MzTabM.h File Reference

#include <OpenMS/FORMAT/MzTabBase.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/METADATA/ID/IdentificationData.h>
#include <OpenMS/METADATA/MetaInfoInterface.h>
#include <set>

Include dependency graph for MzTabM.h:

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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	MzTabMAssayMetaData
	MztabM Assay Metadata. More...
class	MzTabMMSRunMetaData
	MztabM MSRun Metadata. More...
class	MzTabMStudyVariableMetaData
	MztabM StudyVariable Metadata. More...
class	MzTabMDatabaseMetaData
	MztabM Database Metadata. 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

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Class Documentation

OpenMS::MzTabMAssayMetaData

class OpenMS::MzTabMAssayMetaData

MztabM Assay Metadata.

Collaboration diagram for MzTabMAssayMetaData:

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:

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:

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:

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:

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:

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:

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.