PeakGroup Class Reference

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:

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

Public Member Functions
	PeakGroup ()=default
	default constructor
	PeakGroup (int min_abs_charge, int max_abs_charge, bool is_positive)
	Constructor specifying charge range.
	~PeakGroup ()=default
	default destructor
	PeakGroup (const PeakGroup &)=default
	copy constructor
	PeakGroup (PeakGroup &&other)=default
	move constructor
bool	operator< (const PeakGroup &a) const
	comparison operators
bool	operator> (const PeakGroup &a) const
bool	operator== (const PeakGroup &a) const
PeakGroup &	operator= (const PeakGroup &t)=default
	assignment operator
void	updateMonoMassAndIsotopeIntensities (double tol)
	add monoisotopic indices of peaks by offset and discard negative isotope peaks. Total intensity is also updated
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.
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.
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.
void	setScanNumber (int scan_number)
	set scan number
void	setChargeIsotopeCosine (int abs_charge, float cos)
	set per abs_charge isotope cosine
void	setAbsChargeRange (int min_abs_charge, int max_abs_charge)
	set min_abs_charge and max_abs_charge charge range
void	setIsotopeCosine (float cos)
	set isotope cosine score
void	setRepAbsCharge (int max_snr_abs_charge)
	set representative max_snr_abs_charge
void	setMonoisotopicMass (double mono_mass)
	set monoisotopic mass
void	setQscore (double qscore)
	set Qscore - for FLASHIda log file parsing
void	setChargeScore (float charge_score)
	set charge score - for FLASHIda log file parsing
void	setAvgPPMError (float error)
	set average mass ppm error
void	setSNR (float snr)
	set SNR manually - for FLASHIda log file parsing
void	setChargeSNR (int abs_charge, float c_snr)
	set charge SNR manually - for FLASHIda log file parsing
void	setTargeted ()
	set if it is targeted
int	getScanNumber () const
	get scan number
double	getMonoMass () const
	get monoisotopic mass
float	getIntensity () const
	get intensity
float	getChargeSNR (int abs_charge) const
	get per abs_charge SNR
float	getChargeIsotopeCosine (int abs_charge) const
	get per abs_charge isotope cosine
float	getChargeIntensity (int abs_charge) const
	get per abs_charge intenstiy
std::tuple< double, double >	getRepMzRange () const
	get mz range that results in max setQscore
std::tuple< double, double >	getMzRange (int abs_charge) const
	get mz range of the charge
std::tuple< int, int >	getAbsChargeRange () const
	get charge range - the actual charge values
const std::vector< float > &	getIsotopeIntensities () const
	get per isotope intensities
float	getIsotopeCosine () const
	get isotopic cosine score
float	getPeakOccupancy () const
	get the density of the peaks within charge and isotope range
int	getRepAbsCharge () const
	get representative charge
double	getQscore () const
	Get the one-dimensional quality score for this peak group.
double	getQscore2D () const
	Get the two-dimensional quality score incorporating feature-level information.
float	getSNR () const
	get total SNR
float	getChargeScore () const
	get charge score
float	getAvgPPMError () const
	get average mass ppm error;
float	getAvgDaError () const
	get average mass ppm error;
bool	isPositive () const
	get if it is positive mode
bool	isTargeted () const
	get if it is targeted
PeakGroup::TargetDecoyType	getTargetDecoyType () const
	get the target decoy type of this
void	setTargetDecoyType (PeakGroup::TargetDecoyType index)
	for this PeakGroup, specify the target decoy type.
float	getQvalue () const
void	setQvalue (double q)
void	setIsotopeDaDistance (double d)
	set distance between consecutive isotopes
double	getIsotopeDaDistance () const
	get distance between consecutive isotopes
int	getMinNegativeIsotopeIndex () const
	get minimum neagative isotope index
void	setIndex (uint i)
	set index of this peak group
void	setQscore2D (double fqscore)
	Set the two-dimensional quality score for this peak group.
void	setFeatureIndex (uint findex)
	Set the feature index for this peak group.
uint	getIndex () const
	get index of this peak group
uint	getFeatureIndex () const
	Get the feature index associated with this peak group.
std::vector< FLASHHelperClasses::LogMzPeak >::const_iterator	begin () const noexcept
	iterators for the signal LogMz peaks in this PeakGroup
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.
void	push_back (const FLASHHelperClasses::LogMzPeak &pg)
	vector operators for the LogMzPeaks in this PeakGroup
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).

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.
void	updateAvgMassError_ ()
	update avg ppm error
float	getPPMError_ (const LogMzPeak &p) const
	update avg Da error
float	getDaError_ (const LogMzPeak &p) const
	get Da error of a logMzPeak from the closest isotope
void	updateSNR_ (float mul_factor)
	using signal and total (signal + noise) power, update SNR value
void	clear_ ()
	clear peaks
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
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
void	updateChargeRange_ ()
	update the charge range using the calculated per charge information
void	updatePerChargeCos_ (const FLASHHelperClasses::PrecalculatedAveragine &avg, double tol)
	update per charge cosine values
float	getNoisePeakPower_ (const std::vector< LogMzPeak > &noisy_peaks, int z, double tol) const

Private Attributes
std::vector< FLASHHelperClasses::LogMzPeak >	logMzpeaks_
	log Mz peaks
std::vector< FLASHHelperClasses::LogMzPeak >	negative_iso_peaks_
	negative isotope index peaks
std::vector< float >	per_charge_sum_signal_squared_
	per charge summed signal squared, noise pwr, SNR, isotope cosine, and intensity vectors
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.
int	min_abs_charge_ = 0
	charge range
int	max_abs_charge_ = -1
uint	index_ = 0
	peak group index
uint	findex_ = 0
	feature index in which this peak group is included. 0 if not included in any feature
int	scan_number_ = 0
	scan number
bool	is_positive_ = false
	is positive or not
bool	is_targeted_ = false
	if this peak group has been targeted
double	monoisotopic_mass_ = -1.0
	monoisotopic mass
float	intensity_ = 0.f
	summed intensity
PeakGroup::TargetDecoyType	target_decoy_type_ = target
	index to specify if this peak_group is a target, a noise, or a signal decoy.
int	min_negative_isotope_index_ = -1
double	iso_da_distance_ = Constants::ISOTOPE_MASSDIFF_55K_U
	distance between consecutive isotopes. Can be different for decoys
int	max_snr_abs_charge_ = -1
float	isotope_cosine_score_ = 0.f
	cosine score between averagine and the observed isotope pattern
float	charge_score_ = 0.f
	charge fit score
double	qscore_ = .0
	quality score
double	qscore2D_ = -1.0f
	quality score when considering correlation between masses within the same feature.
float	avg_ppm_error_ = 0.f
float	avg_da_error_ = 0.f
float	snr_ = 0.f
	total SNR
float	qvalue_ = 1.f
	q value, only active when FDR report is activated.

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

[in]	min_abs_charge	min Charge
[in]	max_abs_charge	max Charge
[in]	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

[in]	spec	Raw spectrum to extract features from.
[in]	charge_count	Number of charges to include in the feature vector.
[in]	isotope_count	Number of isotopes to include in the feature vector.
[in]	avg	Precalculated averagine model for theoretical isotope patterns.
[in]	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

[in]

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

[in]	noisy_peaks	noisy peaks to calculate power
[in]	z	charge
[in]	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

[in]	spec	raw spectrum
[in]	tol	ppm tolerance
[in]	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

[in]	spec	raw spectrum
[in]	tol	ppm tolerance
[in]	avg	precalculated averagine
[in]	mono_mass	monoisotopic mass
[in]	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

[in]

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

[in]

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

[in]	noisy_peaks	noisy peaks to calculate setQscore
[in]	avg	precalculated averagine
[in]	min_cos	the peak groups with cosine score less than this will have setQscore 0.
[in]	tol	ppm tolerance
[in]	is_low_charge	if set, charge fit score calculation becomes less stroct
[in]	excluded_masses	masses to exclude
[in]	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.