TransitionTSVFile::TSVTransition Struct Reference

Internal structure to represent a transition. More...

#include <OpenMS/ANALYSIS/OPENSWATH/TransitionTSVFile.h>

Collaboration diagram for TransitionTSVFile::TSVTransition:

Public Member Functions
bool	isPeptide () const

Public Attributes
double	precursor = -1
	Precursor m/z.
double	product = -1
	Product m/z (fragment ion m/z)
double	rt_calibrated = -1
	Normalized RT.
std::string	transition_name
	Unique transition name.
double	CE = -1
	Collision Energy.
double	library_intensity = -1
	Library intensity of fragment ion (relative)
std::string	group_id
	Transition group identifier (grouping transitions of the same analyte)
bool	decoy = false
	Whether the transition is a decoy transition.
std::string	PeptideSequence
	Peptide sequence (only AA sequence)
std::vector< std::string >	ProteinName
	List of protein identifiers.
std::string	GeneName
	Gene identifier.
std::string	Annotation
	Fragment ion annotation.
std::string	FullPeptideName
	Full peptide sequence with UniMod modifications.
std::string	CompoundName
	Compound name (for metabolomics)
std::string	SMILES
	SMILES identifier (for metabolomics)
std::string	SumFormula
	Molecular formula (for metabolomics)
std::string	Adducts
	Adducts (for metabolomics)
std::string	precursor_charge
	Precursor charge state.
std::string	peptide_group_label
	Peptide group identifier (grouping isotopically labelled peptides)
std::string	label_type
	Type of label that was used (e.g. "heavy" or "light")
std::string	fragment_charge = "NA"
	Fragment ion charge state.
int	fragment_nr = -1
	Fragment number (e.g. "7" for a y7 ion)
double	fragment_mzdelta = -1
	Fragment m/z delta to theoretical ion.
double	drift_time = -1
	Ion mobility drift time.
int	fragment_modification = 0
	Fragment modification.
std::string	fragment_type
	Fragment type (e.g. "y" for a y7 ion)
std::vector< std::string >	uniprot_id
	List of UniProt identifiers of associated proteins.
bool	detecting_transition = true
	Whether to use transition to detect peak group,.
bool	identifying_transition = false
	Whether to use transition for peptidoform inference using IPF.
bool	quantifying_transition = true
	Whether to use transition to quantify peak group.
std::vector< std::string >	peptidoforms
	List of peptidoforms.

Detailed Description

Internal structure to represent a transition.

Internal structure to represent a single line from a transition input file (one transition).

Member Function Documentation

isPeptide()

bool isPeptide ( ) const

inline

Whether the transition represents a peptide (by convention, if the (metabolic) compound name field is empty, it is a peptide.)

Member Data Documentation

Adducts

std::string Adducts

Adducts (for metabolomics)

Annotation

std::string Annotation

Fragment ion annotation.

CE

double CE = -1

Collision Energy.

CompoundName

std::string CompoundName

Compound name (for metabolomics)

decoy

bool decoy = false

Whether the transition is a decoy transition.

detecting_transition

bool detecting_transition = true

Whether to use transition to detect peak group,.

drift_time

double drift_time = -1

Ion mobility drift time.

fragment_charge

std::string fragment_charge = "NA"

Fragment ion charge state.

fragment_modification

int fragment_modification = 0

Fragment modification.

fragment_mzdelta

double fragment_mzdelta = -1

Fragment m/z delta to theoretical ion.

fragment_nr

int fragment_nr = -1

Fragment number (e.g. "7" for a y7 ion)

fragment_type

std::string fragment_type

Fragment type (e.g. "y" for a y7 ion)

FullPeptideName

std::string FullPeptideName

Full peptide sequence with UniMod modifications.

GeneName

std::string GeneName

Gene identifier.

group_id

std::string group_id

Transition group identifier (grouping transitions of the same analyte)

identifying_transition

bool identifying_transition = false

Whether to use transition for peptidoform inference using IPF.

label_type

std::string label_type

Type of label that was used (e.g. "heavy" or "light")

library_intensity

double library_intensity = -1

Library intensity of fragment ion (relative)

peptide_group_label

std::string peptide_group_label

Peptide group identifier (grouping isotopically labelled peptides)

PeptideSequence

std::string PeptideSequence

Peptide sequence (only AA sequence)

peptidoforms

std::vector<std::string> peptidoforms

List of peptidoforms.

precursor

double precursor = -1

Precursor m/z.

precursor_charge

std::string precursor_charge

Precursor charge state.

product

double product = -1

Product m/z (fragment ion m/z)

ProteinName

std::vector<std::string> ProteinName

List of protein identifiers.

quantifying_transition

bool quantifying_transition = true

Whether to use transition to quantify peak group.

rt_calibrated

double rt_calibrated = -1

Normalized RT.

SMILES

std::string SMILES

SMILES identifier (for metabolomics)

SumFormula

std::string SumFormula

Molecular formula (for metabolomics)

transition_name

std::string transition_name

Unique transition name.

uniprot_id

std::vector<std::string> uniprot_id

List of UniProt identifiers of associated proteins.