| OpenMS 2.5.0

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>`

## 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.