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 by QScore calculation. DeconvolvedSpectrum consists of PeakGroups. More...

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

Public Types
enum	DecoyFlag { target = 0, charge_decoy, noise_decoy, isotope_decoy }
	decoy flag. This flag specifies if a PeakGroup is a target, charge decoy, noise decoy, or isotope decoy. More...

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

void	updateIsotopeCosineSNRAvgErrorAndQScore (const FLASHDeconvHelperStructs::PrecalculatedAveragine &avg, double min_cos)
	Update isotope cosine sore and qscore. Mono mass is also updated one last time. SNR, per charge SNR, and avg errors are updated here. More...

std::vector< LogMzPeak >	recruitAllPeaksInSpectrum (const MSSpectrum &spec, double tol, const FLASHDeconvHelperStructs::PrecalculatedAveragine &avg, double mono_mass, const std::unordered_set< int > &excluded_integer_mzs_, int charge_offset=0, double charge_multiple=1.0, double mz_off=.0)
	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...

bool	isSignalMZ (double mz, 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). Assume logMzPeaks are sorted. 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_qscore_charge)
	set representative max_qscore_charge More...

void	setQScore (float qscore)
	set Q score - 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 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...

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

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...

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::DecoyFlag	getDecoyFlag () const
	get the decoy flag of this More...

void	setDecoyFlag (PeakGroup::DecoyFlag index)
	for this PeakGroup, specify the decoy flag. More...

float	getQvalue (PeakGroup::DecoyFlag flag=PeakGroup::DecoyFlag::target) const
	get calculated qvalue More...

void	setQvalue (float q, PeakGroup::DecoyFlag flag)
	set qvalue. More...

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

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

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

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

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

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[] (Size i) const

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

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 ()

Private Types
typedef FLASHDeconvHelperStructs::LogMzPeak	LogMzPeak

typedef FLASHDeconvHelperStructs::PrecalculatedAveragine	PrecalculatedAveragine

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

void	updateChargeFitScoreAndChargeIntensities_ ()
	update chargefit score and also update per charge intensities here. More...

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

void	updateAvgDaError_ ()
	update avg Da error More...

float	getAbsPPMError_ (const LogMzPeak &p) const
	get ppm error of a logMzPeak More...

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

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

Private Attributes
std::vector< Matrix< float > >	dl_matrices_
	Encoded matrix for DL scoring. More...

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_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...

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...

float	intensity_

PeakGroup::DecoyFlag	decoy_flag_ = target
	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	avg_da_error_ = 0

float	snr_ = 0

std::map< PeakGroup::DecoyFlag, float >	qvalue_
	qvalues with different decoy flags 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 by QScore calculation. DeconvolvedSpectrum consists of PeakGroups.

Member Typedef Documentation

◆ LogMzPeak

typedef FLASHDeconvHelperStructs::LogMzPeak LogMzPeak

private

◆ PrecalculatedAveragine

typedef FLASHDeconvHelperStructs::PrecalculatedAveragine PrecalculatedAveragine

private

Member Enumeration Documentation

◆ DecoyFlag

enum DecoyFlag

decoy flag. This flag specifies if a PeakGroup is a target, charge decoy, noise decoy, or isotope decoy.

Enumerator
target
charge_decoy
noise_decoy
isotope_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

◆ begin() [1/2]

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

noexcept

iterators for the signal LogMz peaks in this PeakGroup

◆ 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

◆ getAbsDaError_()

float getAbsDaError_ ( LogMzPeak & p ) const

private

get Da error of a logMzPeak from the closest isotope

◆ getAbsPPMError_()

float getAbsPPMError_ ( const LogMzPeak & p ) const

private

get ppm error of a logMzPeak

◆ 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

◆ getDecoyFlag()

PeakGroup::DecoyFlag getDecoyFlag ( ) const

get the decoy flag of this

◆ 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

◆ 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 ( PeakGroup::DecoyFlag flag = PeakGroup::DecoyFlag::target ) const

get calculated qvalue

◆ getRepAbsCharge()

int getRepAbsCharge ( ) const

get representative charge

◆ getRepMzRange()

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

get mz range that results in max QScore

◆ getScanNumber()

int getScanNumber ( ) const

get scan number

◆ getSNR()

float getSNR ( ) const

get total SNR

◆ isPositive()

bool isPositive ( ) const

get if it is positive mode

◆ isSignalMZ()

bool isSignalMZ	(	double	mz,
		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). Assume logMzPeaks are sorted.

◆ 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[] ( Size i ) const

◆ push_back()

void push_back ( const FLASHDeconvHelperStructs::LogMzPeak & pg )

vector operators for the LogMzPeaks in this PeakGroup

◆ recruitAllPeaksInSpectrum()

std::vector<LogMzPeak> recruitAllPeaksInSpectrum	(	const MSSpectrum &	spec,
		double	tol,
		const FLASHDeconvHelperStructs::PrecalculatedAveragine &	avg,
		double	mono_mass,
		const std::unordered_set< int > &	excluded_integer_mzs_,
		int	charge_offset = `0`,
		double	charge_multiple = `1.0`,
		double	mz_off = `.0`
	)

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	mass tolerance
avg	precalculated averagine
mono_mass	monoisotopic mass
excluded_integer_mzs_	mzs that will be included - only for decoy generation
charge_offset	charge offset from peaks to recruited peaks
charge_multiple	charge multiplication factor for recruited peaks
mz_off	mz offset for recruited peaks

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

◆ setChargePowers_()

void setChargePowers_	(	int	abs_charge,
		float	signal_pwr,
		float	noise_pwr,
		float	intensity
	)

private

set per abs_charge signal power

◆ 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

◆ setDecoyFlag()

void setDecoyFlag ( PeakGroup::DecoyFlag index )

for this PeakGroup, specify the decoy flag.

◆ 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

◆ setQScore()

void setQScore ( float qscore )

set Q score - for FLASHIda log file parsing

◆ setQvalue()

void setQvalue	(	float	q,
		PeakGroup::DecoyFlag	flag
	)

set qvalue.

◆ setRepAbsCharge()

void setRepAbsCharge ( int max_qscore_charge )

set representative max_qscore_charge

◆ setScanNumber()

void setScanNumber ( int scan_number )

set scan number

◆ setSNR()

void setSNR ( 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 )

◆ updateAvgDaError_()

void updateAvgDaError_ ( )

private

update avg Da error

◆ updateAvgPPMError_()

void updateAvgPPMError_ ( )

private

update avg ppm error

◆ updateChargeFitScoreAndChargeIntensities_()

void updateChargeFitScoreAndChargeIntensities_ ( )

private

update chargefit score and also update per charge intensities here.

◆ updateIsotopeCosineSNRAvgErrorAndQScore()

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

Update isotope cosine sore and qscore. Mono mass is also updated one last time. SNR, per charge SNR, and avg errors are updated here.

Parameters

avg	precalculated averagine
min_cos	the peak groups with cosine score less than this will have QScore 0.

◆ updateMonomassAndIsotopeIntensities()

void updateMonomassAndIsotopeIntensities ( )

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

◆ updateSNR_()

void updateSNR_ ( )

private

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

Member Data Documentation

◆ avg_da_error_

float avg_da_error_ = 0

private

◆ avg_ppm_error_

float avg_ppm_error_ = 0

private

◆ charge_score_

float charge_score_

private

◆ decoy_flag_

PeakGroup::DecoyFlag decoy_flag_ = target

private

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

◆ dl_matrices_

std::vector<Matrix<float> > dl_matrices_

private

Encoded matrix for DL scoring.

◆ index_

uint index_ = 0

private

peak group index

◆ intensity_

float 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

◆ min_abs_charge_

int min_abs_charge_ = 0

private

charge range

◆ monoisotopic_mass_

double monoisotopic_mass_ = -1.0

private

information on the deconvolved mass

◆ 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_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_

std::map<PeakGroup::DecoyFlag, float> qvalue_

private

qvalues with different decoy flags

◆ scan_number_

int scan_number_

private

scan number

◆ snr_

float snr_ = 0

private

Public Types

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ LogMzPeak

◆ PrecalculatedAveragine

Member Enumeration Documentation

◆ DecoyFlag

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()

◆ getAbsDaError_()

◆ getAbsPPMError_()

◆ getAvgDaError()

◆ getAvgPPMError()

◆ getChargeIntensity()

◆ getChargeIsotopeCosine()

◆ getChargeScore()

◆ getChargeSNR()

◆ getDecoyFlag()

◆ getIndex()

◆ getIntensity()

◆ getIsotopeCosine()

◆ getIsotopeDaDistance()

◆ getIsotopeIntensities()

◆ getMonoMass()

◆ getMzRange()

◆ getQScore()

◆ getQvalue()

◆ getRepAbsCharge()

◆ getRepMzRange()

◆ getScanNumber()

◆ getSNR()

◆ isPositive()

◆ isSignalMZ()

◆ isTargeted()

◆ operator<()

◆ operator=()

◆ operator==()

◆ operator>()

◆ operator[]()

◆ push_back()

◆ recruitAllPeaksInSpectrum()

◆ reserve()

◆ setAbsChargeRange()

◆ setAvgPPMError()

◆ setChargeIsotopeCosine()

◆ setChargePowers_()

◆ setChargeScore()

◆ setChargeSNR()

◆ setDecoyFlag()

◆ setIndex()

◆ setIsotopeCosine()

◆ setIsotopeDaDistance()

◆ setQScore()

◆ setQvalue()

◆ setRepAbsCharge()

◆ setScanNumber()

◆ setSNR()

◆ setTargeted()

◆ shrink_to_fit()

◆ size()

◆ sort()

◆ swap()

◆ updateAvgDaError_()

◆ updateAvgPPMError_()