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 (const 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 (const 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 (const OpenSwath::SpectrumPtr &spectrum, const 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. These scores use the ion mobilograms from individual peptides in one (or more) frames to compute additional scores.

• driftScoring() performs scoring on fragment ion mobilograms extracted from a DIA frame
• driftScoringMS1() performs scoring on precursor ion mobilograms extracted from a MS1 frame
• driftScoringMS1Contrast() performs cross correlation (contrast) scoring between precursor and fragment ion mobilograms

Member Typedef Documentation

CompoundType

typedef OpenSwath::LightCompound CompoundType

private

TransitionType

typedef OpenSwath::LightTransition TransitionType

private

Constructor & Destructor Documentation

IonMobilityScoring()

IonMobilityScoring

(

)

Constructor.

~IonMobilityScoring()

~IonMobilityScoring

(

)

Destructor.

Member Function Documentation

driftScoring()

static void driftScoring ( const 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

spectrum	The DIA MS2 spectrum found at the peak apex
transitions	The transitions used for scoring
scores	The output scores
drift_lower	Ion Mobility extraction start
drift_upper	Ion Mobility extraction end
drift_target	Ion Mobility extraction target
dia_extraction_window_	m/z extraction width
dia_extraction_ppm_	Whether m/z extraction width is in ppm
use_spline	Whether to use spline for fitting
drift_extra	Extend 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 ( const 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

spectrum	The DIA MS1 spectrum found at the peak apex
transitions	The transitions used for scoring
scores	The output scores
drift_lower	Ion Mobility extraction start
drift_upper	Ion Mobility extraction end
drift_target	Ion Mobility extraction target
dia_extraction_window_	m/z extraction width
dia_extraction_ppm_	Whether m/z extraction width is in ppm
use_spline	Whether to use spline for fitting
drift_extra	Extra extraction to use for drift time (in percent)

Returns

Populates additional scores in the scores object

driftScoringMS1Contrast()

static void driftScoringMS1Contrast ( const OpenSwath::SpectrumPtr &  spectrum, const 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

spectrum	The DIA MS2 spectrum found at the peak apex
ms1spectrum	The DIA MS1 spectrum found at the peak apex
transitions	The transitions used for scoring
scores	The output scores
drift_lower	Ion Mobility extraction start
drift_upper	Ion Mobility extraction end
drift_target	Ion Mobility extraction target
dia_extraction_window_	m/z extraction width
dia_extraction_ppm_	Whether m/z extraction width is in ppm
use_spline	Whether to use spline for fitting
drift_extra	Extra extraction to use for drift time (in percent)

Returns

Populates additional scores in the scores object