affinity-proteomics

v1.0.0 technology usable alone

SDRF template for affinity-based proteomics experiments (Olink, SomaScan). This is the base template for all affinity proteomics experiments.

Key Guidance

The affinity-proteomics template is one of three usable-alone technology templates. It

covers antibody-based (Olink PEA) and aptamer-based (SomaScan) proteomics platforms.

Use this template directly for affinity experiments and combine with an organism template.

Key differences from ms-proteomics:

No sample preparation chemistry columns (no digestion, reduction, alkylation).
characteristics[sample type] is required to distinguish study samples from controls and

reference materials used for assay calibration/quality control.

comment[platform] identifies the specific instrument/platform.
comment[panel name] is RECOMMENDED, but it MUST be provided when comment[platform]

refers to a platform family with multiple panels/menus and the panel/menu cannot be

uniquely inferred (e.g., Olink Target 96, SomaScan Assay v5.0).

comment[quantification unit]: NPX for Olink, RFU for SomaScan.
comment[dilution]: Optional; commonly used for SomaScan workflows.
comment[lot number]: Optional reagent lot for traceability.
comment[normalization method]: How data was normalized (plate control, bridge, etc.).

Mutually exclusive with ms-proteomics and ms-metabolomics.

Inheritance

base → sample-metadata → affinity-proteomics

Combination Rules

Mutually exclusive with: ms-proteomics

Columns

9 own + 24 inherited = 33 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[organism]	required	sample-metadata	Species of the sample using NCBI Taxonomy
Description Species of the sample using NCBI Taxonomy Ontology COB:0000022 Properties allows N/A Validators ontology — ontologies: ncbitaxon The organism should be a valid NCBI Taxonomy term Examples `homo sapiens`, `mus musculus`, `rattus norvegicus`, `saccharomyces cerevisiae`
▶	characteristics[organism part]	required	sample-metadata	Main normalized anatomical term for the sample
Description Main normalized anatomical term for the sample Ontology EFO:0000635 Properties allows N/A allows not available multiple cardinality Validators ontology — ontologies: uberon, bto The organism part should be a valid UBERON or BTO term Examples `liver`, `brain`, `heart`, `blood`
▶	characteristics[biological replicate]	required	sample-metadata	Identifier for the biological replicate (integer starting from 1, or 'pooled' for pooled samples)
Description Identifier for the biological replicate (integer starting from 1, or 'pooled' for pooled samples) Ontology MS:1001809 Properties Validators pattern — pattern: `^\d+$\|^pooled$` Biological replicate should be an integer or 'pooled' for pooled reference samples Examples `1`, `2`, `pooled`
▶	characteristics[sample type]	required	affinity-proteomics	Role of the sample in the assay. Distinguishes study samples from controls/reference materials fo...
Description Role of the sample in the assay. Distinguishes study samples from controls/reference materials for assay interpretation and quality control Ontology PRIDE:0000895 Properties Validators ontology — ontologies: pride Sample type should be a child of PRIDE:0000895 (sample type) Examples `study sample`, `negative control`, `positive control`, `calibrator`, `reference`, `standard`, `buffer control`
▶	comment[platform]	required	affinity-proteomics	Affinity proteomics platform used (e.g. Olink Explore HT, SomaScan Assay 7K)
Description Affinity proteomics platform used (e.g. Olink Explore HT, SomaScan Assay 7K) Properties Validators single_cardinality_validator ontology — ontologies: pride The platform should be a valid PRIDE ontology term for affinity platforms Examples `Olink Explore HT`, `Olink Target 96`, `SomaScan Assay 11K`
▶	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[cell type]	recommended	sample-metadata	Cell type of the sample
Description Cell type of the sample Ontology EFO:0000324 Properties allows N/A allows not available multiple cardinality Validators ontology — ontologies: cl, bto, clo The cell type should be a valid Cell Ontology (CL), BRENDA Tissue Ontology (BTO), or Cell Line Ontology (CLO) term Examples `hepatocyte`, `neuron`, `fibroblast`, `T cell`
▶	characteristics[disease]	recommended	sample-metadata	Disease state of the sample
Description Disease state of the sample Ontology MONDO:0000001 Properties allows N/A allows not available Validators ontology — ontologies: mondo, efo, doid, ncit, pato The disease should be a valid MONDO, EFO, DOID, NCIT, or PATO ontology term. Use 'normal' (PATO:0000461) for healthy samples. Examples `normal`, `breast cancer`, `infection`, `metabolic disease`
▶	comment[panel name]	recommended	affinity-proteomics	Commercial panel/menu identifier within the platform. RECOMMENDED, but MUST be provided when not ...
Description Commercial panel/menu identifier within the platform. RECOMMENDED, but MUST be provided when not uniquely inferable from comment[platform]. Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Panel/menu identifier Examples `Target 96 Inflammation`, `Explore 1536`, `SomaScan 7K`, `SomaScan 11K`
▶	comment[sdrf template]	optional	base	Template name and version used for annotation. Two formats are supported - key=value format (NT=t...
Description Template name and version used for annotation. Two formats are supported - key=value format (NT=template_name;VV=vX.Y.Z) or simple format (template_name vX.Y.Z). Multiple templates can be specified using multiple columns. Ontology PRIDE:0000832 Properties allows not available multiple cardinality Validators pattern — pattern: `^(NT=[\w-]+;VV=v\d+\.\d+\.\d+(-[\w.]+)?\|[\w-]+ v\d+\.\d+\.\d+(-[\w.]+)?)$` 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[tissue supergroup]	optional	sample-metadata	Broader anatomical grouping or system-level bucket for the sample, used alongside the organism pa...
Description Broader anatomical grouping or system-level bucket for the sample, used alongside the organism part for higher-level grouping Properties allows N/A allows not available Validators ontology — ontologies: uberon, bto Tissue supergroup should be a valid broad UBERON or BTO anatomy term when possible Examples `digestive system`, `nervous system`, `cardiovascular system`, `gastrointestinal tract`
▶	characteristics[pooled sample]	optional	sample-metadata	Whether the sample is a pooled sample combining material from multiple biological sources. Use 'n...
Description 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. Ontology NCIT:C165587 Properties allows N/A allows not available Validators values — values: `not pooled`, `pooled` pattern — pattern: `^(not pooled\|pooled\|SN=.+(;SN=.+)*)$` Use 'not pooled', 'pooled', or list sample IDs with SN= prefix Examples `SN=sample1;SN=sample2`
▶	characteristics[material type]	optional	sample-metadata	Type of biological material being analyzed
Description Type of biological material being analyzed Ontology PRIDE:0000837 Properties allows N/A allows not available Validators values — values: `tissue`, `cell`, `cell line`, `organism part`, `whole organism`, `synthetic` Material type
▶	characteristics[tissue mass]	optional	sample-metadata	Mass of tissue used for extraction
Description Mass of tissue used for extraction Ontology OBA:2045411 Properties allows N/A allows not available Validators number_with_unit Tissue mass with unit Examples `50 mg`, `1 g`, `500 ug`
▶	characteristics[biosample accession number]	optional	sample-metadata	BioSample accession number for the sample (e.g., SAMN or SAMEA identifiers)
Description BioSample accession number for the sample (e.g., SAMN or SAMEA identifiers) Ontology NCIT:C175889 Properties allows N/A allows not available Validators accession BioSample accession Examples `SAMN12345678`, `SAMEA12345678`, `SAMD1234567`
▶	characteristics[sampling time]	optional	sample-metadata	Time at which the sample was collected (for longitudinal or time-course studies)
Description Time at which the sample was collected (for longitudinal or time-course studies) Ontology EFO:0000689 Properties allows N/A allows not available Validators number_with_unit Sampling time with unit Examples `0 hour`, `24 hour`, `7 day`, `3 month`
▶	characteristics[treatment]	optional	sample-metadata	Treatment or perturbation applied to the sample (drug, stimulus, environmental stress)
Description Treatment or perturbation applied to the sample (drug, stimulus, environmental stress) Ontology EFO:0000727 Properties allows N/A allows not available Validators ontology — ontologies: ncit, efo Treatment should be a valid ontology term. Use 'untreated' for controls. Examples `untreated`, `LPS stimulation`, `doxorubicin treatment`, `drought stress`, `salt stress`
▶	characteristics[synthetic peptide]	optional	sample-metadata	Whether the sample is a synthetic peptide library or biological material
Description Whether the sample is a synthetic peptide library or biological material Ontology PRIDE:0000495 Properties allows N/A Validators values — values: `synthetic`, `not synthetic` Synthetic peptide status
▶	characteristics[spiked compound]	optional	sample-metadata	Spiked-in compound details using key-value format (CT=compound type, QY=quantity, PS=peptide sequ...
Description Spiked-in compound details using key-value format (CT=compound type, QY=quantity, PS=peptide sequence, AC=UniProt accession, CN=compound name, CV=vendor) Ontology PRIDE:0000496 Properties allows N/A allows not available multiple cardinality Validators pattern — pattern: `^CT=.+(;(QY\|PS\|AC\|CN\|CV\|SP)=.+)*$` Key-value format for spiked compound details (CT=type, SP=species, QY=quantity, PS=sequence, AC=accession, CN=name, CV=vendor) Examples `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	sample-metadata	Enrichment strategy applied to the sample (e.g., phosphopeptide enrichment, crosslinked peptide e...
Description Enrichment strategy applied to the sample (e.g., phosphopeptide enrichment, crosslinked peptide enrichment, glycopeptide enrichment) Ontology EFO:0009090 Properties allows N/A allows not available Validators ontology — ontologies: pride, efo Enrichment type should be a child term of EFO:0009090 (enrichment process) Examples `enrichment of cross-linked peptides`, `enrichment of phosphorylated protein`, `enrichment of glycopeptides`, `enrichment of ubiquitinated proteins`
▶	comment[instrument]	optional	affinity-proteomics	Instrument used for data acquisition (e.g. sequencer, qPCR machine, microarray reader)
Description Instrument used for data acquisition (e.g. sequencer, qPCR machine, microarray reader) Ontology MS:1000031 Properties allows N/A allows not available Validators ontology — ontologies: ms, pride The instrument should be a valid PSI-MS ontology term Examples `Illumina NovaSeq X`, `Illumina NextSeq 2000`, `Agilent SureScan Microarray Scanner`
▶	comment[quantification unit]	optional	affinity-proteomics	Unit of quantification for the assay (platform-specific)
Description Unit of quantification for the assay (platform-specific) Ontology PRIDE:0000392 Properties allows N/A allows not available Validators values — values: `NPX`, `RFU` Quantification unit
▶	comment[plate]	optional	affinity-proteomics	Plate identifier for batch effect analysis
Description Plate identifier for batch effect analysis Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Plate identifier Examples `1`, `2`
▶	comment[normalization method]	optional	affinity-proteomics	Normalization method applied to quantification values
Description Normalization method applied to quantification values Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Normalization method Examples `plate control normalized`, `bridge normalized`, `median normalization`, `not normalized`
▶	comment[dilution]	optional	affinity-proteomics	Sample dilution factor used (commonly used for SomaScan workflows)
Description Sample dilution factor used (commonly used for SomaScan workflows) Ontology OBI:0002483 Properties allows N/A allows not available Validators pattern — pattern: `^((0\.005\|0\.5\|20\|40)%\|[0-9]+(\.[0-9]+)?%?\|1:[0-9]+)$` Dilution factor; SomaScan commonly uses 0.005%, 0.5%, 20%, 40% Examples `0.005%`, `0.5%`, `20%`, `40%`, `1:200`
▶	comment[lot number]	optional	affinity-proteomics	Reagent lot number for traceability
Description Reagent lot number for traceability Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Lot number Examples `SS-2023-001`, `lot_12345`

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
Magnus Palmblad (n.m.palmblad@lumc.nl) - Leiden University Medical Center