metaproteomics

v1.0.0 sample

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.

Key Guidance

The metaproteomics template is aligned with the Genomics Standards Consortium (GSC)

MIxS standard for environmental and host-associated sample metadata.

Template hierarchy:

metaproteomics (this template) - shared environmental context

human-gut - human gut microbiome (MIxS human-gut extension)

soil - soil metaproteomics (MIxS soil extension)

water - aquatic metaproteomics (MIxS water extension)

Usage: combine a child template with ms-proteomics, e.g.:

human-gut + ms-proteomics

soil + ms-proteomics

Key columns:

characteristics[environmental sample type]: Required. ENVO/EFO term describing

the environmental material (soil, seawater, gut microbiome, biofilm).

characteristics[geographic location]: Recommended. GAZ term or coordinates.
characteristics[collection date]: ISO 8601 date of sample collection.
characteristics[environmental medium]: ENVO term for the environmental material.
comment[metagenome accession]: Link to matched metagenome dataset.

PRIDE ontology terms include MIxS cross-references in their definitions

(e.g., MIXS:0001107). Column names use spaces (SDRF convention) rather than

underscores (MIxS convention).

Inheritance

base → metaproteomics

Combination Rules

Requires a technology layer template.
Mutually exclusive with: human, vertebrates, invertebrates, plants
Excludes: sample-metadata

Columns

18 own + 9 inherited = 27 total · click a row for details

	Column	Requirement	Source	Description
▶	source name	required	base	Unique identifier for the biological sample
Description Unique identifier for the biological sample Ontology PRIDE:0000623 Properties
▶	assay name	required	base	Unique identifier for the data acquisition run
Description Unique identifier for the data acquisition run Ontology NCIT:C178857 Properties
▶	technology type	required	base	Type of technology used
Description Type of technology used Ontology PRIDE:0000663 Properties Validators single_cardinality_validator values — values: `proteomic profiling by mass spectrometry`, `protein expression profiling by antibody array`, `protein expression profiling by aptamer array`
▶	comment[technical replicate]	required	base	Identifier for the technical replicate (integer starting from 1)
Description Identifier for the technical replicate (integer starting from 1) Ontology MS:1001808 Properties type: integer
▶	comment[data file]	required	base	Name of the raw data file
Description Name of the raw data file Ontology MS:1003083 Properties
▶	characteristics[environmental sample type]	required	metaproteomics	Type of environmental sample analyzed (ENVO or EFO term). Corresponds to MIxS env_medium (MIXS:0000014).
Description Type of environmental sample analyzed (ENVO or EFO term). Corresponds to MIxS env_medium (MIXS:0000014). Ontology PRIDE:0000993 Properties Validators ontology — ontologies: envo, efo Should be a valid ENVO or EFO term Examples `soil`, `seawater`, `gut microbiome`, `wastewater`, `biofilm`
▶	comment[sdrf version]	recommended	base	Version of the SDRF-Proteomics specification used to annotate this file
Description Version of the SDRF-Proteomics specification used to annotate this file Ontology PRIDE:0000839 Properties Validators semver SDRF specification version Examples `v1.1.0`, `v2.0.0-dev`
▶	characteristics[geographic location]	recommended	metaproteomics	Geographic location where sample was collected (GAZ term or coordinates). Corresponds to MIxS geo...
Description Geographic location where sample was collected (GAZ term or coordinates). Corresponds to MIxS geo_loc_name (MIXS:0000010). Ontology PRIDE:0000995 Properties allows N/A allows not available Validators ontology — ontologies: gaz Should be a valid GAZ term or coordinates Examples `Pacific Ocean`, `Amazon rainforest`, `47.6062 N, 122.3321 W`
▶	characteristics[environmental medium]	recommended	metaproteomics	Environmental material from which the sample was obtained (ENVO term). Corresponds to MIxS env_me...
Description Environmental material from which the sample was obtained (ENVO term). Corresponds to MIxS env_medium (MIXS:0000014). Ontology PRIDE:0000994 Properties allows N/A allows not available Validators ontology — ontologies: envo Should be a valid ENVO environmental material term Examples `soil`, `seawater`, `freshwater`, `feces`, `biofilm`
▶	comment[sdrf template]	optional	base	Template name and version used for annotation. Two formats are supported - key=value format (NT=t...
Description 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. Ontology PRIDE:0000832 Properties allows not available multiple cardinality Validators pattern — pattern: `^(NT=[\w-]+;VV=v\d+\.\d+\.\d+(-[\w.]+)?\|[\w-]+ v\d+\.\d+\.\d+(-[\w.]+)?)$` Template can be specified as 'NT=name;VV=vX.Y.Z' or 'name vX.Y.Z' Examples `NT=human;VV=v1.1.0`, `human v1.1.0`, `NT=ms-proteomics;VV=v1.1.0`, `ms-proteomics v1.1.0`
▶	comment[sdrf annotation tool]	optional	base	Software tool or method used to generate or annotate the SDRF file. Two formats are supported - k...
Description Software tool or method used to generate or annotate the SDRF file. Two formats are supported - key=value format (NT=tool_name;VV=vX.Y.Z) or simple format (tool_name vX.Y.Z). Ontology PRIDE:0000840 Properties allows not available Validators pattern — pattern: `^(NT=[\w-]+;VV=v[\d.]+[\w.-]\|[\w-]+ v[\d.]+[\w.-]\|manual curation)$` Annotation tool can be specified as 'NT=name;VV=vX.Y.Z' or 'name vX.Y.Z' or 'manual curation' Examples `NT=lesSDRF;VV=v0.1.0`, `lesSDRF v0.1.0`, `NT=sdrf-pipelines;VV=v1.0.0`, `sdrf-pipelines v1.0.0`, `manual curation`
▶	comment[sdrf validation hash]	optional	base	Hash value for SDRF validation integrity checking
Description Hash value for SDRF validation integrity checking Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Validation hash string
▶	characteristics[collection date]	optional	metaproteomics	Date when sample was collected (ISO 8601)
Description Date when sample was collected (ISO 8601) Ontology PRIDE:0000996 Properties allows N/A allows not available Validators date Sample collection date Examples `2024`, `2024-01`, `2024-01-15`
▶	characteristics[sample collection method]	optional	metaproteomics	Method used to collect the environmental sample
Description Method used to collect the environmental sample Ontology PRIDE:0000997 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Collection method description Examples `grab sample`, `core sample`, `swab`, `filtration`
▶	characteristics[depth]	optional	metaproteomics	Depth at which sample was collected. Corresponds to MIxS depth (MIXS:0000018).
Description Depth at which sample was collected. Corresponds to MIxS depth (MIXS:0000018). Ontology PRIDE:0000711 Properties allows N/A allows not available Validators number_with_unit Depth with unit Examples `10 m`, `50 cm`, `100 m`
▶	characteristics[altitude]	optional	metaproteomics	Altitude or elevation of sampling site. Corresponds to MIxS elevation (MIXS:0000093).
Description Altitude or elevation of sampling site. Corresponds to MIxS elevation (MIXS:0000093). Ontology PRIDE:0000712 Properties allows N/A allows not available Validators number_with_unit Altitude with unit Examples `500 m`, `1200 m`, `0 m`
▶	characteristics[temperature]	optional	metaproteomics	Temperature at sampling location. Corresponds to MIxS temperature (MIXS:0000113).
Description Temperature at sampling location. Corresponds to MIxS temperature (MIXS:0000113). Ontology PRIDE:0000703 Properties allows N/A allows not available Validators number_with_unit Temperature in Celsius Examples `25 °C`, `4 °C`, `-20 °C`
▶	characteristics[ph]	optional	metaproteomics	pH at sampling location
Description pH at sampling location Ontology PRIDE:0000746 Properties allows N/A allows not available Validators pattern — pattern: `^\d+(\.\d+)?$` pH value Examples `7.0`, `5.5`, `8.2`
▶	characteristics[sample storage]	optional	metaproteomics	Storage conditions for the sample before analysis
Description Storage conditions for the sample before analysis Ontology PRIDE:0000730 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Storage conditions Examples `-80C`, `liquid nitrogen`, `4C`
▶	comment[metagenome accession]	optional	metaproteomics	Accession number for matched metagenome data
Description Accession number for matched metagenome data Ontology PRIDE:0000956 Properties allows N/A allows not available Validators accession Database accession number Examples `MGYA00001234`, `SRP123456`
▶	characteristics[microbiome source]	optional	metaproteomics	Source of the microbiome being studied (e.g., gut microbiome, rhizosphere microbiome)
Description Source of the microbiome being studied (e.g., gut microbiome, rhizosphere microbiome) Ontology PRIDE:0000986 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Microbiome source description Examples `gut microbiome`, `rhizosphere microbiome`, `oral microbiome`, `skin microbiome`
▶	characteristics[biomass estimation]	optional	metaproteomics	Estimated microbial biomass in the sample
Description Estimated microbial biomass in the sample Ontology PRIDE:0000990 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Biomass estimation Examples `1e9 cells/g`, `high biomass`, `low biomass`
▶	characteristics[host contamination]	optional	metaproteomics	Level of host protein contamination if known
Description Level of host protein contamination if known Ontology PRIDE:0000991 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Host contamination level Examples `low (<5%)`, `moderate (5-20%)`, `high (>20%)`
▶	comment[contaminant database]	optional	metaproteomics	Contaminant database(s) used in database search
Description Contaminant database(s) used in database search Ontology PRIDE:0000992 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Contaminant database name(s) Examples `cRAP`, `MaxQuant contaminants`, `cRAP;MaxQuant contaminants`
▶	characteristics[mock community]	optional	metaproteomics	Identifier or name of mock community standard used
Description Identifier or name of mock community standard used Ontology PRIDE:0000987 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Mock community identifier Examples `ZymoBIOMICS Microbial Community Standard`, `ATCC MSA-1000`
▶	characteristics[mock community composition]	optional	metaproteomics	Description of mock community composition (species and ratios)
Description Description of mock community composition (species and ratios) Ontology PRIDE:0000988 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Community composition description Examples `8 bacteria + 2 yeasts at defined ratios`, `even mix of 10 species`
▶	comment[expected organism list]	optional	metaproteomics	Semicolon-separated list of organisms expected in mock community
Description Semicolon-separated list of organisms expected in mock community Ontology PRIDE:0000989 Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Semicolon-separated organism list Examples `E. coli;B. subtilis;S. cerevisiae;L. fermentum`, `Bacillus subtilis;Staphylococcus aureus`

Contributors

Yasset Perez-Riverol (yperez@ebi.ac.uk) - EMBL-EBI
Deepti Jaiswal Kundu (jaiswal@ebi.ac.uk) - EMBL-EBI
Nithu Sara John (nithu@ebi.ac.uk) - EMBL-EBI
Nandana Madhusoodanan (nandana@ebi.ac.uk) - EMBL-EBI
Asier Larrea (alarre@ebi.ac.uk) - EMBL-EBI
Toan Phung (TPhung001@dundee.ac.uk) - University of Dundee
Timo Sachsenberg (timo.sachsenberg@uni-tuebingen.de) - University of Tübingen