- 1. Status of this document
- 2. Abstract
- 3. Motivation
- 4. Specification structure
- 5. The SDRF-Proteomics Format
- 6. Validating SDRF Files
- 7. SDRF-Proteomics: Samples metadata
- 8. SDRF-Proteomics: data files metadata
- 9. Additional SDRF Rules
- 10. Templates
- 11. Factor Values (Study Variables)
- 12. Ontologies and Controlled Vocabularies
- 13. Examples of Annotated Datasets
- 14. Template Definitions
- 14.1. base
- 14.2. sample-metadata
- 14.3. ms-proteomics
- 14.4. affinity-proteomics
- 14.5. human
- 14.6. vertebrates
- 14.7. invertebrates
- 14.8. plants
- 14.9. clinical-metadata
- 14.10. oncology-metadata
- 14.11. dia-acquisition
- 14.12. single-cell
- 14.13. immunopeptidomics
- 14.14. crosslinking
- 14.15. cell-lines
- 14.16. olink
- 14.17. somascan
- 14.18. metaproteomics
- 14.19. human-gut
- 14.20. soil
- 14.21. water
- 15. Intellectual Property Statement
- 16. Copyright Notice
- 17. How to cite
- References
This document provides information to the proteomics community about a proposed standard for sample metadata annotations in public repositories called Sample and Data Relationship Format (SDRF)-Proteomics. Distribution is unlimited.
Version v1.1.0 - 2026-01
The Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) defines community standards for data representation in proteomics to facilitate data comparison, exchange, and verification. This document presents a specification for the Sample and Data Relationship Format (SDRF-Proteomics).
Further detailed information, including any updates to this document, implementations, and examples is available at SDRF GitHub Repository. The official PSI web page for the document is: HUPO-PSI SDRF.
Public proteomics data is valuable, but sample metadata is often missing or stored inconsistently across repositories (e.g., CPTAC uses Excel files, ProteomicsDB captures minimal properties) [1]. This heterogeneity prevents reproducibility and cross-dataset integration.
SDRF-Proteomics addresses this by providing a standard tab-delimited format to capture (Figure 1):
-
Sample metadata and characteristics
-
Data file acquisition parameters
-
Sample-to-file relationships (experimental design)
Figure 1: SDRF-Proteomics captures sample information and its relationship to data files.
The format is fully compatible with MAGE-TAB SDRF, enabling integration with transcriptomics metadata standards.
SDRF-Proteomics uses a two-tier system: this core specification defines the format rules, and templates provide metadata checklists for specific experiment types (Figure 2). Templates are organized in the templates/ directory, each with documentation and example files.
Figure 2: SDRF-Proteomics specification structure. The main specification defines the core rules and is extended by sample templates (human, vertebrates, etc.) and experiment-type templates (crosslinking, immunopeptidomics, etc.).
The official repository is GitHub, where you can find annotated example projects and the official validator sdrf-pipelines.
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Throughout this specification, the keywords "MUST", "REQUIRED", "SHOULD", "RECOMMENDED", and "OPTIONAL" are interpreted as described in RFC 2119. |
SDRF-Proteomics is a tab-delimited file where:
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Each row = one sample linked to one data file
-
Each column = a property (sample characteristic, data file attribute, or factor value)
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Each cell = the property value for that sample/file or a factor value.
Here’s a minimal example:
| source name | characteristics[organism] | characteristics[organism part] | characteristics[disease] | characteristics[biological replicate] | assay name | technology type | comment[proteomics data acquisition method] | comment[label] | comment[instrument] | comment[cleavage agent details] | comment[fraction identifier] | comment[technical replicate] | comment[data file] | factor value[disease] |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
sample_1 |
homo sapiens |
liver |
normal |
1 |
run_1 |
proteomic profiling by mass spectrometry |
data-dependent acquisition |
label free sample |
Q Exactive HF |
NT=Trypsin;AC=MS:1001251 |
1 |
1 |
sample_1.raw |
normal |
sample_2 |
homo sapiens |
liver |
hepatocellular carcinoma |
1 |
run_2 |
proteomic profiling by mass spectrometry |
data-dependent acquisition |
label free sample |
Q Exactive HF |
NT=Trypsin;AC=MS:1001251 |
1 |
1 |
sample_2.raw |
hepatocellular carcinoma |
sample_3 |
homo sapiens |
not available |
not available |
1 |
run_3 |
proteomic profiling by mass spectrometry |
data-dependent acquisition |
label free sample |
Q Exactive HF |
NT=Trypsin;AC=MS:1001251 |
1 |
1 |
sample_3.raw |
not available |
The file is organized into three column sections:
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Sample metadata (
characteristics[…]) - organism, disease, tissue, etc. -
Data file metadata (
comment[…]) - instrument, label, fraction, data file -
Factor values (
factor value[…]) - variables under study for statistical analysis
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The SDRF-Proteomics specification uses Semantic Versioning (MAJOR.MINOR.PATCH). Version numbers are prefixed with "v" (e.g., v1.1.0). Changes are proposed via GitHub pull requests to the dev branch.
For the complete versioning strategy — including template versioning, ontology updates, the deprecation policy, transition timelines, and migration tooling — see Versioning and Deprecation Policy.
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Case sensitivity: Text values are case-insensitive, but column names are case-sensitive. Use lowercase for all column names (e.g.,
source name,characteristics[organism],comment[label]). Incorrect casing likeSource NameorCharacteristics[organism]will cause validation failures. -
Space sensitivity: The SDRF is sensitive to spaces in column names (
sourcename≠source name). Column names must include appropriate spaces (e.g.,source name, notsourcename) but must NOT have a space before the bracket (e.g.,characteristics[organism], notcharacteristics [organism]). -
Column order: The SDRF columns follows some structure; first the sample metadata columns in Chapter 7; then the data file metadata columns in Chapter 8; followed by the factor values columns in [study-variables].
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Extension: The extension of the SDRF file SHOULD be sdrf.tsv (preferred) or .txt.
There are general scenarios where cell values cannot be provided with actual data. The following reserved words MUST be used in these cases. Reserved words MUST be all lowercase (e.g., not available, NOT Not Available or Not available):
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not available: In some cases, the column is mandatory in the format, but for some samples the corresponding value is unknown or could not be determined. In those cases, users SHOULD use not available.
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not applicable: In some cases, the column is mandatory, but for some samples the corresponding value or concept does not apply. In those cases, users SHOULD use not applicable.
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anonymized: In some cases, the value exists but has been intentionally redacted for privacy protection (e.g., in clinical studies with de-identified patient data). In those cases, users SHOULD use anonymized.
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pooled: In some cases, the sample is a pool of multiple samples (e.g., TMT reference channels), and the value cannot be represented as a single value. In those cases, users SHOULD use pooled.
| Term | Meaning | Example | Use Case |
|---|---|---|---|
not available |
Value exists but is unknown or could not be determined |
characteristics[age] = not available |
Patient age was not recorded in the study |
not applicable |
Value or concept does not apply to this sample |
characteristics[age] = not applicable |
Synthetic peptide library has no age |
anonymized |
Value exists but is redacted for privacy protection |
characteristics[age] = anonymized |
Clinical study with de-identified patient data |
pooled |
Value represents a mixture of multiple samples |
characteristics[biological replicate] = pooled |
TMT reference channel pooled from multiple replicates |
Since version 1.1.0, SDRF-Proteomics supports file-level metadata using dedicated columns. These columns provide information about the SDRF file itself, such as the specification version, template(s) used, annotation tool, and validation status. This column-based approach maintains compatibility with spreadsheet applications (Excel, Google Sheets) and existing data processing tools.
The following metadata columns are supported:
| Column | Description | Example Value | Requirement | Ontology Term |
|---|---|---|---|---|
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SDRF-Proteomics specification version used. Should follow semantic versioning format (vMAJOR.MINOR.PATCH) |
v1.1.0 |
RECOMMENDED |
PRIDE:0000839 |
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Template name and version used for annotation. Two formats are supported: simple format ( |
human v1.1.0 or NT=human;VV=v1.1.0 |
OPTIONAL |
PRIDE:0000832 |
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Software tool, script, or method used to generate or annotate the SDRF file. Two formats are supported: simple format ( |
lesSDRF v0.1.0 or NT=lesSDRF;VV=v0.1.0 |
OPTIONAL |
PRIDE:0000840 |
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Cryptographic hash (e.g., SHA-256) generated after successful validation |
sha256:abc123… |
OPTIONAL |
PRIDE:0000834 |
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When combining multiple templates (e.g., human + ms-proteomics), use multiple comment[sdrf template] columns, one per template. The value in each row should be identical for all samples in the file.
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Example of an SDRF file with metadata columns (simplified example showing only select columns; see Chapter 10 for complete required columns):
| source name | characteristics[organism] | characteristics[disease] | assay name | comment[data file] | comment[sdrf version] | comment[sdrf template] | comment[sdrf template] | comment[sdrf annotation tool] |
|---|---|---|---|---|---|---|---|---|
sample_1 |
homo sapiens |
normal |
run_1 |
sample_1.raw |
v1.1.0 |
human v1.1.0 |
ms-proteomics v1.1.0 |
lesSDRF v0.1.0 |
sample_2 |
homo sapiens |
breast cancer |
run_2 |
sample_2.raw |
v1.1.0 |
human v1.1.0 |
ms-proteomics v1.1.0 |
lesSDRF v0.1.0 |
Depending on each section the column headers (property names) will be prefixed with the following prefixes:
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characteristics: Sample metadata (e.g. characteristics[organism]) -
comment: Data file metadata (e.g. comment[data file]) -
factor value: Factor values properties (e.g. factor value[disease])
Each property name MUST be a valid ontology term or a valid controlled vocabulary term. Each section will have some specific order for column headers.
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A list of all controlled vocabularies and ontologies supported are in the Chapter 12 section. On each section we also provide a list of properties that are supported. |
The value for each property, (e.g. characteristics, comment, factor value) corresponding to each sample or data file can be represented in multiple ways.
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Free Text (Human readable): In the free text representation, the value is provided as text without Ontology support (e.g. colon or providing accession numbers). This is only RECOMMENDED when the text inserted in the table is the exact name of an ontology/CV term in EFO. If the term is not in EFO, other ontologies can be used.
| source name | characteristics[organism] |
|---|---|
sample 1 |
homo sapiens |
sample 2 |
homo sapiens |
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Ontology url (Computer readable): Users can provide the corresponding URI (Uniform Resource Identifier) of the ontology/CV term as a value. This is recommended for enriched files where the user does not want to use intermediate tools to map from free text to ontology/CV terms.
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Key=value representation (Human and Computer readable): The current representation aims to provide a mechanism to represent the complete information of the ontology/CV term including Accession, Name and other additional properties. In the key=value pair representation, the Value of the property is represented as an Object with multiple properties, where the key is one of the properties of the object and the value is the corresponding value for the particular key. The key order MUST be
NT(name) first, followed byAC(accession), then any additional keys. An example of key value pairs is post-translational modification (see Protein Modifications):NT=Glu->pyro-Glu;AC=Unimod:27;MT=fixed;PP=Anywhere;TA=E
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Beyond these three representations, SDRF columns may accept additional structured value types such as numbers with units (10 ppm), accession identifiers (SAMN12345678), ISO 8601 dates, semantic versions, and more. Each column’s YAML template definition declares exactly which value types and formats are accepted. For the complete reference of all value types, parsing rules, and their formal patterns, see Value Types Reference in the Templates Guide.
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The official validator for SDRF-Proteomics files is sdrf-pipelines, a Python tool that checks your SDRF file for errors and compliance with the specification.
Installation:
pip install sdrf-pipelinesBasic Validation:
# Validate an SDRF file
parse_sdrf validate-sdrf --sdrf_file your_file.sdrf.tsv
# Validate with a specific template
parse_sdrf validate-sdrf --sdrf_file your_file.sdrf.tsv --template humanFor more information, visit: sdrf-pipelines on GitHub
The Sample metadata section provides information about the samples of origin and their characteristics. Each sample contains a source name (unique identifier) and a set of characteristics columns. The first column of the file should be the source name and the following columns should be the characteristics of the sample. For example, for any proteomics experiment (human, vertebrate, cell line), the following characteristics should be provided:
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source name: Unique sample name (it can be present multiple times if the same sample is used several times in the same dataset)
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characteristics[organism]: The organism of the Sample of origin. Values MUST come from NCBI Taxonomy.
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characteristics[organism part]: The part of organism’s anatomy or substance arising from an organism from which the biomaterial was derived (e.g., liver). Values SHOULD come from UBERON or BTO.
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characteristics[disease]: The disease under study in the Sample. Values SHOULD come from MONDO, EFO, or DOID. For healthy/control samples, use
normal(PATO:0000461) - see Disease Annotation Guidelines. -
characteristics[cell type]: A cell type is a distinct morphological or functional form of cell (e.g., epithelial, glial). Values SHOULD come from Cell Ontology (CL), BTO, or Cell Line Ontology (CLO).
Example:
| source name | characteristics[organism] | characteristics[organism part] | characteristics[disease] | characteristics[cell type] |
|---|---|---|---|---|
sample_treat |
homo sapiens |
liver |
liver cancer |
not available |
sample_control |
homo sapiens |
liver |
liver cancer |
not available |
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Use the OPTIONAL characteristics[biosample accession number] column to link samples to BioSamples [5], enabling cross-database integration with genomics and transcriptomics data. Formats: SAMN* (NCBI) or SAMEA* (EBI).
SDRF-Proteomics uses two REQUIRED columns to track replicates [4]:
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characteristics[biological replicate]: Independent biological samples. Numbering restarts per experimental condition (factor value group).
-
comment[technical replicate]: Repeated measurements of the same sample (e.g., multiple injections)
When no replicates are performed, set both columns to 1. For pooled samples, use pooled for biological replicate.
| source name | characteristics[biological replicate] | comment[fraction identifier] | comment[technical replicate] | comment[data file] |
|---|---|---|---|---|
patient_001 |
1 |
1 |
1 |
P001_F1_TR1.raw |
patient_001 |
1 |
1 |
2 |
P001_F1_TR2.raw |
patient_002 |
2 |
1 |
1 |
P002_F1_TR1.raw |
patient_002 |
2 |
1 |
2 |
P002_F1_TR2.raw |
When multiple samples are pooled into one (e.g., TMT/iTRAQ reference channels for normalization), use the characteristics[pooled sample] column to indicate pooling status. Allowed values:
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not pooled: Regular individual samples
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pooled: Sample is pooled but individual sources are unknown
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SN=sample1;SN=sample2;…: Lists source names of pooled samples when known
Example:
| source name | characteristics[pooled sample] | characteristics[organism] | characteristics[age] | comment[label] | comment[data file] |
|---|---|---|---|---|---|
sample_1 |
not pooled |
homo sapiens |
45Y |
TMT126 |
file01.raw |
sample_2 |
not pooled |
homo sapiens |
52Y |
TMT127N |
file01.raw |
pooled_ref |
SN=sample_1;SN=sample_2 |
homo sapiens |
pooled |
TMT131C |
file01.raw |
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For pooled samples, use pooled for individual-specific fields (biological replicate, age, sex) to indicate a mixture rather than a single sample.
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For detailed guidance on annotating sample metadata, refer to the following conventions documents:
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Sample Metadata Guidelines - Detailed guidelines for age, sex, disease, organism part, cell type, developmental stage, spiked-in samples, and other sample characteristics
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Human Sample Metadata Guidelines - Human-specific metadata including disease staging, treatment history, demographics, and lifestyle factors
The connection between samples and data files is done using properties annotated with the comment prefix. All properties referring to a data file (e.g., MS run file) are annotated with the category comment. This differentiates data file properties from sample properties (characteristics).
For data file metadata (comment columns) that reference ontology terms, use the structured format: NT={term name};AC={accession}
Examples: NT=HCD;AC=PRIDE:0000590, NT=Orbitrap;AC=MS:1000484
This format enables automated validation and software extraction from raw files. Sample metadata (characteristics) can use simple term names since they are typically human-annotated.
The following properties MUST be provided for each data file in mass spectrometry-based proteomics experiments. For affinity-based proteomics (Olink, SomaScan), see the Affinity-Proteomics template for different required columns.
| Column | Requirement | Description | Ontology |
|---|---|---|---|
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REQUIRED |
Unique identifier for an MS run/data file |
Free text |
|
REQUIRED |
Technology used to capture the data |
Fixed values |
|
REQUIRED |
DDA, DIA, PRM, SRM |
PRIDE:0000659 |
|
REQUIRED |
Label applied to sample (or "label free sample") |
PRIDE - Labels |
|
REQUIRED |
Mass spectrometer model |
PSI-MS - Instruments |
|
REQUIRED |
Enzyme information (use "not applicable" for top-down/undigested samples) |
PSI-MS - Cleavage agents |
|
REQUIRED |
Fraction number (1 if not fractionated) |
Integer |
|
REQUIRED |
Technical replicate number (1 if none) |
Integer |
|
REQUIRED |
Name of the raw file |
Free text |
Example:
| source name | assay name | technology type | comment[proteomics data acquisition method] | comment[label] | comment[instrument] | comment[data file] |
|---|---|---|---|---|---|---|
sample_1 |
sample1_run1 |
proteomic profiling by mass spectrometry |
data-dependent acquisition |
label free sample |
Q Exactive HF |
sample1.raw |
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This section applies to mass spectrometry-based proteomics experiments only. For affinity-based proteomics, these properties do not apply. |
For detailed documentation of sample preparation and MS/MS fragmentation properties, see the MS-Proteomics Template:
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Sample preparation: depletion, reduction reagent, alkylation reagent
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Fractionation: fractionation method (used with
comment[fraction identifier]) -
Fragmentation: collision energy, dissociation method
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For HCD (Higher-energy C-trap Dissociation), the canonical accession is MS:1000422 - beam-type collision-induced dissociation. Use NT=beam-type collision-induced dissociation;AC=MS:1000422 or the short label HCD. Do not use PRIDE:0000590 or MS:1002481.
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Proteomics data acquisition method can happen in multiple ways: Data Dependent Acquisition (DDA), Data Independent Acquisition (DIA), and targeted approaches. The SDRF-Proteomics file format REQUIRES capturing the method used for the data acquisition in the comment[proteomics data acquisition method] column. The values MUST be children of the PRIDE ontology term proteomics data acquisition method (PRIDE:0000659). The following values are commonly used:
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The comment[proteomics data acquisition method] column is REQUIRED for all mass spectrometry-based SDRF files. This field must be explicitly specified and cannot be omitted or assumed. |
You can find an example of a DIA experiment in the following link: DIA example
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For DIA experiments, additional properties like MS1 scan range can be captured. See DIA Scan Window Limits in the DIA-Acquisition Template. |
For detailed guidance on data file metadata, refer to the conventions document:
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MS-Proteomics Template - Detailed guidelines for labels, instruments, modifications, cleavage agents, mass tolerances, RAW file URIs, and other data file properties
Some columns can appear multiple times for the same sample. The cardinality rules are:
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Single (1): Column appears exactly once per sample (e.g.,
characteristics[biological replicate]) -
Multiple (*): Column can appear multiple times (e.g.,
comment[modification parameters]can specify multiple post-translational modifications)
Example of multiple comment[modification parameters] columns:
| source name | characteristics[…] | comment[modification parameters] | comment[modification parameters] | … |
|---|---|---|---|---|
sample-1 |
… |
NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=fixed;PP=Anywhere |
NT=Oxidation;AC=UNIMOD:35;TA=M;MT=variable;PP=Anywhere |
… |
Uniqueness constraints ensure data integrity:
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MUST be unique (error):
source name+assay name+comment[label] -
SHOULD be unique (warning):
source name+assay name -
Assay name: Each data file MUST have a unique
assay name
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For multiplexed experiments (TMT, iTRAQ), multiple rows share the same assay name since samples are in one MS run. The comment[label] distinguishes samples within the run.
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A template is a predefined set of metadata columns that ensures consistent annotation for specific experiment types. Templates define REQUIRED, RECOMMENDED, and OPTIONAL columns to make datasets FAIR-compliant.
Templates follow a layered hierarchy:
| Layer | Templates | Description |
|---|---|---|
TECHNOLOGY (required) |
Minimum valid SDRF - choose one |
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SAMPLE (recommended) |
human, vertebrates, invertebrates, plants, clinical-metadata, oncology-metadata |
Organism-specific and clinical metadata |
EXPERIMENT (optional) |
cell-lines, crosslinking, dia-acquisition, single-cell, immunopeptidomics, metaproteomics, olink, somascan |
Methodology-specific columns |
Child templates inherit all columns from parents and may add new columns or strengthen requirements (e.g., optional → required).
Some layers enforce mutually exclusive choices, while others allow combining multiple templates:
| Layer | Templates | Rule |
|---|---|---|
TECHNOLOGY |
|
Mutually exclusive — choose one (REQUIRED) |
SAMPLE |
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Mutually exclusive — choose one based on organism (RECOMMENDED) |
EXPERIMENT (MS) |
|
Can be combined (e.g., |
EXPERIMENT (affinity platform) |
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Mutually exclusive — choose one if using affinity-proteomics (OPTIONAL) |
Templates from different layers can be freely combined. Common valid combinations:
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ms-proteomics+human(human DDA proteomics) -
ms-proteomics+human+dia-acquisition(human DIA proteomics) -
ms-proteomics+human+immunopeptidomics(human immunopeptidomics) -
ms-proteomics+vertebrates+cell-lines(mouse cell line proteomics) -
ms-proteomics+human+crosslinking(human crosslinking MS) -
affinity-proteomics+human+olink(human Olink) -
affinity-proteomics+human+somascan(human SomaScan) -
ms-proteomics+metaproteomics(environmental metaproteomics) -
ms-proteomics+human+metaproteomics(human gut microbiome metaproteomics) -
ms-proteomics+human+single-cell(human single-cell proteomics)
Declare templates using comment[sdrf template] columns. Only list leaf templates (parents are implied). When using multiple templates, add multiple columns with the same name. Two formats are supported:
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Simple format (preferred):
template_name vX.Y.Z -
Key=value format:
NT=template_name;VV=vX.Y.Z
source name ... comment[sdrf template] comment[sdrf template]
sample_1 ... human v1.1.0 crosslinking v1.0.0Common examples:
| Experiment Type | Template Columns |
|---|---|
Human MS proteomics |
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Mouse MS proteomics |
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Human crosslinking |
Two columns: |
Human Olink |
Two columns: |
Sample templates (organism-specific):
| Template | Use For | Key Columns |
|---|---|---|
Human clinical samples |
disease, age, sex, ancestry |
|
Mouse, rat, zebrafish |
disease, developmental stage, strain |
|
Drosophila, C. elegans |
disease, developmental stage, genotype |
|
Arabidopsis, crops |
disease, developmental stage, growth conditions |
Experiment-type templates:
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DIA Acquisition - scan windows, isolation width
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Cell Lines - Cellosaurus integration
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Single-Cell - cell isolation, carrier proteome
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Immunopeptidomics - MHC protein complex, MHC typing
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Crosslinking MS - crosslinker reagents
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Metaproteomics - environmental sample type
Download templates from the templates folder.
You can add custom columns beyond template requirements for study-specific metadata. Rules:
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Use
characteristics[…]for sample metadata,comment[…]for technical metadata -
Column names MUST be valid ontology terms (search OLS)
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Use controlled vocabularies for values when available
See Additional Sample-Related Columns and SDRF Terms Reference for commonly used columns.
To propose a new template, open an issue on GitHub and submit a pull request.
Factor values identify the experimental variables being studied - the conditions you want to compare in your analysis. They highlight which sample characteristics are the focus of your experiment.
Use factor values to indicate:
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The primary variable(s) under investigation
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Conditions being compared (e.g., disease vs. normal, treated vs. untreated)
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Variables that define experimental groups
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Use normal (not "control") in the disease field for healthy samples. "Control" is an experimental design concept, not a disease state. See Disease Annotation Guidelines for details.
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-
Factor value columns SHOULD appear after all characteristics and comment columns
-
Multiple factor values can be used when studying multiple variables
-
The value in a factor value column typically mirrors a characteristics column value
In an experiment comparing tumor vs. normal tissue across different cancer stages:
| source name | … | characteristics[disease] | characteristics[disease staging] | … | factor value[disease] | factor value[disease staging] |
|---|---|---|---|---|---|---|
tumor_sample_1 |
… |
breast carcinoma |
stage II |
… |
breast carcinoma |
stage II |
normal_sample_1 |
… |
normal |
not applicable |
… |
normal |
not applicable |
tumor_sample_2 |
… |
breast carcinoma |
stage III |
… |
breast carcinoma |
stage III |
In this example, both disease and disease staging are factor values because the experiment aims to compare expression differences between disease states and across cancer stages.
SDRF-Proteomics uses ontologies and controlled vocabularies (CVs) to standardize metadata values. The following ontologies are supported:
| Category | Ontology/CV | Description | Notes |
|---|---|---|---|
General Purpose |
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General |
General experimental metadata |
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General |
Phenotype and Trait Ontology |
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General |
Biomedical terminology |
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General |
Proteomics-specific terms |
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Organism and Taxonomy |
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Taxonomy |
Organism classification |
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Anatomy and Cell Types |
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Anatomy |
Cross-species anatomy ontology |
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Cell Type |
Cell type classification |
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Anatomy |
Tissues and cell lines |
||
Anatomy |
Plant anatomy and development |
For plant samples |
|
Anatomy |
Drosophila anatomy |
For Drosophila samples |
|
Anatomy |
C. elegans anatomy |
For C. elegans samples |
|
Anatomy |
Zebrafish anatomy and development |
For zebrafish samples |
|
Disease (see Disease Annotation Guidelines) |
|||
Disease |
Unified disease ontology |
RECOMMENDED |
|
Disease |
Disease terms from EFO |
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Healthy samples |
Use |
||
Cell Lines |
|||
Cell Lines |
Cell line knowledge resource |
RECOMMENDED |
|
Cell Lines |
Cell line ontology |
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Mass Spectrometry and Proteomics |
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MS/Proteomics |
Instruments, methods, parameters |
||
Modifications |
Protein modifications database |
||
Modifications |
Protein modifications ontology |
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Other |
|||
Chemistry |
Chemical Entities of Biological Interest |
||
Environment |
Environmental sample classification |
For metaproteomics |
|
Ancestry |
Human ancestry categories |
For human samples |
|
The following table provides links to example SDRF files for different experiment types. Click "View in Explorer" to open the SDRF file in the interactive viewer.
| Experiment Type | Dataset | Description | View | Source |
|---|---|---|---|---|
Label-free |
PXD008934 |
Human proteome label-free quantification |
||
TMT |
PXD017710 |
TMT-labeled quantitative proteomics |
||
SILAC |
PXD000612 |
SILAC-based quantification |
||
DIA |
PXD018830 |
data-independent acquisition |
||
Phosphoproteomics |
PXD000759 |
PTM enrichment study |
||
Cell lines |
PXD001819 |
Cell line proteomics |
|
💡
|
Use the SDRF Explorer to browse all {total_datasets}+ annotated datasets with filtering, statistics, and interactive viewing. |
A comprehensive collection of annotated projects is available at: Annotated Projects Repository
This section provides the column definitions for each SDRF-Proteomics template. Each template shows only its own columns (not inherited ones). See the "Extends" field to identify which parent template’s columns are also included.
Version: 1.1.0 | Layer: internal | Extends: none | Usable alone: No
Base SDRF template with infrastructure columns (identifiers, data files, versioning) inherited by all proteomics templates. This is a construction artifact and cannot be used directly.
| Column Name | Req. | Description | Validators | Examples |
|---|---|---|---|---|
|
required |
Unique identifier for the biological sample |
||
|
required |
Unique identifier for the data acquisition run |
||
|
required |
Type of technology used |
single value only; values: proteomic profiling by mass spectrometry, protein expression profiling by antibody array, protein expression profiling by aptamer array |
|
|
required |
Identifier for the technical replicate (integer starting from 1) |
||
|
required |
Name of the raw data file |
||
|
recommended |
Version of the SDRF-Proteomics specification used to annotate this file |
semver |
v1.1.0, v2.0.0-dev |
|
optional |
Template name and version used for annotation. Two formats are supported - key=value format (NT=template_name;VV=vX.Y.Z) or simple format (template_name vX.Y.Z). Multiple templates can be specified using multiple columns. |
pattern: Template can be specified as 'NT=name;VV=vX.Y.Z' or 'name vX.Y.Z' |
NT=human;VV=v1.1.0, human v1.1.0, NT=ms-proteomics;VV=v1.1.0, ms-proteomics v1.1.0 |
|
optional |
Software tool or method used to generate or annotate the SDRF file. Two formats are supported - key=value format (NT=tool_name;VV=vX.Y.Z) or simple format (tool_name vX.Y.Z). |
pattern: Annotation tool can be specified as 'NT=name;VV=vX.Y.Z' or 'name vX.Y.Z' or 'manual curation' |
NT=lesSDRF;VV=v0.1.0, lesSDRF v0.1.0, NT=sdrf-pipelines;VV=v1.0.0, sdrf-pipelines v1.0.0, … |
|
optional |
Hash value for SDRF validation integrity checking |
pattern: Validation hash string |
Version: 1.0.0 | Layer: internal | Extends: base | Usable alone: No
SDRF template with shared sample metadata columns (organism, tissue, disease). This is an internal construction layer inherited by technology and organism templates - not used directly.
| Column Name | Req. | Description | Validators | Examples |
|---|---|---|---|---|
|
required |
Species of the sample using NCBI Taxonomy |
ontology: ncbitaxon |
homo sapiens, mus musculus, rattus norvegicus, saccharomyces cerevisiae |
|
required |
Anatomical part of the organism from which sample was derived |
ontology: uberon, bto |
liver, brain, heart, blood |
|
recommended |
Cell type of the sample |
ontology: cl, bto, clo |
hepatocyte, neuron, fibroblast, T cell |
|
required |
Identifier for the biological replicate (integer starting from 1, or 'pooled' for pooled samples) |
pattern: Biological replicate should be an integer or 'pooled' for pooled reference samples |
1, 2, pooled |
|
optional |
Whether the sample is a pooled sample combining material from multiple biological sources. Use 'not pooled' for individual samples, 'pooled' when sources are unknown, or 'SN=sample1;SN=sample2' to list source names. |
values: not pooled, pooled; pattern: Use 'not pooled', 'pooled', or list sample IDs with SN= prefix |
SN=sample1;SN=sample2 |
|
optional |
Classification of the sample role in the experiment. Distinguishes experimental samples from controls, references, and other roles in multiplexed or plate-based experiments. |
ontology: pride |
single cell, reference, bridge, carrier, … |
|
recommended |
Disease state of the sample |
ontology: mondo, efo, doid, ncit, pato |
normal, breast cancer, infection, metabolic disease |
|
optional |
Type of biological material being analyzed |
values: tissue, cell, cell line, organism part, … |
|
|
optional |
Mass of tissue used for extraction |
number with unit (mg, g, ug) |
50 mg, 1 g, 500 ug |
|
optional |
BioSample accession number for the sample (e.g., SAMN or SAMEA identifiers) |
accession: biosample |
SAMN12345678, SAMEA12345678, SAMD1234567 |
|
optional |
Time at which the sample was collected (for longitudinal or time-course studies) |
number with unit (hour, day, minute, week, month, year) |
0 hour, 24 hour, 7 day, 3 month |
|
optional |
Treatment or perturbation applied to the sample (drug, stimulus, environmental stress) |
ontology: ncit, efo |
untreated, LPS stimulation, doxorubicin treatment, drought stress, … |
|
optional |
Whether the sample is a synthetic peptide library or biological material |
values: synthetic, not synthetic |
|
|
optional |
Spiked-in compound details using key-value format (CT=compound type, QY=quantity, PS=peptide sequence, AC=UniProt accession, CN=compound name, CV=vendor) |
pattern: Key-value format for spiked compound details (CT=type, SP=species, QY=quantity, PS=sequence, AC=accession, CN=name, CV=vendor) |
CT=peptide;PS=PEPTIDESEQ;QY=10 fmol, CT=protein;AC=A9WZ33;QY=20 nmol, CT=protein;SP=Homo sapiens;QY=1 pmol;AC=P37840, CT=mixture;CN=iRT mixture;CV=Biognosys;QY=1 pmol |
|
optional |
Enrichment strategy applied to the sample (e.g., phosphopeptide enrichment, crosslinked peptide enrichment, glycopeptide enrichment) |
ontology: pride, efo |
enrichment of cross-linked peptides, enrichment of phosphorylated protein, enrichment of glycopeptides, enrichment of ubiquitinated proteins |
Version: 1.1.0 | Layer: technology | Extends: sample-metadata | Usable alone: Yes
Base SDRF template for mass spectrometry-based proteomics. This is the minimum valid template for any MS experiment.
| Column Name | Req. | Description | Validators | Examples |
|---|---|---|---|---|
|
required |
Type of technology used |
single value only; values: proteomic profiling by mass spectrometry |
|
|
required |
Mass spectrometry acquisition method |
ontology: pride |
data-dependent acquisition, data-independent acquisition, parallel reaction monitoring, selected reaction monitoring |
|
required |
Mass spectrometer instrument used |
ontology: ms, pride |
LTQ Orbitrap, Q Exactive, Orbitrap Fusion Lumos, timsTOF Pro |
|
required |
Enzyme or chemical used for protein digestion |
ontology: ms |
NT=Trypsin;AC=MS:1001251, NT=Lys-C;AC=MS:1001309, NT=Chymotrypsin;AC=MS:1001306 |
|
required |
Labeling strategy used for quantification |
ontology: pride |
label free sample, SILAC light, SILAC heavy, TMT126, … |
|
required |
Fraction number for fractionated samples (integer, use 1 for non-fractionated). In MS proteomics, this identifies the chromatographic or electrophoretic fraction (e.g., SCX, hpHRP, SEC fractions). Each fraction maps to one data file. |
||
|
recommended |
Fragmentation method used in MS/MS |
ontology: ms, pride |
HCD, CID, ETD, EThcD |
|
optional |
Peptide fractionation method used before MS analysis |
ontology: pride |
High-pH reversed-phase chromatography (hpHRP), Strong cation-exchange chromatography (SCX), Strong anion-exchange chromatography (SAX), Size-exclusion chromatography (SEC) |
|
optional |
Collision energy used for fragmentation |
pattern: Collision energy format: {value} {unit} where unit is NCE or eV. For multiple values, use semicolon-separated entries. |
30 NCE, 30% NCE, 27 eV, 25 NCE;27 NCE;30 NCE |
|
recommended |
Precursor mass tolerance for database search |
number with unit (ppm, Da, mmu) |
10 ppm, 20 ppm, 0.5 Da, 20 mmu |
|
recommended |
Fragment mass tolerance for database search |
number with unit (ppm, Da, mmu) |
0.02 Da, 20 ppm, 50 mmu |
|
optional |
Chemical reagent used for disulfide bond reduction |
ontology: pride, ms |
dithiothreitol, tris(2-carboxyethyl)phosphine |
|
optional |
Chemical reagent used for cysteine alkylation |
ontology: pride, ms |
iodoacetamide, chloroacetamide |
|
optional |
Whether abundant protein depletion was performed |
values: no depletion, depletion |
|
|
recommended |
Post-translational modifications searched |
ontology: unimod, mod |
NT=Oxidation;MT=Variable;TA=M;AC=Unimod:35, NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4 |
|
optional |
Mass analyzer used for MS2 acquisition |
ontology: ms |
orbitrap, ion trap, TOF |
|
optional |
Batch identifier for sample preparation (plate, chip, processing batch). Useful for batch effect correction in multi-batch experiments. |
pattern: Sample preparation batch identifier |
plate1, batch_20220601, prep_A |
|
optional |
Liquid chromatography batch identifier for batch effect tracking (e.g., column changes, LC system swaps) |
pattern: LC batch identifier |
LC1, column_A |
|
optional |
Date of MS data acquisition (ISO 8601 format recommended). Useful for tracking instrument drift and batch effects. |
pattern: Acquisition date/time |
2022-06-01, 2022-06-01T18:28:37 |
|
optional |
MS method-defined minimum precursor (MS1) m/z setting used to acquire the data |
m/z value |
100m/z, 200m/z, 350.5m/z |
|
optional |
MS method-defined maximum precursor (MS1) m/z setting used to acquire the data |
m/z value |
1200m/z, 1600m/z, 2000m/z |
|
optional |
MS method-defined minimum precursor charge state setting used to acquire the data |
pattern: Integer charge state |
1, 2 |
|
optional |
MS method-defined maximum precursor charge state setting used to acquire the data |
pattern: Integer charge state |
6, 7, 8 |
|
optional |
LC method-defined minimum retention time setting used to acquire the data (in minutes) |
pattern: Numeric retention time in minutes |
0, 5, 10.5 |
|
optional |
LC method-defined maximum retention time setting used to acquire the data (in minutes) |
pattern: Numeric retention time in minutes |
60, 90, 120 |
|
optional |
MS method-defined minimum ion mobility setting used to acquire the data (1/K0 or Vs/cm2) |
pattern: Numeric ion mobility value |
0.6, 0.7 |
|
optional |
MS method-defined maximum ion mobility setting used to acquire the data (1/K0 or Vs/cm2) |
pattern: Numeric ion mobility value |
1.3, 1.4, 1.6 |
|
optional |
MS method-defined minimum product ion (MS2) m/z setting used to acquire the data |
m/z value |
100m/z, 200m/z |
|
optional |
MS method-defined maximum product ion (MS2) m/z setting used to acquire the data |
m/z value |
1800m/z, 2000m/z |
|
optional |
MS method-defined minimum product ion (MS3) m/z setting used to acquire the data |
m/z value |
100m/z, 200m/z |
|
optional |
MS method-defined maximum product ion (MS3) m/z setting used to acquire the data |
m/z value |
1500m/z, 2000m/z |
|
optional |
m/z scan range for MS1 spectra as an interval. Alternative to separate ms min mz / ms max mz columns |
m/z range interval |
400m/z-1200m/z, 350m/z-1600m/z |
|
optional |
m/z scan range for MS2 spectra as an interval. Alternative to separate ms2 min mz / ms2 max mz columns |
m/z range interval |
100m/z-2000m/z, 200m/z-1800m/z |
|
optional |
m/z scan range for MS3 spectra as an interval. Alternative to separate ms3 min mz / ms3 max mz columns |
m/z range interval |
100m/z-1500m/z, 200m/z-2000m/z |
|
optional |
Conditions used for peptide/protein elution |
pattern: Free-text elution conditions |
0.1% TFA in water, 80% acetonitrile, gradient 5-35% ACN in 60 min |
Version: 1.0.0 | Layer: technology | Extends: sample-metadata | Usable alone: Yes
SDRF template for affinity-based proteomics experiments (Olink, SomaScan). This is the base template for all affinity proteomics experiments.
| Column Name | Req. | Description | Validators | Examples |
|---|---|---|---|---|
|
required |
Type of technology used |
single value only; values: protein expression profiling by antibody array, protein expression profiling by aptamer array |
|
|
required |
Affinity proteomics platform used (e.g. Olink Explore HT, SomaScan Assay 7K) |
single value only; ontology: pride |
Olink Explore HT, Olink Target 96, SomaScan Assay 11K |
|
optional |
Instrument used for data acquisition (e.g. sequencer, qPCR machine, microarray reader) |
ontology: ms, pride |
Illumina NovaSeq X, Illumina NextSeq 2000, Agilent SureScan Microarray Scanner |
|
recommended |
Name of the commercial panel used |
pattern: Panel name |
Olink Explore 3072, Olink Explore 1536, Olink Target 96 Inflammation, SomaScan 7K, … |
|
optional |
Version of the assay panel |
pattern: Panel version |
v4.1, 2023-01, 7K v4.1 |
|
optional |
Unit of quantification for the assay (platform-specific) |
values: NPX, RFU |
|
|
optional |
Plate identifier for batch effect analysis |
pattern: Plate identifier |
1, 2 |
|
recommended |
Type of biological matrix used as input (e.g. serum, plasma, CSF, urine) |
ontology: uberon, bto |
serum, plasma, cerebrospinal fluid, urine, … |
|
optional |
Normalization method applied to quantification values |
pattern: Normalization method |
plate control normalized, bridge normalized, median normalization, not normalized |
|
optional |
Fraction or dilution series identifier. While fractionation is rare in affinity proteomics, dilution series are used in some protocols (e.g. SomaScan alternative matrix validation). |
pattern: Fraction or dilution identifier |
1, 2, 3 |
Version: 1.1.0 | Layer: sample | Extends: sample-metadata | Usable alone: No
Human SDRF template with human-specific sample metadata fields. Must be combined with a technology template (ms-proteomics or affinity-proteomics).
| Column Name | Req. | Description | Validators | Examples |
|---|---|---|---|---|
|
required |
(override: requirement set to required) |
||
|
recommended |
Ancestry or ethnic background of the donor |
ontology: hancestro |
European, African, Asian, Hispanic or Latin American |
|
required |
Age of the donor at sample collection |
pattern: Age format: 45Y, 6M, 30Y6M (Y>M>W>D order), ranges like 40Y-50Y, or comparison operators like >18Y, >=21Y, <65Y. Use "not available" if unknown, "anonymized" if redacted, or "pooled" for pooled samples. |
45Y, 6M, 30Y6M, 30Y6M2W, … |
|
required |
Biological sex of the donor |
values: male, female, intersex |
|
|
optional |
Developmental stage of the donor |
ontology: efo |
adult, embryonic stage, fetal stage, infant stage |
|
recommended |
Unique identifier for the donor individual |
identifier |
patient_001, donor-A1, subject_12, anonymized, … |
Version: 1.1.0 | Layer: sample | Extends: sample-metadata | Usable alone: No
SDRF template for non-human vertebrate samples (mammals, birds, fish, reptiles, amphibians). Must be combined with a technology template (ms-proteomics or affinity-proteomics).
| Column Name | Req. | Description | Validators | Examples |
|---|---|---|---|---|
|
required |
(override: requirement set to required) |
||
|
required |
Developmental stage of the organism |
ontology: efo |
adult, embryo, juvenile, larval stage |
|
recommended |
Strain or breed of the organism |
ontology: ncbitaxon |
C57BL/6, Sprague-Dawley, BALB/c, Wistar |
|
recommended |
Biological sex of the organism |
values: male, female, hermaphrodite |
Version: 1.1.0 | Layer: sample | Extends: sample-metadata | Usable alone: No
SDRF template for invertebrate samples (Drosophila, C. elegans, insects, etc.). Must be combined with a technology template (ms-proteomics or affinity-proteomics).
| Column Name | Req. | Description | Validators | Examples |
|---|---|---|---|---|
|
required |
(override: requirement set to required) |
||
|
required |
Developmental stage of the organism |
ontology: efo |
adult stage, larval stage, pupal stage, embryonic stage |
|
required |
Strain of the organism |
ontology: ncbitaxon |
Oregon-R, w1118, N2, Canton-S |
|
optional |
Genotype of the organism |
pattern: Genotype notation following standard conventions |
wild type, daf-2(e1370), w[*]; P{GAL4} |
Version: 1.1.0 | Layer: sample | Extends: sample-metadata | Usable alone: No
SDRF template for plant samples (Arabidopsis, crops, etc.). Must be combined with a technology template (ms-proteomics or affinity-proteomics).
| Column Name | Req. | Description | Validators | Examples |
|---|---|---|---|---|
|
ontology: uberon, bto, po |
flower bud, leaf, root, seed |
||
|
required |
(override: requirement set to required) |
||
|
required |
Developmental stage of the plant |
ontology: efo |
seedling stage, flowering stage, rosette growth stage, senescent stage |
|
recommended |
Cultivar, ecotype, or accession of the plant |
pattern: Plant cultivar or ecotype name |
Col-0, Ler-0, Nipponbare, B73 |
|
recommended |
Growth conditions for the plant |
pattern: Description of growth conditions |
long day (16h light/8h dark), short day (8h light/16h dark), continuous light, greenhouse |
|
recommended |
(override: requirement set to recommended) |
Version: 1.0.0 | Layer: sample | Extends: sample-metadata | Usable alone: No
SDRF template for clinical study samples with treatment, demographics, and lifestyle metadata. Applicable to any organism. Combine with organism template (human, vertebrates) and technology template (ms-proteomics, affinity-proteomics).
| Column Name | Req. | Description | Validators | Examples |
|---|---|---|---|---|
|
required |
(override: requirement set to required) |
||
|
optional |
Chemical compound or drug applied to sample |
ontology: chebi, ncit, efo |
doxorubicin, cisplatin, tamoxifen, metformin |
|
optional |
Dose or concentration of compound treatment |
number with unit (mg/kg, uM, nM, mg, ug, mg/mL, ug/mL, mM) |
10 mg/kg, 50 uM, 100 nM, 5 mg |
|
optional |
Duration of treatment exposure |
number with unit (hour, day, minute, week, month) |
24 hour, 5 day, 30 minute, 2 week |
|
optional |
Treatment status at time of sampling |
values: pre-treatment, on treatment, post-treatment, treatment naive |
|
|
optional |
Response to treatment (for studies measuring therapeutic outcomes) |
ontology: ncit |
complete response, partial response, progressive disease, stable disease |
|
optional |
Pre-existing medical conditions or comorbidities |
ontology: mondo, efo, doid |
diabetes mellitus, hypertension, obesity |
|
optional |
Body mass index (BMI) in kg/m^2 |
pattern: Numeric BMI value |
24.5, 31.2, 18.7 |
|
optional |
Patient smoking status |
ontology: ncit |
never smoker, former smoker, current smoker |
|
optional |
Menopausal status for female patients |
values: pre-menopausal, peri-menopausal, post-menopausal |
|
|
optional |
Method of genetic modification (knockout, knockdown, overexpression, transduction) |
ontology: efo |
knockout, knockdown, overexpression, transduction, … |
|
optional |
Observable characteristics or traits (drug sensitivity, molecular markers, expression phenotypes) |
ontology: pato, efo |
drug resistant, HER2-positive, high expresser, wild-type phenotype |
|
optional |
Body weight of the subject |
number with unit (kg, g, lb) |
70 kg, 55 kg, 154 lb |
|
optional |
Height of the subject |
number with unit (cm, m) |
175 cm, 1.75 m, 160 cm |
|
optional |
Specific anatomical location or context of sampling within the organism part |
ontology: uberon, bto |
tumor, normal tissue adjacent to tumor, left ventricle, frontal cortex |
|
optional |
Known genetic variant, mutation, or genotype of the subject |
pattern: Genotype as free text (gene name + variant) |
BRCA1 mutation carrier, KRAS G12D mutant, wild type, TP53 R175H |
Version: 1.0.0 | Layer: sample | Extends: clinical-metadata | Usable alone: No
SDRF template for cancer/oncology study samples with tumor staging, grading, and clinical outcome metadata. Extends clinical-metadata with oncology-specific columns. Combine with organism template (human, vertebrates) and technology template (ms-proteomics, affinity-proteomics).
| Column Name | Req. | Description | Validators | Examples |
|---|---|---|---|---|
|
optional |
Disease progression stage (stage I-IV, chronic phase, end stage) |
ontology: ncit, efo |
stage I, stage II, stage III, stage IV, … |
|
optional |
Histological tumor grade (describes how abnormal cells look) |
ontology: ncit |
grade 1, grade 2, grade 3, grade 4, … |
|
optional |
TNM staging notation (describes extent of cancer spread) |
ontology: ncit |
T2N1M0, T3N0M0, T1N0M0, T4N2M1 |
|
optional |
Tumor size measurement |
number with unit (cm, mm) |
2.5 cm, 15 mm, 0.8 cm |
|
optional |
Tumor mass/weight measurement |
number with unit (g, mg) |
15 g, 250 mg |
|
optional |
Cancer molecular or histologic subtype |
ontology: ncit |
luminal A, luminal B, HER2-enriched, triple-negative, … |
|
optional |
Location where cancer has spread from primary site |
ontology: uberon, bto |
liver, lung, bone, brain |
|
optional |
Specific anatomical location of biopsy |
ontology: uberon, bto |
breast, colon, prostate, lung |
|
optional |
Free-text clinical details (receptor status, treatment history, surgical details) |
pattern: Free-text clinical data |
ER+/PR+/HER2-, prior chemotherapy with doxorubicin, surgical resection performed |
|
optional |
Relevant medical history information for the patient |
pattern: Free-text clinical history |
family history of breast cancer, previous radiation therapy, no significant medical history |
|
optional |
Patient survival time for survival analysis studies |
number with unit (month, year, day, week) |
24 month, 3 year, 180 day |
|
optional |
Time of last clinical follow-up for longitudinal studies |
number with unit (month, year, day, week) |
36 month, 5 year, 365 day |
|
optional |
Number of mitoses per high-power field (indicator of tumor proliferation) |
pattern: Mitotic rate as count or count per HPF |
5, 12/10 HPF, 3/10 HPF |
|
optional |
Dukes staging for colorectal cancer (A, B, C, D) |
values: A, B, C, D |
|
|
optional |
Ann Arbor staging for lymphoma (I, II, III, IV with optional A/B suffix) |
pattern: Ann Arbor stage (I-IV with optional A/B suffix for symptoms, E for extranodal, S for spleen) |
IA, IIB, IIIA, IVB, … |
|
optional |
Gleason score for prostate cancer grading (sum of two pattern grades, range 2-10) |
pattern: Gleason score as sum (e.g., 7) or component pattern (e.g., 3+4) |
7, 3+4, 4+3, 9, … |
|
optional |
Weiss scoring system for adrenal cortical carcinoma (low or high) |
values: low, high |
Version: 1.1.0 | Layer: experiment | Extends: ms-proteomics | Usable alone: No
SDRF template for Data-independent acquisition (DIA) experiments. Extends ms-proteomics with DIA-specific columns.
| Column Name | Req. | Description | Validators | Examples |
|---|---|---|---|---|
|
required |
Mass spectrometry acquisition method (restricted to DIA for this template) |
single value only; values: Data-independent acquisition |
|
|
recommended |
Lower m/z limit of the DIA scan window |
pattern: m/z value as a number |
400, 350.5 |
|
recommended |
Upper m/z limit of the DIA scan window |
pattern: m/z value as a number |
1200, 1000 |
|
recommended |
Width of the isolation window in m/z units |
pattern: Width in m/z |
25, 8, 4 |
|
recommended |
Specific DIA method variant used |
ontology: pride |
SWATH-MS, MSE, All ion fragmentation, diaPASEF |
Version: 1.0.0 | Layer: experiment | Extends: ms-proteomics | Usable alone: No
SDRF template for single-cell proteomics (SCP) experiments. Works with any organism - combine with appropriate sample template (human, vertebrates, invertebrates, or plants). Aligned with Nature Methods SCP guidelines (Gatto et al., 2023).
| Column Name | Req. | Description | Validators | Examples |
|---|---|---|---|---|
|
recommended |
(override: requirement set to recommended) |
||
|
required |
Method used to isolate single cells (FACS, cellenONE, LCM, etc.) |
values: FACS, cellenONE, microfluidics, laser capture microdissection, … |
|
|
required |
Unique identifier for each single cell within the experiment. Required per SCP guidelines for tracking cells through analysis. |
identifier |
cell_001, SC_A1, well_B3, barcode_ATCGATCG, … |
|
recommended |
Batch identifier for sample preparation (plate, chip, processing batch). Critical for batch effect correction. |
||
|
recommended |
Number of cells per well/reaction. Use 1 for true single cells, higher numbers for small pools. |
pattern: Number of cells |
1, 5, 10, 100 |
|
recommended |
TMT/TMTpro channel used for the carrier proteome |
pattern: TMT channel label for carrier |
TMT131C, TMTpro134N, TMT126 |
|
recommended |
TMT/TMTpro channel used for the reference sample (for normalization across sets) |
pattern: TMT channel label for reference |
TMT131N, TMTpro133C, TMT127N |
|
optional |
Forward scatter (FSC) value from flow cytometry - proxy for cell size |
pattern: FSC value (numeric) |
316.0, 250 |
|
optional |
Side scatter (SSC) value from flow cytometry - proxy for cell granularity/complexity |
pattern: SSC value (numeric) |
301.0, 184 |
|
optional |
Markers used for cell sorting/enrichment with optional intensity values |
pattern: Enrichment marker(s) and optional intensity |
CD45+, GFP+, CD3+CD4+, CD34:APC-Cy7-A=276.0, … |
|
optional |
Viability status of the cell at isolation |
values: live, viable, dead, unknown |
|
|
optional |
Cell cycle phase if determined (e.g., by FACS or computational inference) |
values: G1, S, G2, G2/M, … |
|
|
optional |
Physical diameter of the isolated cell if measured (in micrometers) |
number with unit (um, μm) |
15 um, 20.5 um, 12 μm |
|
optional |
X,Y coordinates if cells were isolated from a spatial context (e.g., LCM from tissue) |
pattern: Spatial coordinates |
X=100;Y=250, X=50.5;Y=120.3 |
|
optional |
Tissue section identifier for spatially resolved single-cell proteomics |
pattern: Tissue section identifier |
section_001, slide_A_section_3 |
|
optional |
Nozzle diameter used for FACS-based single cell isolation (in micrometers) |
number with unit (um, μm) |
70 um, 100 um, 130 μm |
|
optional |
Sorting mode used during FACS isolation |
values: single cell, purity, yield, 4-way purity |
|
|
optional |
Type and manufacturer of the microfluidics chip used for single cell isolation |
pattern: Chip type/manufacturer identifier |
Fluidigm C1, Cellenion cellenCHIP, nanowell chip |
|
optional |
Model of the laser capture microdissection microscope used for cell isolation |
pattern: LCM microscope model name |
Leica LMD7, Zeiss PALM MicroBeam, Thermo LCM |
|
optional |
Version of the nanoPOTS chip used for single cell sample preparation |
pattern: nanoPOTS chip version identifier |
nanoPOTS v1, nanoPOTS v2, 9-well chip |
Version: 1.0.0 | Layer: experiment | Extends: ms-proteomics | Usable alone: No
SDRF template for immunopeptidomics experiments (MHC-bound peptide identification). Works with any organism - combine with appropriate sample template (human for HLA typing, vertebrates for H-2/MHC typing in mouse, etc.).
| Column Name | Req. | Description | Validators | Examples |
|---|---|---|---|---|
|
required |
MHC protein complex targeted for immunopeptidome enrichment (GO:0042611) |
values: MHC class I protein complex, MHC class II protein complex, non-classical MHC protein complex, mutant MHC protein complex, MHC protein complex with serotype |
|
|
required |
Method used to enrich MHC-bound peptides |
values: immunoaffinity purification, immunoaffinity purification (iodoacetamide), mild acid elution, detergent lysis |
|
|
recommended |
MHC alleles expressed by the sample (PRIDE:0000893) following IPD-MHC nomenclature (https://www.ebi.ac.uk/ipd/mhc/). Use IPD-IMGT/HLA notation for human (HLA-A*02:01), H-2 notation for mouse (H-2Kb, H-2Db), or appropriate IPD-MHC notation for other species. Multiple alleles can be separated by semicolons. |
pattern: MHC allele notation (HLA for human, H-2 for mouse). Supports multi-allele (semicolon-separated), 2-4 field resolution. |
HLA-A*02:01, HLA-B*07:02, HLA-A*02:01;HLA-B*07:02;HLA-C*07:02, HLA-A*02:01:01, … |
|
optional |
MHC typing method used (PRIDE:0000894). Values mapped to NCIT where available: NGS-based typing (NCIT:C101293), sequence-based typing (NCIT:C130180), PCR-SSO (NCIT:C130181), PCR-SSP (NCIT:C130179), PCR-based genotyping (NCIT:C17003) |
values: NGS-based typing, sequence-based typing, PCR-SSO, PCR-SSP, … |
|
|
recommended |
Antibody clone used for MHC immunoprecipitation |
pattern: Antibody clone name |
W6/32, BB7.2 |
Version: 1.0.0 | Layer: experiment | Extends: ms-proteomics | Usable alone: No
SDRF template for crosslinking mass spectrometry (XL-MS) experiments. Extends ms-proteomics with crosslinking-specific columns for data analysis.
| Column Name | Req. | Description | Validators | Examples |
|---|---|---|---|---|
|
recommended |
MS-based cross-linking methodology used to identify this as a crosslinking dataset |
values: cross-linking mass spectrometry |
|
|
recommended |
(override: requirement set to recommended) |
||
|
required |
Cross-linker compound with structured properties for analysis tools. Format: NT=name;AC=accession;CL=cleavable;TA=targets;MH/ML=stub masses Uses XLMOD ontology (parent term XLMOD:00004). |
structured_kv |
NT=DSS;AC=XLMOD:02001, NT=BS3;AC=XLMOD:02000, NT=DSSO;AC=XLMOD:02010;CL=yes;TA=K,S,T,Y,nterm;MH=54.01;ML=85.98, NT=EDC;AC=XLMOD:02009;CL=no;TA=K,D,E |
|
required |
Fragmentation method used in MS2. Critical for cleavable crosslinkers (DSSO, DSBU) which generate diagnostic stub ions under specific fragmentation conditions. |
ontology: ms, pride |
HCD, CID, ETD, EThcD, … |
|
recommended |
Collision energy used for fragmentation. Important for cleavable crosslinker analysis. |
pattern: Collision energy format: {value} {unit} where unit is NCE or eV. For stepped collision energies, use semicolon-separated values or 'stepped' prefix. |
30 NCE, 30% NCE, 27 eV, 25 NCE;27 NCE;30 NCE, … |
|
recommended |
Method used to enrich crosslinked peptides before MS analysis |
ontology: pride, ms |
size exclusion chromatography, strong cation exchange chromatography, high-pH reversed-phase chromatography, FAIMS |
|
optional |
Maximum Cα-Cα distance constraint provided by the crosslinker (for structural interpretation) |
number with unit (Å) |
30 Å, 26.4 Å, 11.4 Å |
|
optional |
Concentration of crosslinking reagent used |
number with unit (mM, uM, µM) |
2 mM, 500 uM, 1 mM |
|
optional |
Duration of the crosslinking reaction |
number with unit (min, h, s) |
30 min, 1 h, 45 min |
|
optional |
Temperature at which crosslinking was performed |
number with unit (°C) |
25°C, 4°C, 37°C, room temperature |
|
optional |
Molar ratio of crosslinker to protein |
pattern: Ratio format (e.g., 50:1 or 1:1 w/w) |
3001, 6001, 1:1 w/w |
|
optional |
Reagent used to quench the crosslinking reaction |
pattern: Chemical name of quenching reagent |
Tris-HCl, ammonium bicarbonate, glycine |
Version: 1.1.0 | Layer: experiment | Extends: sample-metadata | Usable alone: No
SDRF template for cell line samples with Cellosaurus-based annotation. Cell lines can originate from any organism - combine with appropriate organism template (human for HeLa, vertebrates for NIH 3T3, invertebrates for Sf9).
| Column Name | Req. | Description | Validators | Examples |
|---|---|---|---|---|
|
required |
Name of the cell line |
ontology: clo, bto, efo |
HeLa, HEK293, MCF7, A549 |
|
required |
Disease state of the donor tissue from which the cell line was established |
||
|
required |
Cellosaurus accession number for the cell line |
accession: cellosaurus |
CVCL_0030, CVCL_0004 |
|
recommended |
Official Cellosaurus name for the cell line |
||
|
optional |
Tissue or organ from which the cell line was derived |
ontology: uberon, bto |
cervix, kidney, breast |
|
recommended |
Passage number of the cell line used in the experiment |
pattern: Passage number should be an integer or range |
10, 15-20, 5 |
|
optional |
BioBank or source from which the cell line was obtained |
pattern: Source of the cell line |
ATCC, DSMZ, ECACC, Sigma-Aldrich |
|
optional |
Method used to authenticate the cell line identity |
pattern: Authentication method used |
STR profiling, SNP fingerprinting, cytogenetic analysis |
|
recommended |
Culture medium used to grow the cell line |
ontology: ncit |
DMEM, RPMI 1640, MEM, Ham’s F-12 |
|
optional |
Developmental stage of the donor from which the cell line was derived |
ontology: efo |
adult, embryonic, fetal, neonatal |
|
optional |
Ancestry category of the cell line donor (if known) |
ontology: hancestro |
European, African, East Asian, South Asian |
|
recommended |
Storage temperature of the cell line (in Celsius) |
number with unit (°C) |
-80 °C, -20 °C, 4 °C |
Version: 1.0.0 | Layer: experiment | Extends: affinity-proteomics | Usable alone: No
SDRF template for Olink Proximity Extension Assay (PEA) experiments. Extends affinity-proteomics with Olink-specific columns.
| Column Name | Req. | Description | Validators | Examples |
|---|---|---|---|---|
|
required |
Specific Olink panel name |
pattern: Olink panel name |
Target 96 Inflammation, Target 96 Cardiovascular II, Explore 384 Cardiometabolic, Explore 1536, … |
|
required |
Olink platform version |
values: Olink Target 96, Olink Explore 384, Olink Explore HT, Olink Reveal |
|
|
recommended |
Normalization method applied to NPX values |
values: plate control normalized, intensity normalized, bridge normalized, not normalized |
|
|
optional |
Reagent lot number for traceability |
pattern: Lot number |
lot_2023_001, B12345 |
Version: 1.0.0 | Layer: experiment | Extends: affinity-proteomics | Usable alone: No
SDRF template for SomaScan aptamer-based proteomics experiments. Extends affinity-proteomics with SomaScan-specific columns.
| Column Name | Req. | Description | Validators | Examples |
|---|---|---|---|---|
|
required |
SomaScan assay menu (number of aptamers/proteins measured) |
values: SomaScan 1.1K, SomaScan 1.3K, SomaScan 5K, SomaScan 7K, SomaScan 11K |
|
|
required |
SomaScan instrument/platform version |
values: SomaScan Assay, SomaScan Assay v4, SomaScan Assay v4.1 |
|
|
recommended |
Sample dilution factor used |
pattern: Standard SomaScan dilution factors |
0.005%, 0.5%, 20%, 40% |
|
optional |
Reagent lot number for traceability |
pattern: Lot number |
SS-2023-001, lot_12345 |
Version: 1.0.0 | Layer: sample | Extends: base | Usable alone: No
Base SDRF template for metaproteomics experiments (microbial community proteomics). Extends base directly and defines MIxS-aligned sample metadata. When combined with ms-proteomics, sample-metadata columns (organism, disease, cell type) are excluded. Use a child template (human-gut, soil, water) for environment-specific fields.
| Column Name | Req. | Description | Validators | Examples |
|---|---|---|---|---|
|
required |
Type of environmental sample analyzed (ENVO or EFO term). Corresponds to MIxS env_medium (MIXS:0000014). |
ontology: envo, efo |
soil, seawater, gut microbiome, wastewater, … |
|
recommended |
Geographic location where sample was collected (GAZ term or coordinates). Corresponds to MIxS geo_loc_name (MIXS:0000010). |
ontology: gaz |
Pacific Ocean, Amazon rainforest, 47.6062 N, 122.3321 W |
|
recommended |
Environmental material from which the sample was obtained (ENVO term). Corresponds to MIxS env_medium (MIXS:0000014). |
ontology: envo |
soil, seawater, freshwater, feces, … |
|
optional |
Date when sample was collected (ISO 8601) |
date |
2024, 2024-01, 2024-01-15 |
|
optional |
Method used to collect the environmental sample |
pattern: Collection method description |
grab sample, core sample, swab, filtration |
|
optional |
Depth at which sample was collected. Corresponds to MIxS depth (MIXS:0000018). |
number with unit (m, cm, mm) |
10 m, 50 cm, 100 m |
|
optional |
Altitude or elevation of sampling site. Corresponds to MIxS elevation (MIXS:0000093). |
number with unit (m) |
500 m, 1200 m, 0 m |
|
optional |
Temperature at sampling location. Corresponds to MIxS temperature (MIXS:0000113). |
number with unit (°C) |
25 °C, 4 °C, -20 °C |
|
optional |
pH at sampling location |
pattern: pH value |
7.0, 5.5, 8.2 |
|
optional |
Storage conditions for the sample before analysis |
pattern: Storage conditions |
-80C, liquid nitrogen, 4C |
|
optional |
Accession number for matched metagenome data |
accession: |
MGYA00001234, SRP123456 |
|
optional |
Source of the microbiome being studied (e.g., gut microbiome, rhizosphere microbiome) |
pattern: Microbiome source description |
gut microbiome, rhizosphere microbiome, oral microbiome, skin microbiome |
|
optional |
Estimated microbial biomass in the sample |
pattern: Biomass estimation |
1e9 cells/g, high biomass, low biomass |
|
optional |
Level of host protein contamination if known |
pattern: Host contamination level |
low (<5%), moderate (5-20%), high (>20%) |
|
optional |
Contaminant database(s) used in database search |
pattern: Contaminant database name(s) |
cRAP, MaxQuant contaminants, cRAP;MaxQuant contaminants |
|
optional |
Identifier or name of mock community standard used |
pattern: Mock community identifier |
ZymoBIOMICS Microbial Community Standard, ATCC MSA-1000 |
|
optional |
Description of mock community composition (species and ratios) |
pattern: Community composition description |
8 bacteria + 2 yeasts at defined ratios, even mix of 10 species |
|
optional |
Semicolon-separated list of organisms expected in mock community |
pattern: Semicolon-separated organism list |
E. coli;B. subtilis;S. cerevisiae;L. fermentum, Bacillus subtilis;Staphylococcus aureus |
Version: 1.0.0 | Layer: sample | Extends: metaproteomics | Usable alone: No
SDRF template for human gut metaproteomics. Extends metaproteomics with host-associated columns aligned with the GSC MIxS human-gut extension (0016004). Combine with ms-proteomics for MS acquisition columns.
| Column Name | Req. | Description | Validators | Examples |
|---|---|---|---|---|
|
required |
Host organism for host-associated microbiome samples |
ontology: ncbitaxon |
Homo sapiens |
|
recommended |
De-identified unique identifier for the host subject. Corresponds to MIxS host_subject_id (MIXS:0000861). |
identifier |
subject_001, patient_A, anonymized |
|
recommended |
Host disease diagnoses. Corresponds to MIxS host_disease_stat (MIXS:0000031). |
ontology: mondo, doid |
inflammatory bowel disease, colorectal cancer, healthy |
|
recommended |
Body site where sample was obtained. Corresponds to MIxS host_body_site (MIXS:0000867). |
ontology: uberon, bto |
stool, oral cavity, colon |
|
optional |
Age of host at the time of sampling. Corresponds to MIxS host_age (MIXS:0000255). |
pattern: Age in standard format (Y=year, M=month, W=week, D=day, H=hour) |
45Y, 8W, 3M |
|
optional |
Sex of the host organism. Corresponds to MIxS host_sex (MIXS:0000811). |
values: male, female, intersex |
|
|
optional |
Body mass index (weight/height^2). Corresponds to MIxS host_body_mass_index (MIXS:0000317). |
pattern: BMI numeric value |
22.5, 30.1, 18.5 |
|
optional |
Height of the host. Corresponds to MIxS host_height (MIXS:0000264). |
number with unit (cm, m) |
175 cm, 1.75 m |
|
optional |
Total mass of the host. Corresponds to MIxS host_tot_mass (MIXS:0000263). |
number with unit (kg, g) |
70 kg, 85 kg |
|
optional |
Ethnicity of the host. Corresponds to MIxS ethnicity (MIXS:0000895). |
pattern: Ethnicity description |
European, East Asian, African |
|
optional |
Diet type of the host. Corresponds to MIxS host_diet (MIXS:0000869). |
pattern: Diet description |
omnivore, vegan, western diet, high-fiber |
|
optional |
Special dietary restrictions. Corresponds to MIxS special_diet (MIXS:0000905). |
pattern: Special diet description |
gluten-free, low FODMAP, ketogenic |
|
optional |
Content of last meal and time since feeding. Corresponds to MIxS host_last_meal (MIXS:0000870). |
pattern: Last meal description |
breakfast 4 hours prior, fasting 12 hours |
|
optional |
History of GI tract disorders. Corresponds to MIxS gastroint_disord (MIXS:0000280). |
pattern: GI disorder description |
Crohn’s disease, ulcerative colitis, irritable bowel syndrome, none |
|
optional |
History of liver disorders. Corresponds to MIxS liver_disord (MIXS:0000282). |
pattern: Liver disorder description |
none, fatty liver disease, hepatitis |
|
optional |
Recent antibiotic exposure of the host |
pattern: Antibiotic treatment description |
none, amoxicillin 7 days prior, broad-spectrum |
|
optional |
Medication codes (IHMC). Corresponds to MIxS ihmc_medication_code (MIXS:0000884). |
pattern: Medication code(s) |
none, A02BC01, N02BE01 |
|
optional |
Substance produced by the body where sample was obtained. Corresponds to MIxS host_body_product (MIXS:0000888). |
pattern: Body product description |
stool, mucus, saliva |
|
optional |
Core body temperature at sample collection. Corresponds to MIxS host_body_temp (MIXS:0000874). |
number with unit (°C) |
36.6 °C, 37.2 °C |
|
optional |
Type of perturbation applied. Corresponds to MIxS perturbation (MIXS:0000754). |
pattern: Perturbation description |
antibiotic administration, dietary intervention, none |
|
optional |
Chemical compounds administered to the host. Corresponds to MIxS chem_administration (MIXS:0000751). |
pattern: Chemical administration description |
metformin 500mg daily, probiotics, none |
Version: 1.0.0 | Layer: sample | Extends: metaproteomics | Usable alone: No
SDRF template for soil metaproteomics. Extends metaproteomics with soil-specific columns aligned with the GSC MIxS soil extension (0016012). Combine with ms-proteomics for MS acquisition columns.
| Column Name | Req. | Description | Validators | Examples |
|---|---|---|---|---|
|
recommended |
Soil classification type (ENVO term) |
ontology: envo |
sandy loam, clay, peat, silt |
|
optional |
Soil horizon from which sample was collected |
values: O horizon, A horizon, B horizon, C horizon, … |
|
|
optional |
Land use type at sampling site |
pattern: Land use type |
agricultural, forest, urban, grassland, … |
|
optional |
Dominant vegetation at sampling site |
pattern: Vegetation description |
deciduous forest, corn field, prairie, tropical rainforest |
|
optional |
Total organic carbon content. Corresponds to MIxS tot_org_carb (MIXS:0000533). |
pattern: Total organic carbon with unit |
15.2 g/kg, 2.5 % |
|
optional |
Total nitrogen content. Corresponds to MIxS tot_nitro_content (MIXS:0000530). |
pattern: Total nitrogen with unit |
1.2 g/kg, 0.15 % |
|
optional |
Water content of soil sample. Corresponds to MIxS water_content (MIXS:0000185). |
pattern: Water content with unit |
25 %, 0.25 g/g |
|
optional |
Soil texture measurement (sand/silt/clay percentages). Corresponds to MIxS soil_text_measure (MIXS:0000335). |
pattern: Soil texture description |
sand 60%;silt 25%;clay 15%, loamy sand |
|
optional |
Current vegetation type at sampling site. Corresponds to MIxS cur_vegetation (MIXS:0000312). |
ontology: envo |
grassland, deciduous forest, cropland |
|
optional |
Crop rotation history. Corresponds to MIxS crop_rotation (MIXS:0000318). |
pattern: Crop rotation description |
corn-soybean rotation, wheat-fallow, continuous corn |
|
optional |
Type of perturbation applied. Corresponds to MIxS perturbation (MIXS:0000754). |
pattern: Perturbation description |
fertilizer application, tillage, none |
|
optional |
Chemical compounds administered to the site. Corresponds to MIxS chem_administration (MIXS:0000751). |
pattern: Chemical administration description |
nitrogen fertilizer, pesticide, none |
Version: 1.0.0 | Layer: sample | Extends: metaproteomics | Usable alone: No
SDRF template for aquatic metaproteomics. Extends metaproteomics with water-specific columns aligned with the GSC MIxS water extension (0016014). Combine with ms-proteomics for MS acquisition columns.
| Column Name | Req. | Description | Validators | Examples |
|---|---|---|---|---|
|
recommended |
Type of water body from which sample was collected (ENVO term) |
ontology: envo |
ocean, lake, river, estuary, … |
|
optional |
Salinity measurement. Corresponds to MIxS salinity (MIXS:0000183). |
pattern: Salinity value with unit or descriptive term |
35 PSU, freshwater, brackish |
|
optional |
Dissolved oxygen concentration. Corresponds to MIxS diss_oxygen (MIXS:0000119). |
pattern: Dissolved oxygen with unit or descriptive term |
8.5 mg/L, hypoxic, anoxic |
|
optional |
Chlorophyll concentration if measured |
number with unit (ug/L, mg/L) |
2.5 ug/L, 0.1 mg/L |
|
optional |
Ecological depth zone of the sampling site |
values: epipelagic, mesopelagic, bathypelagic, abyssopelagic, … |
|
|
optional |
Turbidity measurement. Corresponds to MIxS turbidity (MIXS:0000191). |
pattern: Turbidity with unit |
5.2 NTU, 12 FNU |
|
optional |
Alkalinity measurement. Corresponds to MIxS alkalinity (MIXS:0000421). |
number with unit (mg/L, meq/L) |
120 mg/L, 2.5 meq/L |
|
optional |
Nitrate concentration. Corresponds to MIxS nitrate (MIXS:0000425). |
number with unit (mg/L, umol/L) |
0.5 mg/L, 10 umol/L |
|
optional |
Phosphate concentration. Corresponds to MIxS phosphate (MIXS:0000505). |
number with unit (mg/L, umol/L) |
0.1 mg/L, 1.5 umol/L |
|
optional |
Electrical conductivity of water sample. Corresponds to MIxS conduc (MIXS:0000544). |
pattern: Conductivity with unit |
450 uS/cm, 1.2 mS/cm |
|
optional |
Total dissolved solids (TDS) concentration in the water sample. |
number with unit (mg/L, g/L) |
350 mg/L, 1.2 g/L |
|
optional |
Light intensity at sampling depth. Corresponds to MIxS light_intensity (MIXS:0000706). |
pattern: Light intensity with unit |
500 lux, 100 umol/m2/s |
|
optional |
Water current velocity. Corresponds to MIxS current (MIXS:0000051). |
number with unit (m/s, cm/s, knots) |
0.5 m/s, 15 cm/s |
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Copyright © Proteomics Standards Initiative (2020). All Rights Reserved.
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Please cite this document as:
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 Oct 6;12(1):5854. doi: 10.1038/s41467-021-26111-3. PMID: 34615866; PMCID: PMC8494749. [Manuscript - https://www.nature.com/articles/s41467-021-26111-3]
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[2] A. Gonzalez-Beltran, E. Maguire, S.A. Sansone, P. Rocca-Serra, linkedISA: semantic representation of ISA-Tab experimental metadata, BMC Bioinformatics 15 Suppl 14 (2014) S4. doi:10.1186/1471-2105-15-S14-S4
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[3] T.F. Rayner, P. Rocca-Serra, P.T. Spellman, et al., A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB, BMC Bioinformatics 7 (2006) 489. doi:10.1186/1471-2105-7-489
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[4] P. Blainey, M. Krzywinski, N. Altman, Points of significance: replication, Nat Methods 11(9) (2014) 879-80. doi:10.1038/nmeth.3091
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[5] D. Gupta, I. Liyanage, Y. Perez-Riverol, et al., BioSamples database: the global hub for sample metadata and multi-omics integration, Nucleic Acids Res (2025). doi:10.1093/nar/gkaf1133