OpenMS  2.7.0
Public Member Functions | Static Public Member Functions | Private Types | List of all members
IonMobilityScoring Class Reference

A class that calls the ion mobility scoring routines. More...

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

Public Member Functions

 IonMobilityScoring ()
 Constructor. More...
 
 ~IonMobilityScoring ()
 Destructor. More...
 

Static Public Member Functions

static void driftScoring (OpenSwath::SpectrumPtr spectrum, const std::vector< TransitionType > &transitions, OpenSwath_Scores &scores, const double drift_lower, const double drift_upper, const double drift_target, const double dia_extraction_window_, const bool dia_extraction_ppm_, const bool use_spline, const double drift_extra)
 Performs scoring of the ion mobility dimension in MS2. More...
 
static void driftScoringMS1 (OpenSwath::SpectrumPtr spectrum, const std::vector< TransitionType > &transitions, OpenSwath_Scores &scores, const double drift_lower, const double drift_upper, const double drift_target, const double dia_extract_window_, const bool dia_extraction_ppm_, const bool use_spline, const double drift_extra)
 Performs scoring of the ion mobility dimension in MS1. More...
 
static void driftScoringMS1Contrast (OpenSwath::SpectrumPtr spectrum, OpenSwath::SpectrumPtr ms1spectrum, const std::vector< TransitionType > &transitions, OpenSwath_Scores &scores, const double drift_lower, const double drift_upper, const double dia_extract_window_, const bool dia_extraction_ppm_, const double drift_extra)
 Performs scoring of the ion mobility dimension in MS1 and MS2 (contrast) More...
 

Private Types

typedef OpenSwath::LightCompound CompoundType
 
typedef OpenSwath::LightTransition TransitionType
 

Detailed Description

A class that calls the ion mobility scoring routines.

Use this class to invoke the individual OpenSWATH ion mobility scoring routines.

Member Typedef Documentation

◆ CompoundType

◆ TransitionType

Constructor & Destructor Documentation

◆ IonMobilityScoring()

Constructor.

◆ ~IonMobilityScoring()

Destructor.

Member Function Documentation

◆ driftScoring()

static void driftScoring ( OpenSwath::SpectrumPtr  spectrum,
const std::vector< TransitionType > &  transitions,
OpenSwath_Scores scores,
const double  drift_lower,
const double  drift_upper,
const double  drift_target,
const double  dia_extraction_window_,
const bool  dia_extraction_ppm_,
const bool  use_spline,
const double  drift_extra 
)
static

Performs scoring of the ion mobility dimension in MS2.

Parameters
spectrumThe DIA MS2 spectrum found at the peak apex
transitionsThe transitions used for scoring
scoresThe output scores
drift_lowerIon Mobility extraction start
drift_upperIon Mobility extraction end
drift_targetIon Mobility extraction target
dia_extraction_window_m/z extraction width
dia_extraction_ppm_Whether m/z extraction width is in ppm
use_splineWhether to use spline for fitting
drift_extraExtend the extraction window to gain a larger field of view beyond drift_upper - drift_lower (in percent)
Returns
Populates additional scores in the scores object

◆ driftScoringMS1()

static void driftScoringMS1 ( OpenSwath::SpectrumPtr  spectrum,
const std::vector< TransitionType > &  transitions,
OpenSwath_Scores scores,
const double  drift_lower,
const double  drift_upper,
const double  drift_target,
const double  dia_extract_window_,
const bool  dia_extraction_ppm_,
const bool  use_spline,
const double  drift_extra 
)
static

Performs scoring of the ion mobility dimension in MS1.

Parameters
spectrumThe DIA MS1 spectrum found at the peak apex
transitionsThe transitions used for scoring
scoresThe output scores
drift_lowerIon Mobility extraction start
drift_upperIon Mobility extraction end
drift_targetIon Mobility extraction target
dia_extraction_window_m/z extraction width
dia_extraction_ppm_Whether m/z extraction width is in ppm
use_splineWhether to use spline for fitting
drift_extraExtra extraction to use for drift time (in percent)
Returns
Populates additional scores in the scores object

◆ driftScoringMS1Contrast()

static void driftScoringMS1Contrast ( OpenSwath::SpectrumPtr  spectrum,
OpenSwath::SpectrumPtr  ms1spectrum,
const std::vector< TransitionType > &  transitions,
OpenSwath_Scores scores,
const double  drift_lower,
const double  drift_upper,
const double  dia_extract_window_,
const bool  dia_extraction_ppm_,
const double  drift_extra 
)
static

Performs scoring of the ion mobility dimension in MS1 and MS2 (contrast)

Parameters
spectrumThe DIA MS2 spectrum found at the peak apex
ms1spectrumThe DIA MS1 spectrum found at the peak apex
transitionsThe transitions used for scoring
scoresThe output scores
drift_lowerIon Mobility extraction start
drift_upperIon Mobility extraction end
drift_targetIon Mobility extraction target
dia_extraction_window_m/z extraction width
dia_extraction_ppm_Whether m/z extraction width is in ppm
use_splineWhether to use spline for fitting
drift_extraExtra extraction to use for drift time (in percent)
Returns
Populates additional scores in the scores object