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. More...

double	product = -1
	Product m/z (fragment ion m/z) More...

double	rt_calibrated = -1
	Normalized RT. More...

String	transition_name = ""
	Unique transition name. More...

double	CE = -1
	Collision Energy. More...

double	library_intensity = -1
	Library intensity of fragment ion (relative) More...

String	group_id = ""
	Transition group identifier (grouping transitions of the same analyte) More...

bool	decoy = false
	Whether the transition is a decoy transition. More...

String	PeptideSequence
	Peptide sequence (only AA sequence) More...

std::vector< String >	ProteinName
	List of protein identifiers. More...

String	GeneName
	Gene identifier. More...

String	Annotation
	Fragment ion annotation. More...

String	FullPeptideName
	Full peptide sequence with UniMod modifications. More...

String	CompoundName
	Compound name (for metabolomics) More...

String	SMILES
	SMILES identifier (for metabolomics) More...

String	SumFormula
	Molecular formula (for metabolomics) More...

String	Adducts
	Adducts (for metabolomics) More...

String	precursor_charge
	Precursor charge state. More...

String	peptide_group_label
	Peptide group identifier (grouping isotopically labelled peptides) More...

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

String	fragment_charge = "NA"
	Fragment ion charge state. More...

int	fragment_nr = -1
	Fragment number (e.g. "7" for a y7 ion) More...

double	fragment_mzdelta = -1
	Fragment m/z delta to theoretical ion. More...

double	drift_time = -1
	Ion mobility drift time. More...

int	fragment_modification = 0
	Fragment modification. More...

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

std::vector< String >	uniprot_id
	List of UniProt identifiers of associated proteins. More...

bool	detecting_transition = true
	Whether to use transition to detect peak group,. More...

bool	identifying_transition = false
	Whether to use transition for peptidoform inference using IPF. More...

bool	quantifying_transition = true
	Whether to use transition to quantify peak group. More...

std::vector< String >	peptidoforms
	List of peptidoforms. More...

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

String Adducts

Adducts (for metabolomics)

◆ Annotation

String Annotation

Fragment ion annotation.

◆ CE

double CE = -1

Collision Energy.

◆ CompoundName

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

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

String fragment_type

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

◆ FullPeptideName

String FullPeptideName

Full peptide sequence with UniMod modifications.

◆ GeneName

String GeneName

Gene identifier.

◆ group_id

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

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

String peptide_group_label

Peptide group identifier (grouping isotopically labelled peptides)

◆ PeptideSequence

String PeptideSequence

Peptide sequence (only AA sequence)

◆ peptidoforms

std::vector<String> peptidoforms

List of peptidoforms.

◆ precursor

double precursor = -1

Precursor m/z.

◆ precursor_charge

String precursor_charge

Precursor charge state.

◆ product

double product = -1

Product m/z (fragment ion m/z)

◆ ProteinName

std::vector<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

String SMILES

SMILES identifier (for metabolomics)

◆ SumFormula

String SumFormula

Molecular formula (for metabolomics)

◆ transition_name

String transition_name = ""

Unique transition name.

◆ uniprot_id

std::vector<String> uniprot_id

List of UniProt identifiers of associated proteins.

Public Member Functions

Public Attributes