OpenMS  3.0.0
MzTab.h File Reference
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Classes

class  MzTabModification
 Data model of MzTab files. More...
 
class  MzTabModificationList
 
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
 

Class Documentation

◆ OpenMS::MzTabModificationMetaData

struct OpenMS::MzTabModificationMetaData
Collaboration diagram for MzTabModificationMetaData:
[legend]
Class Members
MzTabParameter modification
MzTabString position
MzTabString site

◆ OpenMS::MzTabAssayMetaData

struct OpenMS::MzTabAssayMetaData
Collaboration diagram for MzTabAssayMetaData:
[legend]
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:
[legend]
Class Members
MzTabParameter format
MzTabParameterList fragmentation_method
MzTabParameter id_format
MzTabString location

◆ OpenMS::MzTabStudyVariableMetaData

struct OpenMS::MzTabStudyVariableMetaData
Collaboration diagram for MzTabStudyVariableMetaData:
[legend]
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:
[legend]
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:
[legend]
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:
[legend]
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:
[legend]
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:
[legend]
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.