SDRF-Proteomics

1. Status of this Template

This document provides guidelines for annotating SomaScan aptamer-based proteomics experiments in SDRF-Proteomics format.

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

Status: Released

Version: 1.0.0 - 2026-01

2. Abstract

SomaScan is an aptamer-based proteomics platform developed by SomaLogic that uses Slow Off-rate Modified Aptamers (SOMAmer) reagents to measure protein levels. This template extends the affinity-proteomics template with SomaScan-specific metadata fields for menu version, sample matrix, and normalization methods.

3. Template Hierarchy

base
  └── affinity-proteomics
        └── somascan (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 (somascan 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

somascan 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

somascan v1.0.0

5. SomaScan-Specific Columns

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

5.1. Required for SomaScan

ColumnRequirementDescriptionExample Values
comment[somascan menu] REQUIRED SomaScan assay menu (number of aptamers) SomaScan 5K, SomaScan 7K, SomaScan 11K
comment[somascan platform] REQUIRED SomaScan platform version SomaScan Assay v4, SomaScan Assay v4.1

5.2. Recommended for SomaScan

ColumnRequirementDescriptionExample Values
comment[sample matrix] RECOMMENDED Sample matrix type (affects calibration) plasma, serum, EDTA plasma, CSF
comment[dilution] RECOMMENDED Sample dilution factor used 0.005%, 0.5%, 20%, 40%
comment[normalization method] RECOMMENDED Normalization method applied to RFU values hybridization control normalized, median normalized, ANML
comment[QC flag] OPTIONAL Quality control flag PASS, FLAG, FAIL
comment[somascan lot number] OPTIONAL Reagent lot number SS-2023-001

6. SomaScan Assay Menus

SomaScan offers different menu sizes based on the number of protein targets:

6.1. Current Menus

  • SomaScan 7K: ~7,000 protein targets (current standard)

  • SomaScan 11K: ~11,000 protein targets (expanded panel)

6.2. Legacy Menus

  • SomaScan 1.1K: ~1,100 protein targets

  • SomaScan 1.3K: ~1,300 protein targets

  • SomaScan 5K: ~5,000 protein targets

7. Technology Type

For SomaScan experiments, use:

technology type = protein expression profiling by aptamer array

8. Quantification

SomaScan uses RFU (Relative Fluorescence Units):

  • RFU is a measure of fluorescence intensity proportional to protein concentration

  • Higher RFU = higher protein concentration

  • RFU values require normalization for cross-sample comparisons

  • Standard normalization includes hybridization control, median, and plate scaling

Always set:

comment[quantification unit] = RFU

9. Sample Matrix

The sample matrix is critical for SomaScan assays because calibration and expected ranges differ by matrix type:

  • EDTA plasma: Preferred matrix, most validated

  • Serum: Commonly used alternative

  • Citrate/Heparin plasma: Less common

  • CSF: Specialized protocols

  • Cell/Tissue lysates: Research applications

10. Normalization Methods

SomaScan data typically undergoes multiple normalization steps:

  1. Hybridization control normalization: Corrects for hybridization variation

  2. Median normalization: Scales samples to common median

  3. Plate scale normalization: Corrects for plate-to-plate variation

  4. Calibration: Applies standard curve corrections

  5. ANML (Adaptive Normalization by Maximum Likelihood): Advanced cross-study normalization

11. Example SDRF

source name characteristics[organism] characteristics[organism part] characteristics[disease] assay name technology type comment[instrument] comment[somascan menu] comment[somascan platform] comment[quantification unit] comment[sample matrix] comment[normalization method] comment[data file]
patient_001 homo sapiens blood plasma type 2 diabetes mellitus SL0001 protein expression profiling by aptamer array SomaScan Assay 7K SomaScan 7K SomaScan Assay v4.1 RFU EDTA plasma adaptive normalization by maximum likelihood (ANML) somascan_results.adat
patient_002 homo sapiens blood plasma normal SL0002 protein expression profiling by aptamer array SomaScan Assay 7K SomaScan 7K SomaScan Assay v4.1 RFU EDTA plasma adaptive normalization by maximum likelihood (ANML) somascan_results.adat
Sample metadata Data file metadata

12. Data File Formats

SomaScan data files:

  • ADAT: Native SomaScan format (annotated data file)

  • CSV/TSV: Tabular exports of RFU values

The assay name column must match the SampleId column in the ADAT file.

13. Validation

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

14. Template File

16. References