OpenMS  3.0.0
MzTabM.h File Reference
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Classes

struct  CompareMzTabMMatchRef
 Data model of MzTabM files. Please see the official MzTabM specification at https://github.com/HUPO-PSI/mzTab/tree/master/specification_document-releases/2_0-Metabolomics-Release. More...
 
class  MzTabMMetaData
 MztabM Metadata. More...
 
class  MzTabMSmallMoleculeSectionRow
 SML Small molecule section (mztab-m) More...
 
class  MzTabMSmallMoleculeFeatureSectionRow
 SMF Small molecule feature section (mztab-m) More...
 
class  MzTabMSmallMoleculeEvidenceSectionRow
 SME Small molecule evidence section (mztab-m) More...
 
class  MzTabM
 Data model of MzTab-M files Please see the MzTab-M specification at https://github.com/HUPO-PSI/mzTab/blob/master/specification_document-releases/2_0-Metabolomics-Release/mzTab_format_specification_2_0-M_release.adoc#use-cases-for-mztab. More...
 

Namespaces

 OpenMS
 Main OpenMS namespace.
 

Typedefs

typedef std::vector< MzTabMSmallMoleculeSectionRow > MzTabMSmallMoleculeSectionRows
 
typedef std::vector< MzTabMSmallMoleculeFeatureSectionRow > MzTabMSmallMoleculeFeatureSectionRows
 
typedef std::vector< MzTabMSmallMoleculeEvidenceSectionRow > MzTabMSmallMoleculeEvidenceSectionRows
 

Class Documentation

◆ OpenMS::MzTabMAssayMetaData

class OpenMS::MzTabMAssayMetaData

MztabM Assay Metadata.

Collaboration diagram for MzTabMAssayMetaData:
[legend]
Class Members
map< Size, MzTabParameter > custom Additional parameters or values for a given assay.
MzTabString external_uri A reference to further information about the assay.
MzTabInteger ms_run_ref An association from a given assay to the source MS run.
MzTabString name Name of the assay.
MzTabInteger sample_ref An association from a given assay to the sample analysed.

◆ OpenMS::MzTabMMSRunMetaData

class OpenMS::MzTabMMSRunMetaData

MztabM MSRun Metadata.

Collaboration diagram for MzTabMMSRunMetaData:
[legend]
Class Members
MzTabParameter format Parameter specifying the data format of the external MS data file.
map< Size, MzTabParameter > fragmentation_method The type of fragmentation used in a given ms run.
MzTabString hash Hash value of the corresponding external MS data file.
MzTabParameter hash_method Parameter specifying the hash methods.
MzTabParameter id_format Parameter specifying the id format used in the external data file.
MzTabInteger instrument_ref Link to a specific instrument.
MzTabString location Location of the external data file.
map< Size, MzTabParameter > scan_polarity The polarity mode of a given run.

◆ OpenMS::MzTabMStudyVariableMetaData

class OpenMS::MzTabMStudyVariableMetaData

MztabM StudyVariable Metadata.

Collaboration diagram for MzTabMStudyVariableMetaData:
[legend]
Class Members
vector< int > assay_refs References to the IDs of assays grouped in the study variable.
MzTabParameter average_function The function used to calculate the study variable quantification value.
MzTabString description A textual description of the study variable.
MzTabParameterList factors Additional parameters or factors.
MzTabString name Name of the study variable.
MzTabParameter variation_function The function used to calculate the study variable quantification variation value.

◆ OpenMS::MzTabMDatabaseMetaData

class OpenMS::MzTabMDatabaseMetaData

MztabM Database Metadata.

Collaboration diagram for MzTabMDatabaseMetaData:
[legend]
Class Members
MzTabParameter database The description of databases used.
MzTabString prefix The prefix used in the “identifier” column of data tables.
MzTabString uri The URI to the database.
MzTabString version The database version.

◆ OpenMS::MzTabMSmallMoleculeSectionRow

class OpenMS::MzTabMSmallMoleculeSectionRow

SML Small molecule section (mztab-m)

Collaboration diagram for MzTabMSmallMoleculeSectionRow:
[legend]
Class Members
MzTabStringList adducts Adducts.
MzTabParameter best_id_confidence_measure The identification approach with the highest confidence.
MzTabDouble best_id_confidence_value The best confidence measure.
MzTabStringList chemical_formula Potential chemical formula of the reported compound.
MzTabStringList chemical_name Possible chemical/common names or general description.
MzTabStringList database_identifier Names of the used databases.
MzTabStringList inchi InChi of the potential compound identifications.
vector< MzTabOptionalColumnEntry > opt_ Optional columns must start with “opt_”.
MzTabString reliability Reliability of the given small molecule identification.
map< Size, MzTabDouble > small_molecule_abundance_assay The small molecule’s abundance in every assay described in the metadata section.
map< Size, MzTabDouble > small_molecule_abundance_study_variable The small molecule’s abundance in all the study variables described in the metadata section.
map< Size, MzTabDouble > small_molecule_abundance_variation_study_variable A measure of the variability of the study variable abundance measurement.
MzTabStringList smf_id_refs References to all the features on which quantification has been based.
MzTabStringList smiles Molecular structure in SMILES format.
MzTabString sml_identifier The small molecule’s identifier.
MzTabDoubleList theoretical_neutral_mass Precursor theoretical neutral mass.
MzTabStringList uri The source entry’s location.

◆ OpenMS::MzTabMSmallMoleculeFeatureSectionRow

class OpenMS::MzTabMSmallMoleculeFeatureSectionRow

SMF Small molecule feature section (mztab-m)

Collaboration diagram for MzTabMSmallMoleculeFeatureSectionRow:
[legend]
Class Members
MzTabString adduct Adduct.
MzTabInteger charge Precursor ion’s charge.
MzTabDouble exp_mass_to_charge Precursor ion’s m/z.
MzTabParameter isotopomer If de-isotoping has not been performed, then the isotopomer quantified MUST be reported here.
vector< MzTabOptionalColumnEntry > opt_ Optional columns must start with “opt_”.
MzTabDouble retention_time Time point in seconds.
MzTabDouble rt_end The end time of the feature on the retention time axis.
MzTabDouble rt_start The start time of the feature on the retention time axis.
map< Size, MzTabDouble > small_molecule_feature_abundance_assay Feature abundance in every assay.
MzTabInteger sme_id_ref_ambiguity_code Ambiguity in identifications.
MzTabStringList sme_id_refs Reference to the identification evidence.
MzTabString smf_identifier Within file unique identifier for the small molecule feature.

◆ OpenMS::MzTabMSmallMoleculeEvidenceSectionRow

class OpenMS::MzTabMSmallMoleculeEvidenceSectionRow

SME Small molecule evidence section (mztab-m)

Collaboration diagram for MzTabMSmallMoleculeEvidenceSectionRow:
[legend]
Class Members
MzTabString adduct Adduct.
MzTabDouble calc_mass_to_charge Precursor ion’s m/z.
MzTabInteger charge Precursor ion’s charge.
MzTabString chemical_formula The putative molecular formula.
MzTabString chemical_name Possible chemical/common names or general description.
MzTabString database_identifier The putative identification for the small molecule sourced from an external database.
MzTabParameter derivatized_form derivatized form.
MzTabString evidence_input_id Within file unique identifier for the input data used to support this identification e.g. fragment spectrum, RT and m/z pair.
MzTabDouble exp_mass_to_charge Precursor ion’s m/z.
map< Size, MzTabDouble > id_confidence_measure Statistical value or score for the identification.
MzTabParameter identification_method Database search, search engine or process that was used to identify this small molecule.
MzTabString inchi InChi of the potential compound identifications.
MzTabParameter ms_level The highest MS level used to inform identification.
vector< MzTabOptionalColumnEntry > opt_ Optional columns must start with “opt_”.
MzTabInteger rank Rank of the identification (1 = best)
MzTabString sme_identifier Within file unique identifier for the small molecule evidence result.
MzTabString smiles Potential molecular structure as SMILES.
MzTabSpectraRef spectra_ref Reference to a spectrum.
MzTabString uri The source entry’s location.