IonMobilityScoring Class Reference

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

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

Public Member Functions
	IonMobilityScoring ()
	Constructor.
	~IonMobilityScoring ()
	Destructor.

Static Public Member Functions
static void	driftScoring (const SpectrumSequence &spectra, const std::vector< TransitionType > &transitions, OpenSwath_Scores &scores, const double drift_target, RangeMobility im_range, const double dia_extraction_window_, const bool dia_extraction_ppm_, const double drift_extra, const bool apply_im_peak_picking, MobilogramParquetConsumer *mobilogram_consumer=nullptr, const double feature_rt=std::numeric_limits< double >::quiet_NaN(), Int64 feature_id=-1)
	Performs scoring of the ion mobility dimension in MS2.
static void	driftScoringMS1 (const SpectrumSequence &spectra, const std::vector< TransitionType > &transitions, OpenSwath_Scores &scores, const double drift_target, RangeMobility im_range, const double dia_extraction_window_, const bool dia_extraction_ppm_, const double drift_extra, MobilogramParquetConsumer *mobilogram_consumer=nullptr, const double feature_rt=std::numeric_limits< double >::quiet_NaN(), Int64 feature_id=-1)
	Performs scoring of the ion mobility dimension in MS1.
static void	driftScoringMS1Contrast (const SpectrumSequence &spectra, const SpectrumSequence &ms1spectrum, const std::vector< TransitionType > &transitions, OpenSwath_Scores &scores, RangeMobility im_range, const double dia_extraction_window_, const bool dia_extraction_ppm_, const double drift_extra, MobilogramParquetConsumer *mobilogram_consumer=nullptr, const double feature_rt=std::numeric_limits< double >::quiet_NaN(), Int64 feature_id=-1)
	Performs scoring of the ion mobility dimension in MS1 and MS2 (contrast)
static void	driftIdScoring (const SpectrumSequence &spectra, const std::vector< TransitionType > &transitions, MRMTransitionGroupType &transition_group_detection, OpenSwath_Scores &scores, const double drift_target, RangeMobility im_range, const double dia_extract_window_, const bool dia_extraction_ppm_, const double drift_extra, const bool apply_im_peak_picking, MobilogramParquetConsumer *mobilogram_consumer=nullptr, const double feature_rt=std::numeric_limits< double >::quiet_NaN(), Int64 feature_id=-1)
	Performs scoring of the ion mobility dimension for identification transitions against detection transitions.
static void	computeIonMobilogram (const SpectrumSequence &spectra, const RangeMZ &mz_range, const RangeMobility &im_range, double &im, double &intensity, Mobilogram &res, double eps)
	computes ion mobilogram to be used in scoring based on mz_range and im_range. Also integrates intensity in the resulting ion mobility mobilogram in mz_range and im_range across all the entire SpectrumSequence.

Private Types
typedef OpenSwath::LightCompound	CompoundType
typedef OpenSwath::LightTransition	TransitionType
typedef MRMTransitionGroup< MSChromatogram, TransitionType >	MRMTransitionGroupType

Static Private Member Functions
static std::vector< double >	computeGrid_ (const std::vector< Mobilogram > &mobilograms, double eps)
	helper function to computeIonMobilogram. Discretizes ion mobility values into a grid.
static void	alignToGrid_ (const Mobilogram &profile, const std::vector< double > &im_grid, Mobilogram &aligned_profile, double eps, Size &max_peak_idx)
static void	extractIntensities (const std::vector< Mobilogram > &mobilograms, std::vector< std::vector< double > > &int_values)
static std::vector< double >	extractIntensities (const Mobilogram &mobilogram)
	Extracts intensity values from a single Mobilogram object.

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

MRMTransitionGroupType

typedef MRMTransitionGroup< MSChromatogram, TransitionType> MRMTransitionGroupType

private

TransitionType

typedef OpenSwath::LightTransition TransitionType

private

Constructor & Destructor Documentation

IonMobilityScoring()

IonMobilityScoring

(

)

Constructor.

~IonMobilityScoring()

~IonMobilityScoring

(

)

Destructor.

Member Function Documentation

alignToGrid_()

static void alignToGrid_ ( const Mobilogram &  profile, const std::vector< double > &  im_grid, Mobilogram &  aligned_profile, double  eps, Size &  max_peak_idx  )

staticprivate

computeGrid_()

static std::vector< double > computeGrid_ ( const std::vector< Mobilogram > &  mobilograms, double  eps  )

staticprivate

helper function to computeIonMobilogram. Discretizes ion mobility values into a grid.

computeIonMobilogram()

static void computeIonMobilogram ( const SpectrumSequence &  spectra, const RangeMZ &  mz_range, const RangeMobility &  im_range, double &  im, double &  intensity, Mobilogram &  res, double  eps  )

static

computes ion mobilogram to be used in scoring based on mz_range and im_range. Also integrates intensity in the resulting ion mobility mobilogram in mz_range and im_range across all the entire SpectrumSequence.

Note

If there is no signal, mz will be set to -1 and intensity to 0

Parameters

[in]	spectra	Raw data in a spectrumSequence object (can contain 1 or multiple spectra centered around peak apex)
[in]	mz_range	the range across mz to extract
[in]	im_range	the range across im to extract
[out]	im	computed weighted average ion mobility
[out]	intensity	intensity computed intensity
[out]	res	outputted ion mobilogram
[in]	eps	minimum distance to allow for two seperate points

driftIdScoring()

static void driftIdScoring ( const SpectrumSequence &  spectra, const std::vector< TransitionType > &  transitions, MRMTransitionGroupType &  transition_group_detection, OpenSwath_Scores &  scores, const double  drift_target, RangeMobility  im_range, const double  dia_extract_window_, const bool  dia_extraction_ppm_, const double  drift_extra, const bool  apply_im_peak_picking, MobilogramParquetConsumer *  mobilogram_consumer = nullptr, const double  feature_rt = std::numeric_limits< double >::quiet_NaN(), Int64  feature_id = -1  )

static

Performs scoring of the ion mobility dimension for identification transitions against detection transitions.

Parameters

[in]	spectra	Vector of the DIA MS2 spectrum found in SpectrumSequence object (can contain 1 or multiple spectra centered around peak apex)
[in]	transitions	The transitions used for scoring
[in]	transition_group_detection	The detection transition group
[out]	scores	The output scores
[out]	drift_target	Ion Mobility extraction target
[in]	im_range	Ion Mobility extraction range
[in]	dia_extract_window_	m/z extraction width
[in]	dia_extraction_ppm_	Whether m/z extraction width is in ppm
[in]	drift_extra	Extra extraction to use for drift time (in percent)
[in]	apply_im_peak_picking	Apply peak pickng on the ion mobilogram
[in]	mobilogram_consumer	Optional consumer to write out extracted ion mobilograms to disk.
[in]	feature_rt	Optional retention time apex that the extract ion mobilogram corresponds to.
[in]	feature_id	Optional feature id of the retention time apex that the extract ion mobilogram corresponds to.

driftScoring()

static void driftScoring ( const SpectrumSequence &  spectra, const std::vector< TransitionType > &  transitions, OpenSwath_Scores &  scores, const double  drift_target, RangeMobility  im_range, const double  dia_extraction_window_, const bool  dia_extraction_ppm_, const double  drift_extra, const bool  apply_im_peak_picking, MobilogramParquetConsumer *  mobilogram_consumer = nullptr, const double  feature_rt = std::numeric_limits< double >::quiet_NaN(), Int64  feature_id = -1  )

static

Performs scoring of the ion mobility dimension in MS2.

Populates additional scores in the scores object

If apply_im_peak_picking is set to true, peak picking is performed on the Savitzky-Golay smoothed ion mobilogram. This is useful for minimizing interference from co-eluting analytes in the ion mobility dimension (IM) that fall within the current extraction window. This process improves the specificity of analyte detection by dynamically adjusting the IM extraction window to extract only over the IM elution of the highest intensity species. If multiple peaks are present in the IM dimension, lower intensity peaks get discarded.

Parameters

[in]	spectra	Sequence of segments of the DIA MS2 spectrum found at (and around) the peak apex
[in]	transitions	The transitions used for scoring
[out]	scores	The output scores
[out]	drift_target	Ion Mobility extraction target
[in]	im_range	Ion Mobility extraction range
[in]	dia_extraction_window_	m/z extraction width
[in]	dia_extraction_ppm_	Whether m/z extraction width is in ppm
[in]	drift_extra	Extend the extraction window to gain a larger field of view beyond drift_upper - drift_lower (in percent)
[in]	apply_im_peak_picking	Apply peak picking on the ion mobilogram
[in]	mobilogram_consumer	Optional consumer to write out extracted ion mobilograms to disk.
[in]	feature_rt	Optional retention time apex that the extract ion mobilogram corresponds to.
[in]	feature_id	Optional feature id of the retention time apex that the extract ion mobilogram corresponds to.

driftScoringMS1()

static void driftScoringMS1 ( const SpectrumSequence &  spectra, const std::vector< TransitionType > &  transitions, OpenSwath_Scores &  scores, const double  drift_target, RangeMobility  im_range, const double  dia_extraction_window_, const bool  dia_extraction_ppm_, const double  drift_extra, MobilogramParquetConsumer *  mobilogram_consumer = nullptr, const double  feature_rt = std::numeric_limits< double >::quiet_NaN(), Int64  feature_id = -1  )

static

Performs scoring of the ion mobility dimension in MS1.

Populates additional scores in the scores object

Parameters

[in]	spectra	vector containing the DIA MS1 spectra found at (or around) the peak apex
[in]	transitions	The transitions used for scoring
[out]	scores	The output scores
[in]	im_range	Ion Mobility extraction range
[out]	drift_target	Ion Mobility extraction target
[in]	dia_extraction_window_	m/z extraction width
[in]	dia_extraction_ppm_	Whether m/z extraction width is in ppm
[in]	drift_extra	Extra extraction to use for drift time (in percent)
[in]	mobilogram_consumer	Optional consumer to write out extracted ion mobilograms to disk.
[in]	feature_rt	Optional retention time apex that the extract ion mobilogram corresponds to.
[in]	feature_id	Optional feature id of the retention time apex that the extract ion mobilogram corresponds to.

driftScoringMS1Contrast()

static void driftScoringMS1Contrast ( const SpectrumSequence &  spectra, const SpectrumSequence &  ms1spectrum, const std::vector< TransitionType > &  transitions, OpenSwath_Scores &  scores, RangeMobility  im_range, const double  dia_extraction_window_, const bool  dia_extraction_ppm_, const double  drift_extra, MobilogramParquetConsumer *  mobilogram_consumer = nullptr, const double  feature_rt = std::numeric_limits< double >::quiet_NaN(), Int64  feature_id = -1  )

static

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

Populates additional scores in the scores object

Parameters

[in]	spectra	Vector of the DIA MS2 spectrum found in SpectrumSequence object (can contain 1 or multiple spectra centered around peak apex)
[in]	ms1spectrum	The DIA MS1 spectrum found in SpectrumSequence object (can contain 1 or multiple spectra centered around peak apex)
[in]	transitions	The transitions used for scoring
[out]	scores	The output scores
[in]	im_range	the ion mobility range
[in]	dia_extraction_window_	m/z extraction width
[in]	dia_extraction_ppm_	Whether m/z extraction width is in ppm
[in]	drift_extra	Extra extraction to use for drift time (in percent)
[in]	mobilogram_consumer	Optional consumer to write out extracted ion mobilograms to disk.
[in]	feature_rt	Optional retention time apex that the extract ion mobilogram corresponds to.
[in]	feature_id	Optional feature id of the retention time apex that the extract ion mobilogram corresponds to.

extractIntensities() [1/2]

static std::vector< double > extractIntensities ( const Mobilogram &  mobilogram )

staticprivate

Extracts intensity values from a single Mobilogram object.

This function takes a single Mobilogram object and extracts the intensity values, returning them as a vector of doubles.

Parameters

[in]

mobilogram

[in] A const reference to a Mobilogram object from which to extract intensity values.

Returns

A vector of doubles containing the extracted intensity values.

extractIntensities() [2/2]

static void extractIntensities ( const std::vector< Mobilogram > &  mobilograms, std::vector< std::vector< double > > &  int_values  )

staticprivate