SDRF-Proteomics

1. Status

Status: Released

Version: 1.1.0 - 2026-01

2. Abstract

The MS-Proteomics template is the minimum valid SDRF template for mass spectrometry-based proteomics experiments. It includes all columns necessary to describe an MS proteomics dataset.

This template is appropriate for:

  • DDA (Data-Dependent Acquisition) proteomics

  • DIA (Data-Independent Acquisition) proteomics

  • Targeted proteomics (SRM/MRM/PRM)

  • Any experiment using mass spectrometry for protein/peptide detection

3. Template Hierarchy

base
  └── ms-proteomics (THIS TEMPLATE)
        │
        ├── dda-acquisition (DDA-specific columns)
        ├── dia-acquisition (DIA-specific columns)
        ├── crosslinking (XL-MS columns)
        ├── single-cell (SCP columns)
        └── immunopeptidomics (MHC-MS columns)

4. Checklist

4.1. Inherited Columns (from base)

ColumnRequirementDescription
source name REQUIRED Unique identifier for the biological sample
characteristics[organism] REQUIRED Species (NCBI Taxonomy)
characteristics[organism part] REQUIRED Anatomical part
characteristics[cell type] RECOMMENDED Cell type
characteristics[biological replicate] REQUIRED Biological replicate number
assay name REQUIRED Unique identifier for the MS run
technology type REQUIRED "proteomic profiling by mass spectrometry"
comment[technical replicate] RECOMMENDED Technical replicate number
comment[data file] REQUIRED Raw data file name

4.2. MS-Specific Columns

ColumnRequirementDescriptionOntologyExample Values
comment[instrument] REQUIRED Mass spectrometer used MS Q Exactive HF, Orbitrap Fusion Lumos, timsTOF Pro
comment[proteomics data acquisition method] REQUIRED MS acquisition method PRIDE Data-dependent acquisition, Data-independent acquisition
comment[cleavage agent details] REQUIRED Enzyme used for digestion MS NT=Trypsin;AC=MS:1001251
comment[label] REQUIRED Labeling strategy PRIDE label free sample, TMT126, SILAC heavy
comment[fraction identifier] REQUIRED Fraction number (1 for non-fractionated) — 1, 2, 3

5. Field Guidelines

5.1. CV Term Format

For data file metadata columns that reference ontology terms, use the structured CV term format:

NT={term name};AC={accession}

Examples:

  • Dissociation method: NT=HCD;AC=PRIDE:0000590

  • Instrument: NT=Q Exactive HF;AC=MS:1002523

  • Label: NT=TMT126;AC=PRIDE:0000285

Note
 Data file metadata benefits from the structured CV term format because these values are often extracted programmatically from instrument files.

5.2. Label

Column: comment[label]

Ontology: PRIDE:0000514 - Sample label

Describes the isotopic label applied to each sample. All label values MUST be children of PRIDE:0000514 (label free sample, TMT, iTRAQ, SILAC, etc.). Open example SDRF

source name comment[label] comment[data file]
sample_1 TMT126 run1.raw
sample_2 TMT127N run1.raw
Sample metadata Data file metadata

5.3. Cleavage Agents

Column: comment[cleavage agent details]

Ontology: PSI-MS - Cleavage agent name (MS:1001045)

Format: NT=EnzymeName;AC=Accession

Enzyme Value OLS Link

Trypsin

NT=Trypsin;AC=MS:1001251

MS:1001251

Trypsin/P

NT=Trypsin/P;AC=MS:1001313

MS:1001313

Lys-C

NT=Lys-C;AC=MS:1001309

MS:1001309

For top-down/intact proteins, use not applicable. For multiple enzymes, add multiple columns. Open example SDRF

5.4. Protein Modifications

Column: comment[modification parameters]

Ontology: UNIMOD or PSI-MOD

Format: NT=ModificationName;AC=Accession;MT=Type;TA=AminoAcid;PP=Position Open example SDRF

Property Key Values

Name

NT

UNIMOD or PSI-MOD term name

Accession

AC

UNIMOD:X or MOD:X

Type

MT

Fixed, Variable

Target Amino Acid

TA

Single letter codes (e.g., S,T,Y)

Position

PP

Anywhere, Protein N-term, Protein C-term

Common modifications:

Modification Value OLS Link

Carbamidomethyl (fixed)

NT=Carbamidomethyl;AC=UNIMOD:4;MT=Fixed;TA=C;PP=Anywhere

UNIMOD:4

Oxidation (variable)

NT=Oxidation;AC=UNIMOD:35;MT=Variable;TA=M;PP=Anywhere

UNIMOD:35

Phosphorylation (variable)

NT=Phospho;AC=UNIMOD:21;MT=Variable;TA=S,T,Y;PP=Anywhere

UNIMOD:21

5.5. Mass Tolerances

Columns: comment[precursor mass tolerance], comment[fragment mass tolerance]

Format: {value} {unit} where unit is Da or ppm.

Precursor Fragment Instrument Type

10 ppm

20 ppm

Orbitrap MS1/MS2

20 ppm

0.6 Da

Orbitrap MS1, Ion trap MS2

5.6. Fractionation

Column: comment[fractionation method]

Ontology: PRIDE - Fractionation method

Use with comment[fraction identifier] to number fractions.

Method OLS Link

High-pH reversed-phase chromatography

PRIDE:0000564

Strong cation-exchange chromatography

PRIDE:0000561
Note
 For single-shot experiments without fractionation, this column can be omitted or set to not applicable. Open example SDRF

5.7. Dissociation Method

Column: comment[dissociation method]

Ontology: PRIDE - dissociation method (MS:1000044)

All values MUST be children of MS:1000044 from the PRIDE ontology. Use the short acronyms (HCD, CID, ETD, etc.) as term names.

Term (Acronym) OLS Link

HCD

PRIDE:0000590

CID

PRIDE:0000591

ETD

PRIDE:0000593

EThcD

PRIDE:0000594

CV term format: NT=HCD;AC=PRIDE:0000590 Open example SDRF

5.8. Collision Energy

Column: comment[collision energy]

Format: {value} {unit}

Format Example Description

Normalized

27 NCE

Normalized collision energy

Absolute

30 eV

Absolute energy in electron volts

Stepped

22 NCE;26 NCE;30 NCE

Multiple energies (semicolon-separated)
Tip
 For DIA experiments with stepped collision energy, see the DIA template for detailed guidance.

5.9. Sample Preparation

Reduction Reagent: comment[reduction reagent] - DTT, TCEP, beta-mercaptoethanol

Alkylation Reagent: comment[alkylation reagent] - IAA, chloroacetamide

Depletion: comment[depletion] - no depletion, depletion, depleted fraction, bound fraction

6. Usage

6.1. 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. Place these columns at the end of the file.

6.2. Minimal MS Proteomics (non-organism-specific)

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

…​

v1.1.0

ms-proteomics v1.1.0

6.3. Human Samples (Recommended)

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

…​

v1.1.0

human v1.1.0
Note
 The human template inherits from ms-proteomics, so you only need to specify human.

6.4. With Acquisition-Specific Parameters (multiple templates)

When using multiple templates, add multiple comment[sdrf template] columns:

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

…​

v1.1.0

human v1.1.0

dda-acquisition v1.1.0

Each template declares its own version, allowing templates to evolve independently.

7. Validation

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

8. Example

source name characteristics[organism] characteristics[organism part] characteristics[biological replicate] assay name technology type comment[instrument] comment[proteomics data acquisition method] comment[cleavage agent details] comment[label] comment[fraction identifier] comment[data file]
sample_1 homo sapiens liver 1 run_1 proteomic profiling by mass spectrometry Q Exactive HF Data-dependent acquisition NT=Trypsin;AC=MS:1001251 label free sample 1 sample1.raw

10. Ontologies