Class describing a deconvolved mass. A mass contains multiple peaks of different charges and isotope indices. PeakGroup is the set of such peaks representing a single monoisotopic mass. PeakGroup also contains features that define the quality of it. It is used by QScore calculation DeconvolvedSpectrum consists of PeakGroups. More...

#include <OpenMS/ANALYSIS/TOPDOWN/PeakGroup.h>

Collaboration diagram for PeakGroup:

[legend]

Public Member Functions
	PeakGroup ()=default
	default constructor More...

	PeakGroup (const int min_abs_charge, const int max_abs_charge, const bool is_positive)
	Constructor specifying charge range. More...

	~PeakGroup ()
	default destructor More...

	PeakGroup (const PeakGroup &)=default
	copy constructor More...

	PeakGroup (PeakGroup &&other)=default
	move constructor More...

bool	operator< (const PeakGroup &a) const
	comparison operators More...

bool	operator> (const PeakGroup &a) const

bool	operator== (const PeakGroup &a) const

PeakGroup &	operator= (const PeakGroup &t)=default
	assignment operator More...

void	updateMonomassAndIsotopeIntensities ()
	add monoisotopic indices of peaks by offset and discard negative isotope peaks. Total intensity is also updated More...

void	updateIsotopeCosineAndQScore (const FLASHDeconvHelperStructs::PrecalculatedAveragine &avg, double min_cos, double iso_da_distance)

void	recruitAllPeaksInSpectrum (const MSSpectrum &spec, const double tol, const FLASHDeconvHelperStructs::PrecalculatedAveragine &avg, double mono_mass, bool write_detail)
	recruit peaks and then return as a spectrum. More...

void	updateSNR ()
	using signal and total (signal + noise) power, update SNR value More...

bool	isSignalMZ (const double mz, const double tol) const
	determine is an mz is a signal of this peakgroup. Input tol is ppm tolerance (e.g., 10.0 for 10ppm tolerance) More...

void	setScanNumber (const int scan_number)
	set scan number More...

void	setChargeIsotopeCosine (const int abs_charge, const float cos)
	set per abs_charge isotope cosine More...

void	setMaxQScoreMzRange (const double min, const double max)
	set mz range that results in max QScore More...

void	setAbsChargeRange (const int min_abs_charge, const int max_abs_charge)
	set min_abs_charge and max_abs_charge charge range More...

void	setIsotopeCosine (const float cos)
	set isotope cosine score More...

void	setRepAbsCharge (const int max_qscore_charge)
	set representative max_qscore_charge More...

void	setQScore (const float qscore)
	set Q score - for FLASHIda log file parsing More...

void	setChargeScore (const float charge_score)
	set charge score - for FLASHIda log file parsing More...

void	setAvgPPMError (const float error)
	set average mass ppm error More...

void	setSNR (const float snr)
	set SNR manually - for FLASHIda log file parsing More...

void	setChargeSNR (const int abs_charge, const float c_snr)
	set charge SNR manually - for FLASHIda log file parsing More...

void	setTargeted ()
	set if it is targeted More...

void	setSecondBestMonsMass (const double mass)
	set second best monoisotopic mass More...

int	getScanNumber () const
	get scan number More...

double	getMonoMass () const
	get monoisotopic mass More...

double	getSecondBestMonoMass () const
	get second best monoisotopic mass More...

double	getIntensity () const
	get intensity More...

float	getChargeSNR (const int abs_charge) const
	get per abs_charge SNR More...

float	getChargeIsotopeCosine (const int abs_charge) const
	get per abs_charge isotope cosine More...

float	getChargeIntensity (const int abs_charge) const
	get per abs_charge intenstiy More...

std::tuple< double, double >	getMaxQScoreMzRange () const
	get mz range that results in max QScore More...

std::tuple< double, double >	getMzRange (int abs_charge) const
	get mz range of the charge More...

std::tuple< int, int >	getAbsChargeRange () const
	get charge range - the actual charge values More...

std::vector< float >	getIsotopeIntensities () const

float	getIsotopeCosine () const
	get isotopic cosine score More...

int	getRepAbsCharge () const
	get representative charge More...

float	getQScore () const
	get Q score More...

float	getSNR () const
	get total SNR More...

float	getChargeScore () const
	get charge score More...

float	getAvgPPMError () const
	get average mass ppm error; More...

bool	isPositive () const
	get if it is positive mode More...

bool	isTargeted () const
	get if it is targeted More...

int	getDecoyIndex () const

void	setDecoyIndex (int index)

float	getQvalue () const

void	setQvalue (const float q)

float	getQvalueWithChargeDecoyOnly () const

float	getQvalueWithIsotopeDecoyOnly () const

float	getQvalueWithNoiseDecoyOnly () const

void	setQvalueWithChargeDecoyOnly (const float q)

void	setQvalueWithIsotopeDecoyOnly (const float q)

void	setQvalueWithNoiseDecoyOnly (const float q)

void	setIsotopeDaDistance (const double d)

double	getIsotopeDaDistance () const

std::vector< FLASHDeconvHelperStructs::LogMzPeak >::const_iterator	begin () const noexcept

std::vector< FLASHDeconvHelperStructs::LogMzPeak >::const_iterator	end () const noexcept

std::vector< FLASHDeconvHelperStructs::LogMzPeak >::iterator	begin () noexcept

std::vector< FLASHDeconvHelperStructs::LogMzPeak >::iterator	end () noexcept

const FLASHDeconvHelperStructs::LogMzPeak &	operator[] (const Size i) const

void	push_back (const FLASHDeconvHelperStructs::LogMzPeak &pg)

Size	size () const noexcept

void	clear ()

void	reserve (Size n)

bool	empty () const

void	swap (std::vector< FLASHDeconvHelperStructs::LogMzPeak > &x)

void	shrink_to_fit ()

void	sort ()

Public Attributes
std::vector< FLASHDeconvHelperStructs::LogMzPeak >	noisy_peaks

Private Types
typedef FLASHDeconvHelperStructs::LogMzPeak	LogMzPeak

typedef FLASHDeconvHelperStructs::PrecalculatedAveragine	PrecalculatedAveragine

Private Member Functions
void	setChargePowers_ (const int abs_charge, const double signal_pwr, const double noise_pwr, const double intensity)
	set per abs_charge signal power More...

void	updateChargeFitScoreAndChargeIntensities_ ()

void	updateAvgPPMError_ (double iso_da_distance)

Private Attributes
std::vector< FLASHDeconvHelperStructs::LogMzPeak >	logMzpeaks_
	log Mz peaks More...

std::vector< float >	per_charge_signal_pwr_
	per charge SNR, isotope cosine, and intensity vectors More...

std::vector< float >	per_charge_pwr_

std::vector< float >	per_charge_cos_

std::vector< float >	per_charge_int_

std::vector< float >	per_charge_snr_

std::vector< float >	per_isotope_int_
	per isotope intensity. More...

double	max_qscore_mz_end_
	mz range resulting in maximum Q score More...

double	max_qscore_mz_start_

int	min_abs_charge_ = 0
	charge range More...

int	max_abs_charge_ = -1

int	scan_number_
	scan number More...

bool	is_positive_
	is positive or not More...

bool	is_targeted_ = false
	if this peak group has been targeted More...

double	monoisotopic_mass_ = -1.0
	information on the deconvolved mass More...

double	second_best_monomass_ = -1.0

double	intensity_

int	decoy_index_ = 0
	index to specify if this peak_group is a target (0), an isotope decoy (1), a noise (2), or a charge decoy (3) More...

double	iso_da_distance_ = Constants::ISOTOPE_MASSDIFF_55K_U
	distance between consecutive isotopes. Can be different for decoys More...

int	max_qscore_abs_charge_ = -1
	scoring variables More...

float	isotope_cosine_score_ = 0

float	charge_score_

float	qscore_ = .0f

float	avg_ppm_error_ = 0

float	snr_ = 0

float	qvalue_ = 1.0

float	qvalue_with_isotope_decoy_only_ = 1.0

float	qvalue_with_noise_decoy_only_ = 1.0

float	qvalue_with_charge_decoy_only_ = 1.0

Detailed Description

Class describing a deconvolved mass. A mass contains multiple peaks of different charges and isotope indices. PeakGroup is the set of such peaks representing a single monoisotopic mass. PeakGroup also contains features that define the quality of it. It is used by QScore calculation DeconvolvedSpectrum consists of PeakGroups.

Member Typedef Documentation

◆ LogMzPeak

typedef FLASHDeconvHelperStructs::LogMzPeak LogMzPeak

private

◆ PrecalculatedAveragine

typedef FLASHDeconvHelperStructs::PrecalculatedAveragine PrecalculatedAveragine

private

Constructor & Destructor Documentation

◆ PeakGroup() [1/4]

PeakGroup ( )

default

default constructor

◆ PeakGroup() [2/4]

PeakGroup	(	const int	min_abs_charge,
		const int	max_abs_charge,
		const bool	is_positive
	)

explicit

Constructor specifying charge range.

Parameters

min_abs_charge	min Charge
max_abs_charge	max Charge
is_positive	whether MS is positive mode

◆ ~PeakGroup()

~PeakGroup ( )

default destructor

◆ PeakGroup() [3/4]

PeakGroup ( const PeakGroup & )

default

copy constructor

◆ PeakGroup() [4/4]

PeakGroup ( PeakGroup && other )

default

move constructor

Member Function Documentation

◆ begin() [1/2]

std::vector<FLASHDeconvHelperStructs::LogMzPeak>::const_iterator begin ( ) const

noexcept

◆ begin() [2/2]

std::vector<FLASHDeconvHelperStructs::LogMzPeak>::iterator begin ( )

noexcept

◆ clear()

void clear ( )

◆ empty()

bool empty ( ) const

◆ end() [1/2]

std::vector<FLASHDeconvHelperStructs::LogMzPeak>::const_iterator end ( ) const

noexcept

◆ end() [2/2]

std::vector<FLASHDeconvHelperStructs::LogMzPeak>::iterator end ( )

noexcept

◆ getAbsChargeRange()

std::tuple<int, int> getAbsChargeRange ( ) const

get charge range - the actual charge values

◆ getAvgPPMError()

float getAvgPPMError ( ) const

get average mass ppm error;

◆ getChargeIntensity()

float getChargeIntensity ( const int abs_charge ) const

get per abs_charge intenstiy

◆ getChargeIsotopeCosine()

float getChargeIsotopeCosine ( const int abs_charge ) const

get per abs_charge isotope cosine

◆ getChargeScore()

float getChargeScore ( ) const

get charge score

◆ getChargeSNR()

float getChargeSNR ( const int abs_charge ) const

get per abs_charge SNR

◆ getDecoyIndex()

int getDecoyIndex ( ) const

◆ getIntensity()

double getIntensity ( ) const

get intensity

◆ getIsotopeCosine()

float getIsotopeCosine ( ) const

get isotopic cosine score

◆ getIsotopeDaDistance()

double getIsotopeDaDistance ( ) const

◆ getIsotopeIntensities()

std::vector<float> getIsotopeIntensities ( ) const

◆ getMaxQScoreMzRange()

std::tuple<double, double> getMaxQScoreMzRange ( ) const

get mz range that results in max QScore

◆ getMonoMass()

double getMonoMass ( ) const

get monoisotopic mass

◆ getMzRange()

std::tuple<double, double> getMzRange ( int abs_charge ) const

get mz range of the charge

◆ getQScore()

float getQScore ( ) const

get Q score

◆ getQvalue()

float getQvalue ( ) const

◆ getQvalueWithChargeDecoyOnly()

float getQvalueWithChargeDecoyOnly ( ) const

◆ getQvalueWithIsotopeDecoyOnly()

float getQvalueWithIsotopeDecoyOnly ( ) const

◆ getQvalueWithNoiseDecoyOnly()

float getQvalueWithNoiseDecoyOnly ( ) const

◆ getRepAbsCharge()

int getRepAbsCharge ( ) const

get representative charge

◆ getScanNumber()

int getScanNumber ( ) const

get scan number

◆ getSecondBestMonoMass()

double getSecondBestMonoMass ( ) const

get second best monoisotopic mass

◆ getSNR()

float getSNR ( ) const

get total SNR

◆ isPositive()

bool isPositive ( ) const

get if it is positive mode

◆ isSignalMZ()

bool isSignalMZ	(	const double	mz,
		const double	tol
	)		const

determine is an mz is a signal of this peakgroup. Input tol is ppm tolerance (e.g., 10.0 for 10ppm tolerance)

◆ isTargeted()

bool isTargeted ( ) const

get if it is targeted

◆ operator<()

bool operator< ( const PeakGroup & a ) const

comparison operators

◆ operator=()

PeakGroup& operator= ( const PeakGroup & t )

default

assignment operator

◆ operator==()

bool operator== ( const PeakGroup & a ) const

◆ operator>()

bool operator> ( const PeakGroup & a ) const

◆ operator[]()

const FLASHDeconvHelperStructs::LogMzPeak& operator[] ( const Size i ) const

◆ push_back()

void push_back ( const FLASHDeconvHelperStructs::LogMzPeak & pg )

◆ recruitAllPeaksInSpectrum()

void recruitAllPeaksInSpectrum	(	const MSSpectrum &	spec,
		const double	tol,
		const FLASHDeconvHelperStructs::PrecalculatedAveragine &	avg,
		double	mono_mass,
		bool	write_detail
	)

recruit peaks and then return as a spectrum.

◆ reserve()

void reserve ( Size n )

◆ setAbsChargeRange()

void setAbsChargeRange	(	const int	min_abs_charge,
		const int	max_abs_charge
	)

set min_abs_charge and max_abs_charge charge range

◆ setAvgPPMError()

void setAvgPPMError ( const float error )

set average mass ppm error

◆ setChargeIsotopeCosine()

void setChargeIsotopeCosine	(	const int	abs_charge,
		const float	cos
	)

set per abs_charge isotope cosine

◆ setChargePowers_()

void setChargePowers_	(	const int	abs_charge,
		const double	signal_pwr,
		const double	noise_pwr,
		const double	intensity
	)

private

set per abs_charge signal power

◆ setChargeScore()

void setChargeScore ( const float charge_score )

set charge score - for FLASHIda log file parsing

◆ setChargeSNR()

void setChargeSNR	(	const int	abs_charge,
		const float	c_snr
	)

set charge SNR manually - for FLASHIda log file parsing

◆ setDecoyIndex()

void setDecoyIndex ( int index )

◆ setIsotopeCosine()

void setIsotopeCosine ( const float cos )

set isotope cosine score

◆ setIsotopeDaDistance()

void setIsotopeDaDistance ( const double d )

◆ setMaxQScoreMzRange()

void setMaxQScoreMzRange	(	const double	min,
		const double	max
	)

set mz range that results in max QScore

◆ setQScore()

void setQScore ( const float qscore )

set Q score - for FLASHIda log file parsing

◆ setQvalue()

void setQvalue ( const float q )

◆ setQvalueWithChargeDecoyOnly()

void setQvalueWithChargeDecoyOnly ( const float q )

◆ setQvalueWithIsotopeDecoyOnly()

void setQvalueWithIsotopeDecoyOnly ( const float q )

◆ setQvalueWithNoiseDecoyOnly()

void setQvalueWithNoiseDecoyOnly ( const float q )

◆ setRepAbsCharge()

void setRepAbsCharge ( const int max_qscore_charge )

set representative max_qscore_charge

◆ setScanNumber()

void setScanNumber ( const int scan_number )

set scan number

◆ setSecondBestMonsMass()

void setSecondBestMonsMass ( const double mass )

set second best monoisotopic mass

◆ setSNR()

void setSNR ( const float snr )

set SNR manually - for FLASHIda log file parsing

◆ setTargeted()

void setTargeted ( )

set if it is targeted

◆ shrink_to_fit()

void shrink_to_fit ( )

◆ size()

Size size ( ) const

noexcept

◆ sort()

void sort ( )

◆ swap()

void swap ( std::vector< FLASHDeconvHelperStructs::LogMzPeak > & x )

◆ updateAvgPPMError_()

void updateAvgPPMError_ ( double iso_da_distance )

private

◆ updateChargeFitScoreAndChargeIntensities_()

void updateChargeFitScoreAndChargeIntensities_ ( )

private

◆ updateIsotopeCosineAndQScore()

void updateIsotopeCosineAndQScore	(	const FLASHDeconvHelperStructs::PrecalculatedAveragine &	avg,
		double	min_cos,
		double	iso_da_distance
	)

◆ updateMonomassAndIsotopeIntensities()

void updateMonomassAndIsotopeIntensities ( )

add monoisotopic indices of peaks by offset and discard negative isotope peaks. Total intensity is also updated

Parameters

offset isotope index offset

◆ updateSNR()

void updateSNR ( )

using signal and total (signal + noise) power, update SNR value

Member Data Documentation

◆ avg_ppm_error_

float avg_ppm_error_ = 0

private

◆ charge_score_

float charge_score_

private

◆ decoy_index_

int decoy_index_ = 0

private

index to specify if this peak_group is a target (0), an isotope decoy (1), a noise (2), or a charge decoy (3)

◆ intensity_

double intensity_

private

◆ is_positive_

bool is_positive_

private

is positive or not

◆ is_targeted_

bool is_targeted_ = false

private

if this peak group has been targeted

◆ iso_da_distance_

double iso_da_distance_ = Constants::ISOTOPE_MASSDIFF_55K_U

private

distance between consecutive isotopes. Can be different for decoys

◆ isotope_cosine_score_

float isotope_cosine_score_ = 0

private

◆ logMzpeaks_

std::vector<FLASHDeconvHelperStructs::LogMzPeak> logMzpeaks_

private

log Mz peaks

◆ max_abs_charge_

int max_abs_charge_ = -1

private

◆ max_qscore_abs_charge_

int max_qscore_abs_charge_ = -1

private

scoring variables

◆ max_qscore_mz_end_

double max_qscore_mz_end_

private

mz range resulting in maximum Q score

◆ max_qscore_mz_start_

double max_qscore_mz_start_

private

◆ min_abs_charge_

int min_abs_charge_ = 0

private

charge range

◆ monoisotopic_mass_

double monoisotopic_mass_ = -1.0

private

information on the deconvolved mass

◆ noisy_peaks

std::vector<FLASHDeconvHelperStructs::LogMzPeak> noisy_peaks

◆ per_charge_cos_

std::vector<float> per_charge_cos_

private

◆ per_charge_int_

std::vector<float> per_charge_int_

private

◆ per_charge_pwr_

std::vector<float> per_charge_pwr_

private

◆ per_charge_signal_pwr_

std::vector<float> per_charge_signal_pwr_

private

per charge SNR, isotope cosine, and intensity vectors

◆ per_charge_snr_

std::vector<float> per_charge_snr_

private

◆ per_isotope_int_

std::vector<float> per_isotope_int_

private

per isotope intensity.

◆ qscore_

float qscore_ = .0f

private

◆ qvalue_

float qvalue_ = 1.0

private

◆ qvalue_with_charge_decoy_only_

float qvalue_with_charge_decoy_only_ = 1.0

private

◆ qvalue_with_isotope_decoy_only_

float qvalue_with_isotope_decoy_only_ = 1.0

private

◆ qvalue_with_noise_decoy_only_

float qvalue_with_noise_decoy_only_ = 1.0

private

◆ scan_number_

int scan_number_

private

scan number

◆ second_best_monomass_

double second_best_monomass_ = -1.0

private

◆ snr_

float snr_ = 0

private

Public Member Functions

Public Attributes

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ LogMzPeak

◆ PrecalculatedAveragine

Constructor & Destructor Documentation

◆ PeakGroup() [1/4]

◆ PeakGroup() [2/4]

◆ ~PeakGroup()

◆ PeakGroup() [3/4]

◆ PeakGroup() [4/4]

Member Function Documentation

◆ begin() [1/2]

◆ begin() [2/2]

◆ clear()

◆ empty()

◆ end() [1/2]

◆ end() [2/2]

◆ getAbsChargeRange()

◆ getAvgPPMError()

◆ getChargeIntensity()

◆ getChargeIsotopeCosine()

◆ getChargeScore()

◆ getChargeSNR()

◆ getDecoyIndex()

◆ getIntensity()

◆ getIsotopeCosine()

◆ getIsotopeDaDistance()

◆ getIsotopeIntensities()

◆ getMaxQScoreMzRange()

◆ getMonoMass()

◆ getMzRange()

◆ getQScore()

◆ getQvalue()

◆ getQvalueWithChargeDecoyOnly()

◆ getQvalueWithIsotopeDecoyOnly()

◆ getQvalueWithNoiseDecoyOnly()

◆ getRepAbsCharge()

◆ getScanNumber()

◆ getSecondBestMonoMass()

◆ getSNR()

◆ isPositive()

◆ isSignalMZ()

◆ isTargeted()

◆ operator<()

◆ operator=()

◆ operator==()

◆ operator>()

◆ operator[]()

◆ push_back()

◆ recruitAllPeaksInSpectrum()

◆ reserve()

◆ setAbsChargeRange()

◆ setAvgPPMError()

◆ setChargeIsotopeCosine()

◆ setChargePowers_()

◆ setChargeScore()

◆ setChargeSNR()

◆ setDecoyIndex()

◆ setIsotopeCosine()

◆ setIsotopeDaDistance()

◆ setMaxQScoreMzRange()

◆ setQScore()

◆ setQvalue()

◆ setQvalueWithChargeDecoyOnly()

◆ setQvalueWithIsotopeDecoyOnly()

◆ setQvalueWithNoiseDecoyOnly()

◆ setRepAbsCharge()

◆ setScanNumber()

◆ setSecondBestMonsMass()

◆ setSNR()

◆ setTargeted()

◆ shrink_to_fit()

◆ size()

◆ sort()

◆ swap()