mzTab-M v2.0 → v2.1 Changes

The version of the mzTab file. The suffix MUST be "-M" for mzTab for metabolomics (mzTab-M).

Version number of the mzTab format used.

Format: major.minor.patch-variant
Must end with "-M" suffix for metabolomics variant.

Used to ensure compatibility and processing correctness.

Regex
…​.
\d{2}\.\d{0}\.\d{0}-M
…​.

Regex
----
^\d{1}\.\d{1}\.\d{1}-[A-Z]{1}$
----

The ID of the mzTab file, this could be supplied by the repository from which it is downloaded or a local identifier from the lab producing the file. It is not intended to be a globally unique ID but carry some locally useful meaning.

Unique identifier for the mzTab-M document.
REQUIRED. Can be:
- Repository accession number (e.g., MTBLS214)
- Laboratory internal identifier
- Study-specific identifier
NOT intended as a globally unique identifier,
but SHOULD have local meaning within its context.

String

String

The file’s human readable title.

Human-readable title of the experiment or study.
OPTIONAL. SHOULD be:
- Concise but informative
- Reflect the main focus of the study
- Unique within a collection of related studies

String

String

The file’s human readable description.

Detailed description of the experiment or study.
OPTIONAL. SHOULD include:
- Study objectives
- Experimental design overview
- Key methodological approaches
- Any unique aspects of the study
Provides context for understanding the data and its significance.

String

String

A list of parameters describing a sample processing, preparation or handling step similar to a biological or analytical methods report. The order of the sample_processing items should reflect the order these processing steps were performed in. If multiple parameters are given for a step these MUST be separated by a “{vbar}”. If derivatization was performed, it MUST be reported here as a general step, e.g. 'silylation' and the actual derivatization agens MUST be specified in the [derivatization_agent1-n] part.

Parameters specifying sample processing that was applied within one step.

Parameter List

Parameter List

The name of the instrument used in the experiment. Multiple instruments are numbered 1..n.

The instrument’s name.

Parameter

Parameter

—

The instrument’s source used in the experiment. Multiple instruments are numbered [1-n].

The instrument’s ion source.

Parameter

Parameter

—

The instrument’s analyzer type used in the experiment. Multiple instruments are numbered [1-n].

The instrument’s mass analyzer, as defined by the parameter.

Parameter

Parameter List

—

The instrument’s detector type used in the experiment. Multiple instruments are numbered [1-n].

The instrument’s mass analyzer, as defined by the parameter.

Parameter

Parameter

—

Software used to analyze the data and obtain the reported results. The parameter’s value SHOULD contain the software’s version. The order (numbering) should reflect the order in which the tools were used.

The software utilized.

Parameter

Parameter

A software setting used. This field MAY occur multiple times for a single software. The value of this field is deliberately set as a String, since there currently do not exist CV terms for every possible setting.

A software setting used. This field MAY occur multiple times for a single software. The value of this field is deliberately set as a String, since there currently do not exist cvParams for every possible setting.

String

String List

—

A publication associated with this file. Several publications can be given by indicating the number in the square brackets after “publication”. PubMed ids must be prefixed by “pubmed:”, DOIs by “doi:”. Multiple identifiers MUST be separated by “{vbar}”.

The publication item ids referenced by this publication.

String

String List

The contact’s name. Several contacts can be given by indicating the number in the square brackets after "contact". A contact has to be supplied in the format [first name] [initials] [last name] (see example).

The contact’s name.

String

String

—

The contact’s affiliation.

The contact’s affiliation.

String

String

—

The contact’s e-mail address.

The contact’s e-mail address.

String

String

—

A URI pointing to the file’s source data (e.g., a MetaboLights records).

The URI pointing to the external resource.

URI

URI

A URI pointing to an external file with more details about the study design (e.g., an ISA-TAB file).

The URI pointing to the external resource.

URI

URI

The quantification method used in the experiment reported in the file.

The quantification method used in the experiment reported in the file.

Parameter

Parameter

—

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.

The sample’s name.

String

String

The respective species of the samples analysed. For more complex cases, such as metagenomics, optional columns and userParams should be used.

Biological species information on the sample.

Parameter

Parameter List

—

The respective tissue(s) of the sample.

Biological tissue information on the sample.

Parameter

Parameter List

—

The respective cell type(s) of the sample.

Biological cell type information on the sample.

Parameter

Parameter List

—

The respective disease(s) of the sample.

Disease information on the sample.

Parameter

Parameter List

—

A human readable description of the sample.

A free form description of the sample.

String

String

—

Parameters describing the sample’s additional properties. Dates MUST be provided in ISO-8601 format.

Additional user or cv parameters.

Parameter

Parameter List

—

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.

The msRun’s location URI.

URI

URI

—

If different instruments are used in different runs, this attribute can be used to link a specific instrument to a specific run.

Sample reference.

Integer

Integer

—

A 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.

The format of the MS run file.

Parameter

Parameter

—

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.

The format of the IDs in the MS run file.

Parameter

Parameter

—

An identifier for the MS run based on the Universal Spectrum Identifier (USI) specification.
Implied within the USI is an MS run identifier. Every deposited MS run can be referenced with a shortened form: mzspec:<collection>:<msRun>. More info on the standard can be found: https://www.psidev.info/usi.
Since an MS run may be represented in several formats (with potentially slightly different data associated with the spectrum), a format suffix MAY be specified (e.g. mzspec:<collection>:<msRun>.RAW) to signify that a specific file type is meant.
If specified, the format suffix should align with the ms_run[1-n]-format parameter and the ms_run[1-n]-location suffix defined in the metadata section.

(not present)

String

(not present)

(not present)

The type(s) of fragmentation used in a given ms run.

The fragmentation methods applied during this msRun.

Parameter

Parameter List

—

The polarity mode of a given run. Usually only one value SHOULD be given here except for the case of mixed polarity runs.

The scan polarity/polarities used during this msRun.

Parameter

Parameter List

—

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.

The file hash value of this msRun’s data file.

String

String

—

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.

The method used to calculate the hash.

Parameter

Parameter

—

A name for each assay, to serve as a list of the assays that MUST be reported in the following tables.

The assay name.

String

String

Additional parameters or values for a given assay.

Additional user or cv parameters.

Parameter

Parameter List

—

A reference to further information about the assay, for example via a reference to an object within an ISA-TAB file.

An external URI to further information about this assay.

URI

URI

—

An association from a given assay to the sample analysed.

Sample reference.

{SAMPLE_ID}

Integer

—

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.

The ms run(s) referenced by this assay.

{MS_RUN_ID}

Integer List

—

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“.

The study variable value. Encoded according to the datatype declared on the referenced study_variable_group: either a literal value (for xsd: datatypes) or a Parameter (for the Parameter datatype, e.g. [NO, NO:12345, Male,] or [,,Male,]).*

String

Study Variable List

Bar-separated references to the IDs of assays grouped in the study variable.

The assays referenced by this study variable.

{ASSAY_ID}, …​

Integer List

—

A textual description of the study variable.

A free-form description of this study variable.

String

String

—

A reference to the study_variable_group that this study variable belongs to, allowing study variables to be linked to the experimental design factors they represent.

(not present)

{STUDY_VARIABLE_GROUP_ID}

(not present)

(not present)

A parameter defining the group to which the study variable belongs. This allows grouping of related study variables that belong to the same experimental design factor in multi-factorial designs. The parameter can be either a CV Parameter or a user-defined parameter. At least one study_variable_group MUST be defined. For software that does not capture study variables, a single study_variable_group MUST be reported, linking to the single study variable. This single study_variable_group MUST have the identifier “undefined”. Added in mzTab-M 2.1.

The study variable group name.

Parameter

Parameter

A textual description of the study variable group.

Description of the study variable group.

String

String

—

The statistical type of the group variable, which determines how the values should be interpreted in a statistical analysis context. The type MUST be a term from the STATO ontology, and SHOULD be one of the examples below. While the type also has implications for how the variables are encoded/decoded, that information goes into the study_variable_group[1-n]-datatype.

The following data types are supported:

* categorical – [STATO, STATO:0000252, categorical variable] is a variable that can only assume a finite number of values without inherent ordering. In programming languages often represented as enums, factors (in R), or strings.

* ordinal – [STATO, STATO:0000228, ordinal variable] Ordered variable where the sequence matters but intervals between levels are undefined. These values represent categories with a defined sequence or ranking. Example: disease severity (mild, moderate, severe), confidence levels (low, medium, high).

* continuous – [STATO, STATO:0000251, continuous variable] is a variable that can take any value within a range on a continuous scale. Example: temperature, height, concentration, time.

Tools and parsers implementing mzTab-M SHOULD apply the appropriate data type interpretation when reading study_variable_group data and constructing analysis data structures (e.g., data frames, matrices, or tables).

The study variable group type, as defined by the parameter.

Parameter

Parameter

—

The datatype of the group variable, which determines how they can be encoded and parsed in mzTab-M files, and how the values could be handled in programming languages.

Producers of mzTab-M 2.1.0 SHOULD provide a datatype for each study_variable_group to simplify interpretation by downstream consumers of the format. The field is not mandatory, but its presence removes ambiguity about how the associated values are encoded and should be parsed.

The following datatypes are supported:

* xsd:string – Character string.
* xsd:integer – Arbitrary‑size integer.
* xsd:decimal – Arbitrary‑precision decimal number.
* xsd:boolean – Boolean value (true / false).
* xsd:date – Calendar date, encoded in ISO 8601 format (YYYY-MM-DD).
* xsd:time – Time of day, encoded in ISO 8601 format (hh:mm:ss, optional fractional seconds and timezone).
* xsd:dateTime – Combined date and time, encoded in ISO 8601 format (YYYY-MM-DDThh:mm:ss, with optional fractional seconds and timezone, e.g. YYYY-MM-DDThh:mm:ssZ).
* xsd:anyURI – A Uniform Resource Identifier reference.

Tools and parsers implementing mzTab-M SHOULD apply the appropriate data type interpretation when reading study_variable_group data and constructing analysis data structures (e.g., data frames, matrices, or tables).

The datatype of the group variable, which determines how they can be encoded and parsed in mzTab-M files, and how the values could be handled in programming languages.

Producers of mzTab-M 2.1.0 SHOULD provide a datatype for each study_variable_group to simplify interpretation by downstream consumers of the format. The field is not mandatory, but its presence removes ambiguity about how the associated values are encoded and should be parsed.

The following datatypes are supported:

* xsd:string – Character string.
* xsd:integer – Arbitrary‑size integer.
* xsd:decimal – Arbitrary‑precision decimal number.
* xsd:boolean – Boolean value (true / false).
* xsd:date – Calendar date, encoded in ISO 8601 format (YYYY-MM-DD).
* xsd:time – Time of day, encoded in ISO 8601 format (hh:mm:ss, optional fractional seconds and timezone).
* xsd:dateTime – Combined date and time, encoded in ISO 8601 format (YYYY-MM-DDThh:mm:ss, with optional fractional seconds and timezone, e.g. YYYY-MM-DDThh:mm:ssZ).
* xsd:anyURI – A Uniform Resource Identifier reference.
* Parameter – The values of the linked study_variables are reported as a Parameter (user-defined or CV Parameter), using the standard mzTab-M Parameter syntax [CV, accession, name, value].

Writers MUST ensure that the values of the study_variable entries belonging to the same study_variable_group all have the same type (e.g. string, number, …​) and use the same convention of reporting the value directly or as a Parameter, consistent with the datatype declared on the group. If the study_variable_group defines the datatype as Parameter, the CVParam qualifying the study_variable_group itself can be of a different CV origin than the CVParams used in the linked study_variable values.

Tools and parsers implementing mzTab-M SHOULD apply the appropriate data type interpretation when reading study_variable_group data and constructing analysis data structures (e.g., data frames, matrices, or tables).

String (constrained)

Parameter

An optional parameter specifying the unit of the study variable group (e.g., day, hour, concentration, etc.). This SHOULD only be used for numeric or scalar values.

The study variable group unit, as defined by the parameter.

Parameter

Parameter

—

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.

The function used to calculate the study variable quantification value and the operation used is not arithmetic mean (default). e.g. geometric mean, median.

Parameter

Parameter

—

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”.

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.

Parameter

Parameter

—

Any additional parameters describing the analysis reported.

Any additional parameters describing the analysis reported.

Parameter

Parameter List

A string describing the labels of the controlled vocabularies/ontologies used in the mzTab file as a short-hand e.g. "MS" for PSI-MS.

The abbreviated CV label.

String

String

—

A string describing the full names of the controlled vocabularies/ontologies used in the mzTab file.

The full name of this CV, for humans.

String

String

—

A string describing the version of the controlled vocabularies/ontologies used in the mzTab file.

The CV version used when the file was generated.

String

String

—

A string containing the URIs of the controlled vocabularies/ontologies used in the mzTab file. Note: For OBO ontologies, always use an OBO PURL rather than raw repository links to ensure long-term stability. For other ontology formats, please use the fully qualified PURL pointing to the ontology file.

A URI to the CV definition.

String

URI

—

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.

The database name.

Param

Database List

The prefix used in the “identifier” column of data tables. For the “no database” case "null" must be used.

The prefix used in the “identifier” column of data tables. For the 'no database' case 'null' must be used.

String

String

—

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.

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.

String

String

—

The URI to the database. For the “no database” case, "null" must be reported.

The URI to the database. For the “no database” case, 'null' must be reported.

URI

String

—

A description of derivatization agents applied to small molecules, using userParams or CV terms where possible.

A description of derivatization agents applied to small molecules, using userParams or CV terms where possible.

Param

Parameter List

Defines what type of units are reported in the small molecule summary quantification / abundance fields.

Defines what type of units are reported in the small molecule summary quantification / abundance fields

Parameter

Parameter

Defines what type of units are reported in the small molecule feature quantification / abundance fields.

Defines what type of units are reported in the small molecule feature quantification / abundance fields.

Parameter

Parameter

The system used for giving reliability / confidence codes to small molecule identifications MUST be specified if not using the default codes (see [reliability] and for details).

The system used for giving reliability / confidence codes to small molecule identifications MUST be specified if not using the default codes.

Param

Parameter

The type of small molecule confidence measures or scores MUST be reported as a CV parameter [1-n]. The CV parameter definition should formally state whether the ordering is high to low or vice versa. The order of the scores SHOULD reflect their importance for the identification and be used to determine the identification’s rank.

Small molecule identification confidence metrics.<br/>Scoring System
- Use CV parameters numbered [1-n]
- Define score direction (high-to-low or low-to-high)
- Order by importance for identification ranking

Scores determine confidence in molecular identifications

Parameter

Parameter List

Defines the used unit for a column in the small molecule 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-quantification_unit.

Unit definitions for small molecule data columns.

Format
- Pattern: {column_name}={unit_parameter}
- Use CV parameters for units when possible

Important Notes
- Not for quantification columns
- Use small_molecule-quantification_unit for quantification values

String

Column Parameter Mapping List

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.

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.

String

Column Parameter Mapping List

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}.

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}.

String

Column Parameter Mapping List

(not present)

The contact’s orcid id, without https prefix.

(not present)

Regex
----
^[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]{1}$

(not present)

—

(not present)

Additional parameters of the assay, separated by bars.

(not present)

Parameter List

(not present)

(not present)

The protocol(s) referenced by this assay.

(not present)

Integer List

(not present)

(not present)

Additional parameters of the assay, separated by bars.

(not present)

Parameter List

(not present)

(not present)

The ms run(s) referenced by this study variable.

(not present)

Integer List

(not present)

(not present)

The study variable group this study variable belongs to.

(not present)

Integer List

(not present)

(not present)

The protocol name.

(not present)

String

(not present)

—

(not present)

The protocol type, as defined by the parameter.

(not present)

Parameter

(not present)

—

(not present)

Description of the protocol.

(not present)

String

(not present)

—

(not present)

The protocol parameters.

(not present)

Parameter List

(not present)

—

A within file unique identifier for the small molecule.

A within file unique identifier for the small molecule summary.

Integer

Integer

References to all the features on which quantitation has been based (SMF elements) via referencing SMF_ID values. Multiple values SHOULD be provided as a “{vbar}” separated list. This MAY be null only if this is a Summary file.

References to the small molecule features (SMF elements) via referencing SMF_ID values. Multiple values MAY be provided as a {vbar} separated list to indicate which features were used to aggregate the SML row.

{SMF_ID} list

Integer List

A list of “{vbar}” separated possible identifiers for the small molecule; multiple values MUST only be provided to indicate ambiguity in the identification of the molecule and not to demonstrate different identifier types for the same molecule. Alternative identifiers for the same molecule MAY be provided as optional columns.

The database identifier must be preceded by the resource description (prefix) followed by a colon, as specified in the metadata section.

A null value MAY be provided if the identification is sufficiently ambiguous as to be meaningless for reporting or the small molecule has not been identified.

A list of {vbar} separated possible identifiers for the small molecule; multiple values MUST only be provided to indicate ambiguity in the identification of the molecule and not to demonstrate different identifier types for the same molecule. Alternative identifiers for the same molecule MAY be provided as optional columns. The database identifier must be preceded by the resource description (prefix) followed by a colon, as specified in the metadata section. A null value MAY be provided if the identification is sufficiently ambiguous as to be meaningless for reporting or the small molecule has not been identified.

String List

String List

A list of “{vbar}” separated potential chemical formulae of the reported compound. The number of values provided MUST match the number of entities reported under “database_identifier”, even if this leads to redundant reporting of information (i.e. if ambiguity can be resolved in the chemical formula), and the validation software will throw an error if the number of “{vbar}” symbols does not match. “null” values between bars are allowed.

This should be specified in Hill notation (EA Hill 1900), i.e. elements in the order C, H and then alphabetically all other elements. Counts of one may be omitted. Elements should be capitalized properly to avoid confusion (e.g., “CO” vs. “Co”). The chemical formula reported should refer to the neutral form.

*Example N-acetylglucosamine would be encoded by the string “C8H15NO6”*

The chemical formula of the identified compound e.g. in a database, assumed to match the theoretical mass to charge (in some cases this will be the derivatized form, including adducts and protons). This should be specified in Hill notation (EA Hill 1900), i.e. elements in the order C, H and then alphabetically all other elements. Counts of one may be omitted. Elements should be capitalized properly to avoid confusion (e.g., “CO” vs. “Co”). The chemical formula reported should refer to the neutral form. Charge state is reported by the charge field in the SME and SMF section.
Example N-acetylglucosamine would be encoded by the string “C8H15NO6”

String List

String List

A list of “{vbar}” separated potential molecule structures in the simplified molecular-input line-entry system (SMILES) for the small molecule. The number of values provided MUST match the number of entities reported under “database_identifier”, and the validation software will throw an error if the number of “{vbar}” symbols does not match. “null” values between bars are allowed.

The potential molecule’s structure in the simplified molecular-input line-entry system (SMILES) for the small molecule.

String List

String List

A list of “{vbar}” separated potential standard IUPAC International Chemical Identifier (InChI) of the given substance.

The number of values provided MUST match the number of entities reported under “database_identifier”, even if this leads to redundant information being reported (i.e. if ambiguity can be resolved in the InChi), and the validation software will throw an error if the number of “{vbar}” symbols does not match. “null” values between bars are allowed.

A standard IUPAC International Chemical Identifier (InChI) for the given substance.

String List

String List

A list of “{vbar}” separated possible chemical/common names for the small molecule, or general description if a chemical name is unavailable. Multiple names are only to demonstrate ambiguity in the identification. The number of values provided MUST match the number of entities reported under “database_identifier”, and the validation software will throw an error if the number of “{vbar}” symbols does not match. “null” values between bars are allowed.

The small molecule’s chemical/common name, or general description if a chemical name is unavailable.

String List

String List

A URI pointing to the small molecule’s entry in a reference database (e.g., the small molecule’s HMDB or KEGG entry). The number of values provided MUST match the number of entities reported under “database_identifier”, and the validation software will throw an error if the number of “{vbar}” symbols does not match. “null” values between bars are allowed.

A URI pointing to the small molecule’s entry in a database (e.g., the small molecule’s HMDB, Chebi or KEGG entry).

URI List

String List

The small molecule’s precursor’s theoretical neutral mass.

The number of values provided MUST match the number of entities reported under “database_identifier”, and the validation software will throw an error if the number of “{vbar}” symbols does not match. “null” values (in general and between bars) are allowed for molecules that have not been identified only, or for molecules where the neutral mass cannot be calculated. In these cases, the SML entry SHOULD reference features in which exp_mass_to_charge values are captured.

The theoretical neutral mass of the small molecule. This should be calculated from the chemical formula.

Double List

Double List

A “{vbar}” separated list of detected adducts for this this molecule, following the general style in the 2013 IUPAC recommendations on terms relating to MS e.g. [M+H]1+, [M+Na]1+, [M+NH4]1+, [M-H]1-, [M+Cl]1-, [M+H]1+. If the adduct classification is ambiguous with regards to identification evidence it MAY be null.

A {vbar} separated list of the detected adduct ion forms for this small molecule. The terms should follow the general style in the 2013 IUPAC recommendations on terms relating to MS e.g. [M+H]1+, [M+Na]1+, [M+NH4]1+, [M-H]1-, [M+Cl]1-.

Regex List
…​.
\[\d*M([-][\w\d])\]\d*[+-]
…​.*

Regex List
----
^\[\d*M([-][\w\d])\]\d*[+-]$
----*

The reliability of the given small molecule identification. This must be supplied by the resource and MUST be reported as an integer between 1-4:

. identified metabolite (1)
. putatively annotated compound (2)
. putatively characterized compound class (3)
. unknown compound (4)

These MAY be replaced using a suitable CV term in the metadata section e.g. to use MSI recommendation levels (see [small_molecule-identification_reliability] for details).

The following CV terms are already available within the PSI MS CV. Future schemes may be implemented by extending the PSI MS CV with new terms and associated levels.

The MSI has recently discussed an extension of the original four level scheme into a five level scheme MS:1002896 (compound identification confidence level) with levels

["arabic", start=0]
. isolated, pure compound, full stereochemistry (0)
. reference standard match or full 2D structure (1)
. unambiguous diagnostic evidence (literature, database) (2)
. most likely structure, including isomers, substance class or substructure match (3)
. unknown compound (4)

For high-resolution MS, the following term and its levels may be used: MS:1002955 (hr-ms compound identification confidence level) with levels

["arabic", start=1]
. confirmed structure (1)
. probable structure (2)
[loweralpha]
.. unambiguous ms library match (2a)
.. diagnostic evidence (2b)
. tentative candidates (3)
. unequivocal molecular formula (4)
. exact mass (5)

A String data type is set to allow for different systems to be specified in the metadata section.

The reliability of the given small molecule identification. This must be supplied by the resource and should be reported as an integer between 1-4:

1: identified, rigorous. …​
2: identified. …​
3: putatively characterized class. …​
4: unknown. …​

String

String

The approach or database search that identified this small molecule with highest confidence.

The small molecule confidence measure/score of the best identification for this small molecule summary. The type of the value is defined by the best_id_confidence_measure CV parameter. The value is reported in the best_id_confidence_value column.

Parameter

Parameter

The best confidence measure in identification (for this type of score) for the given small molecule across all assays. The type of score MUST be defined in the metadata section. If the small molecule was not identified by the specified search engine, “null” MUST be reported. If the confidence measure does not report a numerical confidence value, “null” SHOULD be reported.

The small molecule confidence measure/score value of the best identification for this small molecule summary.

Double

Double

The small molecule’s abundance in every assay described in the metadata section MUST be reported. Null or zero values may be reported as appropriate. "null" SHOULD be used to report missing quantities, while zero SHOULD be used to indicate a present but not reliably quantifiable value (e.g. below a minimum noise threshold).

The small molecule’s abundance in every assay described in the metadata section MUST be reported. Null or zero values may be reported as appropriate.

Double

Double List

The small molecule’s abundance in all the study variables described in the metadata section (study_variable[1-n]_average_function), calculated using the method as described in the Metadata section (default = arithmetic mean across assays). Null or zero values may be reported as appropriate. "null" SHOULD be used to report missing quantities, while zero SHOULD be used to indicate a present but not reliably quantifiable value (e.g. below a minimum noise threshold).

The small molecule’s abundance in every study variable described in the metadata section. Null or zero values may be reported as appropriate.

Double

Double List

A measure of the variability of the study variable abundance measurement, calculated using the method as described in the metadata section (study_variable[1-n]_average_function), with a default = arithmethic co-efficient of variation of the small molecule’s abundance in the given study variable.

The small molecule’s abundance variation in every study variable described in the metadata section. Null or zero values may be reported as appropriate.

Double

Double List

Additional columns can be added to the end of the small molecule table. These column headers MUST start with the prefix “opt_” followed by the {identifier} of the object they reference: assay, study variable, MS run or “global” (if the value relates to all replicates). Column names MUST only contain the following characters: ‘A’-‘Z’, ‘a’-‘z’, ‘0’-‘9’, ‘’, ‘-’, ‘[’, ‘]’, and ‘:’. CV parameter accessions MAY be used for optional columns following the format: opt_{identifier}_cv_{accession}_{parameter name}. Spaces within the parameter’s name MUST be replaced by ‘’.

Additional columns can be added to the end of the small molecule table. These column headers MUST start with the prefix “opt_” followed by the {identifier} of the object they reference: assay, study variable, MS run or “global” (if the value relates to all replicates). Column names MUST only contain the following characters: 'A'-'Z', 'a'-'z', '0'-'9', '', '-', '[', ']', and ':'. CV parameter accessions MAY be used for optional columns following the format: opt{identifier}_cv_{accession}_{parameter name}. Spaces within the parameter’s name MUST be replaced by '_'.

Column

Optional Column

A within file unique identifier for the small molecule feature.

A within file unique identifier for the small molecule feature.

Integer

Integer

References to the identification evidence (SME elements) via referencing SME_ID values. Multiple values MAY be provided as a “{vbar}” separated list to indicate ambiguity in the identification or to indicate that different types of data supported the identifiction (see SME_ID_REF_ambiguity_code). For the case of a consensus approach where multiple adduct forms are used to infer the SML ID, different features should just reference the same SME_ID value(s).

References to the identification evidence (SME elements) via referencing SME_ID values. Multiple values MAY be provided as a {vbar} separated list to indicate ambiguity in the identification or to indicate that different types of data supported the identifiction (see sme_id_ref_ambiguity_code). For the case of a consensus approach where multiple adduct forms are used to infer the SML ID, different features should just reference the same SME_ID value(s).

{SME_ID} list

Integer List

If multiple values are given under SME_ID_REFS, one of the following codes MUST be provided. 1=Ambiguous identification; 2=Only different evidence streams for the same molecule with no ambiguity; 3=Both ambiguous identification and multiple evidence streams. If there are no or one value under SME_ID_REFs, this MUST be reported as null.

If multiple values are given under SME_ID_REFS, one of the following codes MUST be provided. 1=Ambiguous identification; 2=Only different evidence streams for the same molecule with no ambiguity; 3=Both ambiguous identification and multiple evidence streams. If there are no or one value under SME_ID_REFs, this MUST be reported as null.

Integer

Integer

The assumed classification of this molecule’s adduct ion after detection, following the general style in the 2013 IUPAC recommendations on terms relating to MS e.g. [M+H]1+, [M+Na]1+, [M+NH4]1+, [M-H]1-, [M+Cl]1-, [M+H]1+.

The assumed classification of this molecule’s adduct ion after detection, following the general style in the 2013 IUPAC recommendations on terms relating to MS e.g. [M+H]1+, [M+Na]1+, [M+NH4]1+, [M-H]1-, [M+Cl]1-.

Regex
…​.
\[\d*M([-][\w\d])\]\d*[+-]
…​.*

String

If de-isotoping has not been performed, then the isotopomer quantified MUST be reported here e.g. “+1”, “+2”, “13C peak” using CV terms, otherwise (i.e. for approaches where SMF rows are de-isotoped features) this MUST be null.

If de-isotoping has not been performed, then the isotopomer quantified MUST be reported here e.g. “+1”, “+2”, “13C peak” using CV terms, otherwise (i.e. for approaches were SMF rows are de-isotoped features) this MUST be null.

Parameter

Parameter

The experimental mass/charge value for the feature, by default assumed to be the mean across assays or a representative value. For approaches that report isotopomers as SMF rows, then the m/z of the isotopomer MUST be reported here.

The experimental mass/charge value for the feature, by default assumed to be the mean across assays or a representative value. For approaches that report isotopomers as SMF rows, then the m/z of the isotopomer MUST be reported here.

Double

Double

The feature’s charge value using positive integers both for positive and negative polarity modes. Is nullable in the SMF table but if identification is precised the charge is expected to expected to be known.

The feature’s charge value using positive integers both for positive and negative polarity modes.

Integer

Integer

The apex of the feature on the retention time axis, in a Master or aggregate MS run. Retention time MUST be reported in seconds. Retention time values for individual MS runs (i.e. before alignment) MAY be reported as optional columns. Retention time SHOULD only be null in the case of direct infusion MS or other techniques where a retention time value is absent or unknown. Relative retention time or retention time index values MAY be reported as optional columns, and could be considered for inclusion in future versions of mzTab as appropriate.

The apex of the feature on the retention time axis, in a Master or aggregate MS run. Retention time MUST be reported in seconds. Retention time values for individual MS runs (i.e. before alignment) MAY be reported as optional columns. Retention time SHOULD only be null in the case of direct infusion MS or other techniques where a retention time value is absent or unknown. Relative retention time or retention time index values MAY be reported as optional columns, and could be considered for inclusion in future versions of mzTab as appropriate.

Double

Double