MzTab.h File Reference

#include <OpenMS/FORMAT/SVOutStream.h>
#include <OpenMS/FORMAT/MzTabBase.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/METADATA/PeptideEvidence.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
#include <optional>

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Classes
class	MzTabModification
	Data model of MzTab files. More...
class	MzTabModificationList
struct	MzTabModificationMetaData
struct	MzTabAssayMetaData
struct	MzTabMSRunMetaData
struct	MzTabStudyVariableMetaData
class	MzTabMetaData
	all meta data of a mzTab file. Please refer to specification for documentation. More...
struct	MzTabProteinSectionRow
	PRT - Protein section (Table based) More...
struct	MzTabProteinSectionRow::RowCompare
	Comparison operator for sorting rows. More...
struct	MzTabPeptideSectionRow
	PEP - Peptide section (Table based) More...
struct	MzTabPeptideSectionRow::RowCompare
	Comparison operator for sorting rows. More...
struct	MzTabPSMSectionRow
	PSM - PSM section (Table based) More...
struct	MzTabPSMSectionRow::RowCompare
	Comparison operator for sorting rows. More...
struct	MzTabSmallMoleculeSectionRow
	SML Small molecule section (table based) More...
struct	MzTabNucleicAcidSectionRow
	NUC - Nucleic acid section (table-based) More...
struct	MzTabNucleicAcidSectionRow::RowCompare
	Comparison operator for sorting rows. More...
struct	MzTabOligonucleotideSectionRow
	OLI - Oligonucleotide section (table-based) More...
struct	MzTabOligonucleotideSectionRow::RowCompare
	Comparison operator for sorting rows. More...
struct	MzTabOSMSectionRow
	OSM - OSM (oligonucleotide-spectrum match) section (table-based) More...
struct	MzTabOSMSectionRow::RowCompare
	Comparison operator for sorting rows. More...
class	MzTab
	Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/. More...
class	MzTab::IDMzTabStream
class	MzTab::CMMzTabStream

Namespaces
	OpenMS
	Main OpenMS namespace.

Typedefs
typedef std::vector< MzTabProteinSectionRow >	MzTabProteinSectionRows
typedef std::vector< MzTabPeptideSectionRow >	MzTabPeptideSectionRows
typedef std::vector< MzTabPSMSectionRow >	MzTabPSMSectionRows
typedef std::vector< MzTabSmallMoleculeSectionRow >	MzTabSmallMoleculeSectionRows
typedef std::vector< MzTabNucleicAcidSectionRow >	MzTabNucleicAcidSectionRows
typedef std::vector< MzTabOligonucleotideSectionRow >	MzTabOligonucleotideSectionRows
typedef std::vector< MzTabOSMSectionRow >	MzTabOSMSectionRows

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Class Documentation

OpenMS::MzTabModificationMetaData

struct OpenMS::MzTabModificationMetaData

Collaboration diagram for MzTabModificationMetaData:

Class Members
MzTabParameter	modification
MzTabString	position
MzTabString	site

OpenMS::MzTabAssayMetaData

struct OpenMS::MzTabAssayMetaData

Collaboration diagram for MzTabAssayMetaData:

Class Members
vector< int >	ms_run_ref
map< Size, MzTabModificationMetaData >	quantification_mod
MzTabParameter	quantification_reagent
MzTabString	sample_ref

OpenMS::MzTabMSRunMetaData

struct OpenMS::MzTabMSRunMetaData

Collaboration diagram for MzTabMSRunMetaData:

Class Members
MzTabParameter	format
MzTabParameterList	fragmentation_method
MzTabParameter	id_format
MzTabString	location

OpenMS::MzTabStudyVariableMetaData

struct OpenMS::MzTabStudyVariableMetaData

Collaboration diagram for MzTabStudyVariableMetaData:

Class Members
vector< int >	assay_refs
MzTabString	description
vector< int >	sample_refs

OpenMS::MzTabPeptideSectionRow

struct OpenMS::MzTabPeptideSectionRow

PEP - Peptide section (Table based)

Collaboration diagram for MzTabPeptideSectionRow:

Class Members
MzTabString	accession	The protein’s accession.
map< Size, MzTabDouble >	best_search_engine_score	Search engine(s) score(s) for the peptide.
MzTabInteger	charge	Precursor ion’s charge.
MzTabString	database	Name of the sequence database.
MzTabString	database_version	Version (and optionally # of entries).
MzTabDouble	mass_to_charge	Precursor ion’s m/z.
MzTabModificationList	modifications	Modifications identified in the peptide.
vector< MzTabOptionalColumnEntry >	opt_	Optional columns must start with “opt_”.
map< Size, MzTabDouble >	peptide_abundance_assay
map< Size, MzTabDouble >	peptide_abundance_std_error_study_variable
map< Size, MzTabDouble >	peptide_abundance_stdev_study_variable
map< Size, MzTabDouble >	peptide_abundance_study_variable
MzTabInteger	reliability	(1-3) 0=null Identification reliability for the peptide.
MzTabDoubleList	retention_time	Time points in seconds. Semantics may vary.
MzTabDoubleList	retention_time_window
MzTabParameterList	search_engine	Search engine(s) that identified the peptide.
map< Size, map< Size, MzTabDouble > >	search_engine_score_ms_run
MzTabString	sequence	The peptide’s sequence.
MzTabSpectraRef	spectra_ref	Spectra identifying the peptide.
MzTabBoolean	unique	0=false, 1=true, null else: Peptide is unique for the protein.
MzTabString	uri	Location of the PSMs source entry.

OpenMS::MzTabSmallMoleculeSectionRow

struct OpenMS::MzTabSmallMoleculeSectionRow

SML Small molecule section (table based)

Collaboration diagram for MzTabSmallMoleculeSectionRow:

Class Members
map< Size, MzTabDouble >	best_search_engine_score	Search engine(s) identifications score(s).
MzTabDouble	calc_mass_to_charge	Precursor ion’s m/z.
MzTabInteger	charge	Precursor ion’s charge.
MzTabString	chemical_formula	Chemical formula of the identified compound.
MzTabString	database	Name of the used database.
MzTabString	database_version	String Version of the database (and optionally # of compounds).
MzTabString	description	Human readable description (i.e. the name)
MzTabDouble	exp_mass_to_charge	Precursor ion’s m/z.
MzTabStringList	identifier	The small molecule’s identifier.
MzTabString	inchi_key	InChi Key of the identified compound.
MzTabString	modifications	Modifications identified on the small molecule.
vector< MzTabOptionalColumnEntry >	opt_	Optional columns must start with “opt_”.
MzTabInteger	reliability	(1-3) The identification reliability.
MzTabDoubleList	retention_time	Time points in seconds. Semantics may vary.
MzTabParameterList	search_engine	Search engine(s) identifying the small molecule.
map< Size, map< Size, MzTabDouble > >	search_engine_score_ms_run
map< Size, MzTabDouble >	smallmolecule_abundance_assay
map< Size, MzTabDouble >	smallmolecule_abundance_std_error_study_variable
map< Size, MzTabDouble >	smallmolecule_abundance_stdev_study_variable
map< Size, MzTabDouble >	smallmolecule_abundance_study_variable
MzTabString	smiles	Molecular structure in SMILES format.
MzTabString	species	Human readable name of the species.
MzTabSpectraRef	spectra_ref	Spectra identifying the small molecule.
MzTabInteger	taxid	NEWT taxonomy for the species.
MzTabString	uri	The source entry’s location.

OpenMS::MzTabNucleicAcidSectionRow

struct OpenMS::MzTabNucleicAcidSectionRow

NUC - Nucleic acid section (table-based)

Collaboration diagram for MzTabNucleicAcidSectionRow:

Class Members
MzTabString	accession	The nucleic acid’s accession.
MzTabStringList	ambiguity_members	Alternative nucleic acid identifications.
map< Size, MzTabDouble >	best_search_engine_score	Best search engine(s) score(s) (over all MS runs)
MzTabDouble	coverage	(0-1) Fraction of nucleic acid sequence identified.
MzTabString	database	Name of the sequence database.
MzTabString	database_version	Version of the sequence database.
MzTabString	description	Human readable description (i.e. the name)
MzTabStringList	go_terms	List of GO terms for the nucleic acid.
MzTabModificationList	modifications	Modifications identified in the nucleic acid.
map< Size, MzTabInteger >	num_oligos_distinct_ms_run
map< Size, MzTabInteger >	num_oligos_unique_ms_run
map< Size, MzTabInteger >	num_osms_ms_run
vector< MzTabOptionalColumnEntry >	opt_	Optional Columns must start with “opt_”
MzTabInteger	reliability
MzTabParameterList	search_engine	Search engine(s) that identified the nucleic acid.
map< Size, map< Size, MzTabDouble > >	search_engine_score_ms_run
MzTabString	species	Human readable name of the species.
MzTabInteger	taxid	NEWT taxonomy for the species.
MzTabString	uri	Location of the nucleic acid’s source entry.

OpenMS::MzTabOligonucleotideSectionRow

struct OpenMS::MzTabOligonucleotideSectionRow

OLI - Oligonucleotide section (table-based)

Collaboration diagram for MzTabOligonucleotideSectionRow:

Class Members
MzTabString	accession	The nucleic acid’s accession.
map< Size, MzTabDouble >	best_search_engine_score	Search engine(s) score(s) for the match.
MzTabInteger	end
MzTabModificationList	modifications	Modifications identified in the oligonucleotide.
vector< MzTabOptionalColumnEntry >	opt_	Optional columns must start with “opt_”.
MzTabString	post
MzTabString	pre
MzTabInteger	reliability	(1-3) 0=null Identification reliability for the match.
MzTabDoubleList	retention_time	Time points in seconds. Semantics may vary.
MzTabDoubleList	retention_time_window
MzTabParameterList	search_engine	Search engine(s) that identified the match.
map< Size, map< Size, MzTabDouble > >	search_engine_score_ms_run	Search engine(s) score(s) per individual MS run.
MzTabString	sequence	The oligonucleotide’s sequence.
MzTabInteger	start
MzTabBoolean	unique	0=false, 1=true, null else: Oligonucleotide maps uniquely to the nucleic acid sequence.
MzTabString	uri	Location of the oligonucleotide's source entry.

OpenMS::MzTabOSMSectionRow

struct OpenMS::MzTabOSMSectionRow

OSM - OSM (oligonucleotide-spectrum match) section (table-based)

Collaboration diagram for MzTabOSMSectionRow:

Class Members
MzTabDouble	calc_mass_to_charge	The theoretical m/z ratio of the oligonucleotide.
MzTabInteger	charge	The charge of the experimental precursor ion.
MzTabDouble	exp_mass_to_charge	The m/z ratio of the experimental precursor ion.
MzTabModificationList	modifications	Modifications identified in the oligonucleotide.
vector< MzTabOptionalColumnEntry >	opt_	Optional columns must start with “opt_”.
MzTabInteger	reliability	(1-3) 0=null Identification reliability for the match.
MzTabDoubleList	retention_time	Time points in seconds. Semantics may vary.
MzTabParameterList	search_engine	Search engine(s) that identified the match.
map< Size, MzTabDouble >	search_engine_score	Search engine(s) score(s) for the match.
MzTabString	sequence	The oligonucleotide’s sequence.
MzTabSpectraRef	spectra_ref	Reference to the spectrum underlying the match.
MzTabString	uri	Location of the OSM’s source entry.