FLASHDeconv algorithm: ultrafast mass deconvolution algorithm for top down mass spectrometry dataset From MSSpectrum, this class outputs DeconvolvedSpectrum. Deconvolution takes three steps: i) decharging and select candidate masses - speed up via binning ii) collecting isotopes from the candidate masses and deisotope - peak groups are defined here iii) scoring and filter out low scoring masses (i.e., peak groups) More...

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

Inheritance diagram for SpectralDeconvolution:

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Collaboration diagram for SpectralDeconvolution:

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Public Types
typedef FLASHHelperClasses::PrecalculatedAveragine	PrecalculatedAveragine

typedef FLASHHelperClasses::LogMzPeak	LogMzPeak

Public Member Functions
	SpectralDeconvolution ()
	default constructor More...

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

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

SpectralDeconvolution &	operator= (const SpectralDeconvolution &fd)=default
	assignment operator More...

SpectralDeconvolution &	operator= (SpectralDeconvolution &&fd)=default
	move assignment operator More...

	~SpectralDeconvolution ()=default
	destructor More...

void	performSpectrumDeconvolution (const MSSpectrum &spec, int scan_number, const PeakGroup &precursor_peak_group)
	main deconvolution function that generates the deconvolved target and dummy spectrum based on the original spectrum. More...

DeconvolvedSpectrum &	getDeconvolvedSpectrum ()
	return deconvolved spectrum More...

const PrecalculatedAveragine &	getAveragine ()
	get calculated averagine. Call after calculateAveragine is called. More...

void	setAveragine (const PrecalculatedAveragine &avg)
	set calculated averagine More...

void	setTargetMasses (const std::vector< double > &masses, bool exclude=false)
	set targeted or excluded masses for targeted deconvolution. Masses are targeted or excluded in all ms levels. More...

void	calculateAveragine (bool use_RNA_averagine)
	precalculate averagine (for predefined mass bins) to speed up averagine generation More...

void	setToleranceEstimation ()
	when estimating tolerance, max_mass_dalton_tolerance_ should be large More...

void	setTargetDecoyType (PeakGroup::TargetDecoyType target_decoy_type, const DeconvolvedSpectrum &target_dspec_for_decoy_calcualtion)

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...

virtual	~DefaultParamHandler ()
	Destructor. More...

DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...

void	setParameters (const Param &param)
	Sets the parameters. More...

const Param &	getParameters () const
	Non-mutable access to the parameters. More...

const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...

const String &	getName () const
	Non-mutable access to the name. More...

void	setName (const String &name)
	Mutable access to the name. More...

const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

Static Public Member Functions
static int	getNominalMass (double mass)
	convert double to nominal mass More...

static float	getCosine (const std::vector< float > &a, int a_start, int a_end, const IsotopeDistribution &b, int offset, int min_iso_len)

static float	getIsotopeCosineAndIsoOffset (double mono_mass, const std::vector< float > &per_isotope_intensities, int &offset, const PrecalculatedAveragine &avg, int iso_int_shift, int window_width, const std::vector< double > &excluded_masses)
	Examine intensity distribution over isotope indices. Also determines the most plausible isotope index or, monoisotopic mono_mass. More...

Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
	Writes all parameters to meta values. More...

Static Public Attributes
static const int	min_iso_size = 2
	minimum isotopologue count in a peak group More...

Protected Member Functions
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method. More...

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Private Member Functions
void	updateLogMzPeaks_ ()
	generate log mz peaks from the input spectrum More...

void	binLogMzPeaks_ (Size bin_number, std::vector< float > &binned_log_mz_peak_intensities)
	generate mz bins and intensity per mz bin from log mz peaks More...

double	getMassFromMassBin_ (Size mass_bin, double bin_mul_factor) const
	get mass value for input mass bin: used for debugging More...

double	getMzFromMzBin_ (Size mass_bin, double bin_mul_factor) const
	get mz value for input mz bin: used for debugging More...

void	generatePeakGroupsFromSpectrum_ ()
	Generate peak groups from the input spectrum. More...

Matrix< int >	updateMassBins_ (const std::vector< float > &mz_intensities)
	Update binned_log_masses_. It select candidate mass bins using the universal pattern, eliminate possible harmonic masses. This function does not perform deisotoping. More...

Matrix< int >	filterMassBins_ (const std::vector< float > &mass_intensities)
	Subfunction of updateMassBins_. More...

void	updateCandidateMassBins_ (std::vector< float > &mass_intensities, const std::vector< float > &mz_intensities)
	Subfunction of updateMassBins_. It select candidate masses and update binned_log_masses_ using the universal pattern, eliminate possible harmonic masses. More...

void	getCandidatePeakGroups_ (const Matrix< int > &per_mass_abs_charge_ranges)
	For selected masses in binned_log_masses_, select the peaks from the original spectrum. Also isotopic peaks are clustered in this function. More...

void	setFilters_ ()
	Make the universal pattern. More...

void	scoreAndFilterPeakGroups_ ()
	function for peak group scoring and filtering More...

void	removeChargeErrorPeakGroups_ (DeconvolvedSpectrum &dspec, const PeakGroup::TargetDecoyType &target_decoy_type) const
	filter out charge error masses More...

void	removeExcludedMasses_ (DeconvolvedSpectrum &dspec, std::vector< double > excluded_masses, double tol) const
	filter out excluded masses More...

void	setTargetPrecursorCharge_ ()

void	prepareSignalDecoyExclusions_ ()
	prepare signal decoy exclusions for decoy runs More...

void	prepareNoiseDecoySpectrum_ (const MSSpectrum &spec)
	prepare noise decoy spectrum by filtering signal peaks More...

void	registerPrecursorForMSn_ (const PeakGroup &precursor_peak_group)
	register precursor information for MSn spectra (n > 1) More...

bool	isPeakGroupInExcludedMassForDecoyRuns_ (const PeakGroup &peak_group, double tol, int offset=0) const

Static Private Member Functions
static double	getBinValue_ (Size bin, double min_value, double bin_mul_factor)
	static function that converts bin to value More...

static Size	getBinNumber_ (double value, double min_value, double bin_mul_factor)
	static function that converts value to bin More...

static void	removeOverlappingPeakGroups_ (DeconvolvedSpectrum &dspec, double tol, PeakGroup::TargetDecoyType target_decoy_type=PeakGroup::TargetDecoyType::target)
	filter out overlapping masses More...

Private Attributes
int	allowed_iso_error_ = -1
	FLASHDeconv parameters. More...

int	min_abs_charge_
	min charge and max charge subject to analysis, set by users More...

int	max_abs_charge_

bool	is_positive_
	is positive mode More...

double	min_mass_
	mass ranges of deconvolution, set by users More...

double	max_mass_

int	current_max_charge_
	current_max_charge_: controlled by precursor charge for MSn n>1; otherwise just max_abs_charge_ More...

double	current_max_mass_
	max mass is controlled by precursor mass for MSn n>1; otherwise just max_mass More...

double	current_min_mass_
	max mass is max_mass for MS1 and 50 for MS2 More...

double	noise_iso_delta_ = .9444
	isotope distance for noise decoy. This distance has been determined so i) it is close to the mass of 13C - 12C yet is not close to any correct isotope distances of different charges (from 1 to 10). More...

DoubleList	tolerance_
	tolerance in ppm for each MS level More...

DoubleList	bin_mul_factors_
	bin multiplication factor (log mz * bin_mul_factors_ = bin number) - for fast convolution, binning is used More...

DoubleList	min_isotope_cosine_
	Isotope cosine threshold for each MS level. More...

DoubleList	min_snr_
	snr threshold for each MS level More...

double	min_qscore_ = .2
	minimum Qscore of a deconvolved mass More...

const DeconvolvedSpectrum *	target_dspec_for_decoy_calculation_
	the peak group vector from normal run. This is used when dummy masses are generated. More...

PeakGroup::TargetDecoyType	target_decoy_type_ = PeakGroup::TargetDecoyType::target
	PeakGroup::TargetDecoyType values. More...

FLASHHelperClasses::PrecalculatedAveragine	avg_
	precalculated averagine distributions for fast averagine generation More...

boost::dynamic_bitset	target_mass_bins_
	mass bins that are targeted for FLASHIda global targeting mode More...

std::vector< double >	target_mono_masses_

std::vector< double >	excluded_masses_
	mass bins that are excluded for FLASHIda global targeting mode More...

boost::dynamic_bitset	excluded_mass_bins_for_decoy_runs_
	mass bins that are previously deconvolved and excluded for decoy mass generation More...

std::vector< double >	excluded_peak_masses_for_decoy_runs_

std::vector< double >	excluded_masses_for_decoy_runs_

std::vector< LogMzPeak >	log_mz_peaks_
	Stores log mz peaks. More...

DeconvolvedSpectrum	deconvolved_spectrum_
	selected_peak_groups_ stores the deconvolved mass peak groups More...

boost::dynamic_bitset	binned_log_masses_
	binned_log_masses_ stores the selected bins for this spectrum + overlapped spectrum (previous a few spectra). More...

boost::dynamic_bitset	binned_log_mz_peaks_
	binned_log_mz_peaks_ stores the binned log mz peaks More...

std::vector< double >	universal_pattern_
	This stores the "universal pattern". More...

Matrix< double >	harmonic_pattern_matrix_
	This stores the patterns for harmonic reduction. More...

std::vector< int >	binned_universal_pattern_
	This stores the "universal pattern" in binned dimension. More...

Matrix< int >	binned_harmonic_patterns
	This stores the patterns for harmonic reduction in binned dimension. More...

double	mass_bin_min_value_
	minimum mass and mz values representing the first bin of massBin and mzBin, respectively: to save memory space More...

double	mz_bin_min_value_

uint	ms_level_
	current ms Level More...

double	iso_da_distance_
	isotope dalton distance More...

int	target_precursor_charge_ = 0
	for precursor targetting. More...

double	target_precursor_mz_ = 0

double	max_mass_dalton_tolerance_ = .16
	this is additional mass tolerance in Da to get more high signal-to-ratio peaks in this candidate peakgroup finding More...

Static Private Attributes
static const int	min_support_peak_count_ = 2
	minimum number of peaks supporting a mass More...

Additional Inherited Members
Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters. More...

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes! More...

std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes! More...

String	error_name_
	Name that is displayed in error messages during the parameter checking. More...

bool	check_defaults_
	If this member is set to false no checking if parameters in done;. More...

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;. More...

Detailed Description

FLASHDeconv algorithm: ultrafast mass deconvolution algorithm for top down mass spectrometry dataset From MSSpectrum, this class outputs DeconvolvedSpectrum. Deconvolution takes three steps: i) decharging and select candidate masses - speed up via binning ii) collecting isotopes from the candidate masses and deisotope - peak groups are defined here iii) scoring and filter out low scoring masses (i.e., peak groups)

Member Typedef Documentation

◆ LogMzPeak

typedef FLASHHelperClasses::LogMzPeak LogMzPeak

◆ PrecalculatedAveragine

typedef FLASHHelperClasses::PrecalculatedAveragine PrecalculatedAveragine

Constructor & Destructor Documentation

◆ SpectralDeconvolution() [1/3]

SpectralDeconvolution ( )

default constructor

◆ SpectralDeconvolution() [2/3]

SpectralDeconvolution ( const SpectralDeconvolution & )

default

copy constructor

◆ SpectralDeconvolution() [3/3]

SpectralDeconvolution ( SpectralDeconvolution && other )

default

move constructor

◆ ~SpectralDeconvolution()

~SpectralDeconvolution ( )

default

destructor

Member Function Documentation

◆ binLogMzPeaks_()

void binLogMzPeaks_	(	Size	bin_number,
		std::vector< float > &	binned_log_mz_peak_intensities
	)

private

generate mz bins and intensity per mz bin from log mz peaks

Parameters

bin_number	number of mz bins
binned_log_mz_peak_intensities	intensity per mz bin

◆ calculateAveragine()

void calculateAveragine ( bool use_RNA_averagine )

precalculate averagine (for predefined mass bins) to speed up averagine generation

Parameters

use_RNA_averagine if set, averagine for RNA (nucleotides) is calculated

◆ filterMassBins_()

Matrix<int> filterMassBins_ ( const std::vector< float > & mass_intensities )

private

Subfunction of updateMassBins_.

Parameters

mass_intensities per mass bin intensity

Returns: a matrix containing charge ranges for all found masses

◆ generatePeakGroupsFromSpectrum_()

void generatePeakGroupsFromSpectrum_ ( )

private

Generate peak groups from the input spectrum.

◆ getAveragine()

const PrecalculatedAveragine& getAveragine ( )

get calculated averagine. Call after calculateAveragine is called.

◆ getBinNumber_()

static Size getBinNumber_	(	double	value,
		double	min_value,
		double	bin_mul_factor
	)

staticprivate

static function that converts value to bin

Parameters

value	value
min_value	minimum value (corresponding to bin number = 0)
bin_mul_factor	bin multiplication factor: bin_number = (bin_value * bin_mul_factors_ - min_value)

Returns: bin corresponding to value

◆ getBinValue_()

static double getBinValue_	(	Size	bin,
		double	min_value,
		double	bin_mul_factor
	)

staticprivate

static function that converts bin to value

Parameters

bin	bin number
min_value	minimum value (corresponding to bin number = 0)
bin_mul_factor	bin multiplication factor: bin_value = (min_value + bin_number/ bin_mul_factors_)

Returns: value corresponding to bin

◆ getCandidatePeakGroups_()

void getCandidatePeakGroups_ ( const Matrix< int > & per_mass_abs_charge_ranges )

private

For selected masses in binned_log_masses_, select the peaks from the original spectrum. Also isotopic peaks are clustered in this function.

Parameters

per_mass_abs_charge_ranges charge range per mass

◆ getCosine()

static float getCosine	(	const std::vector< float > &	a,
		int	a_start,
		int	a_end,
		const IsotopeDistribution &	b,
		int	offset,
		int	min_iso_len
	)

static

calculate cosine between two vectors a and b with additional parameters for fast calculation

Parameters

a	vector a
a_start	non zero start index of a
a_end	non zero end index of a (exclusive)
b	vector b
offset	element index offset between a and b
min_iso_len	minimum isotope size. If isotope size is less than this, return 0

◆ getDeconvolvedSpectrum()

DeconvolvedSpectrum& getDeconvolvedSpectrum ( )

return deconvolved spectrum

◆ getIsotopeCosineAndIsoOffset()

static float getIsotopeCosineAndIsoOffset	(	double	mono_mass,
		const std::vector< float > &	per_isotope_intensities,
		int &	offset,
		const PrecalculatedAveragine &	avg,
		int	iso_int_shift,
		int	window_width,
		const std::vector< double > &	excluded_masses
	)

static

Examine intensity distribution over isotope indices. Also determines the most plausible isotope index or, monoisotopic mono_mass.

Parameters

mono_mass	monoisotopic mass
per_isotope_intensities	vector of intensities associated with each isotope - aggregated through charges
offset	output offset between input monoisotopic mono_mass and determined monoisotopic mono_mass
avg	precalculated averagine
iso_int_shift	isotope shift in per_isotope_intensities.
window_width	isotope offset value range. If -1, set automatically.
excluded_masses	masses not considered in the calculation.

Returns: calculated cosine similarity score

◆ getMassFromMassBin_()

double getMassFromMassBin_	(	Size	mass_bin,
		double	bin_mul_factor
	)		const

private

get mass value for input mass bin: used for debugging

◆ getMzFromMzBin_()

double getMzFromMzBin_	(	Size	mass_bin,
		double	bin_mul_factor
	)		const

private

get mz value for input mz bin: used for debugging

◆ getNominalMass()

static int getNominalMass ( double mass )

static

convert double to nominal mass

◆ isPeakGroupInExcludedMassForDecoyRuns_()

bool isPeakGroupInExcludedMassForDecoyRuns_	(	const PeakGroup &	peak_group,
		double	tol,
		int	offset = `0`
	)		const

private

◆ operator=() [1/2]

SpectralDeconvolution& operator= ( const SpectralDeconvolution & fd )

default

assignment operator

◆ operator=() [2/2]

SpectralDeconvolution& operator= ( SpectralDeconvolution && fd )

default

move assignment operator

◆ performSpectrumDeconvolution()

void performSpectrumDeconvolution	(	const MSSpectrum &	spec,
		int	scan_number,
		const PeakGroup &	precursor_peak_group
	)

main deconvolution function that generates the deconvolved target and dummy spectrum based on the original spectrum.

Parameters

spec	the original spectrum
scan_number	scan number from input spectrum.
precursor_peak_group	precursor peak group

◆ prepareNoiseDecoySpectrum_()

void prepareNoiseDecoySpectrum_ ( const MSSpectrum & spec )

private

prepare noise decoy spectrum by filtering signal peaks

◆ prepareSignalDecoyExclusions_()

void prepareSignalDecoyExclusions_ ( )

private

prepare signal decoy exclusions for decoy runs

◆ registerPrecursorForMSn_()

void registerPrecursorForMSn_ ( const PeakGroup & precursor_peak_group )

private

register precursor information for MSn spectra (n > 1)

◆ removeChargeErrorPeakGroups_()

void removeChargeErrorPeakGroups_	(	DeconvolvedSpectrum &	dspec,
		const PeakGroup::TargetDecoyType &	target_decoy_type
	)		const

private

filter out charge error masses

◆ removeExcludedMasses_()

void removeExcludedMasses_	(	DeconvolvedSpectrum &	dspec,
		std::vector< double >	excluded_masses,
		double	tol
	)		const

private

filter out excluded masses

◆ removeOverlappingPeakGroups_()

static void removeOverlappingPeakGroups_	(	DeconvolvedSpectrum &	dspec,
		double	tol,
		PeakGroup::TargetDecoyType	target_decoy_type = `PeakGroup::TargetDecoyType::target`
	)

staticprivate

filter out overlapping masses

◆ scoreAndFilterPeakGroups_()

void scoreAndFilterPeakGroups_ ( )

private

function for peak group scoring and filtering

◆ setAveragine()

void setAveragine ( const PrecalculatedAveragine & avg )

set calculated averagine

◆ setFilters_()

void setFilters_ ( )

private

Make the universal pattern.

◆ setTargetDecoyType()

void setTargetDecoyType	(	PeakGroup::TargetDecoyType	target_decoy_type,
		const DeconvolvedSpectrum &	target_dspec_for_decoy_calcualtion
	)

set target dummy type for the SpectralDeconvolution run. All masses from the target SpectralDeconvolution run will have the target_decoy_type_.

Parameters

target_decoy_type	This target_decoy_type_ specifies if a PeakGroup is a target (0), charge dummy (1), noise dummy (2), or isotope dummy (3)
target_dspec_for_decoy_calcualtion	target masses from normal deconvolution

◆ setTargetMasses()

void setTargetMasses	(	const std::vector< double > &	masses,
		bool	exclude = `false`
	)

set targeted or excluded masses for targeted deconvolution. Masses are targeted or excluded in all ms levels.

Parameters

masses	target masses to set
exclude	if set, masses are excluded.

◆ setTargetPrecursorCharge_()

void setTargetPrecursorCharge_ ( )

private

◆ setToleranceEstimation()

void setToleranceEstimation ( )

inline

when estimating tolerance, max_mass_dalton_tolerance_ should be large

◆ updateCandidateMassBins_()

void updateCandidateMassBins_	(	std::vector< float > &	mass_intensities,
		const std::vector< float > &	mz_intensities
	)

private

Subfunction of updateMassBins_. It select candidate masses and update binned_log_masses_ using the universal pattern, eliminate possible harmonic masses.

Parameters

mass_intensities	mass bin intensities which are updated in this function
mz_intensities	mz bin intensities

◆ updateLogMzPeaks_()

void updateLogMzPeaks_ ( )

private

generate log mz peaks from the input spectrum

◆ updateMassBins_()

Matrix<int> updateMassBins_ ( const std::vector< float > & mz_intensities )

private

Update binned_log_masses_. It select candidate mass bins using the universal pattern, eliminate possible harmonic masses. This function does not perform deisotoping.

Parameters

mz_intensities per mz bin intensity

Returns: a matrix containing charge ranges for all found masses

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ allowed_iso_error_

int allowed_iso_error_ = -1

private

FLASHDeconv parameters.

allowed isotope error in deconvolved mass to calculate qvalue

◆ avg_

FLASHHelperClasses::PrecalculatedAveragine avg_

private

precalculated averagine distributions for fast averagine generation

◆ bin_mul_factors_

DoubleList bin_mul_factors_

private

bin multiplication factor (log mz * bin_mul_factors_ = bin number) - for fast convolution, binning is used

◆ binned_harmonic_patterns

Matrix<int> binned_harmonic_patterns

private

This stores the patterns for harmonic reduction in binned dimension.

◆ binned_log_masses_

boost::dynamic_bitset binned_log_masses_

private

binned_log_masses_ stores the selected bins for this spectrum + overlapped spectrum (previous a few spectra).

◆ binned_log_mz_peaks_

boost::dynamic_bitset binned_log_mz_peaks_

private

binned_log_mz_peaks_ stores the binned log mz peaks

◆ binned_universal_pattern_

std::vector<int> binned_universal_pattern_

private

This stores the "universal pattern" in binned dimension.

◆ current_max_charge_

int current_max_charge_

private

current_max_charge_: controlled by precursor charge for MSn n>1; otherwise just max_abs_charge_

◆ current_max_mass_

double current_max_mass_

private

max mass is controlled by precursor mass for MSn n>1; otherwise just max_mass

◆ current_min_mass_

double current_min_mass_

private

max mass is max_mass for MS1 and 50 for MS2

◆ deconvolved_spectrum_

DeconvolvedSpectrum deconvolved_spectrum_

private

selected_peak_groups_ stores the deconvolved mass peak groups

◆ excluded_mass_bins_for_decoy_runs_

boost::dynamic_bitset excluded_mass_bins_for_decoy_runs_

private

mass bins that are previously deconvolved and excluded for decoy mass generation

◆ excluded_masses_

std::vector<double> excluded_masses_

private

mass bins that are excluded for FLASHIda global targeting mode

◆ excluded_masses_for_decoy_runs_

std::vector<double> excluded_masses_for_decoy_runs_

private

◆ excluded_peak_masses_for_decoy_runs_

std::vector<double> excluded_peak_masses_for_decoy_runs_

private

◆ harmonic_pattern_matrix_

Matrix<double> harmonic_pattern_matrix_

private

This stores the patterns for harmonic reduction.

◆ is_positive_

bool is_positive_

private

is positive mode

◆ iso_da_distance_

double iso_da_distance_

private

isotope dalton distance

◆ log_mz_peaks_

std::vector<LogMzPeak> log_mz_peaks_

private

Stores log mz peaks.

◆ mass_bin_min_value_

double mass_bin_min_value_

private

minimum mass and mz values representing the first bin of massBin and mzBin, respectively: to save memory space

◆ max_abs_charge_

int max_abs_charge_

private

◆ max_mass_

double max_mass_

private

◆ max_mass_dalton_tolerance_

double max_mass_dalton_tolerance_ = .16

private

this is additional mass tolerance in Da to get more high signal-to-ratio peaks in this candidate peakgroup finding

◆ min_abs_charge_

int min_abs_charge_

private

min charge and max charge subject to analysis, set by users

◆ min_iso_size

const int min_iso_size = 2

static

minimum isotopologue count in a peak group

◆ min_isotope_cosine_

DoubleList min_isotope_cosine_

private

Isotope cosine threshold for each MS level.

◆ min_mass_

double min_mass_

private

mass ranges of deconvolution, set by users

◆ min_qscore_

double min_qscore_ = .2

private

minimum Qscore of a deconvolved mass

◆ min_snr_

DoubleList min_snr_

private

snr threshold for each MS level

◆ min_support_peak_count_

const int min_support_peak_count_ = 2

staticprivate

minimum number of peaks supporting a mass

◆ ms_level_

uint ms_level_

private

current ms Level

◆ mz_bin_min_value_

double mz_bin_min_value_

private

◆ noise_iso_delta_

double noise_iso_delta_ = .9444

private

isotope distance for noise decoy. This distance has been determined so i) it is close to the mass of 13C - 12C yet is not close to any correct isotope distances of different charges (from 1 to 10).

◆ target_decoy_type_

PeakGroup::TargetDecoyType target_decoy_type_ = PeakGroup::TargetDecoyType::target

private

PeakGroup::TargetDecoyType values.

◆ target_dspec_for_decoy_calculation_

const DeconvolvedSpectrum* target_dspec_for_decoy_calculation_

private

the peak group vector from normal run. This is used when dummy masses are generated.

◆ target_mass_bins_

boost::dynamic_bitset target_mass_bins_

private

mass bins that are targeted for FLASHIda global targeting mode

◆ target_mono_masses_

std::vector<double> target_mono_masses_

private

◆ target_precursor_charge_

int target_precursor_charge_ = 0

private

for precursor targetting.

◆ target_precursor_mz_

double target_precursor_mz_ = 0

private

◆ tolerance_

DoubleList tolerance_

private

tolerance in ppm for each MS level

◆ universal_pattern_

std::vector<double> universal_pattern_

private

This stores the "universal pattern".

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ LogMzPeak

◆ PrecalculatedAveragine

Constructor & Destructor Documentation

◆ SpectralDeconvolution() [1/3]

◆ SpectralDeconvolution() [2/3]

◆ SpectralDeconvolution() [3/3]

◆ ~SpectralDeconvolution()

Member Function Documentation

◆ binLogMzPeaks_()

◆ calculateAveragine()

◆ filterMassBins_()

◆ generatePeakGroupsFromSpectrum_()

◆ getAveragine()

◆ getBinNumber_()

◆ getBinValue_()

◆ getCandidatePeakGroups_()

◆ getCosine()

◆ getDeconvolvedSpectrum()

◆ getIsotopeCosineAndIsoOffset()

◆ getMassFromMassBin_()

◆ getMzFromMzBin_()

◆ getNominalMass()

◆ isPeakGroupInExcludedMassForDecoyRuns_()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ performSpectrumDeconvolution()

◆ prepareNoiseDecoySpectrum_()

◆ prepareSignalDecoyExclusions_()

◆ registerPrecursorForMSn_()

◆ removeChargeErrorPeakGroups_()

◆ removeExcludedMasses_()

◆ removeOverlappingPeakGroups_()

◆ scoreAndFilterPeakGroups_()

◆ setAveragine()

◆ setFilters_()

◆ setTargetDecoyType()

◆ setTargetMasses()

◆ setTargetPrecursorCharge_()

◆ setToleranceEstimation()

◆ updateCandidateMassBins_()

◆ updateLogMzPeaks_()

◆ updateMassBins_()

◆ updateMembers_()

Member Data Documentation

◆ allowed_iso_error_

◆ avg_

◆ bin_mul_factors_

◆ binned_harmonic_patterns

◆ binned_log_masses_

◆ binned_log_mz_peaks_

◆ binned_universal_pattern_

◆ current_max_charge_

◆ current_max_mass_

◆ current_min_mass_

◆ deconvolved_spectrum_

◆ excluded_mass_bins_for_decoy_runs_

◆ excluded_masses_

◆ excluded_masses_for_decoy_runs_

◆ excluded_peak_masses_for_decoy_runs_

◆ harmonic_pattern_matrix_

◆ is_positive_

◆ iso_da_distance_

◆ log_mz_peaks_

◆ mass_bin_min_value_

◆ max_abs_charge_

◆ max_mass_

◆ max_mass_dalton_tolerance_

◆ min_abs_charge_