF-Proteomics? Start here to learn the basics and create your first SDRF file.

Get Started

Validation

Validate your SDRF files using sdrf-pipelines, the official Python validator.

Learn More

Examples

Browse annotated datasets from ProteomeXchange as reference examples.

View Examples

Templates

Core Templates

Organism-based templates for common proteomics experiments.

Human

Clinical and demographic metadata

View Template

Vertebrates

Mouse, rat, zebrafish, etc.

View Template

Invertebrates

Insects, nematodes, etc.

View Template

Plants

Arabidopsis, crops, etc.

View Template

Experiment-specific Templates

Specialized templates for specific experiment types. Released templates are stable; templates under development may change.

Template Description Status Version
Cell Lines Standardized cell line annotation using Cellosaurus Released 1.1.0
DDA Acquisition Data-dependent acquisition experiments Released 1.1.0
DIA Acquisition Data-independent acquisition experiments Released 1.1.0
Affinity Proteomics Olink and SomaScan affinity-based proteomics Released 1.1.0
Crosslinking XL-MS structural proteomics experiments Released 1.0.0
Immunopeptidomics MHC-bound peptide identification Under Development 1.1.0-dev
Metaproteomics Microbial community proteomics Under Development 1.1.0-dev
Single Cell Single cell proteomics experiments Under Development 1.1.0-dev

Metadata Guidelines

Detailed rules for annotating specific types of metadata fields.

Sample Metadata

Age, sex, disease, organism part

View Guidelines

Human Metadata

Disease staging, treatment, demographics

View Guidelines

SDRF Terms

All column terms and allowed values

Browse Terms

Tool Support

A growing ecosystem of tools supports the SDRF-Proteomics format for creating, validating, and analyzing proteomics data.

SDRF Editor

Browser-based editor with ontology autocomplete, bulk editing, and Excel export.

Open Editor

Annotators

Web-based tools for creating and editing SDRF files with ontology support.

View Tools

Validators

Validate your SDRF files against the specification and check ontology terms.

View Tools

Analysis Pipelines

Proteomics workflows that use SDRF as input for automated analysis.

View Tools

Resources

SDRF Explorer

Browse and explore 298+ annotated proteomics datasets with statistics and filtering.

Explore Datasets

Annotated Projects

Collection of SDRF files from ProteomeXchange datasets on GitHub.

Browse on GitHub

Publication

Read the original SDRF-Proteomics publication in Nature Communications.

Read Paper
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Cite SDRF-Proteomics

If you use SDRF-Proteomics in your research, please cite:

Dai C, Füllgrabe A, Pfeuffer J, Solovyeva EM, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, Locard-Paulet M, Turewicz M, Eisenacher M, Uszkoreit J, Van Den Bossche T, Schwämmle V, Webel H, Schulze S, Bouyssié D, Jayaram S, Duggineni VK, Samaras P, Wilhelm M, Choi M, Wang M, Kohlbacher O, Brazma A, Papatheodorou I, Bandeira N, Deutsch EW, Vizcaíno JA, Bai M, Sachsenberg T, Levitsky LI, Perez-Riverol Y. A proteomics sample metadata representation for multiomics integration and big data analysis. Nat Commun. 2021;12:5854.
Read Paper PubMed

Core Contributors and Collaborators

SDRF-Proteomics is developed by a global community of proteomics researchers and bioinformaticians.

EMBL-EBI (U.K.)

  • Yasset Perez-Riverol PRIDE
  • Juan Antonio Vizcaino PRIDE
  • Mathias Walzer PRIDE
  • Anja Fullgrabe Expression Atlas
  • Nancy George Expression Atlas
  • Pablo Moreno Expression Atlas

Tübingen University (Germany)

  • Timo Sachsenberg OpenMS
  • Oliver Alka OpenMS
  • Julianus Pfeuffer OpenMS
  • Jonas Scheid

University of Bergen (Norway)

  • Marc Vaudel
  • Harald Barsnes

University of Gent (Belgium)

  • Niels Hulstaert CompOmics
  • Lennart Martens CompOmics
  • Tim Van Den Bossche CompOmics
  • Tine Claeys CompOmics
  • Caroline Jachmann CompOmics

Other Contributors

  • Lev Levitsky INEPCP RAS, Russia
  • Elizaveta Solovyeva INEPCP RAS, Russia
  • Stefan Schulze U. Pennsylvania, USA
  • Veit Schwammle U. Southern Denmark
  • David Bouyssie U. Toulouse, France
  • Enrique Audain UKSH, Germany
  • Marie Locard-Paulet U. Copenhagen, Denmark
  • Johannes Griss Medical U. Vienna, Austria
  • Chengxin Dai Chongqing U., China
  • Julian Uszkoreit Ruhr-U. Bochum, Germany
  • Alexandra Naba U. Illinois Chicago, USA
  • Joshua Klein Boston U., USA

View all contributors | Want to contribute? Learn how