A container type that gathers peaks similar in m/z and moving along retention time. More...

#include <OpenMS/KERNEL/MassTrace.h>

Collaboration diagram for MassTrace:

Public Types
enum	MT_QUANTMETHOD { MT_QUANT_AREA = 0 , MT_QUANT_MEDIAN , MT_QUANT_HEIGHT , SIZE_OF_MT_QUANTMETHOD }

Public Member Functions
Constructors and Destructor
	MassTrace ()=default
	Default constructor. More...

	MassTrace (const std::list< PeakType > &trace_peaks)

	MassTrace (const std::vector< PeakType > &trace_peaks)
	Detailed constructor for vector. More...

	~MassTrace ()=default
	Destructor. More...

	MassTrace (const MassTrace &)=default
	Copy constructor. More...

MassTrace &	operator= (const MassTrace &)=default
	Assignment operator. More...

PeakType &	operator[] (const Size &mt_idx)
	Random access operator. More...

const PeakType &	operator[] (const Size &mt_idx) const

Accessor methods
Size	getSize () const
	Returns the number of peaks contained in the mass trace. More...

String	getLabel () const
	Gets label of mass trace. More...

void	setLabel (const String &label)
	Sets label of mass trace. More...

double	getCentroidMZ () const
	Returns the centroid m/z. More...

double	getCentroidRT () const
	Returns the centroid RT. More...

double	getCentroidSD () const

void	setCentroidSD (const double &tmp_sd)

double	getFWHM () const

double	getTraceLength () const
	Returns the length of the trace (as difference in RT) More...

std::pair< Size, Size >	getFWHMborders () const

const std::vector< double > &	getSmoothedIntensities () const
	Gets smoothed intensities (empty if no smoothing was explicitly done beforehand!). More...

void	setSmoothedIntensities (const std::vector< double > &db_vec)
	Set smoothed intensities (smoothing is done externally, e.g. by LowessSmoothing). More...

double	getAverageMS1CycleTime () const
	Get average scan time of mass trace. More...

Computational methods
double	computeSmoothedPeakArea () const
	Sum all non-negative (smoothed!) intensities in the mass trace. More...

double	computePeakArea () const
	Sum intensities of all peaks in the mass trace. More...

Size	findMaxByIntPeak (bool use_smoothed_ints=false) const
	Return the index of the mass trace's highest peak within the MassTrace container (based either on raw or smoothed intensities). More...

double	estimateFWHM (bool use_smoothed_ints=false)

void	setQuantMethod (MT_QUANTMETHOD method)
	determine if area or median is used for quantification More...

MT_QUANTMETHOD	getQuantMethod () const
	check if area or median is used for quantification More...

double	computeFwhmAreaSmooth () const
	Compute chromatographic peak area within the FWHM range. More...

double	computeFwhmArea () const

double	getIntensity (bool smoothed) const

double	getMaxIntensity (bool smoothed) const

ConvexHull2D	getConvexhull () const
	Return the mass trace's convex hull. More...

Update methods for centroid RT and m/z
void	updateSmoothedMaxRT ()

void	updateWeightedMeanRT ()
	Compute & update centroid RT as a intensity-weighted mean of RTs. More...

void	updateSmoothedWeightedMeanRT ()

void	updateMedianRT ()
	Compute & update centroid RT as median position of intensities. More...

void	updateMedianMZ ()
	Compute & update centroid m/z as median of m/z values. More...

void	updateMeanMZ ()
	Compute & update centroid m/z as mean of m/z values. More...

void	updateWeightedMeanMZ ()
	Compute & update centroid m/z as weighted mean of m/z values. More...

void	updateWeightedMZsd ()
	Compute & update m/z standard deviation of mass trace as weighted mean of m/z values. More...

Static Public Member Functions
static MT_QUANTMETHOD	getQuantMethod (const String &val)
	converts a string to enum value; returns 'SIZE_OF_MT_QUANTMETHOD' upon error More...

Public Attributes
double	fwhm_mz_avg = 0
	Average FWHM of m/z peaks. More...

Static Public Attributes
static const std::string	names_of_quantmethod [SIZE_OF_MT_QUANTMETHOD]

Private Member Functions
double	computeMedianIntensity_ () const
	median of trace intensities More...

double	linearInterpolationAtY_ (double xA, double xB, double yA, double yB, double y_eval) const

Private Attributes
std::vector< PeakType >	trace_peaks_
	Actual MassTrace container for doing centroid calculation, peak width estimation etc. More...

double	centroid_mz_ = 0.0
	Centroid m/z. More...

double	centroid_sd_ = 0.0
	intensity-weighted STD More...

double	centroid_rt_ = 0.0
	Centroid RT. More...

String	label_
	Trace label. More...

std::vector< double >	smoothed_intensities_
	Container for smoothed intensities. Smoothing must be done externally. More...

double	fwhm_ = 0.0
	FWHM of RT peak. More...

Size	fwhm_start_idx_ = 0
	index into 'trace_peaks_' vector (inclusive) More...

Size	fwhm_end_idx_ = 0
	index into 'trace_peaks_' vector (inclusive) More...

MT_QUANTMETHOD	quant_method_ = MT_QUANT_AREA
	use area under mass trace or the median of intensities More...

Iterators
Enables mutable/immutable access to the mass trace's peaks.
typedef std::vector< PeakType >::iterator	iterator

typedef std::vector< PeakType >::const_iterator	const_iterator

typedef std::vector< PeakType >::reverse_iterator	reverse_iterator

typedef std::vector< PeakType >::const_reverse_iterator	const_reverse_iterator

iterator	begin ()

iterator	end ()

const_iterator	begin () const

const_iterator	end () const

reverse_iterator	rbegin ()

reverse_iterator	rend ()

const_reverse_iterator	rbegin () const

const_reverse_iterator	rend () const

Detailed Description

A container type that gathers peaks similar in m/z and moving along retention time.

Depending on the method of extraction a mass trace could virtually represent a complete extracted ion chromatogram (XIC) or merely a part of it (e.g., a chromatographic peak). The kernel class provides methods for computing mass trace characteristics such as its centroid m/z and retention time. Coeluting mass traces can be further assembled to complete isotope patterns of peptides/metabolites.

Member Typedef Documentation

◆ const_iterator

typedef std::vector<PeakType>::const_iterator const_iterator

◆ const_reverse_iterator

typedef std::vector<PeakType>::const_reverse_iterator const_reverse_iterator

◆ iterator

typedef std::vector<PeakType>::iterator iterator

◆ reverse_iterator

typedef std::vector<PeakType>::reverse_iterator reverse_iterator

Member Enumeration Documentation

◆ MT_QUANTMETHOD

enum MT_QUANTMETHOD

Enumerator
MT_QUANT_AREA	quantify by area
MT_QUANT_MEDIAN	quantify by median of intensities
MT_QUANT_HEIGHT	quantify by peak height
SIZE_OF_MT_QUANTMETHOD

Constructor & Destructor Documentation

◆ MassTrace() [1/4]

MassTrace ( )

default

Default constructor.

◆ MassTrace() [2/4]

MassTrace ( const std::list< PeakType > & trace_peaks )

Detailed constructor (useful, since Mass Traces are commonly assembled by prepending and appending – which is faster using lists)

◆ MassTrace() [3/4]

MassTrace ( const std::vector< PeakType > & trace_peaks )

Detailed constructor for vector.

◆ ~MassTrace()

~MassTrace ( )

default

Destructor.

◆ MassTrace() [4/4]

MassTrace ( const MassTrace & )

default

Copy constructor.

Member Function Documentation

◆ begin() [1/2]

iterator begin ( )

inline

◆ begin() [2/2]

const_iterator begin ( ) const

inline

◆ computeFwhmArea()

double computeFwhmArea ( ) const

◆ computeFwhmAreaSmooth()

double computeFwhmAreaSmooth ( ) const

Compute chromatographic peak area within the FWHM range.

◆ computeMedianIntensity_()

double computeMedianIntensity_ ( ) const

private

median of trace intensities

◆ computePeakArea()

double computePeakArea ( ) const

Sum intensities of all peaks in the mass trace.

◆ computeSmoothedPeakArea()

double computeSmoothedPeakArea ( ) const

Sum all non-negative (smoothed!) intensities in the mass trace.

◆ end() [1/2]

iterator end ( )

inline

◆ end() [2/2]

const_iterator end ( ) const

inline

◆ estimateFWHM()

double estimateFWHM ( bool use_smoothed_ints = false )

Estimate FWHM of chromatographic peak in seconds (based on either raw or smoothed intensities). Uses linear interpolation of the two closest points to the half_max intensity in order to get the RT values at exactly the half_max stores result internally, use getFWHM().

◆ findMaxByIntPeak()

Size findMaxByIntPeak ( bool use_smoothed_ints = false ) const

Return the index of the mass trace's highest peak within the MassTrace container (based either on raw or smoothed intensities).

◆ getAverageMS1CycleTime()

double getAverageMS1CycleTime ( ) const

inline

Get average scan time of mass trace.

◆ getCentroidMZ()

double getCentroidMZ ( ) const

inline

Returns the centroid m/z.

Referenced by CmpMassTraceByMZ::operator()().

◆ getCentroidRT()

double getCentroidRT ( ) const

inline

Returns the centroid RT.

◆ getCentroidSD()

double getCentroidSD ( ) const

inline

◆ getConvexhull()

ConvexHull2D getConvexhull ( ) const

Return the mass trace's convex hull.

◆ getFWHM()

double getFWHM ( ) const

inline

◆ getFWHMborders()

std::pair<Size, Size> getFWHMborders ( ) const

inline

◆ getIntensity()

double getIntensity ( bool smoothed ) const

◆ getLabel()

String getLabel ( ) const

inline

Gets label of mass trace.

◆ getMaxIntensity()

double getMaxIntensity ( bool smoothed ) const

◆ getQuantMethod() [1/2]

MT_QUANTMETHOD getQuantMethod ( ) const

check if area or median is used for quantification

◆ getQuantMethod() [2/2]

static MT_QUANTMETHOD getQuantMethod ( const String & val )

static

converts a string to enum value; returns 'SIZE_OF_MT_QUANTMETHOD' upon error

◆ getSize()

Size getSize ( ) const

inline

Returns the number of peaks contained in the mass trace.

◆ getSmoothedIntensities()

const std::vector<double>& getSmoothedIntensities ( ) const

inline

Gets smoothed intensities (empty if no smoothing was explicitly done beforehand!).

◆ getTraceLength()

double getTraceLength ( ) const

inline

Returns the length of the trace (as difference in RT)

◆ linearInterpolationAtY_()

double linearInterpolationAtY_	(	double	xA,
		double	xB,
		double	yA,
		double	yB,
		double	y_eval
	)		const

private

calculate x coordinate of start/end indexes at half_max calculation is based on (yB - yA) / (xB - xA) = (y_eval - yA) / (xC - xA) solve for xC: xC = xA + ((y_eval - yA) * (xB - xA) / (yB - yA))

◆ operator=()

MassTrace& operator= ( const MassTrace & )

default

Assignment operator.

◆ operator[]() [1/2]

PeakType& operator[] ( const Size & mt_idx )

Random access operator.

◆ operator[]() [2/2]

const PeakType& operator[] ( const Size & mt_idx ) const

◆ rbegin() [1/2]

reverse_iterator rbegin ( )

inline

◆ rbegin() [2/2]

const_reverse_iterator rbegin ( ) const

inline

◆ rend() [1/2]

reverse_iterator rend ( )

inline

◆ rend() [2/2]

const_reverse_iterator rend ( ) const

inline

◆ setCentroidSD()

void setCentroidSD ( const double & tmp_sd )

inline

◆ setLabel()

void setLabel ( const String & label )

inline

Sets label of mass trace.

◆ setQuantMethod()

void setQuantMethod ( MT_QUANTMETHOD method )

determine if area or median is used for quantification

◆ setSmoothedIntensities()

void setSmoothedIntensities ( const std::vector< double > & db_vec )

inline

Set smoothed intensities (smoothing is done externally, e.g. by LowessSmoothing).

◆ updateMeanMZ()

void updateMeanMZ ( )

Compute & update centroid m/z as mean of m/z values.

◆ updateMedianMZ()

void updateMedianMZ ( )

Compute & update centroid m/z as median of m/z values.

◆ updateMedianRT()

void updateMedianRT ( )

Compute & update centroid RT as median position of intensities.

◆ updateSmoothedMaxRT()

void updateSmoothedMaxRT ( )

◆ updateSmoothedWeightedMeanRT()

void updateSmoothedWeightedMeanRT ( )

◆ updateWeightedMeanMZ()

void updateWeightedMeanMZ ( )

Compute & update centroid m/z as weighted mean of m/z values.

◆ updateWeightedMeanRT()

void updateWeightedMeanRT ( )

Compute & update centroid RT as a intensity-weighted mean of RTs.

◆ updateWeightedMZsd()

void updateWeightedMZsd ( )

Compute & update m/z standard deviation of mass trace as weighted mean of m/z values.

Make sure to call update(Weighted)(Mean|Median)MZ() first!
use getCentroidSD() to get result

Member Data Documentation

◆ centroid_mz_

double centroid_mz_ = 0.0

private

Centroid m/z.

◆ centroid_rt_

double centroid_rt_ = 0.0

private

Centroid RT.

◆ centroid_sd_

double centroid_sd_ = 0.0

private

intensity-weighted STD

◆ fwhm_

double fwhm_ = 0.0

private

FWHM of RT peak.

◆ fwhm_end_idx_

Size fwhm_end_idx_ = 0

private

index into 'trace_peaks_' vector (inclusive)

◆ fwhm_mz_avg

double fwhm_mz_avg = 0

Average FWHM of m/z peaks.

◆ fwhm_start_idx_

Size fwhm_start_idx_ = 0

private

index into 'trace_peaks_' vector (inclusive)

◆ label_

String label_

private

Trace label.

◆ names_of_quantmethod

const std::string names_of_quantmethod[SIZE_OF_MT_QUANTMETHOD]

static

◆ quant_method_

MT_QUANTMETHOD quant_method_ = MT_QUANT_AREA

private

use area under mass trace or the median of intensities

◆ smoothed_intensities_

std::vector<double> smoothed_intensities_

private

Container for smoothed intensities. Smoothing must be done externally.

◆ trace_peaks_

std::vector<PeakType> trace_peaks_

private

Actual MassTrace container for doing centroid calculation, peak width estimation etc.

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Static Public Attributes

Private Member Functions

Private Attributes

Iterators

Detailed Description

Member Typedef Documentation

◆ const_iterator

◆ const_reverse_iterator

◆ iterator

◆ reverse_iterator

Member Enumeration Documentation

◆ MT_QUANTMETHOD

Constructor & Destructor Documentation

◆ MassTrace() [1/4]

◆ MassTrace() [2/4]

◆ MassTrace() [3/4]

◆ ~MassTrace()

◆ MassTrace() [4/4]

Member Function Documentation

◆ begin() [1/2]

◆ begin() [2/2]

◆ computeFwhmArea()

◆ computeFwhmAreaSmooth()

◆ computeMedianIntensity_()

◆ computePeakArea()

◆ computeSmoothedPeakArea()

◆ end() [1/2]

◆ end() [2/2]

◆ estimateFWHM()

◆ findMaxByIntPeak()

◆ getAverageMS1CycleTime()

◆ getCentroidMZ()

◆ getCentroidRT()

◆ getCentroidSD()

◆ getConvexhull()

◆ getFWHM()

◆ getFWHMborders()

◆ getIntensity()

◆ getLabel()

◆ getMaxIntensity()

◆ getQuantMethod() [1/2]

◆ getQuantMethod() [2/2]

◆ getSize()

◆ getSmoothedIntensities()

◆ getTraceLength()

◆ linearInterpolationAtY_()

◆ operator=()

◆ operator[]() [1/2]

◆ operator[]() [2/2]

◆ rbegin() [1/2]

◆ rbegin() [2/2]

◆ rend() [1/2]

◆ rend() [2/2]

◆ setCentroidSD()

◆ setLabel()

◆ setQuantMethod()

◆ setSmoothedIntensities()

◆ updateMeanMZ()

◆ updateMedianMZ()

◆ updateMedianRT()

◆ updateSmoothedMaxRT()

◆ updateSmoothedWeightedMeanRT()

◆ updateWeightedMeanMZ()

◆ updateWeightedMeanRT()

◆ updateWeightedMZsd()

Member Data Documentation

◆ centroid_mz_

◆ centroid_rt_

◆ centroid_sd_

◆ fwhm_

◆ fwhm_end_idx_

◆ fwhm_mz_avg

◆ fwhm_start_idx_

◆ label_

◆ names_of_quantmethod

◆ quant_method_