SDRF-Proteomics: Metaproteomics Template

1. Status of this Template

This document provides guidelines for annotating metaproteomics experiments in SDRF-Proteomics format. This template extends the core SDRF-Proteomics specification with metaproteomics-specific metadata fields.

Status: Draft - This template is under active development and may change significantly.

Version: 1.0.0-dev - 2026-01

2. Abstract

Metaproteomics is the study of proteins expressed by microbial communities, analyzing complex samples containing proteins from many different organisms simultaneously. Key applications include gut microbiome characterization, environmental microbiology, host-microbiome interactions, and industrial biotechnology.

Metaproteomics experiments have unique characteristics: multi-organism samples, complex sample matrices, databases constructed from metagenomics data, taxonomic attribution challenges, and critical environmental context metadata. This template defines the additional metadata requirements for annotating metaproteomics datasets.

3. Connections to Other Omics Fields

Metaproteomics data is typically integrated with:

Metagenomics: For database construction and taxonomic context
Metatranscriptomics: For gene expression correlation
16S/ITS amplicon sequencing: For community composition
Metabolomics: For functional interpretation
Environmental databases: ENVO, MIxS standards

When available, linking to related omics datasets is highly RECOMMENDED.

4. Additional Ontologies

In addition to the ontologies supported by the core SDRF-Proteomics specification, metaproteomics templates utilize:

Environment Ontology (ENVO): For environmental sample classification (http://www.obofoundry.org/ontology/envo.html)
Gazetteer (GAZ): For geographic locations
MIxS: Minimum Information about any (x) Sequence standards
NCBI Taxonomy: For organism classification

5. Checklist

This section defines the metadata columns required and recommended for metaproteomics experiments.

5.1. Required Columns

The following columns are REQUIRED for metaproteomics experiments in addition to the core SDRF-Proteomics requirements:

Column Name	Description	Cardinality	Ontology/CV	Example Values
characteristics[environmental sample type]	Type of environmental or biological sample being analyzed	1	ENVO, EFO	soil, marine sediment, human gut, wastewater, rhizosphere, oral cavity, skin
characteristics[sample collection method]	Method used to collect the sample	1	Controlled vocabulary or free text	grab sample, core sampling, swab collection, filtration, fecal collection, biopsy

Column Name

Description

Cardinality

Ontology/CV

Example Values

characteristics[environmental sample type]

Type of environmental or biological sample being analyzed

ENVO, EFO

soil, marine sediment, human gut, wastewater, rhizosphere, oral cavity, skin

characteristics[sample collection method]

Method used to collect the sample

Controlled vocabulary or free text

grab sample, core sampling, swab collection, filtration, fecal collection, biopsy

5.2. Recommended Columns

The following columns are RECOMMENDED for metaproteomics experiments:

Column Name	Description	Cardinality	Ontology/CV	Example Values
characteristics[geographic location]	Geographic location where sample was collected	0..1	GAZ or free text with coordinates	Baltic Sea, Amazon rainforest, lat:52.5 lon:13.4, GAZ:00002459
characteristics[collection date]	Date when sample was collected	0..1	ISO 8601 date format	2024-03-15, 2024-03, March 2024
characteristics[depth]	Depth at which sample was collected (for water/sediment)	0..1	Numeric value with unit	10 m, 0-5 cm, surface
characteristics[altitude]	Altitude/elevation for terrestrial samples	0..1	Numeric value with unit	500 m, 1200 m above sea level
characteristics[temperature]	Environmental temperature at collection	0..1	Numeric value with unit (Celsius)	25 C, 4 C, 37 C
characteristics[pH]	pH of the sample or environment	0..1	Numeric value	7.4, 5.5, 8.2
characteristics[host organism]	Host organism for host-associated microbiomes	0..1	NCBITaxon	homo sapiens, mus musculus, zea mays
characteristics[host disease]	Disease state of host if applicable	0..1	MONDO, EFO	inflammatory bowel disease, normal, colorectal cancer
characteristics[host age]	Age of host organism	0..1	Standard age format	45Y, 8W, 3M
comment[database search strategy]	Strategy for sequence database construction	0..1	Free text description	matched metagenome, RefSeq bacteria, GTDB, UniRef90, custom assembly
comment[metagenome accession]	Accession number for associated metagenome data	0..1	Database accession	SRR12345678, ERR12345678, PRJNA123456
comment[sample storage]	How sample was stored before processing	0..1	Free text description	flash frozen, -80C, RNAlater, 4C for 24h

Column Name

Description

Cardinality

Ontology/CV

Example Values

characteristics[geographic location]

Geographic location where sample was collected

0..1

GAZ or free text with coordinates

Baltic Sea, Amazon rainforest, lat:52.5 lon:13.4, GAZ:00002459

characteristics[collection date]

Date when sample was collected

0..1

ISO 8601 date format

2024-03-15, 2024-03, March 2024

characteristics[depth]

Depth at which sample was collected (for water/sediment)

0..1

Numeric value with unit

10 m, 0-5 cm, surface

characteristics[altitude]

Altitude/elevation for terrestrial samples

0..1

Numeric value with unit

500 m, 1200 m above sea level

characteristics[temperature]

Environmental temperature at collection

0..1

Numeric value with unit (Celsius)

25 C, 4 C, 37 C

characteristics[pH]

pH of the sample or environment

0..1

Numeric value

7.4, 5.5, 8.2

characteristics[host organism]

Host organism for host-associated microbiomes

0..1

NCBITaxon

homo sapiens, mus musculus, zea mays

characteristics[host disease]

Disease state of host if applicable

0..1

MONDO, EFO

inflammatory bowel disease, normal, colorectal cancer

characteristics[host age]

Age of host organism

0..1

Standard age format

45Y, 8W, 3M

comment[database search strategy]

Strategy for sequence database construction

0..1

Free text description

matched metagenome, RefSeq bacteria, GTDB, UniRef90, custom assembly

comment[metagenome accession]

Accession number for associated metagenome data

0..1

Database accession

SRR12345678, ERR12345678, PRJNA123456

comment[sample storage]

How sample was stored before processing

0..1

Free text description

flash frozen, -80C, RNAlater, 4C for 24h

5.3. Environmental Context Columns

5.3.1. Aquatic Samples

Column Name	Description	Example Values
characteristics[water body type]	Type of water body	ocean, lake, river, estuary, pond
characteristics[salinity]	Salinity measurement	35 PSU, freshwater, brackish
characteristics[dissolved oxygen]	Dissolved oxygen concentration	8.5 mg/L, hypoxic, anoxic
characteristics[chlorophyll]	Chlorophyll concentration if measured	2.5 ug/L
characteristics[sampling depth zone]	Ecological depth zone	epipelagic, mesopelagic, benthic

Column Name

Description

Example Values

characteristics[water body type]

Type of water body

ocean, lake, river, estuary, pond

characteristics[salinity]

Salinity measurement

35 PSU, freshwater, brackish

characteristics[dissolved oxygen]

Dissolved oxygen concentration

8.5 mg/L, hypoxic, anoxic

characteristics[chlorophyll]

Chlorophyll concentration if measured

2.5 ug/L

characteristics[sampling depth zone]

Ecological depth zone

epipelagic, mesopelagic, benthic

5.3.2. Soil Samples

Column Name	Description	Example Values
characteristics[soil type]	Soil classification	sandy loam, clay, peat
characteristics[soil horizon]	Soil horizon sampled	A horizon, O horizon, B horizon
characteristics[land use]	Land use type	agricultural, forest, urban, grassland
characteristics[vegetation]	Dominant vegetation	deciduous forest, corn field, prairie

Column Name

Description

Example Values

characteristics[soil type]

Soil classification

sandy loam, clay, peat

characteristics[soil horizon]

Soil horizon sampled

A horizon, O horizon, B horizon

characteristics[land use]

Land use type

agricultural, forest, urban, grassland

characteristics[vegetation]

Dominant vegetation

deciduous forest, corn field, prairie

5.3.3. Host-Associated Samples

Column Name	Description	Example Values
characteristics[body site]	Specific body site for host-associated samples	stool, oral cavity, skin, vaginal
characteristics[host diet]	Diet information for host	omnivore, vegan, western diet, high-fiber
characteristics[antibiotic treatment]	Recent antibiotic exposure	none, amoxicillin 7 days prior, broad-spectrum

Column Name

Description

Example Values

characteristics[body site]

Specific body site for host-associated samples

stool, oral cavity, skin, vaginal

characteristics[host diet]

Diet information for host

omnivore, vegan, western diet, high-fiber

characteristics[antibiotic treatment]

Recent antibiotic exposure

none, amoxicillin 7 days prior, broad-spectrum

6. Organism Annotation in Metaproteomics

The characteristics[organism] column presents a unique challenge in metaproteomics because samples contain multiple organisms. Several approaches are supported:

6.1. Option 1: Use "metagenome" or Environment-Specific Term

For samples where the community composition is unknown or highly complex:

characteristics[organism]	Example Samples
metagenome	General environmental samples
human gut metagenome	Human fecal samples, gut biopsies
soil metagenome	Soil samples
marine metagenome	Ocean water, marine sediment
mouse gut metagenome	Mouse fecal samples

characteristics[organism]

Example Samples

metagenome

General environmental samples

human gut metagenome

Human fecal samples, gut biopsies

soil metagenome

Soil samples

marine metagenome

Ocean water, marine sediment

mouse gut metagenome

Mouse fecal samples

These terms have corresponding NCBITaxon identifiers (e.g., NCBITaxon:749906 for "gut metagenome").

6.2. Option 2: Specify Host Organism

For host-associated microbiomes where host context is important:

characteristics[organism]	characteristics[microbiome source]
homo sapiens	gut microbiome
mus musculus	gut microbiome
arabidopsis thaliana	rhizosphere microbiome

characteristics[organism]

characteristics[microbiome source]

homo sapiens

gut microbiome

mus musculus

gut microbiome

arabidopsis thaliana

rhizosphere microbiome

6.3. Option 3: Multiple Organism Columns

For controlled or known communities (e.g., defined consortia, mock communities):

characteristics[organism]	characteristics[organism]	characteristics[organism]
escherichia coli	bacteroides fragilis	lactobacillus acidophilus

characteristics[organism]

escherichia coli

bacteroides fragilis

lactobacillus acidophilus

Note	The approach should be chosen based on the experimental context and database search strategy used.

7. Database Search Strategy Annotation

Metaproteomics database construction is critical and should be documented:

Strategy	Description	When to Use
Matched metagenome	Database from metagenome of same sample	When metagenome sequencing was performed
Reference database	Public reference database (RefSeq, UniProt)	When no metagenome available
Custom assembly	De novo assembled from sample metagenome	For novel environments
GTDB/UHGG	Genome-resolved metagenome databases	For gut microbiome studies
Hybrid approach	Combination of reference and sample-specific	Complex communities with some known members

Strategy

Description

When to Use

Matched metagenome

Database from metagenome of same sample

When metagenome sequencing was performed

Reference database

Public reference database (RefSeq, UniProt)

When no metagenome available

Custom assembly

De novo assembled from sample metagenome

For novel environments

GTDB/UHGG

Genome-resolved metagenome databases

For gut microbiome studies

Hybrid approach

Combination of reference and sample-specific

Complex communities with some known members

Document the strategy in comment[database search strategy].

8. Mock Community Samples

For defined/mock microbial communities used as standards:

Column Name	Description	Example Values
characteristics[mock community]	Identifier or name of mock community standard	ZymoBIOMICS Microbial Community Standard, ATCC MSA-1000
characteristics[mock community composition]	Description of community composition	8 bacteria + 2 yeasts at defined ratios, even mix of 10 species
comment[expected organism list]	List of organisms expected in mock community	E. coli;B. subtilis;S. cerevisiae;L. fermentum

Column Name

Description

Example Values

characteristics[mock community]

Identifier or name of mock community standard

ZymoBIOMICS Microbial Community Standard, ATCC MSA-1000

characteristics[mock community composition]

Description of community composition

8 bacteria + 2 yeasts at defined ratios, even mix of 10 species

comment[expected organism list]

List of organisms expected in mock community

E. coli;B. subtilis;S. cerevisiae;L. fermentum

9. Example SDRF Files

9.1. Human Gut Microbiome Example

source name	characteristics[organism]	characteristics[environmental sample type]	characteristics[host disease]	...	comment[database search strategy]	comment[metagenome accession]	comment[data file]
subject_001_stool	human gut metagenome	human gut	inflammatory bowel disease	...	matched metagenome	SRR12345678	IBD_001.raw
subject_002_stool	human gut metagenome	human gut	normal	...	matched metagenome	SRR12345679	healthy_002.raw

Sample metadata Data file metadata

9.2. Environmental Sample Example

source name	characteristics[organism]	characteristics[environmental sample type]	characteristics[geographic location]	characteristics[depth]	...	comment[database search strategy]	comment[data file]
baltic_station1_summer	marine metagenome	marine sediment	Baltic Sea	50 m	...	GTDB marine subset	baltic_sed_001.raw
soil_farm_plot1	soil metagenome	agricultural soil	Iowa, USA	0-10 cm	...	custom assembly	soil_plot1.raw

Sample metadata Data file metadata

10. Quality Control Annotations

For metaproteomics, consider documenting:

Column Name	Description	Example Values
comment[biomass estimation]	Estimated microbial biomass in sample	1e9 cells/g, high biomass, low biomass
comment[host contamination]	Level of host protein contamination if known	low (<5%), moderate (5-20%), high (>20%)
comment[contaminant database]	Contaminant databases used in search	cRAP, MaxQuant contaminants

Column Name

Description

Example Values

comment[biomass estimation]

Estimated microbial biomass in sample

1e9 cells/g, high biomass, low biomass

comment[host contamination]

Level of host protein contamination if known

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

comment[contaminant database]

Contaminant databases used in search

cRAP, MaxQuant contaminants

11. Best Practices for Metaproteomics Annotation

Use appropriate organism terms: Choose between metagenome terms, host organism, or explicit multi-organism annotation based on your experimental design.
Document database strategy: The sequence database used dramatically affects results - always document construction strategy.
Link to metagenomics data: When available, provide accession numbers for related metagenome/metatranscriptome data.
Include environmental context: Geographic location, collection date, and environmental parameters enhance data reusability.
Specify host information: For host-associated microbiomes, document host species, health status, and relevant metadata.
Note sample handling: Storage conditions and processing time can affect community composition.
Consider MIxS standards: Align with Minimum Information about any (x) Sequence standards where applicable.
Use controlled vocabularies: Prefer ENVO terms for environmental classification and NCBITaxon for organisms.

12. Template File

The metaproteomics SDRF template file is available in this directory:

metaproteomics-template.sdrf.tsv

13. Validation

Metaproteomics SDRF files should be validated using the sdrf-pipelines tool:

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

Note	Metaproteomics-specific validation rules are under development.

14. Authors and Maintainers

This template was developed by the SDRF-Proteomics community with contributions from metaproteomics researchers.

For questions or suggestions, please open an issue on the GitHub repository.

15. References

Wilmes P, Bond PL. (2004) The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms. Environmental Microbiology.
Muth T, et al. (2015) The MetaProteomeAnalyzer: a powerful open-source software suite for metaproteomics data analysis and interpretation. Journal of Proteome Research.
Chatterjee S, et al. (2023) A comprehensive and scalable database search system for metaproteomics. Nature Communications.
ENVO: Environment Ontology (http://www.obofoundry.org/ontology/envo.html)
MIxS: Minimum Information about any (x) Sequence (https://genomicsstandardsconsortium.github.io/mixs/)