OpenMS  2.8.0
Public Member Functions | Public Attributes | List of all members
TransitionTSVFile::TSVTransition Struct Reference

Internal structure to represent a transition. More...

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

Collaboration diagram for TransitionTSVFile::TSVTransition:
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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< StringProteinName
 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< Stringuniprot_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< Stringpeptidoforms
 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.