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/FLASHDeconvAlgorithm.h>

Inheritance diagram for FLASHDeconvAlgorithm:

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Collaboration diagram for FLASHDeconvAlgorithm:

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Public Types
typedef FLASHDeconvHelperStructs::PrecalculatedAveragine	PrecalculatedAveragine

typedef FLASHDeconvHelperStructs::LogMzPeak	LogMzPeak

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

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

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

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

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

	~FLASHDeconvAlgorithm ()=default
	destructor More...

void	performSpectrumDeconvolution (const MSSpectrum &spec, const std::vector< DeconvolvedSpectrum > &survey_scans, int scan_number, const std::map< int, std::vector< std::vector< float >>> &precursor_map_for_FLASHIda)
	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	setTargetDummyType (PeakGroup::TargetDummyType target_dummy_type, DeconvolvedSpectrum &target_dspec_for_dummy_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 b_size, int offset, int min_iso_size)

static float	getIsotopeCosineAndDetermineIsotopeIndex (double mono_mass, const std::vector< float > &per_isotope_intensities, int &offset, const PrecalculatedAveragine &avg, int iso_int_shift=0, int window_width=-1, int allowed_iso_error_for_second_best_cos=0, PeakGroup::TargetDummyType target_dummy_type=PeakGroup::TargetDummyType::target)
	Examine intensity distribution over isotope indices. Also determines the most plausible isotope index or, monoisotopic mono_mass. More...

static void	addMZsToExcludsionList (const DeconvolvedSpectrum &dspec, std::unordered_set< double > &excluded_mzs)

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...

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	updateMzBins_ (Size bin_number, std::vector< float > &mz_bin_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 More...

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

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

Matrix< int >	updateMassBins_ (const std::vector< float > &mz_intensities)
	Update mass_bins_. 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 mass_bins_ using the universal pattern, eliminate possible harmonic masses. More...

void	getCandidatePeakGroups_ (const Matrix< int > &per_mass_abs_charge_ranges)
	For selected masses in mass_bins_, 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
	filter out charge error masses More...

void	removeOverlappingPeakGroups_ (DeconvolvedSpectrum &dspec, double tol)
	filter out overlapping masses More...

bool	registerPrecursor_ (const std::vector< DeconvolvedSpectrum > &survey_scans, const std::map< int, std::vector< std::vector< float >>> &precursor_map_for_real_time_acquisition)
	register the precursor peak as well as the precursor peak group (or mass) if possible for MSn (n>1) spectrum. Given a precursor peak (found in the original MS n-1 Spectrum) the masses containing the precursor peak are searched. If multiple masses are detected, the one with the best Qscore is selected. For the selected mass, its corresponding peak group (along with precursor peak) is registered. If no such mass exists, only the precursor peak is registered. More...

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...

Private Attributes
int	allowed_iso_error_ = 1
	allowed isotope error in deconvolved mass to calculate qvalue More...

double	min_rt_
	range of RT subject to analysis (in seconds) More...

double	max_rt_

double	min_mz_
	range of mz subject to analysis More...

double	max_mz_

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	intensity_threshold_
	peak intensity threshold subject to analysis 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_
	cosine threshold between observed and theoretical isotope patterns for each MS level More...

DeconvolvedSpectrum *	target_dspec_for_dummy_calcualtion_
	the deconvolved spectrum from normal run. This is used when dummy masses are generated. More...

PeakGroup::TargetDummyType	target_dummy_type_ = PeakGroup::TargetDummyType::target
	PeakGroup::TargetDummyType values. More...

FLASHDeconvHelperStructs::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	previously_deconved_mass_bins_for_dummy_
	mass bins that are previsouly deconvolved and excluded for dummy mass generation More...

std::vector< double >	previously_deconved_mono_masses_for_dummy_

std::unordered_set< double >	excluded_peak_mzs_

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

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

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

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

double	iso_da_distance_
	isotope dalton distance More...

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

Matrix< int >	harmonic_bin_offset_matrix_
	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	isolation_window_size_
	default precursor isolation window size. More...

Static Private Attributes
static const int	min_iso_size_ = 2
	FLASHDeconv parameters. More...

static const int	min_support_peak_count_ = 2
	minimum number of peaks supporting a mass minus one 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 FLASHDeconvHelperStructs::LogMzPeak LogMzPeak

◆ PrecalculatedAveragine

typedef FLASHDeconvHelperStructs::PrecalculatedAveragine PrecalculatedAveragine

Constructor & Destructor Documentation

◆ FLASHDeconvAlgorithm() [1/3]

FLASHDeconvAlgorithm ( )

default constructor

◆ FLASHDeconvAlgorithm() [2/3]

FLASHDeconvAlgorithm ( const FLASHDeconvAlgorithm & )

default

copy constructor

◆ FLASHDeconvAlgorithm() [3/3]

FLASHDeconvAlgorithm ( FLASHDeconvAlgorithm && other )

default

move constructor

◆ ~FLASHDeconvAlgorithm()

~FLASHDeconvAlgorithm ( )

default

destructor

Member Function Documentation

◆ addMZsToExcludsionList()

static void addMZsToExcludsionList	(	const DeconvolvedSpectrum &	dspec,
		std::unordered_set< double > &	excluded_mzs
	)

static

add m/zs in input DeconvolvedSpectrum into exclusion list. The exclusion list is used to generate noise dummy masses.

Parameters

dspec	input DeconvolvedSpectrum
excluded_mzs	mz exclusion list to be updated

◆ 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 mass_bins_, 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	b_size,
		int	offset,
		int	min_iso_size
	)

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
b_size	size of b
offset	element index offset between a and b
min_iso_size	minimum isotope size. If isotope size is less than this, return 0

◆ getDeconvolvedSpectrum()

DeconvolvedSpectrum& getDeconvolvedSpectrum ( )

return deconvolved spectrum

Referenced by TOPPFLASHDeconv::main_().

◆ getIsotopeCosineAndDetermineIsotopeIndex()

static float getIsotopeCosineAndDetermineIsotopeIndex	(	double	mono_mass,
		const std::vector< float > &	per_isotope_intensities,
		int &	offset,
		const PrecalculatedAveragine &	avg,
		int	iso_int_shift = `0`,
		int	window_width = `-1`,
		int	allowed_iso_error_for_second_best_cos = `0`,
		PeakGroup::TargetDummyType	target_dummy_type = `PeakGroup::TargetDummyType::target`
	)

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.
allowed_iso_error_for_second_best_cos	allowed isotope error to calculate the second best cos. If target_dummy_type is not PeakGroup::TargetDummyType::target, the second best cosine and its corresponding offset will be output
target_dummy_type	This target_dummy_type specifies if a PeakGroup is a target (0), charge dummy (1), noise dummy (2), or isotope dummy (3)

Returns: calculated cosine similar score

◆ getMassFromMassBin_()

double getMassFromMassBin_	(	Size	mass_bin,
		double	bin_mul_factor
	)		const

private

get mass value for input mass bin

◆ getMzFromMzBin_()

double getMzFromMzBin_	(	Size	mass_bin,
		double	bin_mul_factor
	)		const

private

get mz value for input mz bin

◆ getNominalMass()

static int getNominalMass ( double mass )

static

convert double to nominal mass

◆ operator=() [1/2]

FLASHDeconvAlgorithm& operator= ( const FLASHDeconvAlgorithm & fd )

default

assignment operator

◆ operator=() [2/2]

FLASHDeconvAlgorithm& operator= ( FLASHDeconvAlgorithm && fd )

default

move assignment operator

◆ performSpectrumDeconvolution()

void performSpectrumDeconvolution	(	const MSSpectrum &	spec,
		const std::vector< DeconvolvedSpectrum > &	survey_scans,
		int	scan_number,
		const std::map< int, std::vector< std::vector< float >>> &	precursor_map_for_FLASHIda
	)

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

Parameters

spec	the original spectrum
survey_scans	the survey scans to assign precursor mass to the deconvolved spectrum.
scan_number	scan number from input spectrum.
precursor_map_for_FLASHIda	deconvolved precursor information from FLASHIda

Referenced by TOPPFLASHDeconv::main_().

◆ registerPrecursor_()

bool registerPrecursor_	(	const std::vector< DeconvolvedSpectrum > &	survey_scans,
		const std::map< int, std::vector< std::vector< float >>> &	precursor_map_for_real_time_acquisition
	)

private

register the precursor peak as well as the precursor peak group (or mass) if possible for MSn (n>1) spectrum. Given a precursor peak (found in the original MS n-1 Spectrum) the masses containing the precursor peak are searched. If multiple masses are detected, the one with the best Qscore is selected. For the selected mass, its corresponding peak group (along with precursor peak) is registered. If no such mass exists, only the precursor peak is registered.

Parameters

survey_scans	the candidate precursor spectra - the user may allow search of previous N survey scans.
precursor_map_for_real_time_acquisition	this contains the deconvolved mass information from FLASHIda runs.

◆ removeChargeErrorPeakGroups_()

void removeChargeErrorPeakGroups_ ( DeconvolvedSpectrum & dspec ) const

private

filter out charge error masses

◆ removeOverlappingPeakGroups_()

void removeOverlappingPeakGroups_	(	DeconvolvedSpectrum &	dspec,
		double	tol
	)

private

filter out overlapping masses

◆ scoreAndFilterPeakGroups_()

void scoreAndFilterPeakGroups_ ( )

private

function for peak group scoring and filtering

◆ setAveragine()

void setAveragine ( const PrecalculatedAveragine & avg )

set calculated averagine

Referenced by TOPPFLASHDeconv::main_().

◆ setFilters_()

void setFilters_ ( )

private

Make the universal pattern.

◆ setTargetDummyType()

void setTargetDummyType	(	PeakGroup::TargetDummyType	target_dummy_type,
		DeconvolvedSpectrum &	target_dspec_for_dummy_calcualtion
	)

set target dummy type for the FLASHDeconvAlgorithm run. All masses from the target FLASHDeconvAlgorithm run will have the target_dummy_type_.

Parameters

target_dummy_type	This target_dummy_type_ specifies if a PeakGroup is a target (0), charge dummy (1), noise dummy (2), or isotope dummy (3)
target_dspec_for_dummy_calcualtion	target masses from normal deconvolution

Referenced by TOPPFLASHDeconv::main_().

◆ 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

exclude if set, masses are excluded.

◆ updateCandidateMassBins_()

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

private

Subfunction of updateMassBins_. It select candidate masses and update mass_bins_ 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 mass_bins_. 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.

◆ updateMzBins_()

void updateMzBins_	(	Size	bin_number,
		std::vector< float > &	mz_bin_intensities
	)

private

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

Parameters

bin_number	number of mz bins
mz_bin_intensities	intensity per mz bin

Member Data Documentation

◆ allowed_iso_error_

int allowed_iso_error_ = 1

private

allowed isotope error in deconvolved mass to calculate qvalue

◆ avg_

FLASHDeconvHelperStructs::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

◆ bin_offsets_

std::vector<int> bin_offsets_

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_masses_

std::vector<double> excluded_masses_

private

mass bins that are excluded for FLASHIda global targeting mode

◆ excluded_peak_mzs_

std::unordered_set<double> excluded_peak_mzs_

private

◆ filter_

std::vector<double> filter_

private

This stores the "universal pattern".

◆ harmonic_bin_offset_matrix_

Matrix<int> harmonic_bin_offset_matrix_

private

This stores the patterns for harmonic reduction in binned dimension.

◆ harmonic_filter_matrix_

Matrix<double> harmonic_filter_matrix_

private

This stores the patterns for harmonic reduction.

◆ intensity_threshold_

double intensity_threshold_

private

peak intensity threshold subject to analysis

◆ is_positive_

bool is_positive_

private

is positive mode

◆ iso_da_distance_

double iso_da_distance_

private

isotope dalton distance

◆ isolation_window_size_

double isolation_window_size_

private

default precursor isolation window size.

◆ 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

◆ mass_bins_

boost::dynamic_bitset mass_bins_

private

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

◆ max_abs_charge_

int max_abs_charge_

private

◆ max_mass_

double max_mass_

private

◆ max_mz_

double max_mz_

private

◆ max_rt_

double max_rt_

private

◆ 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

staticprivate

FLASHDeconv parameters.

minimum isotopologue count in a peak group

◆ min_isotope_cosine_

DoubleList min_isotope_cosine_

private

cosine threshold between observed and theoretical isotope patterns for each MS level

◆ min_mass_

double min_mass_

private

mass ranges of deconvolution, set by users

◆ min_mz_

double min_mz_

private

range of mz subject to analysis

◆ min_rt_

double min_rt_

private

range of RT subject to analysis (in seconds)

◆ min_support_peak_count_

const int min_support_peak_count_ = 2

staticprivate

minimum number of peaks supporting a mass minus one

◆ ms_level_

uint ms_level_

private

current ms Level

◆ mz_bin_min_value_

double mz_bin_min_value_

private

◆ mz_bins_

boost::dynamic_bitset mz_bins_

private

mz_bins_ stores the binned log mz peaks

◆ previously_deconved_mass_bins_for_dummy_

boost::dynamic_bitset previously_deconved_mass_bins_for_dummy_

private

mass bins that are previsouly deconvolved and excluded for dummy mass generation

◆ previously_deconved_mono_masses_for_dummy_

std::vector<double> previously_deconved_mono_masses_for_dummy_

private

◆ target_dspec_for_dummy_calcualtion_

DeconvolvedSpectrum* target_dspec_for_dummy_calcualtion_

private

the deconvolved spectrum from normal run. This is used when dummy masses are generated.

◆ target_dummy_type_

PeakGroup::TargetDummyType target_dummy_type_ = PeakGroup::TargetDummyType::target

private

PeakGroup::TargetDummyType values.

◆ 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

◆ tolerance_

DoubleList tolerance_

private

tolerance in ppm for each MS level

Public Types

Public Member Functions

Static Public Member Functions

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

◆ FLASHDeconvAlgorithm() [1/3]

◆ FLASHDeconvAlgorithm() [2/3]

◆ FLASHDeconvAlgorithm() [3/3]

◆ ~FLASHDeconvAlgorithm()

Member Function Documentation

◆ addMZsToExcludsionList()

◆ calculateAveragine()

◆ filterMassBins_()

◆ generatePeakGroupsFromSpectrum_()

◆ getAveragine()

◆ getBinNumber_()

◆ getBinValue_()

◆ getCandidatePeakGroups_()

◆ getCosine()

◆ getDeconvolvedSpectrum()

◆ getIsotopeCosineAndDetermineIsotopeIndex()

◆ getMassFromMassBin_()

◆ getMzFromMzBin_()

◆ getNominalMass()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ performSpectrumDeconvolution()

◆ registerPrecursor_()

◆ removeChargeErrorPeakGroups_()

◆ removeOverlappingPeakGroups_()

◆ scoreAndFilterPeakGroups_()

◆ setAveragine()

◆ setFilters_()

◆ setTargetDummyType()

◆ setTargetMasses()

◆ updateCandidateMassBins_()

◆ updateLogMzPeaks_()

◆ updateMassBins_()

◆ updateMembers_()

◆ updateMzBins_()

Member Data Documentation

◆ allowed_iso_error_

◆ avg_

◆ bin_mul_factors_

◆ bin_offsets_

◆ current_max_charge_

◆ current_max_mass_

◆ current_min_mass_

◆ deconvolved_spectrum_

◆ excluded_masses_

◆ excluded_peak_mzs_

◆ filter_

◆ harmonic_bin_offset_matrix_

◆ harmonic_filter_matrix_

◆ intensity_threshold_

◆ is_positive_

◆ iso_da_distance_

◆ isolation_window_size_

◆ log_mz_peaks_

◆ mass_bin_min_value_

◆ mass_bins_

◆ max_abs_charge_

◆ max_mass_

◆ max_mz_

◆ max_rt_

◆ min_abs_charge_

◆ min_iso_size_

◆ min_isotope_cosine_

◆ min_mass_

◆ min_mz_

◆ min_rt_