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? Learn the key concepts behind SDRF files and how to fill them in.

Learn the Basics

Template Builder

Build a customized SDRF template by selecting your technology, organism, and experiment type.

Build a Template

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

SDRF templates define the columns and validation rules for different types of proteomics experiments. See the Templates Guide for details on inheritance and combination rules.

Template Layer Description Version
Affinity Proteomics technology SDRF template for affinity-based proteomics experiments (Olink, SomaScan). This is the base template for all affinity... 1.0.0
Ms Proteomics technology Base SDRF template for mass spectrometry-based proteomics. This is the minimum valid template for any MS experiment. 1.1.0
Clinical Metadata sample SDRF template for clinical study samples with treatment, demographics, and lifestyle metadata. Applicable to any orga... 1.0.0
Human sample Human SDRF template with human-specific sample metadata fields. Must be combined with a technology template (ms-prote... 1.1.0
Human Gut sample SDRF template for human gut metaproteomics. Extends metaproteomics with host-associated columns aligned with the GSC ... 1.0.0
Invertebrates sample SDRF template for invertebrate samples (Drosophila, C. elegans, insects, etc.). Must be combined with a technology te... 1.1.0
Metaproteomics sample Base SDRF template for metaproteomics experiments (microbial community proteomics). Extends base directly and defines... 1.0.0
Oncology Metadata sample SDRF template for cancer/oncology study samples with tumor staging, grading, and clinical outcome metadata. Extends c... 1.0.0
Plants sample SDRF template for plant samples (Arabidopsis, crops, etc.). Must be combined with a technology template (ms-proteomic... 1.1.0
Soil sample SDRF template for soil metaproteomics. Extends metaproteomics with soil-specific columns aligned with the GSC MIxS so... 1.0.0
Vertebrates sample SDRF template for non-human vertebrate samples (mammals, birds, fish, reptiles, amphibians). Must be combined with a ... 1.1.0
Water sample SDRF template for aquatic metaproteomics. Extends metaproteomics with water-specific columns aligned with the GSC MIx... 1.0.0
Cell Lines experiment SDRF template for cell line samples with Cellosaurus-based annotation. Cell lines can originate from any organism - c... 1.1.0
Crosslinking experiment SDRF template for crosslinking mass spectrometry (XL-MS) experiments. Extends ms-proteomics with crosslinking-specifi... 1.0.0
Dia Acquisition experiment SDRF template for Data-independent acquisition (DIA) experiments. Extends ms-proteomics with DIA-specific columns. 1.1.0
Immunopeptidomics experiment SDRF template for immunopeptidomics experiments (MHC-bound peptide identification). Works with any organism - combine... 1.0.0
Olink experiment SDRF template for Olink Proximity Extension Assay (PEA) experiments. Extends affinity-proteomics with Olink-specific columns. 1.0.0
Single Cell experiment SDRF template for single-cell proteomics (SCP) experiments. Works with any organism - combine with appropriate sample... 1.0.0
Somascan experiment SDRF template for SomaScan aptamer-based proteomics experiments. Extends affinity-proteomics with SomaScan-specific columns. 1.0.0

Metadata Guidelines

Detailed rules for annotating specific types of metadata fields.

Sample Metadata

Age, sex, disease, organism part

View Guidelines

Templates Guide

Inheritance, layers, combination rules

View Guide

SDRF Terms

All column terms and allowed values

Browse Terms

Example SDRF Files

Curated examples covering different experiment types, labeling strategies, and organisms. Download and use as starting points for your own annotations.

Accession Description Organism Label Templates Rows
PXD004684 Label-free, DDA Homo sapiens label free ms-proteomics, human 15
PXD008934 Label-free, human proteome Homo sapiens label free ms-proteomics, human 35
PXD003772 TMT labeling Mus musculus TMT ms-proteomics, vertebrates 13
PDC000126 TMT labeling, large cohort Homo sapiens TMT ms-proteomics, human 2041
PXD013923 SILAC, phosphoproteomics Homo sapiens SILAC ms-proteomics, human 21
PXD012667 DIA acquisition Homo sapiens label free ms-proteomics, human, dia-acquisition 49
PXD019515 Single-cell proteomics Homo sapiens label free ms-proteomics, human, single-cell 7
PXD003791 Metaproteomics, gut human gut metagenome label free metaproteomics 109
PXD005969 Metaproteomics, human gut extraction methods human gut metagenome label free metaproteomics, human-gut 30
PXD003572 Metaproteomics, soil (Mediterranean dryland) soil metagenome label free metaproteomics, soil 59
PXD009712 Metaproteomics, ocean (Pacific depth profiles) marine metagenome label free metaproteomics, water 74
PXD006439 Label-free, mouse Mus musculus label free ms-proteomics, vertebrates 68
PXD013868 Label-free, plant Arabidopsis thaliana label free ms-proteomics, plants 21

Browse all examples on GitHub →

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