SDRF-Proteomics

1. Status of this document

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

2. Abstract

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.

3. Motivation

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)

sample metadata

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.

4. Specification structure

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.

Logo

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.

Important

Throughout this specification, the keywords "MUST", "REQUIRED", "SHOULD", "RECOMMENDED", and "OPTIONAL" are interpreted as described in RFC 2119.

5. The SDRF-Proteomics Format

SDRF-Proteomics is a tab-delimited file where:

  • Each row = one sample linked to one data file

  • Each column = a property (sample characteristic, data file attribute, or factor value)

  • 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
Sample metadata
Data file metadata
Factor values

The file is organized into three column sections:

  1. Sample metadata (characteristics[…​]) - organism, disease, tissue, etc.

  2. Data file metadata (comment[…​]) - instrument, label, fraction, data file

  3. Factor values (factor value[…​]) - variables under study for statistical analysis

Note

5.1. Versioning

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.

5.2. Format rules

  • 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 like Source Name or Characteristics[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, not sourcename) but must NOT have a space before the bracket (e.g., characteristics[organism], not characteristics [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].

  • Extension: The extension of the SDRF file SHOULD be sdrf.tsv (preferred) or .txt.

5.3. Reserved words

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):

  • 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.

  • 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.

  • 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.

  • 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.

Table 1. Reserved words for SDRF cell values
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

5.4. SDRF file-level metadata

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

comment[sdrf version]

SDRF-Proteomics specification version used. Should follow semantic versioning format (vMAJOR.MINOR.PATCH)

v1.1.0

RECOMMENDED

PRIDE:0000839

comment[sdrf template]

Template name and version used for annotation. Two formats are supported: simple format (name vX.Y.Z) or key=value format (NT=name;VV=vX.Y.Z). Multiple templates can be specified using multiple columns.

human v1.1.0 or NT=human;VV=v1.1.0

OPTIONAL

PRIDE:0000832

comment[sdrf annotation tool]

Software tool, script, or method used to generate or annotate the SDRF file. Two formats are supported: simple format (name vX.Y.Z) or key=value format (NT=name;VV=vX.Y.Z).

lesSDRF v0.1.0 or NT=lesSDRF;VV=v0.1.0

OPTIONAL

PRIDE:0000840

comment[sdrf validation hash]

Cryptographic hash (e.g., SHA-256) generated after successful validation

sha256:abc123…​

OPTIONAL

PRIDE:0000834
Note
 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.

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
Sample metadata Data file metadata

5.5. Table Column headers

Depending on each section the column headers (property names) will be prefixed with the following prefixes:

  • 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.

Note
 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.

5.6. Table Cell values

The value for each property, (e.g. characteristics, comment, factor value) corresponding to each sample or data file can be represented in multiple ways.

  • 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
Sample metadata

  • 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.

  • 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 by AC (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
Note
 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.

6. Validating SDRF Files

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-pipelines

Basic 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 human

For more information, visit: sdrf-pipelines on GitHub

7. SDRF-Proteomics: Samples metadata

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:

  • source name: Unique sample name (it can be present multiple times if the same sample is used several times in the same dataset)

  • characteristics[organism]: The organism of the Sample of origin. Values MUST come from NCBI Taxonomy.

  • characteristics[organism part]: The main normalized anatomical term for the sample (e.g., liver). Values SHOULD come from UBERON or BTO. Use the clearest ontology-backed anatomy term available for cross-study integration; characteristics[tissue supergroup] can be used separately for broader organ/system grouping and characteristics[sampling site] for finer provenance. characteristics[sampling site] may be equal to characteristics[organism part] when no distinction exists.

  • 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
Sample metadata
Note

  • Additional characteristics can be added per experiment type - see SDRF-Proteomics templates for required properties.

  • Column headers SHOULD use EFO ontology terms (e.g., characteristics[organism]) - see Disease Annotation Guidelines.

  • Multiple columns with the same characteristics term are allowed (see Section 9.1), but RECOMMENDED to use more specific terms (e.g., "immunophenotype" instead of duplicate "phenotype").

7.1. BioSamples database integration

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).

7.2. Encoding sample technical and biological replicates

SDRF-Proteomics uses two REQUIRED columns to track replicates [4]:

  • 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
Sample metadata
Data file metadata

7.3. Pooled samples

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:

  • not pooled: Regular individual samples

  • pooled: Sample is pooled but individual sources are unknown

  • 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
Sample metadata
Data file metadata
Tip
 For pooled samples, use pooled for individual-specific fields (biological replicate, age, sex) to indicate a mixture rather than a single sample.

7.4. Sample Metadata Guidelines

For detailed guidance on annotating sample metadata, refer to the following conventions documents:

  • Sample Metadata Guidelines - Detailed guidelines for age, sex, disease, organism part, cell type, developmental stage, spiked-in samples, and other sample characteristics

  • Human Sample Metadata Guidelines - Human-specific metadata including disease staging, treatment history, demographics, and lifestyle factors

8. SDRF-Proteomics: data files metadata

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).

8.1. CV Term Format for Data File Metadata

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

assay name

REQUIRED

Unique identifier for an MS run/data file

Free text

technology type

REQUIRED

Technology used to capture the data

Fixed values

comment[proteomics data acquisition method]

REQUIRED

DDA, DIA, PRM, SRM

PRIDE:0000659

comment[label]

REQUIRED

Label applied to sample (or "label free sample")

PRIDE - Labels

comment[instrument]

REQUIRED

Mass spectrometer model

PSI-MS - Instruments

comment[cleavage agent details]

REQUIRED

Enzyme information (use "not applicable" for top-down/undigested samples)

PSI-MS - Cleavage agents

comment[fraction identifier]

REQUIRED

Fraction number (1 if not fractionated)

Integer

comment[technical replicate]

REQUIRED

Technical replicate number (1 if none)

Integer

comment[data file]

REQUIRED

Name of the raw file (primary/canonical file when the vendor format ships multiple files - see Section 8.2)

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
Sample metadata
Data file metadata

8.2. Vendor formats that ship multiple files (e.g. AB Sciex .wiff + .wiff.scan)

Some vendor formats persist a single MS run as two or more files on disk that are only useful together. The most common case is AB Sciex, where every acquisition produces a .wiff file paired with a .wiff.scan (and sometimes .wiff2) sidecar; tools such as ProteoWizard/Skyline cannot open one without the other. Bruker .d directories, in contrast, are a single logical entity (a folder) and do not require this pattern - reference the .d folder name directly in comment[data file].

To represent these multi-file formats while keeping one row per MS run, SDRF-Proteomics treats one file as the primary/canonical file and the remaining files as auxiliary files described by sidecar columns:

Column Cardinality Description

comment[data file]

1

Name of the primary/canonical file for the MS run (for AB Sciex, the .wiff file).

comment[file uri]

1

URI to retrieve the primary file. The trailing path segment MUST equal comment[data file].

comment[associated data file]

*

Name of an auxiliary file that must be downloaded alongside the primary file (for AB Sciex, the .wiff.scan file). Repeat the column when more than one auxiliary file is required.

comment[associated file uri]

*

URI to retrieve the auxiliary file. The trailing path segment MUST equal the corresponding comment[associated data file]. Repeat in the same order as comment[associated data file].
Note
 When multiple comment[associated data file] / comment[associated file uri] columns are present, consumers MUST pair them positionally (first associated file with first associated URI, second with second, etc.).

Example - AB Sciex (.wiff + .wiff.scan):

source name assay name comment[instrument] comment[data file] comment[file uri] comment[associated data file] comment[associated file uri]

sample_1

sample1_run1

TripleTOF 6600

OA_3.wiff

https://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD073289/OA_3.wiff

OA_3.wiff.scan

https://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD073289/OA_3.wiff.scan
Sample metadata
Data file metadata
Tip
 Once repositories standardise on bundling related files into a single .zip or .tar.gz (as already done for some Bruker timsTOF deposits), comment[data file] and comment[file uri] can reference the archive directly and comment[associated data file] is no longer needed. See the PRIDE submission formats guidelines for the direction of travel.

If a repository already distributes a single canonical archive for one acquisition today (for example a .raw.zip bundle in some metabolomics deposits), that archive can already be recorded directly in comment[data file] and comment[file uri].

8.3. Sample Preparation and Fragmentation (MS-based only)

Note
 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:

  • Sample preparation: depletion, reduction reagent, alkylation reagent

  • Fractionation: fractionation method (used with comment[fraction identifier])

  • Fragmentation: collision energy, dissociation method

Note
 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.

8.4. Proteomics data acquisition method

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:

Important
 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

Tip
 For DIA experiments, additional properties like MS1 scan range can be captured. See DIA Scan Window Limits in the DIA-Acquisition Template.

8.5. MS-Proteomics Template

For detailed guidance on data file metadata, refer to the conventions document:

  • MS-Proteomics Template - Detailed guidelines for labels, instruments, modifications, cleavage agents, mass tolerances, RAW file URIs, and other data file properties

9. Additional SDRF Rules

9.1. Column Cardinality

Some columns can appear multiple times for the same sample. The cardinality rules are:

  • 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

…​
Sample metadata
Data file metadata

9.2. Row Uniqueness Requirements

Uniqueness constraints ensure data integrity:

  • 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

Note
 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.

10. Templates

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.

10.1. Template Architecture

Templates follow a layered hierarchy:

Layer Templates Description

TECHNOLOGY (required)

ms-proteomics, affinity-proteomics, ms-metabolomics

Minimum valid SDRF - choose one

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, lc-ms-metabolomics, gc-ms-metabolomics

Methodology-specific columns

Child templates inherit all columns from parents and may add new columns or strengthen requirements (e.g., optional → required).

10.2. Template Combination Rules

Some layers enforce mutually exclusive choices, while others allow combining multiple templates:

Layer Templates Rule

TECHNOLOGY

ms-proteomics vs affinity-proteomics vs ms-metabolomics

Mutually exclusive — choose one (REQUIRED)

SAMPLE

human vs vertebrates vs invertebrates vs plants

Mutually exclusive — choose one based on organism (RECOMMENDED)

EXPERIMENT (MS)

dia-acquisition, single-cell, crosslinking, immunopeptidomics, metaproteomics

Can be combined (e.g., dia-acquisition + single-cell)

EXPERIMENT (metabolomics)

lc-ms-metabolomics vs gc-ms-metabolomics

Mutually exclusive — choose one when using ms-metabolomics (OPTIONAL)

Templates from different layers can be freely combined. Common valid combinations:

  • 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 (human affinity proteomics, including Olink or SomaScan)

  • ms-metabolomics + human + lc-ms-metabolomics (human LC-MS metabolomics)

  • ms-metabolomics + plants + gc-ms-metabolomics (plant GC-MS metabolomics)

  • ms-proteomics + metaproteomics (environmental metaproteomics)

  • ms-proteomics + human-gut (human gut microbiome metaproteomics)

  • ms-proteomics + human + single-cell (human single-cell proteomics)

10.3. Specifying Templates in SDRF Files

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:

  • 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 v1.0.0

Common examples:

Experiment Type Template Columns

Human MS proteomics

comment[sdrf template] = human v1.1.0

Mouse MS proteomics

comment[sdrf template] = vertebrates v1.1.0

Human crosslinking

Two columns: human v1.1.0 + crosslinking v1.0.0

Human affinity proteomics

Two columns: human v1.1.0 + affinity-proteomics v1.0.0

Human LC-MS metabolomics

Two columns: human v1.1.0 + lc-ms-metabolomics v1.0.0-dev

10.4. Available Templates

Sample templates (organism-specific):

Template Use For Key Columns

Human

Human clinical samples

disease, age, sex, ancestry

Vertebrates

Mouse, rat, zebrafish

disease, developmental stage, strain

Invertebrates

Drosophila, C. elegans

disease, developmental stage, genotype

Plants

Arabidopsis, crops

disease, developmental stage, growth conditions

Experiment-type templates:

Download templates from the templates folder.

10.5. Extending Templates

You can add custom columns beyond template requirements for study-specific metadata. Rules:

  • Use characteristics[…​] for sample metadata, comment[…​] for technical metadata

  • Column names MUST be valid ontology terms (search OLS)

  • Use controlled vocabularies for values when available

See Additional Sample-Related Columns and SDRF Terms Reference for commonly used columns.

10.6. Contributing New Templates

To propose a new template, open an issue on GitHub and submit a pull request.

11. Factor Values (Study Variables)

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.

11.1. Column Format

factor value[{variable name}]

11.2. When to Use Factor Values

Use factor values to indicate:

  • The primary variable(s) under investigation

  • Conditions being compared (e.g., disease vs. normal, treated vs. untreated)

  • Variables that define experimental groups

Note
 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.

11.3. Rules

  • 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

11.4. Example

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
Sample metadata
Factor values

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.

12. Ontologies and Controlled Vocabularies

SDRF-Proteomics uses ontologies and controlled vocabularies (CVs) to standardize metadata values. The following ontologies are supported:

Category Ontology/CV Description Notes

General Purpose

General

Experimental Factor Ontology (EFO)

General experimental metadata

General

PATO

Phenotype and Trait Ontology

General

NCI Thesaurus (NCIT)

Biomedical terminology

General

PRIDE Controlled Vocabulary

Proteomics-specific terms

Organism and Taxonomy

Taxonomy

NCBI Taxonomy (NCBITaxon)

Organism classification

Anatomy and Cell Types

Anatomy

UBERON

Cross-species anatomy ontology

Cell Type

Cell Ontology (CL)

Cell type classification

Anatomy

BRENDA Tissue Ontology (BTO)

Tissues and cell lines

Anatomy

Plant Ontology (PO)

Plant anatomy and development

For plant samples

Anatomy

FlyBase Anatomy (FBbt)

Drosophila anatomy

For Drosophila samples

Anatomy

WormBase Anatomy (WBbt)

C. elegans anatomy

For C. elegans samples

Anatomy

Zebrafish Anatomy (ZFA)

Zebrafish anatomy and development

For zebrafish samples

Disease (see Disease Annotation Guidelines)

Disease

Mondo Disease Ontology (MONDO)

Unified disease ontology

RECOMMENDED

Disease

Experimental Factor Ontology (EFO)

Disease terms from EFO

Healthy samples

Phenotype And Trait Ontology (PATO)

Use normal (PATO:0000461) for healthy samples

Cell Lines

Cell Lines

Cellosaurus

Cell line knowledge resource

RECOMMENDED

Cell Lines

Cell Line Ontology (CLO)

Cell line ontology

Mass Spectrometry and Proteomics

MS/Proteomics

PSI Mass Spectrometry CV (PSI-MS)

Instruments, methods, parameters

Modifications

Unimod

Protein modifications database

Modifications

PSI-MOD CV

Protein modifications ontology

Other

Chemistry

ChEBI

Chemical Entities of Biological Interest

Environment

Environment Ontology (ENVO)

Environmental sample classification

For metaproteomics

Ancestry

Human Ancestry Ontology (HANCESTRO)

Human ancestry categories

For human samples

13. Examples of Annotated Datasets

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

View in Explorer

GitHub

TMT

PXD017710

TMT-labeled quantitative proteomics

View in Explorer

GitHub

SILAC

PXD000612

SILAC-based quantification

View in Explorer

GitHub

DIA

PXD018830

data-independent acquisition

View in Explorer

GitHub

Phosphoproteomics

PXD000759

PTM enrichment study

View in Explorer

GitHub

Cell lines

PXD001819

Cell line proteomics

View in Explorer

GitHub
Tip
 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

14. Template Definitions

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.

14.1. base

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

source name

required

Unique identifier for the biological sample

assay name

required

Unique identifier for the data acquisition run

technology type

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

comment[technical replicate]

required

Identifier for the technical replicate (integer starting from 1)

comment[data file]

required

Name of the raw data file

comment[sdrf version]

recommended

Version of the SDRF-Proteomics specification used to annotate this file

semver

v1.1.0, v2.0.0-dev

comment[sdrf template]

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

comment[sdrf annotation tool]

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, …​

comment[sdrf validation hash]

optional

Hash value for SDRF validation integrity checking

pattern: Validation hash string

14.2. sample-metadata

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

characteristics[organism]

required

Species of the sample using NCBI Taxonomy

ontology: ncbitaxon

homo sapiens, mus musculus, rattus norvegicus, saccharomyces cerevisiae

characteristics[organism part]

required

Main normalized anatomical term for the sample

ontology: uberon, bto

liver, brain, heart, blood

characteristics[tissue supergroup]

optional

Broader anatomical grouping or system-level bucket for the sample, used alongside the organism part for higher-level grouping

ontology: uberon, bto

digestive system, nervous system, cardiovascular system, gastrointestinal tract

characteristics[cell type]

recommended

Cell type of the sample

ontology: cl, bto, clo

hepatocyte, neuron, fibroblast, T cell

characteristics[biological replicate]

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

characteristics[pooled sample]

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

characteristics[sample type]

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, …​

characteristics[disease]

recommended

Disease state of the sample

ontology: mondo, efo, doid, ncit, pato

normal, breast cancer, infection, metabolic disease

characteristics[material type]

optional

Type of biological material being analyzed

values: tissue, cell, cell line, organism part, …​

characteristics[tissue mass]

optional

Mass of tissue used for extraction

number with unit (mg, g, ug)

50 mg, 1 g, 500 ug

characteristics[biosample accession number]

optional

BioSample accession number for the sample (e.g., SAMN or SAMEA identifiers)

accession: biosample

SAMN12345678, SAMEA12345678, SAMD1234567

characteristics[sampling time]

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

characteristics[treatment]

optional

Treatment or perturbation applied to the sample (drug, stimulus, environmental stress)

ontology: ncit, efo

untreated, LPS stimulation, doxorubicin treatment, drought stress, …​

characteristics[synthetic peptide]

optional

Whether the sample is a synthetic peptide library or biological material

values: synthetic, not synthetic

characteristics[spiked compound]

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

characteristics[enrichment process]

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

14.3. ms-proteomics

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

comment[proteomics data acquisition method]

required

Mass spectrometry acquisition method

ontology: pride

data-dependent acquisition, data-independent acquisition, parallel reaction monitoring, selected reaction monitoring

comment[instrument]

required

Mass spectrometer instrument used

ontology: ms, pride

LTQ Orbitrap, Q Exactive, Orbitrap Fusion Lumos, timsTOF Pro

comment[cleavage agent details]

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

comment[label]

required

Labeling strategy used for quantification

ontology: pride

label free sample, SILAC light, SILAC heavy, TMT126, …​

comment[fraction identifier]

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.

comment[dissociation method]

recommended

Fragmentation method used in MS/MS

ontology: ms, pride

HCD, CID, ETD, EThcD

comment[fractionation method]

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)

comment[collision energy]

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

comment[precursor mass tolerance]

recommended

Precursor mass tolerance for database search

number with unit (ppm, Da, mmu)

10 ppm, 20 ppm, 0.5 Da, 20 mmu

comment[fragment mass tolerance]

recommended

Fragment mass tolerance for database search

number with unit (ppm, Da, mmu)

0.02 Da, 20 ppm, 50 mmu

comment[reduction reagent]

optional

Chemical reagent used for disulfide bond reduction

ontology: pride, ms

dithiothreitol, tris(2-carboxyethyl)phosphine

comment[alkylation reagent]

optional

Chemical reagent used for cysteine alkylation

ontology: pride, ms

iodoacetamide, chloroacetamide

characteristics[depletion]

optional

Whether abundant protein depletion was performed

values: no depletion, depletion

comment[modification parameters]

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

comment[ms2 mass analyzer]

optional

Mass analyzer used for MS2 acquisition

ontology: ms

orbitrap, ion trap, TOF

comment[sample preparation batch]

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

comment[lc batch]

optional

Liquid chromatography batch identifier for batch effect tracking (e.g., column changes, LC system swaps)

pattern: LC batch identifier

LC1, column_A

comment[acquisition date]

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

comment[ms min mz]

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

comment[ms max mz]

optional

MS method-defined maximum precursor (MS1) m/z setting used to acquire the data

m/z value

1200m/z, 1600m/z, 2000m/z

comment[ms min charge]

optional

MS method-defined minimum precursor charge state setting used to acquire the data

pattern: Integer charge state

1, 2

comment[ms max charge]

optional

MS method-defined maximum precursor charge state setting used to acquire the data

pattern: Integer charge state

6, 7, 8

comment[ms min rt]

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

comment[ms max rt]

optional

LC method-defined maximum retention time setting used to acquire the data (in minutes)

pattern: Numeric retention time in minutes

60, 90, 120

comment[ms min im]

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

comment[ms max im]

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

comment[ms2 min mz]

optional

MS method-defined minimum product ion (MS2) m/z setting used to acquire the data

m/z value

100m/z, 200m/z

comment[ms2 max mz]

optional

MS method-defined maximum product ion (MS2) m/z setting used to acquire the data

m/z value

1800m/z, 2000m/z

comment[ms3 min mz]

optional

MS method-defined minimum product ion (MS3) m/z setting used to acquire the data

m/z value

100m/z, 200m/z

comment[ms3 max mz]

optional

MS method-defined maximum product ion (MS3) m/z setting used to acquire the data

m/z value

1500m/z, 2000m/z

comment[ms1 scan range]

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

comment[ms2 scan range]

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

comment[ms3 scan range]

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

comment[elution conditions]

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

14.4. affinity-proteomics

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

characteristics[sample type]

required

Role of the sample in the assay. Distinguishes study samples from controls/reference materials for assay interpretation and quality control

ontology: pride

study sample, negative control, positive control, calibrator, …​

comment[platform]

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

comment[instrument]

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

comment[panel name]

recommended

Commercial panel/menu identifier within the platform. RECOMMENDED, but MUST be provided when not uniquely inferable from comment[platform].

pattern: Panel/menu identifier

Target 96 Inflammation, Explore 1536, SomaScan 7K, SomaScan 11K

comment[quantification unit]

optional

Unit of quantification for the assay (platform-specific)

values: NPX, RFU

comment[plate]

optional

Plate identifier for batch effect analysis

pattern: Plate identifier

1, 2

comment[normalization method]

optional

Normalization method applied to quantification values

pattern: Normalization method

plate control normalized, bridge normalized, median normalization, not normalized

comment[dilution]

optional

Sample dilution factor used (commonly used for SomaScan workflows)

pattern: Dilution factor; SomaScan commonly uses 0.005%, 0.5%, 20%, 40%

0.005%, 0.5%, 20%, 40%, …​

comment[lot number]

optional

Reagent lot number for traceability

pattern: Lot number

SS-2023-001, lot_12345

14.5. human

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, affinity-proteomics, or ms-metabolomics).

Column Name Req. Description Validators Examples

characteristics[disease]

required

(override: requirement set to required)

characteristics[ancestry category]

recommended

Ancestry or ethnic background of the donor

ontology: hancestro

European, African, Asian, Hispanic or Latin American

characteristics[age]

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, …​

characteristics[sex]

required

Biological sex of the donor

values: male, female, intersex

characteristics[developmental stage]

optional

Developmental stage of the donor

ontology: efo

adult, embryonic stage, fetal stage, infant stage

characteristics[individual]

recommended

Unique identifier for the donor individual

identifier

patient_001, donor-A1, subject_12, anonymized, …​

14.6. vertebrates

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, affinity-proteomics, or ms-metabolomics).

Column Name Req. Description Validators Examples

characteristics[disease]

required

(override: requirement set to required)

characteristics[developmental stage]

required

Developmental stage of the organism

ontology: efo

adult, embryo, juvenile, larval stage

characteristics[strain or breed]

recommended

Strain or breed of the organism

ontology: ncbitaxon

C57BL/6, Sprague-Dawley, BALB/c, Wistar

characteristics[sex]

recommended

Biological sex of the organism

values: male, female, hermaphrodite

14.7. invertebrates

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, affinity-proteomics, or ms-metabolomics).

Column Name Req. Description Validators Examples

characteristics[disease]

required

(override: requirement set to required)

characteristics[developmental stage]

required

Developmental stage of the organism

ontology: efo

adult stage, larval stage, pupal stage, embryonic stage

characteristics[strain or breed]

required

Strain of the organism

ontology: ncbitaxon

Oregon-R, w1118, N2, Canton-S

characteristics[genotype]

optional

Genotype of the organism

pattern: Genotype notation following standard conventions

wild type, daf-2(e1370), w[*]; P{GAL4}

14.8. plants

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, affinity-proteomics, or ms-metabolomics).

Column Name Req. Description Validators Examples

characteristics[organism part]

ontology: uberon, bto, po

flower bud, leaf, root, seed

characteristics[disease]

required

(override: requirement set to required)

characteristics[developmental stage]

required

Developmental stage of the plant

ontology: efo

seedling stage, flowering stage, rosette growth stage, senescent stage

characteristics[strain or breed]

recommended

Cultivar, ecotype, or accession of the plant

pattern: Plant cultivar or ecotype name

Col-0, Ler-0, Nipponbare, B73

characteristics[growth condition]

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

characteristics[treatment]

recommended

(override: requirement set to recommended)

14.9. clinical-metadata

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, or ms-metabolomics).

Column Name Req. Description Validators Examples

characteristics[disease]

required

(override: requirement set to required)

characteristics[compound]

optional

Chemical compound or drug applied to sample

ontology: chebi, ncit, efo

doxorubicin, cisplatin, tamoxifen, metformin

characteristics[dose]

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

characteristics[exposure duration]

optional

Duration of treatment exposure

number with unit (hour, day, minute, week, month)

24 hour, 5 day, 30 minute, 2 week

characteristics[treatment status]

optional

Treatment status at time of sampling

values: pre-treatment, on treatment, post-treatment, treatment naive

characteristics[treatment response]

optional

Response to treatment (for studies measuring therapeutic outcomes)

ontology: ncit

complete response, partial response, progressive disease, stable disease

characteristics[pre-existing condition]

optional

Pre-existing medical conditions or comorbidities

ontology: mondo, efo, doid

diabetes mellitus, hypertension, obesity

characteristics[body mass index]

optional

Body mass index (BMI) in kg/m^2

pattern: Numeric BMI value

24.5, 31.2, 18.7

characteristics[smoking status]

optional

Patient smoking status

ontology: ncit

never smoker, former smoker, current smoker

characteristics[menopausal status]

optional

Menopausal status for female patients

values: pre-menopausal, peri-menopausal, post-menopausal

characteristics[genetic modification]

optional

Method of genetic modification (knockout, knockdown, overexpression, transduction)

ontology: efo

knockout, knockdown, overexpression, transduction, …​

characteristics[phenotype]

optional

Observable characteristics or traits (drug sensitivity, molecular markers, expression phenotypes)

ontology: pato, efo

drug resistant, HER2-positive, high expresser, wild-type phenotype

characteristics[weight]

optional

Body weight of the subject

number with unit (kg, g, lb)

70 kg, 55 kg, 154 lb

characteristics[height]

optional

Height of the subject

number with unit (cm, m)

175 cm, 1.75 m, 160 cm

characteristics[sampling site]

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

characteristics[genotype]

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

14.10. oncology-metadata

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, or ms-metabolomics).

Column Name Req. Description Validators Examples

characteristics[disease staging]

optional

Disease progression stage (stage I-IV, chronic phase, end stage)

ontology: ncit, efo

stage I, stage II, stage III, stage IV, …​

characteristics[tumor grading]

optional

Histological tumor grade (describes how abnormal cells look)

ontology: ncit

grade 1, grade 2, grade 3, grade 4, …​

characteristics[tumor stage]

optional

TNM staging notation (describes extent of cancer spread)

ontology: ncit

T2N1M0, T3N0M0, T1N0M0, T4N2M1

characteristics[tumor size]

optional

Tumor size measurement

number with unit (cm, mm)

2.5 cm, 15 mm, 0.8 cm

characteristics[tumor mass]

optional

Tumor mass/weight measurement

number with unit (g, mg)

15 g, 250 mg

characteristics[histologic subtype]

optional

Cancer molecular or histologic subtype

ontology: ncit

luminal A, luminal B, HER2-enriched, triple-negative, …​

characteristics[metastasis site]

optional

Location where cancer has spread from primary site

ontology: uberon, bto

liver, lung, bone, brain

characteristics[biopsy site]

optional

Specific anatomical location of biopsy

ontology: uberon, bto

breast, colon, prostate, lung

characteristics[clinical data]

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

characteristics[clinical history]

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

characteristics[survival time]

optional

Patient survival time for survival analysis studies

number with unit (month, year, day, week)

24 month, 3 year, 180 day

characteristics[last follow up]

optional

Time of last clinical follow-up for longitudinal studies

number with unit (month, year, day, week)

36 month, 5 year, 365 day

characteristics[mitotic rate]

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

characteristics[dukes stage]

optional

Dukes staging for colorectal cancer (A, B, C, D)

values: A, B, C, D

characteristics[ann arbor stage]

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, …​

characteristics[gleason score]

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, …​

characteristics[weiss grade]

optional

Weiss scoring system for adrenal cortical carcinoma (low or high)

values: low, high

14.11. dia-acquisition

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

comment[proteomics data acquisition method]

required

Mass spectrometry acquisition method (restricted to DIA for this template)

single value only; values: Data-independent acquisition

comment[scan window lower limit]

recommended

Lower m/z limit of the DIA scan window

pattern: m/z value as a number

400, 350.5

comment[scan window upper limit]

recommended

Upper m/z limit of the DIA scan window

pattern: m/z value as a number

1200, 1000

comment[isolation window width]

recommended

Width of the isolation window in m/z units

pattern: Width in m/z

25, 8, 4

comment[dia method]

recommended

Specific DIA method variant used

ontology: pride

SWATH-MS, MSE, All ion fragmentation, diaPASEF

14.12. single-cell

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

characteristics[sample type]

recommended

(override: requirement set to recommended)

characteristics[single cell isolation protocol]

required

Method used to isolate single cells (FACS, cellenONE, LCM, etc.)

values: FACS, cellenONE, microfluidics, laser capture microdissection, …​

characteristics[cell identifier]

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, …​

comment[sample preparation batch]

recommended

Batch identifier for sample preparation (plate, chip, processing batch). Critical for batch effect correction.

characteristics[cells per well]

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

comment[carrier channel]

recommended

TMT/TMTpro channel used for the carrier proteome

pattern: TMT channel label for carrier

TMT131C, TMTpro134N, TMT126

comment[reference channel]

recommended

TMT/TMTpro channel used for the reference sample (for normalization across sets)

pattern: TMT channel label for reference

TMT131N, TMTpro133C, TMT127N

characteristics[forward scatter]

optional

Forward scatter (FSC) value from flow cytometry - proxy for cell size

pattern: FSC value (numeric)

316.0, 250

characteristics[side scatter]

optional

Side scatter (SSC) value from flow cytometry - proxy for cell granularity/complexity

pattern: SSC value (numeric)

301.0, 184

characteristics[enrichment marker]

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, …​

characteristics[cell viability]

optional

Viability status of the cell at isolation

values: live, viable, dead, unknown

characteristics[cell cycle phase]

optional

Cell cycle phase if determined (e.g., by FACS or computational inference)

values: G1, S, G2, G2/M, …​

characteristics[cell diameter]

optional

Physical diameter of the isolated cell if measured (in micrometers)

number with unit (um, μm)

15 um, 20.5 um, 12 μm

characteristics[spatial coordinates]

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

comment[tissue section]

optional

Tissue section identifier for spatially resolved single-cell proteomics

pattern: Tissue section identifier

section_001, slide_A_section_3

comment[facs nozzle size]

optional

Nozzle diameter used for FACS-based single cell isolation (in micrometers)

number with unit (um, μm)

70 um, 100 um, 130 μm

comment[facs sorting mode]

optional

Sorting mode used during FACS isolation

values: single cell, purity, yield, 4-way purity

comment[microfluidics chip type]

optional

Type and manufacturer of the microfluidics chip used for single cell isolation

pattern: Chip type/manufacturer identifier

Fluidigm C1, Cellenion cellenCHIP, nanowell chip

comment[lcm microscope model]

optional

Model of the laser capture microdissection microscope used for cell isolation

pattern: LCM microscope model name

Leica LMD7, Zeiss PALM MicroBeam, Thermo LCM

comment[nanopots chip version]

optional

Version of the nanoPOTS chip used for single cell sample preparation

pattern: nanoPOTS chip version identifier

nanoPOTS v1, nanoPOTS v2, 9-well chip

14.13. immunopeptidomics

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

characteristics[mhc protein complex]

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

characteristics[immunopeptidome enrichment method]

required

Method used to enrich MHC-bound peptides

values: immunoaffinity purification, immunoaffinity purification (iodoacetamide), mild acid elution, detergent lysis

characteristics[mhc typing]

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, …​

characteristics[mhc typing method]

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, …​

characteristics[antibody enrichment]

recommended

Antibody clone used for MHC immunoprecipitation

pattern: Antibody clone name

W6/32, BB7.2

14.14. crosslinking

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

comment[chemical cross-linking coupled with ms]

recommended

MS-based cross-linking methodology used to identify this as a crosslinking dataset

values: cross-linking mass spectrometry

characteristics[enrichment process]

recommended

(override: requirement set to recommended)

comment[cross-linker]

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

comment[dissociation method]

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, …​

comment[collision energy]

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, …​

comment[crosslink enrichment method]

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

characteristics[crosslink distance]

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

comment[crosslinker concentration]

optional

Concentration of crosslinking reagent used

number with unit (mM, uM, µM)

2 mM, 500 uM, 1 mM

characteristics[crosslinking reaction time]

optional

Duration of the crosslinking reaction

number with unit (min, h, s)

30 min, 1 h, 45 min

characteristics[crosslinking temperature]

optional

Temperature at which crosslinking was performed

number with unit (°C)

25°C, 4°C, 37°C, room temperature

comment[crosslinker to protein ratio]

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

comment[quenching reagent]

optional

Reagent used to quench the crosslinking reaction

pattern: Chemical name of quenching reagent

Tris-HCl, ammonium bicarbonate, glycine

14.15. cell-lines

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

characteristics[cell line]

required

Name of the cell line

ontology: clo, bto, efo

HeLa, HEK293, MCF7, A549

characteristics[disease]

required

Disease state of the donor tissue from which the cell line was established

characteristics[cellosaurus accession]

required

Cellosaurus accession number for the cell line

accession: cellosaurus

CVCL_0030, CVCL_0004

characteristics[cellosaurus name]

recommended

Official Cellosaurus name for the cell line

characteristics[sampling site]

optional

Original source term, local provenance, or finer tissue-of-origin context for the cell line

ontology: uberon, bto

cervix, kidney, breast

characteristics[passage number]

recommended

Passage number of the cell line used in the experiment

pattern: Passage number should be an integer or range

10, 15-20, 5

characteristics[biorepository]

optional

BioBank or source from which the cell line was obtained

pattern: Source of the cell line

ATCC, DSMZ, ECACC, Sigma-Aldrich

characteristics[cell line authentication]

optional

Method used to authenticate the cell line identity

pattern: Authentication method used

STR profiling, SNP fingerprinting, cytogenetic analysis

characteristics[culture medium]

recommended

Culture medium used to grow the cell line

ontology: ncit

DMEM, RPMI 1640, MEM, Ham’s F-12

characteristics[developmental stage]

optional

Developmental stage of the donor from which the cell line was derived

ontology: efo

adult, embryonic, fetal, neonatal

characteristics[ancestry category]

optional

Ancestry category of the cell line donor (if known)

ontology: hancestro

European, African, East Asian, South Asian

characteristics[sample storage temperature]

recommended

Storage temperature of the cell line (in Celsius)

number with unit (°C)

-80 °C, -20 °C, 4 °C

14.16. metaproteomics

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

characteristics[environmental sample type]

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, …​

characteristics[geographic location]

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

characteristics[environmental medium]

recommended

Environmental material from which the sample was obtained (ENVO term). Corresponds to MIxS env_medium (MIXS:0000014).

ontology: envo

soil, seawater, freshwater, feces, …​

characteristics[collection date]

optional

Date when sample was collected (ISO 8601)

date

2024, 2024-01, 2024-01-15

characteristics[sample collection method]

optional

Method used to collect the environmental sample

pattern: Collection method description

grab sample, core sample, swab, filtration

characteristics[depth]

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

characteristics[altitude]

optional

Altitude or elevation of sampling site. Corresponds to MIxS elevation (MIXS:0000093).

number with unit (m)

500 m, 1200 m, 0 m

characteristics[temperature]

optional

Temperature at sampling location. Corresponds to MIxS temperature (MIXS:0000113).

number with unit (°C)

25 °C, 4 °C, -20 °C

characteristics[ph]

optional

pH at sampling location

pattern: pH value

7.0, 5.5, 8.2

characteristics[sample storage]

optional

Storage conditions for the sample before analysis

pattern: Storage conditions

-80C, liquid nitrogen, 4C

comment[metagenome accession]

optional

Accession number for matched metagenome data

accession:

MGYA00001234, SRP123456

characteristics[microbiome source]

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

characteristics[biomass estimation]

optional

Estimated microbial biomass in the sample

pattern: Biomass estimation

1e9 cells/g, high biomass, low biomass

characteristics[host contamination]

optional

Level of host protein contamination if known

pattern: Host contamination level

low (<5%), moderate (5-20%), high (>20%)

comment[contaminant database]

optional

Contaminant database(s) used in database search

pattern: Contaminant database name(s)

cRAP, MaxQuant contaminants, cRAP;MaxQuant contaminants

characteristics[mock community]

optional

Identifier or name of mock community standard used

pattern: Mock community identifier

ZymoBIOMICS Microbial Community Standard, ATCC MSA-1000

characteristics[mock community composition]

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

comment[expected organism list]

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

14.17. human-gut

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

source name[sample name]

required

Reference to the Sample. This term is used for cross-reference samples in SDRF for proteomics (MIXS:0001107).

identifier

Sample_1, Sample_2

characteristics[host organism]

required

Host organism for host-associated microbiome samples

ontology: ncbitaxon

Homo sapiens

characteristics[host subject id]

recommended

De-identified unique identifier for the host subject. Corresponds to MIxS host_subject_id (MIXS:0000861).

identifier

subject_001, patient_A, anonymized

characteristics[host disease status]

recommended

Host disease diagnoses. Corresponds to MIxS host_disease_stat (MIXS:0000031).

ontology: mondo, doid

inflammatory bowel disease, colorectal cancer, healthy

characteristics[host body site]

recommended

Body site where sample was obtained. Corresponds to MIxS host_body_site (MIXS:0000867).

ontology: uberon, bto

stool, oral cavity, colon

characteristics[host genotype]

recommended

Observed genotype MIXS:0000365.

ontology: efo, gene

homozygous, heterozygous

characteristics[host phenotype]

recommended

Phenotype of human or other host MIXS:0000274.

ontology: pato, hp

polydactyly, arachnodactyly

characteristics[host age]

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

characteristics[host sex]

optional

Sex of the host organism. Corresponds to MIxS host_sex (MIXS:0000811).

values: male, female, intersex

characteristics[host body-mass index]

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

characteristics[host height]

optional

Height of the host. Corresponds to MIxS host_height (MIXS:0000264).

number with unit (cm, m)

175 cm, 1.75 m

characteristics[host total mass]

optional

Total mass of the host. Corresponds to MIxS host_tot_mass (MIXS:0000263).

number with unit (kg, g)

70 kg, 85 kg

characteristics[ethnicity]

optional

Ethnicity of the host. Corresponds to MIxS ethnicity (MIXS:0000895).

pattern: Ethnicity description

European, East Asian, African

characteristics[host diet]

optional

Diet type of the host. Corresponds to MIxS host_diet (MIXS:0000869).

pattern: Diet description

omnivore, vegan, western diet, high-fiber

characteristics[special diet]

optional

Special dietary restrictions. Corresponds to MIxS special_diet (MIXS:0000905).

pattern: Special diet description

gluten-free, low FODMAP, ketogenic

characteristics[host last meal]

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

characteristics[host family relationship]

optional

Relationships to other hosts in the same study; can include multiple relationships MIXS:0000872.

pattern: family relationship description

father, daughter

characteristics[host occupation]

optional

Most frequent job performed by subject MIXS:0000896.

pattern: occupation description

teacher, engineer

characteristics[gastrointestinal tract disorder]

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

characteristics[liver disorder]

optional

History of liver disorders. Corresponds to MIxS liver_disord (MIXS:0000282).

pattern: Liver disorder description

none, fatty liver disease, hepatitis

characteristics[antibiotic treatment]

optional

Recent antibiotic exposure of the host

pattern: Antibiotic treatment description

none, amoxicillin 7 days prior, broad-spectrum

characteristics[ihmc medication code]

optional

Medication codes (IHMC). Corresponds to MIxS ihmc_medication_code (MIXS:0000884).

pattern: Medication code(s)

none, A02BC01, N02BE01

characteristics[host body product]

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

characteristics[host body temperature]

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

characteristics[perturbation]

optional

Type of perturbation applied. Corresponds to MIxS perturbation (MIXS:0000754).

pattern: Perturbation description

antibiotic administration, dietary intervention, none

characteristics[chemical administration]

optional

Chemical compounds administered to the host. Corresponds to MIxS chem_administration (MIXS:0000751).

pattern: Chemical administration description

metformin 500mg daily, probiotics

characteristics[host pulse]

optional

Resting pulse, measured as beats per minutes (MIXS:0000333).

number with unit (bpm)

65 bpm, 72 bpm, 85 bpm

characteristics[observed host symbionts]

optional

The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host (MIXS:0001298).

ontology:

characteristics[medical history performed]

optional

Whether full medical history was collected (MIXS:0000897).

pattern: Medical history performed description

45 year old male with a 2 week history of stomach pain.

characteristics[project name]

optional

Name of the project within which the sequencing was organized (MIXS:0000092).

identifier

Human_microbiome_project

comment[sample storage temperature]

optional

Temperature at which sample was stored (MIXS:0000110).

number with unit (°C)

-80 °C, -20 °C

comment[sample storage location]

optional

Location at which sample was stored (MIXS:0000755).

pattern: storage location description

freezer, room

comment[sample storage duration]

optional

Duration for which the sample was stored (MIXS:0000116).

pattern: storage duration description

40 days, 6 months

comment[sample volume or weight for DNA extraction]

optional

Volume (ml) or mass (g) of total collected sample processed for DNA extraction (MIXS:0000111).

number with unit (ml,g)

1 ml, 2 g

comment[organism count]

optional

Total cell count of any organism per gram, volume, or area of sample, including count (MIXS:0000103).

number with unit (CFU/ml)

500 CFU/ml, 2000 CFU/ml

comment[oxygenation status of sample]

optional

Oxygenation status of sample (MIXS:0000753).

number with unit (mmHg)

80 mmHg, 100 mmHg

comment[miscellaneous parameter]

optional

Any other measurement performed or parameter collected, that is not listed here (MIXS:0000752).

pattern: miscellaneous parameter description

none

14.18. soil

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

source name[sample name]

required

Reference to the Sample. This term is used for cross-reference samples in SDRF for proteomics (MIXS:0001107).

identifier

Sample_1, Sample_2

project name

required

Name of the project within which the sequencing was organized (MIXS:0000092).

identifier

Bermuda_Atlantic_Time-series_Study, Metaproteomes_of_Seawater_Microbial_Communities

characteristics[soil type]

recommended

Soil classification type (ENVO term)

ontology: envo

sandy loam, clay, peat, silt

characteristics[elevation]

optional

Height of the sampling site above mean sea level.

values: 10 feet, 30 feet, 2 cm

characteristics[slope gradient]

optional

The angle between ground surface and a horizontal line (MIxS:0000646).

values: 10 %, 30 %

characteristics[slope aspect]

optional

The direction a slope faces (MIxS:0000647).

values: 300 degrees, north west, south

characteristics[profile position]

optional

Cross-sectional position in the hillslope where sample was collected (MIxS:0001084).

values: summit, shoulder, backslope

characteristics[drainage classification]

optional

Drainage classification from a standard system such as the USDA system (MIxS:0001085).

values: well drained, poorly drained, very poorly drained

characteristics[current land use]

optional

Present state of sample site (MIXS:0001080).

pattern: Land use type

agricultural, forest, urban, grassland, …​

characteristics[current vegetation]

optional

Current vegetation type at sampling site. Corresponds to MIxS cur_vegetation (MIXS:0000312).

ontology: envo

grassland, deciduous forest, cropland

comment[current vegetation method]

optional

method used in vegetation classification (MIXS:0000314).

values: vegetation survey, quadrant sampling

characteristics[history of previous land use]

optional

Previous land use and dates (MIXS:0000315).

values: agricultural land 15 years, grassland forest 5 years

comment[history of previous land use method]

optional

Reference or method used in determining previous land use (MIXS:0000316).

values: land registry records, historical archives

characteristics[crop rotation]

optional

Crop rotation history. Corresponds to MIxS crop_rotation (MIXS:0000318).

pattern: Crop rotation description

corn-soybean rotation, wheat-fallow, continuous corn

characteristics[history of agrochemical additions]

optional

Addition of fertilizers, pesticides, etc. - amount and time of applications (MIXS:0000639).

values: urea 2mg/L, 2020-01-01, superphosphate 5mg/L, 2019-02-19

characteristics[history of tillage]

optional

tilling methods (MIXS:0001081).

values: chisel, digging spade

characteristics[history of fire]

optional

evidence of fire (MIXS:0001086).

date

09-10-2025, 10-02-2002

characteristics[history of flooding]

optional

evidence of flooding (MIXS:0000319).

date

09-10-2025, 10-02-2002

characteristics[history of extreme event]

optional

events that may have affected microbial populations (MIXS:0000320).

date

09-10-2025, 10-02-2002

characteristics[soil horizon]

optional

Soil horizon from which sample was collected

values: O horizon, A horizon, B horizon, C horizon, …​

comment[horizon method]

optional

method used in determining the horizon (MIXS:0000321).

pattern: Horizon method description

USDA Field Book, FAO Guidelines for Soil Profile Description, none

characteristics[soil taxonomic of FAO classification]

optional

Soil classification from the FAO World soil distribution (MIxS:0001083)

values: acrisols, calcisols, durisols, gleysols

characteristics[link classification information]

optional

Link to digitized soil maps or other soil classification information (MIXS:0000329).

pattern: URL, DOI, or PMID linking to classification information

https://example.com/soil-map, doi:10.1000/xyz123, PMID:12345678

characteristics[soil taxonomic local classification]

optional

Soil classification based on local soil classification system (MIXS:0000330).

pattern: Local soil classification term or description

Chernozem, Podzol, Local classification type A

characteristics[soil local classification method]

optional

Method used for local soil classification, including reference to the classification system or methodology applied (MIXS:0000331).

pattern: Description or reference to the local soil classification method

FAO soil classification guidelines, USDA Soil Taxonomy methodology, National soil classification system (UK)

characteristics[soil texture]

optional

The relative proportion of different grain sizes of mineral particles in a soil, expressed as percentages of sand, silt, and clay, optionally including a textural class (MIXS:0000335).

pattern: Soil texture expressed as percentages and/or textural class

40% sand 40% silt 20% clay, 30-50 silty clay loam, silty clay loam

characteristics[soil texture method]

optional

Method used to determine soil texture, including reference to the analytical or classification approach applied.(MIXS:0000336)

pattern: Description or reference to the soil texture determination method

Hydrometer method, Laser diffraction particle size analysis, Pipette method

characteristics[link climate information]

optional

Link to climate resource associated with the sampling site. (MIXS:0000328)

pattern: URL, DOI, or PMID linking to climate information

https://climate-data.org/location123, doi:10.1000/climate456, PMID:98765432

characteristics[mean annual temperature]

optional

Mean annual temperature at the sampling site, typically expressed in degrees Celsius.(MIXS:0000135)

values:

12.5 oC, 25 oC

characteristics[mean seasonal temperature]

optional

Mean seasonal temperature range or average during a defined season at the sampling site. (MIXS:0000136)

pattern: Seasonal temperature description or value

summer 18°C, winter -2 to 5°C

characteristics[mean annual precipitation]

optional

Total annual precipitation at the sampling site, typically measured in millimeters per year.(MIXS:0000140)

numeric

800/year, 1200.5/year

characteristics[mean seasonal precipitation]

optional

Precipitation amount during a defined season at the sampling site. (MIXS:0000141)

pattern: Seasonal precipitation description or value

summer 120 mm, winter 300 mm

characteristics[pH method]

optional

Method used to determine pH in the sample.(MIXS:0001106)

pattern: Description of pH measurement method

pH measured in water (1:2.5 soil:solution ratio), pH measured in CaCl2 solution

characteristics[organic matter]

optional

Organic matter content of the sample.(MIXS:0000204)

number with unit ()

5.2 %, 12 %

characteristics[total organic carbon]

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 %

characteristics[total organic carbon method]

optional

Method used to determine total organic carbon.(MIXS:0000337)

pattern: Description of TOC measurement method

dry combustion method, Walkley-Black method

characteristics[organic nitrogen]

optional

Organic nitrogen content of the sample.(MIXS:0000205)

number with unit ()

0.2 %, 1.5 %

characteristics[total nitrogen content]

optional

Total nitrogen content of the sample.(MIXS:0000530)

number with unit ()

0.5 %, 2.1 %

characteristics[total nitrogen content method]

optional

Method used to determine total nitrogen content.(MIXS:0000338)

pattern: Description of nitrogen measurement method

Kjeldahl method, Dumas combustion method

characteristics[water content]

optional

Water content of soil sample. Corresponds to MIxS water_content (MIXS:0000185).

pattern: Water content with unit

25 %, 0.25 g/g

characteristics[soil water content method]

optional

Method used to determine soil water content.(MIXS:0000323)

pattern: Description of water content measurement method

gravimetric method, time-domain reflectometry

comment[microbial biomass]

optional

Microbial biomass present in the sample.(MIXS:0000650)

number with unit ()

250 mg/kg, 1200 mg/kg

comment[microbial biomass method]

optional

Method used to determine microbial biomass.(MIXS:0000339)

pattern: Description of microbial biomass measurement method

chloroform fumigation extraction, substrate-induced respiration

characteristics[extreme unusual properties of heavy metals]

optional

Concentration of heavy metals in the sample, including elements such as lead, cadmium, mercury, and others.(MIXS:0000652)

pattern: Heavy metal concentrations with units or description

Pb 50 mg/kg; Cd 2 mg/kg, Hg 0.5 mg/kg

characteristics[extreme unusual properties of heavy metals method]

optional

Method used to determine heavy metal concentrations in the sample.(MIXS:0000343)

pattern: Description of heavy metal measurement method

ICP-MS analysis, Atomic absorption spectroscopy

characteristics[aluminum saturation]

optional

Aluminum saturation of the soil, typically expressed as a percentage of cation exchange capacity occupied by aluminum.(MIXS:0000607)

number with unit ()

15 %, 45.5 %

characteristics[aluminum saturation method]

optional

Method used to determine aluminum saturation in the sample.(MIXS:0000324)

pattern: Description of aluminum saturation measurement method

KCl extraction followed by titration, ICP-OES after extraction

characteristics[sieving]

optional

Size of mesh used to sieve the sample prior to analysis.(MIXS:0000322)

pattern: Sieve size or description

2 mm mesh, 500 µm sieve

comment[sample volume or weight for DNA extraction]

optional

Volume or weight of sample used for DNA extraction.(MIXS:0000111)

pattern: Sample amount with unit

0.5 g, 10 mL

characteristics[pooling of DNA extracts]

optional

Whether multiple DNA extracts were pooled prior to sequencing.(MIXS:0000325)

pattern: Indication of DNA extract pooling

yes, pooled from 3 replicates, no

comment[storage conditions]

optional

Storage conditions of the sample prior to analysis, including temperature and duration if known.(MIXS:0000327)

pattern: Storage condition description

-80°C for 6 months, 4°C short-term storage, room temperature

comment[link to additional analysis]

optional

Link to additional analysis results or external resources related to the sample.(MIXS:0000340)

pattern: URL, DOI, or PMID linking to additional analysis

https://example.com/analysis-results, doi:10.1000/analysis123, PMID:12345678

comment[miscellaneous parameter]

optional

Any additional parameter not captured by other fields; should include a name and value.(MIXS:0000752)

pattern: Parameter name and value in key:value format

{'enzyme_activity': 'high'}, {'soil_color': 'dark brown'}

14.19. water

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

source name[sample name]

required

Reference to the Sample. This term is used for cross-reference samples in SDRF for proteomics (MIXS:0001107).

identifier

Sample_1, Sample_2

project name

required

Name of the project within which the sequencing was organized (MIXS:0000092).

identifier

Bermuda_Atlantic_Time-series_Study, Metaproteomes_of_Seawater_Microbial_Communities

characteristics[sampling depth zone]

recommended

Ecological depth zone of the sampling site

values: epipelagic, mesopelagic, bathypelagic, abyssopelagic, …​

characteristics[elevation]

recommended

Height of the sampling site above mean sea level.

number with unit (feet, cm)

10 feet, 30 feet, 2 cm

characteristics[tidal stage]

recommended

Stage of tide (MIXS:0000750).

values: high tide, low tide

characteristics[total depth of water volume]

recommended

Measurement of total depth of water column (MIXS:0000634).

number with unit (m)

35 m, 10 m, 200 m

characteristics[water current]

recommended

Measured speed and direction of water flow

number with unit (m/s)

0.35 m/s, 0.10 m/s

characteristics[mean friction velocity]

recommended

Measurement of mean friction velocity (MIXS:0000498).

number with unit (m/s)

0.035 m/s, 0.010 m/s

characteristics[mean peak friction velocity]

recommended

Measurement of mean peak friction velocity (MIXS:0000502).

number with unit (m/s)

0.015 m/s, 0.045 m/s

characteristics[pressure]

recommended

Pressure to which the sample is subject to, in atmospheres (MIXS:0000412)

number with unit (dbar)

15 dbar, 25 dbar

characteristics[salinity]

optional

Salinity measurement. Corresponds to MIxS salinity (MIXS:0000183).

pattern: Salinity value with unit or descriptive term

35 PSU, freshwater, brackish

characteristics[conductivity]

optional

Electrical conductivity of water sample. Corresponds to MIxS conduc (MIXS:0000544).

pattern: Conductivity with unit

450 uS/cm, 1.2 mS/cm

characteristics[density]

optional

Density of the sample, which is its mass per unit volume (aka volumetric mass density) (MIXS:0000435).

number with unit (kg/m3)

1022 kg/m3, 1050 kg/m3

characteristics[redox potential]

optional

Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential (MIXS:0000182).

number with unit (V)

1.2 V, 0.80 V

characteristics[fluorescence]

optional

Raw or converted fluorescence of water (MIXS:0000704).

number with unit (RFU)

1.2 RFU, 3.8 RFU

characteristics[light intensity]

optional

Light intensity at sampling depth. Corresponds to MIxS light_intensity (MIXS:0000706).

pattern: Light intensity with unit

500 lux, 100 umol/m2/s

characteristics[turbidity]

optional

Turbidity measurement. Corresponds to MIxS turbidity (MIXS:0000191).

pattern: Turbidity with unit

5.2 NTU, 12 FNU

characteristics[downward PAR]

optional

Visible waveband radiance and irradiance measurements in the water column (MIXS:0000703).

number with unit (µmol)

120 µmol, 15 µmol

characteristics[photon flux]

optional

Measurement of photon flux (MIXS:0000725).

number with unit (µmol)

120 µmol, 15 µmol

characteristics[nitrate]

optional

Nitrate concentration. Corresponds to MIxS nitrate (MIXS:0000425).

number with unit (mg/L, umol/L)

0.5 mg/L, 10 umol/L

characteristics[nitrite]

optional

Nitrite concentration. Corresponds to MIxS nitrite (MIXS:0000426).

number with unit (mg/L)

0.5 mg/L, 1 mg/L

characteristics[nitrogen]

optional

Nitrogen concentration. Corresponds to MIxS nitrogen (MIXS:0000504).

number with unit (mg/L)

10 mg/L, 15 mg/L

characteristics[ammonium]

optional

Ammonium concentration. Corresponds to MIxS ammonium (MIXS:0000427).

number with unit (mg/L)

1 mg/L, 1.5 mg/L

characteristics[phosphate]

optional

Phosphate concentration. Corresponds to MIxS phosphate (MIXS:0000505).

number with unit (mg/L, umol/L)

0.1 mg/L, 1.5 umol/L

characteristics[dissolved inorganic nitrogen]

optional

Dissolved inorganic nitrogen concentration (MIXS:0000698).

number with unit (mmol/L)

761 mmol/L, 500 mmol/L

characteristics[total inorganic nitrogen]

optional

total inorganic nitrogen concentration (MIXS:0000745).

number with unit (mg/L)

76 mg/L, 40 mg/L

characteristics[total dissolved nitrogen]

optional

total dissolved nitrogen concentration (MIXS:0000744).

number with unit (mg/L)

76 mg/L, 40 mg/L

characteristics[dissolved inorganic phosphorus]

optional

Dissolved inorganic phosphorus concentration (MIXS:0000106).

number with unit (mmol/L)

76 mmol/L, 56 mmol/L

characteristics[total nitrogen concentration]

optional

total nitrogen concentration (MIXS:0000102).

number with unit (mmol/L)

76 mmol/L, 56 mmol/L

characteristics[total phosphorus]

optional

total phosphorus concentration. Corresponds to MIxS total phosphorus (MIXS:0000117).

number with unit (mg/L)

0.03 mg/L, 0.05mg/L

characteristics[soluble reactive phosphorus]

optional

soluble reactive phosphorus concentration (MIXS:0000738).

number with unit (mg/L)

0.1 mg/L, 0.2 mg/L

characteristics[silicate]

optional

ssilicate concentration. Corresponds to MIxS(MIXS:0000184).

number with unit (mmol/L)

0.05 mmol/L, 0.08 mmol/L

characteristics[alkalinity]

optional

Alkalinity measurement. Corresponds to MIxS alkalinity (MIXS:0000421).

number with unit (mg/L, meq/L)

120 mg/L, 2.5 meq/L

characteristics[alkalinity method]

optional

Method used for alkalinity measurement (MIXS:0000298).

identifier

titration

characteristics[calcium]

optional

Calcium concentration. Corresponds to MIxS(MIXS:0000421).

number with unit (mmol/L)

0.2 mmol/L, 2.5 mmol/L

characteristics[magnesium]

optional

Magnesium concentration. Corresponds to MIxS(MIXS:0000431).

number with unit (mmol/kg)

25 mmol/kg, 52.8 mmol/kg

characteristics[potassium]

optional

Potassium concentration. Corresponds to MIxS(MIXS:0000430).

number with unit (mg/L)

463 mg/L, 300 mg/L

characteristics[sodium]

optional

Sodium concentration. Corresponds to MIxS(MIXS:0000428).

number with unit (mg/L)

10.5 mg/L, 12 mg/L

characteristics[chloride]

optional

Sodium concentration. Corresponds to MIxS(MIXS:0000429).

number with unit (mg/L)

5000 mg/L, 3500 mg/L

characteristics[sulfate]

optional

Sulfate concentration. Corresponds to MIxS(MIXS:0000423).

number with unit (mmol/L)

5 mmol/L, 3.5 mmol/L

characteristics[sulfide]

optional

Sulfide concentration. Corresponds to MIxS(MIXS:0000424).

number with unit (mmol/L)

2 mmol/L, 1.5 mmol/L

characteristics[bromide]

optional

Bromide concentration. Corresponds to MIxS(MIXS:0000176).

number with unit (ppm)

0.05 ppm, 0.01 ppm

characteristics[atmospheric data]

optional

Measurement of atmospheric data; can include multiple data (MIXS:0001097).

pattern: Diet description

wind speed; 9 knots, humidity; 75%

characteristics[dissolved organic carbon]

optional

Dissolved organic carbon concentration. Corresponds to MIxS (MIXS:0000433)

number with unit (mmol/L)

197 mmol/L, 75 mmol/L

characteristics[dissolved inorganic carbon]

optional

Dissolved inorganic carbon concentration. Corresponds to MIxS (MIXS:0000434)

number with unit (mmol/kg)

2059 mmol/kg, 1075 mmol/kg

characteristics[dissolved carbon dioxide]

optional

Dissolved carbon dioxide concentration. Corresponds to MIxS (MIXS:0000436)

number with unit (mg/L)

5 mg/L, 10 mg/L

characteristics[dissolved oxygen]

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

characteristics[dissolved hydrogen]

optional

Dissolved hydrogen concentration. Corresponds to MIxS (MIXS:0000205).

number with unit (mmol/L)

0.3 mmol/L, 0.5 mmol/L

characteristics[dissolved organic nitrogen]

optional

Dissolved organic nitrogen concentration. Corresponds to MIxS (MIXS:0000162).

number with unit (mmol/L)

0.04 mmol/L, 0.05 mmol/L

characteristics[organic carbon]

optional

Organic carbon concentration. Corresponds to MIxS (MIXS:0000508).

number with unit (ug/L)

1.5 ug/L, 1 ug/L

characteristics[organic matter]

optional

Organic matter concentration. Corresponds to MIxS (MIXS:0000204).

number with unit (ug/L)

1.75 ug/L, 1 ug/L

characteristics[organic nitrogen]

optional

Organic nitrogen concentration. Corresponds to MIxS (MIXS:0000205).

number with unit (umol/L)

4 umol/L, 1 umol/L

characteristics[particulate organic carbon]

optional

Particulate organic carbon concentration. Corresponds to MIxS (MIXS:0000515).

number with unit (umol/L)

1.92 umol/L, 1 umol/L

characteristics[particulate organic nitrogen]

optional

Particulate organic nitrogen concentration. Corresponds to MIxS (MIXS:0000719).

number with unit (umol/L)

0.3 umol/L, 0.5 umol/L

characteristics[total particulate carbon]

optional

Total particulate carbon content. Corresponds to MIxS (MIXS:0000747).

number with unit (umol/L, ug/L)

35 umol/L, 5 ug/L

characteristics[carbon nitrogen ratio]

optional

Carbon to nitrogen concentration. Corresponds to MIxS (MIXS:0000310).

pattern: carbon nitrogen measurement value

0.475, 0.34576

characteristics[suspended particulate matter]

optional

Suspended particulate matter concentration. Corresponds to MIxS (MIXS:0000741).

number with unit (mg/L)

0.5 mg/L, 1 mg/L

characteristics[chlorophyll]

optional

Chlorophyll concentration if measured

number with unit (ug/L, mg/L)

2.5 ug/L, 0.1 mg/L

characteristics[primary production]

optional

Primary production measurement

number with unit (mg/m3/day, g/m2/day)

100 mg/m3/day, 10 g/m2/day

comment[bacterial production]

optional

bacterial production measurement (MIXS:0000683)

number with unit (mg/m3/day)

5 mg/m3/day, 10 mg/m3/day

characteristics[bacterial respiration]

optional

bacterial respiration measurement (MIXS:0000684)

number with unit (ug/m3/day, umolO2/L/hr)

300 umolO2/L/hr, 100 umolO2/L/hr

characteristics[bacterial carbon production]

optional

bacterial carbon production measurement (MIXS:0000173)

number with unit (ug/L/hr)

2.53 ug/L/hr, 1.23 ug/L/hr

characteristics[aminopeptidase activity]

optional

Aminopeptidase activity measurement (MIXS:0000172)

number with unit (mol/L/hr)

0.253 mol/L/hr, 0.123 mol/L/hr

characteristics[glucosidase activity]

optional

glucosidase activity measurement (MIXS:0000137)

number with unit (mol/L/hr)

5 mol/L/hr, 3 mol/L/hr

characteristics[phaeopigments]

optional

phaeopigments concentration (MIXS:0000180)

number with unit (mg/m3)

2.5 mg/m3, 3 mg/m3

characteristics[biomass]

optional

Total cell count of any organism (MIXS:0000174)

number with unit (ton, kg, g)

25 g, 3 kg

comment[organism count]

optional

phaeopigments concentration (MIXS:0000103)

number with unit (CFU/ml)

500 CFU/ml, 2000 CFU/ml

comment[oxygenation status of sample]

optional

Oxygenation status of sample (MIXS:0000753).

number with unit (mmHg)

80 mmHg, 100 mmHg

characteristics[alkyl diethers]

optional

Alkyl diethers concentration (MIXS:0000490).

number with unit (mol/L)

0.005 mol/L, 0.003 mol/L

characteristics[diether lipids]

optional

Diether lipids concentration (MIXS:0000178).

number with unit (ng/L)

0.5 ng/L, 0.3 ng/L

characteristics[bishomohopanol]

optional

Bishomohopanol concentration (MIXS:0000175).

number with unit (ug/L, ug/g)

14 ug/L, 4 ug/g

characteristics[phospholipid fatty acid]

optional

Phospholipid fatty acid concentration (MIXS:0000181).

pattern: Phospholipid fatty acid name and measurement value

Linoleic acid; 2.8 mg/L, Palmitic acid; 1.5 mg/L

characteristics[petroleum hydrocarbon]

optional

Petroleum hydrocarbon concentration (MIXS:0000516).

number with unit (umol/L)

0.05 umol/L, 0.02 umol/L

comment[sample storage temperature]

optional

Temperature at which sample was stored (MIXS:0000110).

number with unit (°C)

-80 °C, -20 °C

comment[sample storage location]

optional

Location at which sample was stored (MIXS:0000755).

pattern: storage location description

freezer, room

comment[sample storage duration]

optional

Duration for which the sample was stored (MIXS:0000116).

pattern: storage duration description

40 days, 6 months

comment[sample volume or weight for DNA extraction]

optional

Volume or weight of sample used for DNA extraction.(MIXS:0000111)

pattern: Sample amount with unit

0.5 g, 10 mL

comment[size-fraction lower threshold]

optional

mesh/pore size used to pre-filter/pre-sort the sample (MIXS:0000735).

number with unit (um)

0.1 um, 0.2 um

comment[size-fraction upper threshold]

optional

Mesh or pore size of the device used to retain the sample (MIXS:0000736).

number with unit (um)

10 um, 20 um

characteristics[perturbation]

optional

Type of perturbation applied. Corresponds to MIxS perturbation (MIXS:0000754).

pattern: Perturbation description

antibiotic administration, dietary intervention, none

comment[miscellaneous parameter]

optional

Any additional parameter not captured by other fields; should include a name and value.(MIXS:0000752)

pattern: Parameter name and value in key:value format

{'enzyme_activity': 'high'}, {'soil_color': 'dark brown'}

14.20. gc-ms-metabolomics

Version: 1.0.0-dev | Layer: experiment | Extends: ms-metabolomics | Usable alone: No

SDRF template for GC-MS-based metabolomics experiments. Extends ms-metabolomics with derivatization and GC-specific columns.

Column Name Req. Description Validators Examples

technology type

required

(override: requirement set to required)

single value only; values: GC-MS-based metabolomics

comment[ion source]

required

(override: requirement set to required)

values: electron ionization, chemical ionization, electron impact ionization

comment[derivatization]

required

Derivatization protocol applied to the sample prior to GC injection. Use none if no derivatization was performed (e.g. volatiles analysis).

pattern: Free-text derivatization protocol

MSTFA, MOX + MSTFA, BSTFA, methoximation followed by trimethylsilylation, …​

comment[derivatization agent]

recommended

Chemical reagent(s) used for derivatization

ontology: chebi

N-methyl-N-(trimethylsilyl)trifluoroacetamide, N,O-bis(trimethylsilyl)trifluoroacetamide, methoxyamine hydrochloride

comment[gc column]

recommended

GC column used for separation, including stationary phase and dimensions

pattern: Free-text GC column description

DB-5MS 30 m x 0.25 mm x 0.25 um, HP-5MS 30 m x 0.25 mm x 0.25 um, Rxi-5Sil MS 30 m x 0.25 mm x 0.25 um

comment[carrier gas]

optional

Carrier gas used in the GC system

values: helium, hydrogen, nitrogen

comment[oven program]

optional

Free-text description of the GC oven temperature program

pattern: Free-text oven program description

60C 1 min, ramp 10C/min to 300C, hold 5 min, 70C 2 min, ramp 5C/min to 320C, hold 10 min

14.21. lc-ms-metabolomics

Version: 1.0.0-dev | Layer: experiment | Extends: ms-metabolomics | Usable alone: No

SDRF template for LC-MS-based metabolomics experiments. Extends ms-metabolomics with chromatography-specific columns.

Column Name Req. Description Validators Examples

technology type

required

(override: requirement set to required)

single value only; values: LC-MS-based metabolomics

comment[chromatography type]

required

Chromatography mode used for separation. Should be a CHMO term (e.g. CHMO:0002302 reversed-phase chromatography, CHMO:0001025 hydrophilic interaction chromatography).

pattern: Chromatography type as a CHMO-style ontology term (NT=…​;AC=CHMO:NNNNNNN) or one of the common short names. Strict CHMO ontology validation is a follow-up.

NT=reversed-phase chromatography;AC=CHMO:0002302, NT=hydrophilic interaction chromatography;AC=CHMO:0001025, reversed-phase chromatography, hydrophilic interaction chromatography

comment[chromatography column]

recommended

LC column used for separation, including manufacturer, model, and dimensions

pattern: Free-text chromatography column description

Waters ACQUITY HSS T3 100 x 2.1 mm 1.8 um, Phenomenex Kinetex C18 150 x 2.1 mm 2.6 um, SeQuant ZIC-pHILIC 150 x 2.1 mm 5 um

comment[mobile phase a]

optional

Composition of mobile phase A

pattern: Free-text composition of mobile phase A

0.1% formic acid in water, 10 mM ammonium acetate in water pH 9.0, 5 mM ammonium formate in water

comment[mobile phase b]

optional

Composition of mobile phase B

pattern: Free-text composition of mobile phase B

0.1% formic acid in acetonitrile, 10 mM ammonium acetate in 90% acetonitrile pH 9.0, methanol

comment[gradient]

optional

Free-text description of the chromatographic gradient program

pattern: Free-text gradient description

5% B 0-1 min, ramp to 95% B at 15 min, hold 3 min, re-equilibrate, isocratic 50% B for 10 min, 0-100% B in 30 min

comment[flow rate]

optional

Mobile-phase flow rate

number with unit (nL/min, uL/min, mL/min)

300 nL/min, 250 uL/min, 0.4 mL/min

14.22. ms-metabolomics

Version: 1.0.0-dev | Layer: technology | Extends: sample-metadata | Usable alone: Yes

Base SDRF template for mass spectrometry-based metabolomics. This is the parent template for LC-MS and GC-MS metabolomics experiments.

Column Name Req. Description Validators Examples

technology type

required

Type of technology used

single value only; values: metabolite profiling by mass spectrometry, LC-MS-based metabolomics, GC-MS-based metabolomics

comment[instrument]

required

Mass spectrometer instrument used

ontology: psi-ms, pride

Q Exactive, Xevo G2-S QTof, Orbitrap Fusion Lumos, timsTOF Pro

comment[ion source]

required

Ion source used for ionization (e.g. ESI, APCI, EI, MALDI). Should be a child of MS:1000008.

ontology: psi-ms

electrospray ionization, atmospheric pressure chemical ionization, electron ionization, matrix-assisted laser desorption ionization

comment[scan polarity]

required

Scan polarity (positive scan, negative scan, or polarity switching). Polarity switching is reserved for true in-method switching producing a single file; otherwise use two rows per sample (one per polarity).

single value only; values: positive scan, negative scan, polarity switching

comment[acquisition method]

required

Mass spectrometry acquisition method (DDA, DIA, SIM, MRM, full scan)

ontology: pride

data-dependent acquisition, data-independent acquisition, selected reaction monitoring, parallel reaction monitoring, …​

comment[metabolite assignment file]

recommended

Pointer to the metabolite assignment file (MAF) for this assay. Per-assay constant — the same value is repeated across all rows of the same assay. Mirrors the MetaboBank semantics of Comment[Metabolite Assignment File].

pattern: Path or filename of the MAF file

m_MTBLS1129_LC-MS_positive_reverse-phase_metabolite_profiling_v2_maf.tsv, maf_pos_lipidomics.tsv

comment[extraction method]

recommended

Sample extraction method used to obtain the metabolite fraction

pattern: Free-text extraction method, optionally CHMO-style NT=…​;AC=CHMO:NNNNNNN

methanol-water extraction, MTBE extraction, Bligh-Dyer extraction, Folch extraction, …​

comment[extraction solvent]

optional

Solvent or solvent mixture used for metabolite extraction

ontology: chebi

methanol, chloroform, methyl tert-butyl ether, acetonitrile

characteristics[analyte class]

recommended

Class of metabolites targeted by the extraction and acquisition method

values: polar metabolites, lipids, amino acids, fatty acids, …​

comment[internal standard]

optional

Internal standard(s) spiked into the sample for normalization or retention-time calibration

ontology: chebi

caffeine-d9, L-tryptophan-d5, palmitic acid-d31

characteristics[sample matrix]

recommended

Type of biological matrix used as input (e.g. serum, plasma, CSF, urine, tissue extract)

ontology: uberon, bto

serum, plasma, cerebrospinal fluid, urine, …​

comment[sample preparation batch]

optional

Batch identifier for sample preparation (plate, chip, processing batch). Useful for batch-effect correction.

pattern: Sample preparation batch identifier

plate1, batch_20220601, prep_A

comment[lc batch]

optional

Liquid chromatography batch identifier for batch-effect tracking (e.g. column changes, LC system swaps)

pattern: LC batch identifier

LC1, column_A

comment[acquisition date]

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

comment[ms2 mass analyzer]

optional

Mass analyzer used for MS2 acquisition

ontology: psi-ms

orbitrap, ion trap, TOF

comment[ms min mz]

optional

MS method-defined minimum precursor (MS1) m/z setting used to acquire the data

m/z value

100m/z, 200m/z

comment[ms max mz]

optional

MS method-defined maximum precursor (MS1) m/z setting used to acquire the data

m/z value

1200m/z, 1600m/z

comment[ms1 scan range]

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

70m/z-1000m/z, 100m/z-1500m/z

comment[ms2 scan range]

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

50m/z-1000m/z, 100m/z-1500m/z

comment[precursor mass tolerance]

optional

Precursor mass tolerance for feature detection / database search

number with unit (ppm, Da, mmu)

5 ppm, 10 ppm, 0.01 Da

comment[fragment mass tolerance]

optional

Fragment mass tolerance for feature detection / database search

number with unit (ppm, Da, mmu)

0.02 Da, 20 ppm

comment[collision energy]

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, 25 eV, 25 NCE;27 NCE;30 NCE

comment[raw data file md5]

optional

MD5 integrity hash for the raw data file referenced in comment[data file]. Mirrors MetaboBank Comment[Raw Data File md5].

pattern: 32-character hex MD5 hash

d41d8cd98f00b204e9800998ecf8427e, 9e107d9d372bb6826bd81d3542a419d6

comment[processed data file]

optional

Pointer to the processed data file (e.g. peak table, feature matrix). Mirrors MetaboBank Comment[Processed Data File].

pattern: Path or filename of the processed data file

features_pos.tsv, peak_table_lipidomics.csv

comment[processed data file md5]

optional

MD5 integrity hash for the processed data file. Mirrors MetaboBank Comment[Processed Data File md5].

pattern: 32-character hex MD5 hash

d41d8cd98f00b204e9800998ecf8427e

comment[metabolite assignment file md5]

optional

MD5 integrity hash for the metabolite assignment file. Mirrors MetaboBank Comment[Metabolite Assignment File md5].

pattern: 32-character hex MD5 hash

d41d8cd98f00b204e9800998ecf8427e

15. Intellectual Property Statement

The PSI takes no position regarding the validity or scope of any intellectual property or other rights that might be claimed to pertain to the implementation or use of the technology described in this document or the extent to which any license under such rights might or might not be available; neither does it represent that it has made any effort to identify any such rights. Copies of claims of rights made available for publication and any assurances of licenses to be made available or the result of an attempt made to obtain a general license or permission for the use of such proprietary rights by implementers or users of this specification can be obtained from the PSI Chair.

The PSI invites any interested party to bring to its attention any copyrights, patents or patent applications, or other proprietary rights which may cover technology that may be required to practice this recommendation. Please address the information to the PSI Chair (see contacts information at PSI website).

16. Copyright Notice

Copyright © Proteomics Standards Initiative (2020). All Rights Reserved.

This document and translations of it may be copied and furnished to others, and derivative works that comment on or otherwise explain it or assist in its implementation may be prepared, copied, published, and distributed, in whole or in part, without the restriction of any kind, provided that the above copyright notice and this paragraph are included on all such copies and derivative works. However, this document itself may not be modified in any way, such as by removing the copyright notice or references to the PSI or other organizations, except as needed for the purpose of developing Proteomics Recommendations in which case the procedures for copyrights defined in the PSI Document process must be followed, or as required to translate it into languages other than English.

The limited permissions granted above are perpetual and will not be revoked by the PSI or its successors or assigns.

This document and the information contained herein is provided on an "AS IS" basis and THE PROTEOMICS STANDARDS INITIATIVE DISCLAIMS ALL WARRANTIES, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY WARRANTY THAT THE USE OF THE INFORMATION HEREIN WILL NOT INFRINGE ANY RIGHTS OR ANY IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE."

17. How to cite

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]

References

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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

  • [4] P. Blainey, M. Krzywinski, N. Altman, Points of significance: replication, Nat Methods 11(9) (2014) 879-80. doi:10.1038/nmeth.3091

  • [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