MRMTransitionGroupPicker Class Reference

The MRMTransitionGroupPicker finds peaks in chromatograms that belong to the same precursors. More...

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

Inheritance diagram for MRMTransitionGroupPicker:

Public Member Functions
template<typename SpectrumT , typename TransitionT >
void	pickTransitionGroup (MRMTransitionGroup< SpectrumT, TransitionT > &transition_group)
	Pick a group of chromatograms belonging to the same peptide. More...
template<typename SpectrumT , typename TransitionT >
MRMFeature	createMRMFeature (const MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, std::vector< SpectrumT > &picked_chroms, const std::vector< SpectrumT > &smoothed_chroms, const int chr_idx, const int peak_idx)
	Create feature from a vector of chromatograms and a specified peak. More...
template<typename SpectrumT >
void	remove_overlapping_features (std::vector< SpectrumT > &picked_chroms, double best_left, double best_right)
	Remove overlapping features. More...
void	findLargestPeak (const std::vector< MSChromatogram > &picked_chroms, int &chr_idx, int &peak_idx)
	Find largest peak in a vector of chromatograms. More...
void	findWidestPeakIndices (const std::vector< MSChromatogram > &picked_chroms, Int &chrom_idx, Int &point_idx) const
	Given a vector of chromatograms, find the indices of the chromatogram containing the widest peak and of the position of highest intensity. More...
	MRMTransitionGroupPicker ()
	Constructor. More...
	~MRMTransitionGroupPicker () override
	Destructor. More...
Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...
	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...
virtual	~DefaultParamHandler ()
	Destructor. More...
virtual DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...
virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...
void	setParameters (const Param &param)
	Sets the parameters. More...
const Param &	getParameters () const
	Non-mutable access to the parameters. More...
const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...
const String &	getName () const
	Non-mutable access to the name. More...
void	setName (const String &name)
	Mutable access to the name. More...
const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

Protected Member Functions
void	updateMembers_ () override
	Synchronize members with param class. More...
MRMTransitionGroupPicker &	operator= (const MRMTransitionGroupPicker &rhs)
	Assignment operator is protected for algorithm. More...
template<typename SpectrumT , typename TransitionT >
const SpectrumT &	selectChromHelper_ (const MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, const String &native_id)
	Select matching precursor or fragment ion chromatogram. More...
template<typename SpectrumT , typename TransitionT >
double	computeQuality_ (const MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, const std::vector< SpectrumT > &picked_chroms, const int chr_idx, const double best_left, const double best_right, String &outlier)
	Compute transition group quality (higher score is better) More...
template<typename SpectrumT >
void	recalculatePeakBorders_ (const std::vector< SpectrumT > &picked_chroms, double &best_left, double &best_right, double max_z)
	Recalculate the borders of the peak. More...
Resampling methods
template<typename SpectrumT >
void	prepareMasterContainer_ (const SpectrumT &ref_chromatogram, SpectrumT &master_peak_container, double left_boundary, double right_boundary)
	Create an empty master peak container that has the correct mz / RT values set. More...
template<typename SpectrumT >
SpectrumT	resampleChromatogram_ (const SpectrumT &chromatogram, const SpectrumT &master_peak_container, double left_boundary, double right_boundary)
	Resample a container at the positions indicated by the master peak container. More...
Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes
String	peak_integration_
String	background_subtraction_
bool	recalculate_peaks_
bool	use_precursors_
bool	use_consensus_
bool	compute_peak_quality_
bool	compute_peak_shape_metrics_
bool	compute_total_mi_
double	min_qual_
int	stop_after_feature_
double	stop_after_intensity_ratio_
double	min_peak_width_
double	recalculate_peaks_max_z_
double	resample_boundary_
String	boundary_selection_method_
	Which method to use for selecting peaks' boundaries. More...
PeakPickerMRM	picker_
PeakIntegrator	pi_
Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters. More...
Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes! More...
std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes! More...
String	error_name_
	Name that is displayed in error messages during the parameter checking. More...
bool	check_defaults_
	If this member is set to false no checking if parameters in done;. More...
bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;. More...

Detailed Description

The MRMTransitionGroupPicker finds peaks in chromatograms that belong to the same precursors.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
stop_after_feature	int	-1		Stop finding after feature (ordered by intensity; -1 means do not stop).
stop_after_intensity_ratio	float	0.0001		Stop after reaching intensity ratio
min_peak_width	float	-1		Minimal peak width (s), discard all peaks below this value (-1 means no action).
peak_integration	string	original	original, smoothed	Calculate the peak area and height either the smoothed or the raw chromatogram data.
background_subtraction	string	none	none, original, exact	Remove background from peak signal using estimated noise levels. The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation.
recalculate_peaks	string	false	true, false	Tries to get better peak picking by looking at peak consistency of all picked peaks. Tries to use the consensus (median) peak border if the variation within the picked peaks is too large.
use_precursors	string	false	true, false	Use precursor chromatogram for peak picking (note that this may lead to precursor signal driving the peak picking)
use_consensus	string	true	true, false	Use consensus peak boundaries when computing transition group picking (if false, compute independent peak boundaries for each transition)
recalculate_peaks_max_z	float	1		Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries. If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0).
minimal_quality	float	-10000		Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold
resample_boundary	float	15		For computing peak quality, how many extra seconds should be sample left and right of the actual peak
compute_peak_quality	string	false	true, false	Tries to compute a quality value for each peakgroup and detect outlier transitions. The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad.
compute_peak_shape_metrics	string	false	true, false	Calculates various peak shape metrics (e.g., tailing) that can be used for downstream QC/QA.
compute_total_mi	string	false	true, false	Compute mutual information metrics for individual transitions that can be used for OpenSWATH/IPF scoring.
boundary_selection_method	string	largest	largest, widest	Method to use when selecting the best boundaries for peaks.
PeakPickerMRM:sgolay_frame_length	int	15		The number of subsequent data points used for smoothing. This number has to be uneven. If it is not, 1 will be added.
PeakPickerMRM:sgolay_polynomial_order	int	3		Order of the polynomial that is fitted.
PeakPickerMRM:gauss_width	float	50		Gaussian width in seconds, estimated peak size.
PeakPickerMRM:use_gauss	string	true	false, true	Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)
PeakPickerMRM:peak_width	float	-1		Force a certain minimal peak_width on the data (e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off.
PeakPickerMRM:signal_to_noise	float	1	min: 0	Signal-to-noise threshold at which a peak will not be extended any more. Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured.
PeakPickerMRM:sn_win_len	float	1000		Signal to noise window length.
PeakPickerMRM:sn_bin_count	int	30		Signal to noise bin count.
PeakPickerMRM:write_sn_log_messages	string	true	true, false	Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin
PeakPickerMRM:remove_overlapping_peaks	string	false	false, true	Try to remove overlapping peaks during peak picking
PeakPickerMRM:method	string	corrected	legacy, corrected, crawdad	Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram).
PeakIntegrator:integration_type	string	intensity_sum	intensity_sum, simpson, trapezoid	The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration.
PeakIntegrator:baseline_type	string	base_to_base	base_to_base, vertical_division, vertical_division_min, vertical_division_max	The baseline type to use in estimateBackground() based on the peak boundaries. A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base).
PeakIntegrator:fit_EMG	string	false	false, true	Fit the chromatogram/spectrum to the EMG peak model.

Note:

• If a section name is documented, the documentation is displayed as tooltip.
• Advanced parameter names are italic.

It is called through pickTransitionGroup which will accept an MRMTransitionGroup filled with n chromatograms and perform the following steps:

• Step 1: find features (peaks) in individual chromatograms
• Step 2: merge these features to consensus features that span multiple chromatograms

Step 1 is performed by smoothing the individual chromatogram and applying the PeakPickerHiRes.

Step 2 is performed by finding the largest peak overall and use this to create a feature, propagating this through all chromatograms.

Constructor & Destructor Documentation

MRMTransitionGroupPicker()

MRMTransitionGroupPicker

(

)

Constructor.

~MRMTransitionGroupPicker()

~MRMTransitionGroupPicker ( )

override

Destructor.

Member Function Documentation

computeQuality_()

double computeQuality_ ( const MRMTransitionGroup< SpectrumT, TransitionT > &  transition_group, const std::vector< SpectrumT > &  picked_chroms, const int  chr_idx, const double  best_left, const double  best_right, String &  outlier  )

inlineprotected

Compute transition group quality (higher score is better)

This is only based on the co-elution of the chromatograms and internal consistency without any library information.

For the final score (larger is better), consider these scores:

• missing_peaks (the more peaks are missing, the worse)
• multiple_peaks
• mean of the shapes (1 is very good, 0 is bad)
• mean of the coelutions (0 is good, 1 is ok, above 1 is pretty bad)

These scores are similar to the ones computed by MRMFeatureFinderScoring and a simple sum of these scores is returned.

left_borders / right_borders might not have the same length since we might have peaks missing!!

References OpenMS::Constants::k, LOG_DEBUG, mean_and_stddev::mean(), OpenSwath::Scoring::normalizedCrossCorrelation(), and OpenSwath::Scoring::xcorrArrayGetMaxPeak().

createMRMFeature()

MRMFeature createMRMFeature ( const MRMTransitionGroup< SpectrumT, TransitionT > &  transition_group, std::vector< SpectrumT > &  picked_chroms, const std::vector< SpectrumT > &  smoothed_chroms, const int  chr_idx, const int  peak_idx  )

inline

Create feature from a vector of chromatograms and a specified peak.

References PeakIntegrator::PeakArea::apex_pos, PeakIntegrator::PeakArea::area, PeakIntegrator::PeakBackground::area, PeakIntegrator::PeakShapeMetrics::asymmetry_factor, PeakIntegrator::PeakShapeMetrics::baseline_delta_2_height, MRMTransitionGroup< ChromatogramType, TransitionType >::chromatogramIdsMatch(), PeakIntegrator::PeakShapeMetrics::end_position_at_10, PeakIntegrator::PeakShapeMetrics::end_position_at_5, PeakIntegrator::PeakShapeMetrics::end_position_at_50, MRMTransitionGroup< ChromatogramType, TransitionType >::getChromatograms(), Feature::getConvexHulls(), MRMTransitionGroup< ChromatogramType, TransitionType >::getPrecursorChromatograms(), MRMTransitionGroup< ChromatogramType, TransitionType >::getTransitionGroupID(), MRMTransitionGroup< ChromatogramType, TransitionType >::getTransitions(), PeakIntegrator::PeakArea::height, PeakIntegrator::PeakBackground::height, PeakIntegrator::PeakArea::hull_points, MRMTransitionGroup< ChromatogramType, TransitionType >::isInternallyConsistent(), OpenMS::Constants::k, LOG_DEBUG, LOG_WARN, OPENMS_PRECONDITION, PeakIntegrator::PeakShapeMetrics::points_across_baseline, PeakIntegrator::PeakShapeMetrics::points_across_half_height, OpenSwath::Scoring::rankedMutualInformation(), ConvexHull2D::setHullPoints(), Peak2D::setIntensity(), MetaInfoInterface::setMetaValue(), Peak2D::setMZ(), Feature::setOverallQuality(), Feature::setQuality(), Peak2D::setRT(), PeakIntegrator::PeakShapeMetrics::slope_of_baseline, PeakIntegrator::PeakShapeMetrics::start_position_at_10, PeakIntegrator::PeakShapeMetrics::start_position_at_5, PeakIntegrator::PeakShapeMetrics::start_position_at_50, PeakIntegrator::PeakShapeMetrics::tailing_factor, PeakIntegrator::PeakShapeMetrics::total_width, PeakIntegrator::PeakShapeMetrics::width_at_10, PeakIntegrator::PeakShapeMetrics::width_at_5, and PeakIntegrator::PeakShapeMetrics::width_at_50.

findLargestPeak()

void findLargestPeak	(	const std::vector< MSChromatogram > &	picked_chroms,
		int &	chr_idx,
		int &	peak_idx
	)

Find largest peak in a vector of chromatograms.

findWidestPeakIndices()

void findWidestPeakIndices	(	const std::vector< MSChromatogram > &	picked_chroms,
		Int &	chrom_idx,
		Int &	point_idx
	)		const

Given a vector of chromatograms, find the indices of the chromatogram containing the widest peak and of the position of highest intensity.

Parameters

[in]	picked_chroms	The vector of chromatograms
[out]	chrom_idx	The index of the chromatogram containing the widest peak
[out]	point_idx	The index of the point with highest intensity

operator=()

MRMTransitionGroupPicker& operator= ( const MRMTransitionGroupPicker &  rhs )

protected

Assignment operator is protected for algorithm.

pickTransitionGroup()

void pickTransitionGroup ( MRMTransitionGroup< SpectrumT, TransitionT > &  transition_group )

inline

Pick a group of chromatograms belonging to the same peptide.

Will identify peaks in a set of chromatograms that belong to the same peptide. The chromatograms are given in the MRMTransitionGroup container which also contains the mapping of the chromatograms to their metadata. Only chromatograms from detecting transitions are used for peak picking. Identifying transitions will be processed alongside but do not contribute to the meta-data, e.g. total_xic or peak_apices_sum.

The resulting features are added to the MRMTransitionGroup. Each feature contains the following meta-data:

• PeptideRef
• leftWidth
• rightWidth
• total_xic (fragment trace XIC sum)
• peak_apices_sum

References MRMTransitionGroup< ChromatogramType, TransitionType >::addFeature(), MRMTransitionGroup< ChromatogramType, TransitionType >::chromatogramIdsMatch(), MRMTransitionGroup< ChromatogramType, TransitionType >::getChromatograms(), Peak2D::getIntensity(), MetaInfoInterface::getMetaValue(), ChromatogramSettings::getNativeID(), MRMTransitionGroup< ChromatogramType, TransitionType >::getPrecursorChromatograms(), MRMTransitionGroup< ChromatogramType, TransitionType >::getTransition(), MRMTransitionGroup< ChromatogramType, TransitionType >::getTransitions(), MRMTransitionGroup< ChromatogramType, TransitionType >::hasTransition(), MRMTransitionGroup< ChromatogramType, TransitionType >::isInternallyConsistent(), OpenMS::Constants::k, OPENMS_PRECONDITION, and MSChromatogram::sortByIntensity().

prepareMasterContainer_()

void prepareMasterContainer_ ( const SpectrumT &  ref_chromatogram, SpectrumT &  master_peak_container, double  left_boundary, double  right_boundary  )

inlineprotected

Create an empty master peak container that has the correct mz / RT values set.

The empty master peak container fill be filled with mz / RT values at the positions where the reference chromatogram has values. The container will only be populated between the boundaries given. The output container will contain peaks with mz / RT values but all intensity values will be zero.

Parameters

ref_chromatogram	Reference chromatogram containing mz / RT values (possibly beyond the desired range)
master_peak_container	Output container to be populated
left_boundary	Left boundary of values the container should be populated with
right_boundary	Right boundary of values the container should be populated with

References OPENMS_PRECONDITION.

recalculatePeakBorders_()

void recalculatePeakBorders_ ( const std::vector< SpectrumT > &  picked_chroms, double &  best_left, double &  best_right, double  max_z  )

inlineprotected

Recalculate the borders of the peak.

By collecting all left and right borders of contained peaks, a consensus peak is computed. By looking at the means and standard deviations of all the peak borders it is estimated whether the proposed peak border deviates too much from the consensus one. If the deviation is too high (in this case), then we fall back to the "consensus" (a median here).

References OpenMS::Constants::k, LOG_DEBUG, and OpenMS::Math::mean().

remove_overlapping_features()

void remove_overlapping_features ( std::vector< SpectrumT > &  picked_chroms, double  best_left, double  best_right  )

inline

Remove overlapping features.

Remove features that are within the current seed (between best_left and best_right) or overlap with it. An overlapping feature is defined as a feature that has either of its borders within the border of the current peak

Directly adjacent features are allowed, e.g. they can share one border.

References OpenMS::Constants::k.

resampleChromatogram_()

SpectrumT resampleChromatogram_ ( const SpectrumT &  chromatogram, const SpectrumT &  master_peak_container, double  left_boundary, double  right_boundary  )

inlineprotected

Resample a container at the positions indicated by the master peak container.

Parameters

chromatogram	Container with the input data
master_peak_container	Container with the mz / RT values at which to resample
left_boundary	Left boundary of values the container should be resampled
right_boundary	Right boundary of values the container should be resampled

Returns

A container which contains the data from the input chromatogram resampled at the positions of the master container

References LinearResamplerAlign::raster().

selectChromHelper_()

const SpectrumT& selectChromHelper_ ( const MRMTransitionGroup< SpectrumT, TransitionT > &  transition_group, const String &  native_id  )

inlineprotected

Select matching precursor or fragment ion chromatogram.

References MRMTransitionGroup< ChromatogramType, TransitionType >::getChromatogram(), MRMTransitionGroup< ChromatogramType, TransitionType >::getPrecursorChromatogram(), MRMTransitionGroup< ChromatogramType, TransitionType >::hasChromatogram(), and MRMTransitionGroup< ChromatogramType, TransitionType >::hasPrecursorChromatogram().

updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

Member Data Documentation

background_subtraction_

String background_subtraction_

protected

boundary_selection_method_

String boundary_selection_method_

protected

Which method to use for selecting peaks' boundaries.

Valid values are: "largest", "widest"

compute_peak_quality_

bool compute_peak_quality_

protected

compute_peak_shape_metrics_

bool compute_peak_shape_metrics_

protected

compute_total_mi_

bool compute_total_mi_

protected

min_peak_width_

double min_peak_width_

protected

min_qual_

double min_qual_

protected

peak_integration_

String peak_integration_

protected

pi_

PeakIntegrator pi_

protected

picker_

PeakPickerMRM picker_

protected

recalculate_peaks_

bool recalculate_peaks_

protected

recalculate_peaks_max_z_

double recalculate_peaks_max_z_

protected

resample_boundary_

double resample_boundary_

protected

stop_after_feature_

int stop_after_feature_

protected

stop_after_intensity_ratio_

double stop_after_intensity_ratio_

protected

use_consensus_

bool use_consensus_

protected

use_precursors_

bool use_precursors_

protected