SDRF template for Data-independent acquisition (DIA) experiments. Extends ms-proteomics with DIA-specific columns.
The dia-acquisition template restricts the acquisition method to Data-independent
acquisition and adds DIA-specific window parameters.
Key guidance:
comment[proteomics data acquisition method]: Automatically restricted toData-independent acquisition. This is enforced by the template.
comment[scan window lower limit] / comment[scan window upper limit]: The overallm/z range of the DIA method (e.g., 400-1200 for a typical SWATH experiment).
comment[isolation window width]: Width of individual isolation windows in m/z.Common values: 25 (wide SWATH), 8 (narrow windows), 4 (high-resolution DIA).
comment[dia method]: The specific DIA variant used. Common values:SWATH-MS, diaPASEF (Bruker timsTOF), MSE (Waters), All ion fragmentation.
This template inherits all ms-proteomics columns (instrument, label, cleavage agent, etc.).
The ms-proteomics range columns (ms min/max mz, rt, im) are also relevant for DIA methods.
| Column | Requirement | Source | Description | |
|---|---|---|---|---|
| ▶ | source name | required | base | Unique identifier for the biological sample |
| ▶ | assay name | required | base | Unique identifier for the data acquisition run |
| ▶ | technology type | required | base | Type of technology used |
|
Type of technology used
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) |
| ▶ | comment[data file] | required | base | Name of the raw data file |
| ▶ | characteristics[organism] | required | sample-metadata | Species of the sample using NCBI Taxonomy |
|
Species of the sample using NCBI Taxonomy
allows N/A
ontology
— ontologies: ncbitaxon
The organism should be a valid NCBI Taxonomy term
homo sapiens, mus musculus, rattus norvegicus, saccharomyces cerevisiae
|
||||
| ▶ | characteristics[organism part] | required | sample-metadata | Main normalized anatomical term for the sample |
|
Main normalized anatomical term for the sample
allows N/A
allows not available
multiple cardinality
ontology
— ontologies: uberon, bto
The organism part should be a valid UBERON or BTO term
liver, brain, heart, blood
|
||||
| ▶ | characteristics[biological replicate] | required | sample-metadata | Identifier for the biological replicate (integer starting from 1, or 'pooled' for pooled samples) |
|
Identifier for the biological replicate (integer starting from 1, or 'pooled' for pooled samples)
pattern
— pattern:
^\d+$|^pooled$
Biological replicate should be an integer or 'pooled' for pooled reference samples
1, 2, pooled
|
||||
| ▶ | comment[proteomics data acquisition method] | required | dia-acquisition | Mass spectrometry acquisition method (restricted to DIA for this template) |
|
Mass spectrometry acquisition method (restricted to DIA for this template)
single_cardinality_validator
values
— values:
Data-independent acquisition
This template requires Data-independent acquisition
|
||||
| ▶ | comment[instrument] | required | ms-proteomics | Mass spectrometer instrument used |
|
Mass spectrometer instrument used
multiple cardinality
ontology
— ontologies: ms, pride
The instrument should be a valid MS or PRIDE ontology term
LTQ Orbitrap, Q Exactive, Orbitrap Fusion Lumos, timsTOF Pro
|
||||
| ▶ | comment[cleavage agent details] | required | ms-proteomics | Enzyme or chemical used for protein digestion |
|
Enzyme or chemical used for protein digestion
allows N/A
ontology
— ontologies: ms
The cleavage agent details should be valid MS ontology terms
NT=Trypsin;AC=MS:1001251, NT=Lys-C;AC=MS:1001309, NT=Chymotrypsin;AC=MS:1001306
|
||||
| ▶ | comment[label] | required | ms-proteomics | Labeling strategy used for quantification |
|
Labeling strategy used for quantification
ontology
— ontologies: pride
The label should be a valid PRIDE ontology term
label free sample, SILAC light, SILAC heavy, TMT126, iTRAQ114
|
||||
| ▶ | comment[fraction identifier] | required | ms-proteomics | Fraction number for fractionated samples (integer, use 1 for non-fractionated). In MS proteomics,... |
|
Fraction number for fractionated samples (integer, use 1 for non-fractionated). In MS proteomics, this identifies the chromatographic or electrophoretic fraction (e.g., SCX, hpHRP, SEC fractions). Each fraction maps to one data file.
type: integer
|
||||
| ▶ | comment[sdrf version] | recommended | base | Version of the SDRF-Proteomics specification used to annotate this file |
|
Version of the SDRF-Proteomics specification used to annotate this file
semver
SDRF specification version
v1.1.0, v2.0.0-dev
|
||||
| ▶ | characteristics[cell type] | recommended | sample-metadata | Cell type of the sample |
|
Cell type of the sample
allows N/A
allows not available
multiple cardinality
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
hepatocyte, neuron, fibroblast, T cell
|
||||
| ▶ | characteristics[disease] | recommended | sample-metadata | Disease state of the sample |
|
Disease state of the sample
allows N/A
allows not available
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.
normal, breast cancer, infection, metabolic disease
|
||||
| ▶ | comment[dissociation method] | recommended | ms-proteomics | Fragmentation method used in MS/MS |
|
Fragmentation method used in MS/MS
allows N/A
allows not available
ontology
— ontologies: ms, pride
Dissociation method should be a child term of MS:1000044
HCD, CID, ETD, EThcD
|
||||
| ▶ | comment[precursor mass tolerance] | recommended | ms-proteomics | Precursor mass tolerance for database search |
|
Precursor mass tolerance for database search
allows N/A
allows not available
number_with_unit
Mass tolerance with unit (ppm, Da, or mmu)
10 ppm, 20 ppm, 0.5 Da, 20 mmu
|
||||
| ▶ | comment[fragment mass tolerance] | recommended | ms-proteomics | Fragment mass tolerance for database search |
|
Fragment mass tolerance for database search
allows N/A
allows not available
number_with_unit
Mass tolerance with unit (ppm, Da, or mmu)
0.02 Da, 20 ppm, 50 mmu
|
||||
| ▶ | comment[modification parameters] | recommended | ms-proteomics | Post-translational modifications searched |
|
Post-translational modifications searched
allows N/A
allows not available
multiple cardinality
ontology
— ontologies: unimod, mod
The modification parameters should be valid Unimod or PSI-MOD terms
NT=Oxidation;MT=Variable;TA=M;AC=Unimod:35, NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4
|
||||
| ▶ | comment[scan window lower limit] | recommended | dia-acquisition | Lower m/z limit of the DIA scan window |
|
Lower m/z limit of the DIA scan window
allows N/A
allows not available
pattern
— pattern:
^\d+(\.\d+)?$
m/z value as a number
400, 350.5
|
||||
| ▶ | comment[scan window upper limit] | recommended | dia-acquisition | Upper m/z limit of the DIA scan window |
|
Upper m/z limit of the DIA scan window
allows N/A
allows not available
pattern
— pattern:
^\d+(\.\d+)?$
m/z value as a number
1200, 1000
|
||||
| ▶ | comment[isolation window width] | recommended | dia-acquisition | Width of the isolation window in m/z units |
|
Width of the isolation window in m/z units
allows N/A
allows not available
pattern
— pattern:
^\d+(\.\d+)?$
Width in m/z
25, 8, 4
|
||||
| ▶ | comment[dia method] | recommended | dia-acquisition | Specific DIA method variant used |
|
Specific DIA method variant used
allows N/A
allows not available
ontology
— ontologies: pride
Should be a valid PRIDE ontology term for DIA methods
SWATH-MS, MSE, All ion fragmentation, diaPASEF
|
||||
| ▶ | comment[sdrf template] | optional | base | Template name and version used for annotation. Two formats are supported - key=value format (NT=t... |
|
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.
allows not available
multiple cardinality
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'
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... |
|
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).
allows not available
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'
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 |
|
Hash value for SDRF validation integrity checking
allows N/A
allows not available
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... |
|
Broader anatomical grouping or system-level bucket for the sample, used alongside the organism part for higher-level grouping
allows N/A
allows not available
ontology
— ontologies: uberon, bto
Tissue supergroup should be a valid broad UBERON or BTO anatomy term when possible
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... |
|
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.
allows N/A
allows not available
values
— values:
not pooled, pooled
pattern
— pattern:
^(not pooled|pooled|SN=.+(;SN=.+)*)$
Use 'not pooled', 'pooled', or list sample IDs with SN= prefix
SN=sample1;SN=sample2
|
||||
| ▶ | characteristics[sample type] | optional | sample-metadata | Classification of the sample role in the experiment. Distinguishes experimental samples from cont... |
|
Classification of the sample role in the experiment. Distinguishes experimental samples from controls, references, and other roles in multiplexed or plate-based experiments.
allows N/A
allows not available
ontology
— ontologies: pride
Sample type should be a child of PRIDE:0000895 (sample type)
single cell, reference, bridge, carrier, pooled, empty, quality control sample, negative control
|
||||
| ▶ | characteristics[material type] | optional | sample-metadata | Type of biological material being analyzed |
|
Type of biological material being analyzed
allows N/A
allows not available
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 |
|
Mass of tissue used for extraction
allows N/A
allows not available
number_with_unit
Tissue mass with unit
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) |
|
BioSample accession number for the sample (e.g., SAMN or SAMEA identifiers)
allows N/A
allows not available
accession
BioSample accession
SAMN12345678, SAMEA12345678, SAMD1234567
|
||||
| ▶ | characteristics[sampling time] | optional | sample-metadata | Time at which the sample was collected (for longitudinal or time-course studies) |
|
Time at which the sample was collected (for longitudinal or time-course studies)
allows N/A
allows not available
number_with_unit
Sampling time with unit
0 hour, 24 hour, 7 day, 3 month
|
||||
| ▶ | characteristics[treatment] | optional | sample-metadata | Treatment or perturbation applied to the sample (drug, stimulus, environmental stress) |
|
Treatment or perturbation applied to the sample (drug, stimulus, environmental stress)
allows N/A
allows not available
ontology
— ontologies: ncit, efo
Treatment should be a valid ontology term. Use 'untreated' for controls.
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 |
|
Whether the sample is a synthetic peptide library or biological material
allows N/A
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... |
|
Spiked-in compound details using key-value format (CT=compound type, QY=quantity, PS=peptide sequence, AC=UniProt accession, CN=compound name, CV=vendor)
allows N/A
allows not available
multiple cardinality
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)
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... |
|
Enrichment strategy applied to the sample (e.g., phosphopeptide enrichment, crosslinked peptide enrichment, glycopeptide enrichment)
allows N/A
allows not available
ontology
— ontologies: pride, efo
Enrichment type should be a child term of EFO:0009090 (enrichment process)
enrichment of cross-linked peptides, enrichment of phosphorylated protein, enrichment of glycopeptides, enrichment of ubiquitinated proteins
|
||||
| ▶ | comment[fractionation method] | optional | ms-proteomics | Peptide fractionation method used before MS analysis |
|
Peptide fractionation method used before MS analysis
allows N/A
allows not available
ontology
— ontologies: pride
Fractionation method should be a child term of PRIDE:0000550
High-pH reversed-phase chromatography (hpHRP), Strong cation-exchange chromatography (SCX), Strong anion-exchange chromatography (SAX), Size-exclusion chromatography (SEC)
|
||||
| ▶ | comment[collision energy] | optional | ms-proteomics | Collision energy used for fragmentation |
|
Collision energy used for fragmentation
allows N/A
allows not available
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.
30 NCE, 30% NCE, 27 eV, 25 NCE;27 NCE;30 NCE
|
||||
| ▶ | comment[reduction reagent] | optional | ms-proteomics | Chemical reagent used for disulfide bond reduction |
|
Chemical reagent used for disulfide bond reduction
allows N/A
allows not available
ontology
— ontologies: pride, ms
Reduction reagent should be a valid PRIDE or MS ontology term
dithiothreitol, tris(2-carboxyethyl)phosphine
|
||||
| ▶ | comment[alkylation reagent] | optional | ms-proteomics | Chemical reagent used for cysteine alkylation |
|
Chemical reagent used for cysteine alkylation
allows N/A
allows not available
ontology
— ontologies: pride, ms
Alkylation reagent should be a valid PRIDE or MS ontology term
iodoacetamide, chloroacetamide
|
||||
| ▶ | characteristics[depletion] | optional | ms-proteomics | Whether abundant protein depletion was performed |
|
Whether abundant protein depletion was performed
allows N/A
allows not available
values
— values:
no depletion, depletion
Depletion status
|
||||
| ▶ | comment[ms2 mass analyzer] | optional | ms-proteomics | Mass analyzer used for MS2 acquisition |
|
Mass analyzer used for MS2 acquisition
allows N/A
allows not available
ontology
— ontologies: ms
Should be a valid MS ontology term
orbitrap, ion trap, TOF
|
||||
| ▶ | comment[sample preparation batch] | optional | ms-proteomics | Batch identifier for sample preparation (plate, chip, processing batch). Useful for batch effect ... |
|
Batch identifier for sample preparation (plate, chip, processing batch). Useful for batch effect correction in multi-batch experiments.
allows N/A
allows not available
pattern
— pattern:
^.+$
Sample preparation batch identifier
plate1, batch_20220601, prep_A
|
||||
| ▶ | comment[lc batch] | optional | ms-proteomics | Liquid chromatography batch identifier for batch effect tracking (e.g., column changes, LC system swaps) |
|
Liquid chromatography batch identifier for batch effect tracking (e.g., column changes, LC system swaps)
allows N/A
allows not available
pattern
— pattern:
^.+$
LC batch identifier
LC1, column_A
|
||||
| ▶ | comment[acquisition date] | optional | ms-proteomics | Date of MS data acquisition (ISO 8601 format recommended). Useful for tracking instrument drift a... |
|
Date of MS data acquisition (ISO 8601 format recommended). Useful for tracking instrument drift and batch effects.
allows N/A
allows not available
pattern
— pattern:
^.+$
Acquisition date/time
2022-06-01, 2022-06-01T18:28:37
|
||||
| ▶ | comment[ms min mz] | optional | ms-proteomics | MS method-defined minimum precursor (MS1) m/z setting used to acquire the data |
|
MS method-defined minimum precursor (MS1) m/z setting used to acquire the data
allows N/A
allows not available
mz_value
Precursor m/z value with unit
100m/z, 200m/z, 350.5m/z
|
||||
| ▶ | comment[ms max mz] | optional | ms-proteomics | MS method-defined maximum precursor (MS1) m/z setting used to acquire the data |
|
MS method-defined maximum precursor (MS1) m/z setting used to acquire the data
allows N/A
allows not available
mz_value
Precursor m/z value with unit
1200m/z, 1600m/z, 2000m/z
|
||||
| ▶ | comment[ms min charge] | optional | ms-proteomics | MS method-defined minimum precursor charge state setting used to acquire the data |
|
MS method-defined minimum precursor charge state setting used to acquire the data
allows N/A
allows not available
pattern
— pattern:
^\d+$
Integer charge state
1, 2
|
||||
| ▶ | comment[ms max charge] | optional | ms-proteomics | MS method-defined maximum precursor charge state setting used to acquire the data |
|
MS method-defined maximum precursor charge state setting used to acquire the data
allows N/A
allows not available
pattern
— pattern:
^\d+$
Integer charge state
6, 7, 8
|
||||
| ▶ | comment[ms min rt] | optional | ms-proteomics | LC method-defined minimum retention time setting used to acquire the data (in minutes) |
|
LC method-defined minimum retention time setting used to acquire the data (in minutes)
allows N/A
allows not available
pattern
— pattern:
^[\d.]+$
Numeric retention time in minutes
0, 5, 10.5
|
||||
| ▶ | comment[ms max rt] | optional | ms-proteomics | LC method-defined maximum retention time setting used to acquire the data (in minutes) |
|
LC method-defined maximum retention time setting used to acquire the data (in minutes)
allows N/A
allows not available
pattern
— pattern:
^[\d.]+$
Numeric retention time in minutes
60, 90, 120
|
||||
| ▶ | comment[ms min im] | optional | ms-proteomics | MS method-defined minimum ion mobility setting used to acquire the data (1/K0 or Vs/cm2) |
|
MS method-defined minimum ion mobility setting used to acquire the data (1/K0 or Vs/cm2)
allows N/A
allows not available
pattern
— pattern:
^[\d.]+$
Numeric ion mobility value
0.6, 0.7
|
||||
| ▶ | comment[ms max im] | optional | ms-proteomics | MS method-defined maximum ion mobility setting used to acquire the data (1/K0 or Vs/cm2) |
|
MS method-defined maximum ion mobility setting used to acquire the data (1/K0 or Vs/cm2)
allows N/A
allows not available
pattern
— pattern:
^[\d.]+$
Numeric ion mobility value
1.3, 1.4, 1.6
|
||||
| ▶ | comment[ms2 min mz] | optional | ms-proteomics | MS method-defined minimum product ion (MS2) m/z setting used to acquire the data |
|
MS method-defined minimum product ion (MS2) m/z setting used to acquire the data
allows N/A
allows not available
mz_value
Product ion m/z value with unit
100m/z, 200m/z
|
||||
| ▶ | comment[ms2 max mz] | optional | ms-proteomics | MS method-defined maximum product ion (MS2) m/z setting used to acquire the data |
|
MS method-defined maximum product ion (MS2) m/z setting used to acquire the data
allows N/A
allows not available
mz_value
Product ion m/z value with unit
1800m/z, 2000m/z
|
||||
| ▶ | comment[ms3 min mz] | optional | ms-proteomics | MS method-defined minimum product ion (MS3) m/z setting used to acquire the data |
|
MS method-defined minimum product ion (MS3) m/z setting used to acquire the data
allows N/A
allows not available
mz_value
Product ion m/z value with unit
100m/z, 200m/z
|
||||
| ▶ | comment[ms3 max mz] | optional | ms-proteomics | MS method-defined maximum product ion (MS3) m/z setting used to acquire the data |
|
MS method-defined maximum product ion (MS3) m/z setting used to acquire the data
allows N/A
allows not available
mz_value
Product ion m/z value with unit
1500m/z, 2000m/z
|
||||
| ▶ | comment[ms1 scan range] | optional | ms-proteomics | m/z scan range for MS1 spectra as an interval. Alternative to separate ms min mz / ms max mz columns |
|
m/z scan range for MS1 spectra as an interval. Alternative to separate ms min mz / ms max mz columns
allows N/A
allows not available
mz_range_interval
m/z range interval for MS1 spectra
400m/z-1200m/z, 350m/z-1600m/z
|
||||
| ▶ | comment[ms2 scan range] | optional | ms-proteomics | m/z scan range for MS2 spectra as an interval. Alternative to separate ms2 min mz / ms2 max mz columns |
|
m/z scan range for MS2 spectra as an interval. Alternative to separate ms2 min mz / ms2 max mz columns
allows N/A
allows not available
mz_range_interval
m/z range interval for MS2 spectra
100m/z-2000m/z, 200m/z-1800m/z
|
||||
| ▶ | comment[ms3 scan range] | optional | ms-proteomics | m/z scan range for MS3 spectra as an interval. Alternative to separate ms3 min mz / ms3 max mz columns |
|
m/z scan range for MS3 spectra as an interval. Alternative to separate ms3 min mz / ms3 max mz columns
allows N/A
allows not available
mz_range_interval
m/z range interval for MS3 spectra
100m/z-1500m/z, 200m/z-2000m/z
|
||||
| ▶ | comment[elution conditions] | optional | ms-proteomics | Conditions used for peptide/protein elution |
|
Conditions used for peptide/protein elution
allows N/A
allows not available
pattern
— pattern:
^.+$
Free-text elution conditions
0.1% TFA in water, 80% acetonitrile, gradient 5-35% ACN in 60 min
|
||||