SDRF-Proteomics

1. Status of this Template

This document provides guidelines for annotating Olink Proximity Extension Assay (PEA) experiments in SDRF-Proteomics format.

Type: Platform-Specific Template (extends affinity-proteomics)

Status: Released

Version: 1.0.0 - 2026-01

2. Abstract

Olink proteomics uses Proximity Extension Assay (PEA) technology to measure protein levels in biological samples. This template extends the affinity-proteomics template with Olink-specific metadata fields for panel information, NPX normalization, and quality control.

3. Template Hierarchy

base
  └── affinity-proteomics
        └── olink (THIS TEMPLATE)

4. Usage

4.1. File Metadata Columns

SDRF files SHOULD include metadata columns to specify version and template information. Only list leaf templates; parent templates are implied by inheritance (olink inherits from affinity-proteomics). Place these columns at the end of the file.

Non-human samples:

…​ comment[sdrf version] comment[sdrf template]

…​

v1.1.0

olink v1.0.0

Human samples - use multiple template columns:

…​ comment[sdrf version] comment[sdrf template] comment[sdrf template]

…​

v1.1.0

human v1.1.0

olink v1.0.0

5. Olink-Specific Columns

In addition to all columns from affinity-proteomics, the following Olink-specific columns are available:

5.1. Required for Olink

ColumnRequirementDescriptionExample Values
comment[olink panel] REQUIRED Specific Olink panel name Target 96 Inflammation, Explore 384 Cardiometabolic, Explore 1536
comment[olink platform] REQUIRED Olink instrument/platform version Olink Target 96, Olink Explore 384, Olink Explore HT

5.2. Recommended for Olink

ColumnRequirementDescriptionExample Values
comment[NPX normalization] RECOMMENDED Normalization method applied to NPX values plate control normalized, intensity normalized, bridge normalized
comment[QC warning] OPTIONAL Quality control warnings if any QC pass, below LOD, plate effect warning
comment[olink lot number] OPTIONAL Reagent lot number for traceability lot_2023_001, B12345

6.1. Target 96 Panels

Individual panels measuring 92 proteins each:

  • Target 96 Inflammation

  • Target 96 Cardiovascular II

  • Target 96 Cardiovascular III

  • Target 96 Neurology

  • Target 96 Oncology II

  • Target 96 Oncology III

  • Target 96 Metabolism

6.2. Explore Panels

High-throughput panels:

  • Olink Explore 384 (384 proteins)

  • Olink Explore 1536 (1536 proteins)

  • Olink Explore 3072 (3072 proteins)

  • Olink Explore HT (5400+ proteins)

7. Technology Type

For Olink experiments, use:

technology type = protein expression profiling by antibody array

8. Quantification

Olink uses NPX (Normalized Protein eXpression) units:

  • NPX is a log2 scale relative quantification

  • Higher NPX = higher protein concentration

  • NPX values are comparable within a study after proper normalization

  • Cross-study comparisons require bridge normalization

Always set:

comment[quantification unit] = NPX

9. Example SDRF

source name characteristics[organism] characteristics[organism part] characteristics[disease] assay name technology type comment[instrument] comment[olink panel] comment[olink platform] comment[quantification unit] comment[NPX normalization] comment[data file]
patient_001 homo sapiens blood plasma rheumatoid arthritis XB6 protein expression profiling by antibody array Olink Explore HT Olink Explore 1536 Olink Explore HT NPX plate control normalized olink_npx.csv
patient_002 homo sapiens blood plasma normal XB65 protein expression profiling by antibody array Olink Explore HT Olink Explore 1536 Olink Explore HT NPX plate control normalized olink_npx.csv
Sample metadata Data file metadata

10. Data File Formats

Olink data files typically contain:

  • NPX CSV/Excel: Normalized protein expression values

  • Parquet: Large datasets in efficient columnar format

The assay name column must match the Sample ID column in the Olink output file.

11. Validation

pip install sdrf-pipelines
parse_sdrf validate-sdrf --sdrf_file your_file.sdrf.tsv --template olink

12. Template File

14. References