Metadata

Properties

Name (Alias)	Type (Default)	Constraints	Description
prefix	str (MTD)	required pattern: MTD Validation type: error	Metadata section prefix identifier.<br/><br/>Value must be 'MTD'. Used to identify metadata lines in the mzTab-M file format.
mztab_version (mzTab-version)	str (2.1.0-M)	required pattern: ^\d{1}\.\d{1}\.\d{1}-[A-Z]{1}$ Validation type: error	Version number of the mzTab format used.<br/><br/>Format: `major.minor.patch-variant`<br/>Must end with "-M" suffix for metabolomics variant.<br/><br/>Used to ensure compatibility and processing correctness.
mztab_id (mzTab-ID)	str	required Validation type: error	Unique identifier for the mzTab-M document.<br/>REQUIRED. Can be:<br/>- Repository accession number (e.g., MTBLS214)<br/>- Laboratory internal identifier<br/>- Study-specific identifier<br/>NOT intended as a globally unique identifier,<br/>but SHOULD have local meaning within its context.
title	str	-	Human-readable title of the experiment or study.<br/>OPTIONAL. SHOULD be:<br/>- Concise but informative<br/>- Reflect the main focus of the study<br/>- Unique within a collection of related studies
description	str	-	Detailed description of the experiment or study.<br/>OPTIONAL. SHOULD include:<br/>- Study objectives<br/>- Experimental design overview<br/>- Key methodological approaches<br/>- Any unique aspects of the study<br/>Provides context for understanding the data and its significance.
contact	List of Contact	-	Contact information for study personnel.<br/><br/>Format<br/>- Name: `[first name] [initials] [last name]`<br/>- Multiple contacts numbered `[1-n]`<br/><br/>Fields<br/>- Name of the contact person<br/>- Institutional affiliation<br/>- Email address
publication	List of Publication	-	Associated research publications.<br/><br/>Reference Format<br/>- PubMed IDs: prefix with `pubmed:`<br/>- DOIs: prefix with `doi:`<br/>- Multiple IDs: separate with `|`<br/><br/>Multiple publications numbered `[1-n]`
uri	List of Uri	-	A URI pointing to the file's source data (e.g., a MetaboLights records).
external_study_uri	List of Uri	-	A URI pointing to an external file with more details about the study design (e.g., an ISA-TAB file).
instrument	List of Instrument	-	Mass spectrometry instrument specifications.<br/><br/>Each instrument includes:<br/>- `name`: Full instrument name and model<br/>- `source`: Ion source type (e.g., ESI, MALDI)<br/>- `analyzer`: Mass analyzer(s) used (e.g., quadrupole, TOF)<br/>- `detector`: Detector type<br/><br/>Multiple instruments are numbered `[1-n]`. Referenced by `instrument_ref` in `ms_run` entries.
quantification_method	Parameter	required Validation type: error	The quantification method used in the experiment reported in the file.
sample	List of Sample	-	Specification of sample. A name for each sample to serve as a list of the samples that MUST be reported in the following tables. Samples MUST be reported if a statistical design is being captured (i.e. bio or tech replicates). If the type of replicates are not known, samples SHOULD NOT be reported. species: The respective species of the samples analysed. For more complex cases, such as metagenomics, optional columns and userParams should be used.tissue: The respective tissue(s) of the sample. cell_type: The respective cell type(s) of the sample. disease: The respective disease(s) of the sample. description: A human readable description of the sample. custom: Custom parameters describing the sample's additional properties. Dates MUST be provided in ISO-8601 format.
sample_processing	List of SampleProcessing	-	Sample preparation and processing steps.<br/><br/>Processing Documentation<br/>- Sequential steps numbered `[1-n]` in order of execution<br/>- Multiple parameters per step separated by `|`<br/><br/>Special Cases<br/>- Derivatization:<br/> - Report general step (e.g., 'silylation')<br/> - Specify agents in derivatization_agent field<br/><br/>Follows biological/analytical methods report format
software	List of Software	required min: 1 Validation type: error	Analysis software specifications.<br/><br/>For each software entry:<br/>- Include version information<br/>- Number entries (`[1-n]`) to reflect usage order<br/>- Settings can be specified multiple times per software<br/>- Use string values for settings without CV terms
derivatization_agent	List of Parameter	-	A description of derivatization agents applied to small molecules, using userParams or CV terms where possible.
ms_run	List of MsRun	required min: 1 Validation type: error	Specification of ms_run. location: Location of the external data file e.g. raw files on which analysis has been performed. If the actual location of the MS run is unknown, a “null” MUST be used as a place holder value, since the [1-n] cardinality is referenced elsewhere. If pre-fractionation has been performed, then [1-n] ms_runs SHOULD be created per assay.instrument_ref: If different instruments are used in different runs, instrument_ref can be used to link a specific instrument to a specific run. format: Parameter specifying the data format of the external MS data file. If ms_run[1-n]-format is present, ms_run[1-n]-id_format SHOULD also be present, following the parameters specified in Table 1. id_format: Parameter specifying the id format used in the external data file. If ms_run[1-n]-id_format is present, ms_run[1-n]-format SHOULD also be present.fragmentation_method: The type(s) of fragmentation used in a given ms run.scan_polarity: The polarity mode of a given run. Usually only one value SHOULD be given here except for the case of mixed polarity runs.hash: Hash value of the corresponding external MS data file defined in ms_run[1-n]-location. If ms_run[1-n]-hash is present, ms_run[1-n]-hash_method SHOULD also be present.hash_method: A parameter specifying the hash methods used to generate the String in ms_run[1-n]-hash. Specifics of the hash method used MAY follow the definitions of the mzML format. If ms_run[1-n]-hash is present, ms_run[1-n]-hash_method SHOULD also be present.
assay	List of Assay	required min: 1 Validation type: error	Specification of assay. (empty) name: A name for each assay, to serve as a list of the assays that MUST be reported in the following tables. custom: Additional custom parameters or values for a given assay. external_uri: An external reference uri to further information about the assay, for example via a reference to an object within an ISA-TAB file. sample_ref: An association from a given assay to the sample analysed. ms_run_ref: An association from a given assay to the source MS run. All assays MUST reference exactly one ms_run unless a workflow with pre-fractionation is being encoded, in which case each assay MUST reference n ms_runs where n fractions have been collected. Multiple assays SHOULD reference the same ms_run to capture multiplexed experimental designs.
study_variable	List of StudyVariable	required min: 1 Validation type: error	Specification of study_variable. (empty) name: A name for each study variable (experimental condition or factor), to serve as a list of the study variables that MUST be reported in the following tables. For software that does not capture study variables, a single study variable MUST be reported, linking to all assays. This single study variable MUST have the identifier “undefined“. assay_refs: Bar-separated references to the IDs of assays grouped in the study variable. average_function: The function used to calculate the study variable quantification value and the operation used is not arithmetic mean (default) e.g. “geometric mean”, “median”. The 1-n refers to different study variables. variation_function: The function used to calculate the study variable quantification variation value if it is reported and the operation used is not coefficient of variation (default) e.g. “standard error”. description: A textual description of the study variable. factors: Additional parameters or factors, separated by bars, that are known about study variables allowing the capture of more complex, such as nested designs.
custom	List of Parameter	-	Any additional parameters describing the analysis reported.
cv	List of CV (PydanticUndefined)	required min: 1 Validation type: error	Controlled vocabulary specifications.<br/><br/>Fields<br/>- `label`: Short identifier (e.g., 'MS' for PSI-MS)<br/>- `full_name`: Complete ontology name<br/>- `version`: CV/ontology version<br/>- `uri`: Reference URI for the vocabulary
small_molecule_quantification_unit (small_molecule-quantification_unit)	Parameter	required Validation type: error	Defines what type of units are reported in the small molecule summary quantification / abundance fields
small_molecule_feature_quantification_unit (small_molecule_feature-quantification_unit)	Parameter	required Validation type: error	Defines what type of units are reported in the small molecule feature quantification / abundance fields.
small_molecule_identification_reliability (small_molecule-identification_reliability)	Parameter	required Validation type: error	The system used for giving reliability / confidence codes to small molecule identifications MUST be specified if not using the default codes.
database	List of Database	required min: 1 Validation type: error	Specification of databases. (empty): The description of databases used. For cases, where a known database has not been used for identification, a userParam SHOULD be inserted to describe any identification performed. e.g. de novo. If no identification has been performed at all then 'no database' should be inserted followed by null. prefix: The prefix used in the “identifier” column of data tables. For the 'no database' case 'null' must be used. version: The database version is mandatory where identification has been performed. This may be a formal version number e.g. “1.4.1”, a date of access “2016-10-27” (ISO-8601 format) or “Unknown” if there is no suitable version that can be annotated. uri: The URI to the database. For the 'no database' case, 'null' must be reported.
id_confidence_measure	List of Parameter	required min: 1 Validation type: error	Small molecule identification confidence metrics.<br/>Scoring System<br/>- Use CV parameters numbered `[1-n]`<br/>- Define score direction (high-to-low or low-to-high)<br/>- Order by importance for identification ranking<br/><br/>Scores determine confidence in molecular identifications
colunit_small_molecule (colunit-small_molecule)	List of ColumnParameterMapping	-	Unit definitions for small molecule data columns.<br/><br/>Format<br/>- Pattern: `{column_name}={unit_parameter}`<br/>- Use CV parameters for units when possible<br/><br/>Important Notes<br/>- Not for quantification columns<br/>- Use `small_molecule-quantification_unit` for quantification values
colunit_small_molecule_feature (colunit-small_molecule_feature)	List of ColumnParameterMapping	-	Defines the used unit for a column in the small molecule feature section. The format of the value has to be {column name}={Parameter defining the unit}. This field MUST NOT be used to define a unit for quantification columns. The unit used for small molecule quantification values MUST be set in small_molecule_feature-quantification_unit.
colunit_small_molecule_evidence (colunit-small_molecule_evidence)	List of ColumnParameterMapping	-	Defines the used unit for a column in the small molecule evidence section. The format of the value has to be {column name}={Parameter defining the unit}.