Class describing a deconvolved mass. A mass contains multiple (LogMz) 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 for PeakGroupScoring calculation. DeconvolvedSpectrum consists of PeakGroups. More...

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

Collaboration diagram for PeakGroup:

[legend]

Public Types
enum	TargetDecoyType { target = 0 , noise_decoy , signal_decoy }

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

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

	~PeakGroup ()=default
	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 (double tol)
	add monoisotopic indices of peaks by offset and discard negative isotope peaks. Total intensity is also updated More...

int	updateQscore (const std::vector< LogMzPeak > &noisy_peaks, const FLASHHelperClasses::PrecalculatedAveragine &avg, double min_cos, double tol, bool is_low_charge, const std::vector< double > &excluded_masses, bool is_last=false)
	Update setQscore. Cosine and SNRs are also updated. More...

std::vector< LogMzPeak >	recruitAllPeaksInSpectrum (const MSSpectrum &spec, double tol, const FLASHHelperClasses::PrecalculatedAveragine &avg, double mono_mass, bool renew_signal_peaks=true)
	given a monoisotopic mass, recruit raw peaks from the raw input spectrum and add to this peakGroup. This is a bit time-consuming and is done for only a small number of selected high-quality peakgroups. More...

std::vector< LogMzPeak >	getNoisyPeaks (const MSSpectrum &spec, double tol, const FLASHHelperClasses::PrecalculatedAveragine &avg) const
	Get noisy peaks for this PeakGroup without modifying any state (const-safe). This is a const alternative to recruitAllPeaksInSpectrum(..., false) for use in output/write functions. More...

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

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

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

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

void	setRepAbsCharge (int max_snr_abs_charge)
	set representative max_snr_abs_charge More...

void	setMonoisotopicMass (double mono_mass)
	set monoisotopic mass More...

void	setQscore (double qscore)
	set Qscore - for FLASHIda log file parsing More...

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

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

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

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

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

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

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

float	getIntensity () const
	get intensity More...

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

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

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

std::tuple< double, double >	getRepMzRange () const
	get mz range that results in max setQscore 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...

const std::vector< float > &	getIsotopeIntensities () const
	get per isotope intensities More...

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

float	getPeakOccupancy () const
	get the density of the peaks within charge and isotope range More...

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

double	getQscore () const
	Get the one-dimensional quality score for this peak group. More...

double	getQscore2D () const
	Get the two-dimensional quality score incorporating feature-level information. More...

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

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

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

float	getAvgDaError () 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...

PeakGroup::TargetDecoyType	getTargetDecoyType () const
	get the target decoy type of this More...

void	setTargetDecoyType (PeakGroup::TargetDecoyType index)
	for this PeakGroup, specify the target decoy type. More...

float	getQvalue () const

void	setQvalue (double q)

void	setIsotopeDaDistance (double d)
	set distance between consecutive isotopes More...

double	getIsotopeDaDistance () const
	get distance between consecutive isotopes More...

int	getMinNegativeIsotopeIndex () const
	get minimum neagative isotope index More...

void	setIndex (uint i)
	set index of this peak group More...

void	setQscore2D (double fqscore)
	Set the two-dimensional quality score for this peak group. More...

void	setFeatureIndex (uint findex)
	Set the feature index for this peak group. More...

uint	getIndex () const
	get index of this peak group More...

uint	getFeatureIndex () const
	Get the feature index associated with this peak group. More...

std::vector< FLASHHelperClasses::LogMzPeak >::const_iterator	begin () const noexcept
	iterators for the signal LogMz peaks in this PeakGroup More...

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

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

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

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

std::vector< float >	getMassErrors (bool ppm=true) const
	Get mass errors for each isotope index in this peak group. More...

void	push_back (const FLASHHelperClasses::LogMzPeak &pg)
	vector operators for the LogMzPeaks in this PeakGroup More...

FLASHHelperClasses::LogMzPeak &	back ()

Size	size () const noexcept

void	reserve (Size n)

bool	empty () const

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

void	sort ()

std::tuple< std::vector< double >, std::vector< double > >	getDLVector (const MSSpectrum &spec, const Size charge_count, const Size isotope_count, const FLASHHelperClasses::PrecalculatedAveragine &avg, double tol)
	Get deep learning feature vectors (signal and noise). More...

Private Types
typedef FLASHHelperClasses::LogMzPeak	LogMzPeak

typedef FLASHHelperClasses::PrecalculatedAveragine	PrecalculatedAveragine

Private Member Functions
void	updateChargeFitScoreAndChargeIntensities_ (bool is_low_charge)
	update chargefit score and also update per charge intensities here. More...

void	updateAvgMassError_ ()
	update avg ppm error More...

float	getPPMError_ (const LogMzPeak &p) const
	update avg Da error More...

float	getDaError_ (const LogMzPeak &p) const
	get Da error of a logMzPeak from the closest isotope More...

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

void	clear_ ()
	clear peaks More...

void	getPerIsotopeIntensities_ (std::vector< float > &intensities, int &min_isotope_index, int &max_isotope_index, int abs_charge, int min_negative_isotope_index, double tol)
	calculate per isotope intensities. When abs_charge == 0, all peaks are considered More...

void	updatePerChargeInformation_ (const std::vector< LogMzPeak > &noisy_peaks, double tol, bool is_last)
	update per charge intensities, noise power, and squared intensities. used for SNR estimation More...

void	updateChargeRange_ ()
	update the charge range using the calculated per charge information More...

void	updatePerChargeCos_ (const FLASHHelperClasses::PrecalculatedAveragine &avg, double tol)
	update per charge cosine values More...

float	getNoisePeakPower_ (const std::vector< LogMzPeak > &noisy_peaks, int z, double tol) const

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

std::vector< FLASHHelperClasses::LogMzPeak >	negative_iso_peaks_
	negative isotope index peaks More...

std::vector< float >	per_charge_sum_signal_squared_
	per charge summed signal squared, noise pwr, SNR, isotope cosine, and intensity vectors More...

std::vector< float >	per_charge_noise_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...

int	min_abs_charge_ = 0
	charge range More...

int	max_abs_charge_ = -1

uint	index_ = 0
	peak group index More...

uint	findex_ = 0
	feature index in which this peak group is included. 0 if not included in any feature More...

int	scan_number_ = 0
	scan number More...

bool	is_positive_ = false
	is positive or not More...

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

double	monoisotopic_mass_ = -1.0
	monoisotopic mass More...

float	intensity_ = 0.f
	summed intensity More...

PeakGroup::TargetDecoyType	target_decoy_type_ = target
	index to specify if this peak_group is a target, a noise, or a signal decoy. More...

int	min_negative_isotope_index_ = -1

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

int	max_snr_abs_charge_ = -1

float	isotope_cosine_score_ = 0.f
	cosine score between averagine and the observed isotope pattern More...

float	charge_score_ = 0.f
	charge fit score More...

double	qscore_ = .0
	quality score More...

double	qscore2D_ = -1.0f
	quality score when considering correlation between masses within the same feature. More...

float	avg_ppm_error_ = 0.f

float	avg_da_error_ = 0.f

float	snr_ = 0.f
	total SNR More...

float	qvalue_ = 1.f
	q value, only active when FDR report is activated. More...

Detailed Description

Class describing a deconvolved mass. A mass contains multiple (LogMz) 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 for PeakGroupScoring calculation. DeconvolvedSpectrum consists of PeakGroups.

Member Typedef Documentation

◆ LogMzPeak

typedef FLASHHelperClasses::LogMzPeak LogMzPeak

private

◆ PrecalculatedAveragine

typedef FLASHHelperClasses::PrecalculatedAveragine PrecalculatedAveragine

private

Member Enumeration Documentation

◆ TargetDecoyType

enum TargetDecoyType

target decoy type of PeakGroup. This specifies if a PeakGroup is a target (0), noise decoy (1),or signal decoy (2)

Enumerator
target
noise_decoy
signal_decoy

Constructor & Destructor Documentation

◆ PeakGroup() [1/4]

PeakGroup ( )

default

default constructor

◆ PeakGroup() [2/4]

PeakGroup	(	int	min_abs_charge,
		int	max_abs_charge,
		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

default destructor

◆ PeakGroup() [3/4]

PeakGroup ( const PeakGroup & )

default

copy constructor

◆ PeakGroup() [4/4]

PeakGroup ( PeakGroup && other )

default

move constructor

Member Function Documentation

◆ back()

FLASHHelperClasses::LogMzPeak& back ( )

◆ begin() [1/2]

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

noexcept

iterators for the signal LogMz peaks in this PeakGroup

◆ begin() [2/2]

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

noexcept

◆ clear_()

void clear_ ( )

private

clear peaks

◆ empty()

bool empty ( ) const

◆ end() [1/2]

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

noexcept

◆ end() [2/2]

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

noexcept

◆ getAbsChargeRange()

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

get charge range - the actual charge values

◆ getAvgDaError()

float getAvgDaError ( ) const

get average mass ppm error;

◆ getAvgPPMError()

float getAvgPPMError ( ) const

get average mass ppm error;

◆ getChargeIntensity()

float getChargeIntensity ( int abs_charge ) const

get per abs_charge intenstiy

◆ getChargeIsotopeCosine()

float getChargeIsotopeCosine ( int abs_charge ) const

get per abs_charge isotope cosine

◆ getChargeScore()

float getChargeScore ( ) const

get charge score

◆ getChargeSNR()

float getChargeSNR ( int abs_charge ) const

get per abs_charge SNR

◆ getDaError_()

float getDaError_ ( const LogMzPeak & p ) const

private

get Da error of a logMzPeak from the closest isotope

◆ getDLVector()

std::tuple<std::vector<double>, std::vector<double> > getDLVector	(	const MSSpectrum &	spec,
		const Size	charge_count,
		const Size	isotope_count,
		const FLASHHelperClasses::PrecalculatedAveragine &	avg,
		double	tol
	)

Get deep learning feature vectors (signal and noise).

Parameters

spec	Raw spectrum to extract features from.
charge_count	Number of charges to include in the feature vector.
isotope_count	Number of isotopes to include in the feature vector.
avg	Precalculated averagine model for theoretical isotope patterns.
tol	Tolerance in ppm for peak matching.

Returns: Tuple of (signal_vector, noise_vector) for ML model input.

◆ getFeatureIndex()

uint getFeatureIndex ( ) const

Get the feature index associated with this peak group.

The feature index identifies which traced feature (isotope pattern across multiple scans) this peak group belongs to.

Returns: The feature index. Returns 0 if no feature has been assigned (default initialization).

◆ getIndex()

uint getIndex ( ) const

get index of this peak group

◆ getIntensity()

float getIntensity ( ) const

get intensity

◆ getIsotopeCosine()

float getIsotopeCosine ( ) const

get isotopic cosine score

◆ getIsotopeDaDistance()

double getIsotopeDaDistance ( ) const

get distance between consecutive isotopes

◆ getIsotopeIntensities()

const std::vector<float>& getIsotopeIntensities ( ) const

get per isotope intensities

◆ getMassErrors()

std::vector<float> getMassErrors ( bool ppm = true ) const

Get mass errors for each isotope index in this peak group.

Calculates the average mass error for peaks at each isotope index, comparing observed masses to theoretical masses from the averagine model.

Parameters

ppm	If true (default), returns errors in parts-per-million (ppm). If false, returns errors in Daltons (Da).

Returns: Vector of average mass errors, one per unique isotope index present in the peak group. Returns an empty vector if no peaks are present.

◆ getMinNegativeIsotopeIndex()

int getMinNegativeIsotopeIndex ( ) const

get minimum neagative isotope index

◆ getMonoMass()

double getMonoMass ( ) const

get monoisotopic mass

◆ getMzRange()

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

get mz range of the charge

◆ getNoisePeakPower_()

float getNoisePeakPower_	(	const std::vector< LogMzPeak > &	noisy_peaks,
		int	z,
		double	tol
	)		const

private

calculate noisy peak power. The goal of this function is to group noisy peaks that are possibly from the same molecule and sum their intensities before calculate power

Parameters

noisy_peaks	noisy peaks to calculate power
z	charge
tol	ppm tolerance

Returns: calculated noise power

◆ getNoisyPeaks()

std::vector<LogMzPeak> getNoisyPeaks	(	const MSSpectrum &	spec,
		double	tol,
		const FLASHHelperClasses::PrecalculatedAveragine &	avg
	)		const

Get noisy peaks for this PeakGroup without modifying any state (const-safe). This is a const alternative to recruitAllPeaksInSpectrum(..., false) for use in output/write functions.

Parameters

spec	raw spectrum
tol	ppm tolerance
avg	precalculated averagine

Returns: returns the noisy peaks - raw peaks within range that don't match the isotope pattern

◆ getPeakOccupancy()

float getPeakOccupancy ( ) const

get the density of the peaks within charge and isotope range

Get the density of peaks within charge and isotope range.

Returns: Peak occupancy value (0-1) representing the fraction of expected peaks that are present

◆ getPerIsotopeIntensities_()

void getPerIsotopeIntensities_	(	std::vector< float > &	intensities,
		int &	min_isotope_index,
		int &	max_isotope_index,
		int	abs_charge,
		int	min_negative_isotope_index,
		double	tol
	)

private

calculate per isotope intensities. When abs_charge == 0, all peaks are considered

◆ getPPMError_()

float getPPMError_ ( const LogMzPeak & p ) const

private

update avg Da error

◆ getQscore()

double getQscore ( ) const

Get the one-dimensional quality score for this peak group.

The Q-score represents the confidence/quality of the peak group based on isotope pattern matching, charge state consistency, and signal-to-noise ratio.

Returns: Quality score in range [0, 1], where higher values indicate better quality. Returns 0.0 if the score has not been calculated (default initialization).

◆ getQscore2D()

double getQscore2D ( ) const

Get the two-dimensional quality score incorporating feature-level information.

The 2D Q-score extends the 1D score by incorporating additional dimensions such as retention time consistency, ion mobility correlation, or MS1-MS2 relationship. This score is typically set after feature tracing/grouping across scans.

Returns: The maximum of the 1D Q-score and the 2D Q-score, in range [0, 1]. If the 2D score has not been set (initialized to -1.0), effectively returns the 1D Q-score.

◆ getQvalue()

float getQvalue ( ) const

Get q value

◆ getRepAbsCharge()

int getRepAbsCharge ( ) const

get representative charge

◆ getRepMzRange()

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

get mz range that results in max setQscore

◆ getScanNumber()

int getScanNumber ( ) const

get scan number

◆ getSNR()

float getSNR ( ) const

get total SNR

◆ getTargetDecoyType()

PeakGroup::TargetDecoyType getTargetDecoyType ( ) const

get the target decoy type of this

◆ isPositive()

bool isPositive ( ) const

get if it is positive mode

◆ 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 FLASHHelperClasses::LogMzPeak& operator[] ( Size i ) const

◆ push_back()

void push_back ( const FLASHHelperClasses::LogMzPeak & pg )

vector operators for the LogMzPeaks in this PeakGroup

◆ recruitAllPeaksInSpectrum()

std::vector<LogMzPeak> recruitAllPeaksInSpectrum	(	const MSSpectrum &	spec,
		double	tol,
		const FLASHHelperClasses::PrecalculatedAveragine &	avg,
		double	mono_mass,
		bool	renew_signal_peaks = `true`
	)

given a monoisotopic mass, recruit raw peaks from the raw input spectrum and add to this peakGroup. This is a bit time-consuming and is done for only a small number of selected high-quality peakgroups.

Parameters

spec	raw spectrum
tol	ppm tolerance
avg	precalculated averagine
mono_mass	monoisotopic mass
renew_signal_peaks	Whether or not the signal peaks should be renewed during recruitment

Returns: returns the noisy peaks for this peakgroup - i.e., the raw peaks within the range of this peakGroup that are not matched to any istope of this peakGroup mass.

◆ reserve()

void reserve ( Size n )

◆ setAbsChargeRange()

void setAbsChargeRange	(	int	min_abs_charge,
		int	max_abs_charge
	)

set min_abs_charge and max_abs_charge charge range

◆ setAvgPPMError()

void setAvgPPMError ( float error )

set average mass ppm error

◆ setChargeIsotopeCosine()

void setChargeIsotopeCosine	(	int	abs_charge,
		float	cos
	)

set per abs_charge isotope cosine

◆ setChargeScore()

void setChargeScore ( float charge_score )

set charge score - for FLASHIda log file parsing

◆ setChargeSNR()

void setChargeSNR	(	int	abs_charge,
		float	c_snr
	)

set charge SNR manually - for FLASHIda log file parsing

◆ setFeatureIndex()

void setFeatureIndex ( uint findex )

Set the feature index for this peak group.

Associates this peak group with a feature (traced isotope pattern across scans).

Parameters

findex The feature index to assign to this peak group.

◆ setIndex()

void setIndex ( uint i )

set index of this peak group

◆ setIsotopeCosine()

void setIsotopeCosine ( float cos )

set isotope cosine score

◆ setIsotopeDaDistance()

void setIsotopeDaDistance ( double d )

set distance between consecutive isotopes

◆ setMonoisotopicMass()

void setMonoisotopicMass ( double mono_mass )

set monoisotopic mass

◆ setQscore()

void setQscore ( double qscore )

set Qscore - for FLASHIda log file parsing

◆ setQscore2D()

void setQscore2D ( double fqscore )

Set the two-dimensional quality score for this peak group.

The 2D Q-score incorporates feature-level information such as retention time consistency or ion mobility correlation across multiple scans.

Parameters

fqscore The 2D quality score to set, typically in range [0, 1].

◆ setQvalue()

void setQvalue ( double q )

set peakGroup q value

◆ setRepAbsCharge()

void setRepAbsCharge ( int max_snr_abs_charge )

set representative max_snr_abs_charge

◆ setScanNumber()

void setScanNumber ( int scan_number )

set scan number

◆ setSNR()

void setSNR ( float snr )

set SNR manually - for FLASHIda log file parsing

◆ setTargetDecoyType()

void setTargetDecoyType ( PeakGroup::TargetDecoyType index )

for this PeakGroup, specify the target decoy type.

◆ setTargeted()

void setTargeted ( )

set if it is targeted

◆ size()

Size size ( ) const

noexcept

◆ sort()

void sort ( )

◆ swap()

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

◆ updateAvgMassError_()

void updateAvgMassError_ ( )

private

update avg ppm error

◆ updateChargeFitScoreAndChargeIntensities_()

void updateChargeFitScoreAndChargeIntensities_ ( bool is_low_charge )

private

update chargefit score and also update per charge intensities here.

◆ updateChargeRange_()

void updateChargeRange_ ( )

private

update the charge range using the calculated per charge information

◆ updateMonoMassAndIsotopeIntensities()

void updateMonoMassAndIsotopeIntensities ( double tol )

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

◆ updatePerChargeCos_()

void updatePerChargeCos_	(	const FLASHHelperClasses::PrecalculatedAveragine &	avg,
		double	tol
	)

private

update per charge cosine values

◆ updatePerChargeInformation_()

void updatePerChargeInformation_	(	const std::vector< LogMzPeak > &	noisy_peaks,
		double	tol,
		bool	is_last
	)

private

update per charge intensities, noise power, and squared intensities. used for SNR estimation

◆ updateQscore()

int updateQscore	(	const std::vector< LogMzPeak > &	noisy_peaks,
		const FLASHHelperClasses::PrecalculatedAveragine &	avg,
		double	min_cos,
		double	tol,
		bool	is_low_charge,
		const std::vector< double > &	excluded_masses,
		bool	is_last = `false`
	)

Update setQscore. Cosine and SNRs are also updated.

Parameters

noisy_peaks	noisy peaks to calculate setQscore
avg	precalculated averagine
min_cos	the peak groups with cosine score less than this will have setQscore 0.
tol	ppm tolerance
is_low_charge	if set, charge fit score calculation becomes less stroct
excluded_masses	masses to exclude
is_last	if this is set, it means that PeakGroupScoring calculation is at its last iteration. More detailed noise power calculation is activated and mono mass is not recalibrated.

Returns: returns isotope offset after isotope cosine calculation

◆ updateSNR_()

void updateSNR_ ( float mul_factor )

private

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

Member Data Documentation

◆ avg_da_error_

float avg_da_error_ = 0.f

private

◆ avg_ppm_error_

float avg_ppm_error_ = 0.f

private

◆ charge_score_

float charge_score_ = 0.f

private

charge fit score

◆ findex_

uint findex_ = 0

private

feature index in which this peak group is included. 0 if not included in any feature

◆ index_

uint index_ = 0

private

peak group index

◆ intensity_

float intensity_ = 0.f

private

summed intensity

◆ is_positive_

bool is_positive_ = false

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.f

private

cosine score between averagine and the observed isotope pattern

◆ logMzpeaks_

std::vector<FLASHHelperClasses::LogMzPeak> logMzpeaks_

private

log Mz peaks

◆ max_abs_charge_

int max_abs_charge_ = -1

private

◆ max_snr_abs_charge_

int max_snr_abs_charge_ = -1

private

scoring variables the charge for which the charge SNR is maximized

◆ min_abs_charge_

int min_abs_charge_ = 0

private

charge range

◆ min_negative_isotope_index_

int min_negative_isotope_index_ = -1

private

up to which negative isotope index should be considered for isotope pattern matching. By considering negative isotopes, one can reduce isotope index error.

◆ monoisotopic_mass_

double monoisotopic_mass_ = -1.0

private

monoisotopic mass

◆ negative_iso_peaks_

std::vector<FLASHHelperClasses::LogMzPeak> negative_iso_peaks_

private

negative isotope index peaks

◆ per_charge_cos_

std::vector<float> per_charge_cos_

private

◆ per_charge_int_

std::vector<float> per_charge_int_

private

◆ per_charge_noise_pwr_

std::vector<float> per_charge_noise_pwr_

private

◆ per_charge_snr_

std::vector<float> per_charge_snr_

private

◆ per_charge_sum_signal_squared_

std::vector<float> per_charge_sum_signal_squared_

private

per charge summed signal squared, noise pwr, SNR, isotope cosine, and intensity vectors

◆ per_isotope_int_

std::vector<float> per_isotope_int_

private

per isotope intensity.

◆ qscore2D_

double qscore2D_ = -1.0f

private

quality score when considering correlation between masses within the same feature.

◆ qscore_

double qscore_ = .0

private

quality score

◆ qvalue_

float qvalue_ = 1.f

private

q value, only active when FDR report is activated.

◆ scan_number_

int scan_number_ = 0

private

scan number

◆ snr_

float snr_ = 0.f

private

total SNR

◆ target_decoy_type_

PeakGroup::TargetDecoyType target_decoy_type_ = target

private

index to specify if this peak_group is a target, a noise, or a signal decoy.

Public Types

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ LogMzPeak

◆ PrecalculatedAveragine

Member Enumeration Documentation

◆ TargetDecoyType

Constructor & Destructor Documentation

◆ PeakGroup() [1/4]

◆ PeakGroup() [2/4]

◆ ~PeakGroup()

◆ PeakGroup() [3/4]

◆ PeakGroup() [4/4]

Member Function Documentation

◆ back()

◆ begin() [1/2]

◆ begin() [2/2]

◆ clear_()

◆ empty()

◆ end() [1/2]

◆ end() [2/2]

◆ getAbsChargeRange()

◆ getAvgDaError()

◆ getAvgPPMError()

◆ getChargeIntensity()

◆ getChargeIsotopeCosine()

◆ getChargeScore()

◆ getChargeSNR()

◆ getDaError_()

◆ getDLVector()

◆ getFeatureIndex()

◆ getIndex()

◆ getIntensity()

◆ getIsotopeCosine()

◆ getIsotopeDaDistance()

◆ getIsotopeIntensities()

◆ getMassErrors()

◆ getMinNegativeIsotopeIndex()

◆ getMonoMass()

◆ getMzRange()

◆ getNoisePeakPower_()

◆ getNoisyPeaks()

◆ getPeakOccupancy()

◆ getPerIsotopeIntensities_()

◆ getPPMError_()

◆ getQscore()

◆ getQscore2D()

◆ getQvalue()

◆ getRepAbsCharge()

◆ getRepMzRange()

◆ getScanNumber()

◆ getSNR()

◆ getTargetDecoyType()

◆ isPositive()

◆ isTargeted()

◆ operator<()

◆ operator=()

◆ operator==()

◆ operator>()

◆ operator[]()

◆ push_back()

◆ recruitAllPeaksInSpectrum()

◆ reserve()

◆ setAbsChargeRange()

◆ setAvgPPMError()

◆ setChargeIsotopeCosine()

◆ setChargeScore()

◆ setChargeSNR()

◆ setFeatureIndex()

◆ setIndex()

◆ setIsotopeCosine()

◆ setIsotopeDaDistance()

◆ setMonoisotopicMass()

◆ setQscore()

◆ setQscore2D()

◆ setQvalue()