▶ source name
required
base Unique identifier for the biological sample
Description
Unique identifier for the biological sample
▶ assay name
required
base Unique identifier for the data acquisition run
Description
Unique identifier for the data acquisition run
▶ technology type
required
lc-ms-metabolomics Type of technology used
Description
Type of technology used
Validators
single_cardinality_validator
values
— values:
LC-MS-based metabolomics
For lc-ms-metabolomics the technology type must be 'LC-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)
▶ comment[data file]
required
base Name of the raw data file
Description
Name of the raw data file
▶ characteristics[organism]
required
sample-metadata Species of the sample using NCBI Taxonomy
Description
Species of the sample using NCBI Taxonomy
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
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)
Validators
pattern
— pattern:
^\d+$|^pooled$
Biological replicate should be an integer or 'pooled' for pooled reference samples
▶ comment[instrument]
required
ms-metabolomics Mass spectrometer instrument used
Description
Mass spectrometer instrument used
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.
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).
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)
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[chromatography type]
required
lc-ms-metabolomics Chromatography mode used for separation. Should be a CHMO term (e.g. CHMO:0002302 reversed-phase ...
Description
Chromatography mode used for separation. Should be a CHMO term (e.g. CHMO:0002302 reversed-phase chromatography, CHMO:0001025 hydrophilic interaction chromatography).
Validators
pattern
— pattern:
^(NT=.+;AC=CHMO:\d{7}|reversed-phase chromatography|hydrophilic interaction chromatography|normal-phase chromatography|ion-exchange chromatography|size-exclusion chromatography)$
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.
Examples
NT=reversed-phase chromatography;AC=CHMO:0002302, NT=hydrophilic interaction chromatography;AC=CHMO:0001025, reversed-phase chromatography, hydrophilic interaction chromatography
▶ 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
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
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
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[chromatography column]
recommended
lc-ms-metabolomics LC column used for separation, including manufacturer, model, and dimensions
Description
LC column used for separation, including manufacturer, model, and dimensions
Properties
allows N/A
allows not available
Validators
pattern
— pattern:
^.+$
Free-text chromatography column description
Examples
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[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.
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).
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.
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.
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
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
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)
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)
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)
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
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)
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)
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
▶ 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
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
Properties
allows N/A
allows not available
Validators
mz_value
Precursor m/z value with unit
▶ 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
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.
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.
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
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
Properties
allows N/A
allows not available
Validators
number_with_unit
Mass tolerance with unit (ppm, Da, or mmu)
▶ comment[collision energy]
optional
ms-metabolomics Collision energy used for fragmentation
Description
Collision energy used for fragmentation
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
▶ comment[mobile phase a]
optional
lc-ms-metabolomics Composition of mobile phase A
Description
Composition of mobile phase A
Properties
allows N/A
allows not available
Validators
pattern
— pattern:
^.+$
Free-text composition of mobile phase A
Examples
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
lc-ms-metabolomics Composition of mobile phase B
Description
Composition of mobile phase B
Properties
allows N/A
allows not available
Validators
pattern
— pattern:
^.+$
Free-text composition of mobile phase B
Examples
0.1% formic acid in acetonitrile, 10 mM ammonium acetate in 90% acetonitrile pH 9.0, methanol
▶ comment[gradient]
optional
lc-ms-metabolomics Free-text description of the chromatographic gradient program
Description
Free-text description of the chromatographic gradient program
Properties
allows N/A
allows not available
Validators
pattern
— pattern:
^.+$
Free-text gradient description
Examples
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
lc-ms-metabolomics Mobile-phase flow rate
Description
Mobile-phase flow rate
Properties
allows N/A
allows not available
Validators
number_with_unit
Flow rate with unit
Examples
300 nL/min, 250 uL/min, 0.4 mL/min