ms-metabolomics

v1.0.0-dev technology usable alone

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

Key Guidance

The ms-metabolomics template is a usable-alone technology template for mass-spectrometry-based

metabolomics. It is the third sibling technology under sample-metadata, alongside ms-proteomics

and affinity-proteomics, and is mutually exclusive with both. It serves as the parent for the

technique-specific templates lc-ms-metabolomics and gc-ms-metabolomics.

Combine with an organism template (human, vertebrates, invertebrates, plants) to add

species-specific columns. Add clinical-metadata or oncology-metadata for clinical studies.

Naming conventions follow SDRF-Proteomics: lowercase column names, comment[...]/characteristics[...]

brackets, and the flat row model (one row = one sample x acquisition). MetaboBank

(MAGE-TAB-style) submissions can be mapped onto this template via the mapping document at

docs/mappings/metabobank-sdrf-mapping.md.

Key annotation guidance:

comment[scan polarity]: Use positive scan (MS:1000130) or negative scan (MS:1000129)

for single-polarity acquisitions. Reserve polarity switching only for true in-method

polarity switching that produces a single combined raw file. When a sample is acquired in

both POS and NEG modes producing two distinct raw files, use TWO ROWS per source name —

one row per (source name x polarity), each with its own comment[data file].

comment[ion source]: PSI-MS term (MS:1000008 child) such as ESI, APCI, EI, MALDI.

Children of this template (lc-ms / gc-ms) further constrain the set of valid sources.

comment[acquisition method]: Free-text or PRIDE term — DDA, DIA, SIM, MRM, full scan.
comment[data file] (inherited from base): vendor raw or open format (mzML, mzXML, .raw, .d).
comment[metabolite assignment file]: Per-assay constant pointer to the MAF result file.

Repeated identically across all rows of the same assay for SDRF self-containment, mirroring

MetaboBank semantics.

comment[*md5] columns: Optional MD5 integrity hashes for raw / processed / MAF files.

32-character lowercase or uppercase hex.

Mutually exclusive with ms-proteomics and affinity-proteomics.

Inheritance

base → sample-metadata → ms-metabolomics

Combination Rules

Mutually exclusive with: ms-proteomics, affinity-proteomics

Columns

26 own + 24 inherited = 50 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	ms-metabolomics	Type of technology used
Description Type of technology used Ontology PRIDE:0000663 Properties Validators single_cardinality_validator values — values: `metabolite profiling by mass spectrometry`, `LC-MS-based metabolomics`, `GC-MS-based metabolomics`
▶	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`
▶	comment[instrument]	required	ms-metabolomics	Mass spectrometer instrument used
Description Mass spectrometer instrument used Ontology MS:1000031 Properties multiple cardinality Validators ontology — ontologies: psi-ms, pride The instrument should be a valid PSI-MS or PRIDE ontology term Examples `Q Exactive`, `Xevo G2-S QTof`, `Orbitrap Fusion Lumos`, `timsTOF Pro`
▶	comment[ion source]	required	ms-metabolomics	Ion source used for ionization (e.g. ESI, APCI, EI, MALDI). Should be a child of MS:1000008.
Description Ion source used for ionization (e.g. ESI, APCI, EI, MALDI). Should be a child of MS:1000008. Ontology MS:1000008 Properties Validators ontology — ontologies: psi-ms Ion source should be a child term of MS:1000008 Examples `electrospray ionization`, `atmospheric pressure chemical ionization`, `electron ionization`, `matrix-assisted laser desorption ionization`
▶	comment[scan polarity]	required	ms-metabolomics	Scan polarity (positive scan, negative scan, or polarity switching). Polarity switching is reserv...
Description 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). Ontology MS:1000465 Properties Validators single_cardinality_validator values — values: `positive scan`, `negative scan`, `polarity switching` Scan polarity must be one of positive scan, negative scan, polarity switching
▶	comment[acquisition method]	required	ms-metabolomics	Mass spectrometry acquisition method (DDA, DIA, SIM, MRM, full scan)
Description Mass spectrometry acquisition method (DDA, DIA, SIM, MRM, full scan) Ontology PRIDE:0000659 Properties Validators ontology — ontologies: pride Acquisition method should be a valid PRIDE ontology term Examples `data-dependent acquisition`, `data-independent acquisition`, `selected reaction monitoring`, `parallel reaction monitoring`, `full scan`
▶	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[metabolite assignment file]	recommended	ms-metabolomics	Pointer to the metabolite assignment file (MAF) for this assay. Per-assay constant — the same val...
Description 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]. Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Path or filename of the MAF file Examples `m_MTBLS1129_LC-MS_positive_reverse-phase_metabolite_profiling_v2_maf.tsv`, `maf_pos_lipidomics.tsv`
▶	comment[extraction method]	recommended	ms-metabolomics	Sample extraction method used to obtain the metabolite fraction
Description Sample extraction method used to obtain the metabolite fraction Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Free-text extraction method, optionally CHMO-style NT=...;AC=CHMO:NNNNNNN Examples `methanol-water extraction`, `MTBE extraction`, `Bligh-Dyer extraction`, `Folch extraction`, `NT=methanol-water extraction;AC=CHMO:0001568`
▶	characteristics[analyte class]	recommended	ms-metabolomics	Class of metabolites targeted by the extraction and acquisition method
Description Class of metabolites targeted by the extraction and acquisition method Properties allows N/A allows not available Validators values — values: `polar metabolites`, `lipids`, `amino acids`, `fatty acids`, `bile acids`, `nucleotides`, … Analyte class describes the metabolite fraction targeted
▶	characteristics[sample matrix]	recommended	ms-metabolomics	Type of biological matrix used as input (e.g. serum, plasma, CSF, urine, tissue extract)
Description Type of biological matrix used as input (e.g. serum, plasma, CSF, urine, tissue extract) Properties allows N/A allows not available Validators ontology — ontologies: uberon, bto Sample matrix should be a valid UBERON or BTO term Examples `serum`, `plasma`, `cerebrospinal fluid`, `urine`, `tissue extract`
▶	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[sample type]	optional	sample-metadata	Classification of the sample role in the experiment. Distinguishes experimental samples from cont...
Description 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:0000895 Properties allows N/A allows not available Validators ontology — ontologies: pride Sample type should be a child of PRIDE:0000895 (sample type) Examples `single cell`, `reference`, `bridge`, `carrier`, `pooled`, `empty`, `quality control sample`, `negative control`
▶	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[extraction solvent]	optional	ms-metabolomics	Solvent or solvent mixture used for metabolite extraction
Description Solvent or solvent mixture used for metabolite extraction Properties allows N/A allows not available Validators ontology — ontologies: chebi Extraction solvent should be a valid ChEBI term when possible Examples `methanol`, `chloroform`, `methyl tert-butyl ether`, `acetonitrile`
▶	comment[internal standard]	optional	ms-metabolomics	Internal standard(s) spiked into the sample for normalization or retention-time calibration
Description Internal standard(s) spiked into the sample for normalization or retention-time calibration Properties allows N/A allows not available multiple cardinality Validators ontology — ontologies: chebi Internal standard should be a valid ChEBI term when possible Examples `caffeine-d9`, `L-tryptophan-d5`, `palmitic acid-d31`
▶	comment[sample preparation batch]	optional	ms-metabolomics	Batch identifier for sample preparation (plate, chip, processing batch). Useful for batch-effect ...
Description Batch identifier for sample preparation (plate, chip, processing batch). Useful for batch-effect correction. Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Sample preparation batch identifier Examples `plate1`, `batch_20220601`, `prep_A`
▶	comment[lc batch]	optional	ms-metabolomics	Liquid chromatography batch identifier for batch-effect tracking (e.g. column changes, LC system swaps)
Description Liquid chromatography batch identifier for batch-effect tracking (e.g. column changes, LC system swaps) Properties allows N/A allows not available Validators pattern — pattern: `^.+$` LC batch identifier Examples `LC1`, `column_A`
▶	comment[acquisition date]	optional	ms-metabolomics	Date of MS data acquisition (ISO 8601 format recommended). Useful for tracking instrument drift a...
Description Date of MS data acquisition (ISO 8601 format recommended). Useful for tracking instrument drift and batch effects. Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Acquisition date/time Examples `2022-06-01`, `2022-06-01T18:28:37`
▶	comment[ms2 mass analyzer]	optional	ms-metabolomics	Mass analyzer used for MS2 acquisition
Description Mass analyzer used for MS2 acquisition Ontology MS:1000443 Properties allows N/A allows not available Validators ontology — ontologies: psi-ms Should be a valid PSI-MS ontology term Examples `orbitrap`, `ion trap`, `TOF`
▶	comment[ms min mz]	optional	ms-metabolomics	MS method-defined minimum precursor (MS1) m/z setting used to acquire the data
Description MS method-defined minimum precursor (MS1) m/z setting used to acquire the data Ontology PRIDE:0000476 Properties allows N/A allows not available Validators mz_value Precursor m/z value with unit Examples `100m/z`, `200m/z`
▶	comment[ms max mz]	optional	ms-metabolomics	MS method-defined maximum precursor (MS1) m/z setting used to acquire the data
Description MS method-defined maximum precursor (MS1) m/z setting used to acquire the data Ontology PRIDE:0000477 Properties allows N/A allows not available Validators mz_value Precursor m/z value with unit Examples `1200m/z`, `1600m/z`
▶	comment[ms1 scan range]	optional	ms-metabolomics	m/z scan range for MS1 spectra as an interval. Alternative to separate ms min mz / ms max mz columns.
Description m/z scan range for MS1 spectra as an interval. Alternative to separate ms min mz / ms max mz columns. Ontology PRIDE:0001008 Properties allows N/A allows not available Validators mz_range_interval m/z range interval for MS1 spectra Examples `70m/z-1000m/z`, `100m/z-1500m/z`
▶	comment[ms2 scan range]	optional	ms-metabolomics	m/z scan range for MS2 spectra as an interval. Alternative to separate ms2 min mz / ms2 max mz columns.
Description m/z scan range for MS2 spectra as an interval. Alternative to separate ms2 min mz / ms2 max mz columns. Ontology PRIDE:0001009 Properties allows N/A allows not available Validators mz_range_interval m/z range interval for MS2 spectra Examples `50m/z-1000m/z`, `100m/z-1500m/z`
▶	comment[precursor mass tolerance]	optional	ms-metabolomics	Precursor mass tolerance for feature detection / database search
Description Precursor mass tolerance for feature detection / database search Ontology PRIDE:0000575 Properties allows N/A allows not available Validators number_with_unit Mass tolerance with unit (ppm, Da, or mmu) Examples `5 ppm`, `10 ppm`, `0.01 Da`
▶	comment[fragment mass tolerance]	optional	ms-metabolomics	Fragment mass tolerance for feature detection / database search
Description Fragment mass tolerance for feature detection / database search Ontology PRIDE:0000576 Properties allows N/A allows not available Validators number_with_unit Mass tolerance with unit (ppm, Da, or mmu) Examples `0.02 Da`, `20 ppm`
▶	comment[collision energy]	optional	ms-metabolomics	Collision energy used for fragmentation
Description Collision energy used for fragmentation Ontology MS:1000045 Properties allows N/A allows not available Validators pattern — pattern: `^\d+(\.\d+)?%?\s(NCE\|eV)(;\d+(\.\d+)?%?\s(NCE\|eV))*$` Collision energy format: {value} {unit} where unit is NCE or eV. For multiple values, use semicolon-separated entries. Examples `30 NCE`, `25 eV`, `25 NCE;27 NCE;30 NCE`
▶	comment[raw data file md5]	optional	ms-metabolomics	MD5 integrity hash for the raw data file referenced in comment[data file]. Mirrors MetaboBank Com...
Description MD5 integrity hash for the raw data file referenced in comment[data file]. Mirrors MetaboBank Comment[Raw Data File md5]. Properties allows N/A allows not available Validators pattern — pattern: `^[a-fA-F0-9]{32}$` 32-character hex MD5 hash Examples `d41d8cd98f00b204e9800998ecf8427e`, `9e107d9d372bb6826bd81d3542a419d6`
▶	comment[processed data file]	optional	ms-metabolomics	Pointer to the processed data file (e.g. peak table, feature matrix). Mirrors MetaboBank Comment[...
Description Pointer to the processed data file (e.g. peak table, feature matrix). Mirrors MetaboBank Comment[Processed Data File]. Properties allows N/A allows not available Validators pattern — pattern: `^.+$` Path or filename of the processed data file Examples `features_pos.tsv`, `peak_table_lipidomics.csv`
▶	comment[processed data file md5]	optional	ms-metabolomics	MD5 integrity hash for the processed data file. Mirrors MetaboBank Comment[Processed Data File md5].
Description MD5 integrity hash for the processed data file. Mirrors MetaboBank Comment[Processed Data File md5]. Properties allows N/A allows not available Validators pattern — pattern: `^[a-fA-F0-9]{32}$` 32-character hex MD5 hash Examples `d41d8cd98f00b204e9800998ecf8427e`
▶	comment[metabolite assignment file md5]	optional	ms-metabolomics	MD5 integrity hash for the metabolite assignment file. Mirrors MetaboBank Comment[Metabolite Assi...
Description MD5 integrity hash for the metabolite assignment file. Mirrors MetaboBank Comment[Metabolite Assignment File md5]. Properties allows N/A allows not available Validators pattern — pattern: `^[a-fA-F0-9]{32}$` 32-character hex MD5 hash Examples `d41d8cd98f00b204e9800998ecf8427e`

Contributors

Yasset Perez-Riverol (yperez@ebi.ac.uk) - EMBL-EBI
Mathias Mattano (mmattano@bmb.sdu.dk) - University of Southern Denmark
Deepti Jaiswal Kundu (jaiswal@ebi.ac.uk) - EMBL-EBI