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...

void	performSpectrumDeconvolution (const MSSpectrum &spec, const std::vector< DeconvolvedSpectrum > &survey_scans, const int scan_number, const bool write_detail, const std::map< int, std::vector< std::vector< double >>> &precursor_map_for_FLASHIda)
	main deconvolution function that generates the deconvolved and decoy deconvolved spectrum from the original spectrum. More...

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

DeconvolvedSpectrum &	getDecoyDeconvolvedSpectrum ()
	return decoy deconvolved spectrum More...

const PrecalculatedAveragine &	getAveragine ()
	get calculated averagine. This should be called after calculateAveragine is called. More...

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

void	setTargetMasses (const std::vector< double > &masses)
	set targeted masses for targeted deconvolution. Masses are targeted in all ms levels More...

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

void	addExcludedMonoMass (const double m)

void	clearExcludedMonoMasses ()

void	setDecoyFlag (int flag)
	set decoy_flag_ More...

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...

virtual 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 (const 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)

static float	getIsotopeCosineAndDetermineIsotopeIndex (const double mono_mass, const std::vector< float > &per_isotope_intensities, int &offset, int &second_best_iso_offset, const PrecalculatedAveragine &avg, int window_width=-1, int allowed_iso_error=1)
	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...

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_ (const MSSpectrum *spec)
	generate log mz peaks from the input spectrum More...

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

void	unionPrevMassBins_ ()
	this function takes the previous deconvolution results (from ovelapped spectra) for sensitive deconvolution of the current spectrum 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	removeHarmonicsPeakGroups_ (DeconvolvedSpectrum &dpec)

void	removeOverlappingPeakGroups_ (DeconvolvedSpectrum &dpec, const double tol, const int iso_length=1)
	filter out overlapping masses More...

void	filterPeakGroupsByIsotopeCosine_ (const int current_max_mass_count)
	Filter out masses with low isotope cosine scores, only retaining current_max_mass_count masses. More...

bool	registerPrecursor (const std::vector< DeconvolvedSpectrum > &survey_scans, const std::map< int, std::vector< std::vector< double >>> &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_ (const Size bin, const double min_value, const double bin_width)
	static function that converts bin to value More...

static Size	getBinNumber_ (const double value, const double min_value, const double bin_width)
	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...

bool	write_detail_ = false
	to store detailed information More...

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

double	max_mass_

int	current_min_charge_
	current_min_charge_ charge: 1 for MSn n>1; otherwise just min_abs_charge_ More...

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...

const IntList	min_support_peak_count_ = {3,3,3,3,3,3,3,3}
	minimum number of peaks supporting a mass More...

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

DoubleList	bin_width_
	bin size for first stage of mass selection - for fast convolution, binning is used More...

DoubleList	min_isotope_cosine_
	cosine threshold between observed and theoretical isotope patterns for each MS level More...

int	decoy_run_flag_ = 0
	max mass count per spectrum for each MS level More...

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

std::vector< std::vector< Size > >	prev_mass_bins_ms1_
	The data structures for spectra overlapping. More...

std::vector< std::map< int, std::vector< Size > > >	prev_mass_bins_ms2_

std::vector< double >	prev_rts_ms1_

std::vector< double >	prev_rts_ms2_

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

std::vector< double >	target_masses_

boost::dynamic_bitset	excluded_mass_bins_
	mass bins that are excluded for decoy More...

std::vector< double >	excluded_masses_

const std::vector< int >	harmonic_charges_ {2, 3, 5, 7}
	harmonic charge factors that will be considered for harmonic mass reduction. For example, 2 is for 1/2 charge harmonic component reduction More...

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

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

DeconvolvedSpectrum	decoy_deconvolved_spectrum_
	decoy_deconvolved_spectrum_ stores the deconvolved decoy 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...

boost::dynamic_bitset	mz_bins_for_edge_effect_
	mz_bins_for_edge_effect_ stores the binned log mz peaks, considering edge effect 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_

int	ms_level_
	current ms Level More...

const int	low_charge_ = 6
	high and low charges are differently deconvolved. This value determines the (inclusive) threshold for low charge. More...

double	isolation_window_size_
	default precursor isolation window size. More...

const int	max_peak_count_ = 30000
	allowed maximum peak count per spectrum - intensity based. More...

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

static const int	charge_decoy_ = 1

static const int	noise_decoy_ = 2

static const int	isotope_decoy_ = 3

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

Member Function Documentation

◆ addExcludedMonoMass()

void addExcludedMonoMass ( const double m )

Referenced by TOPPFLASHDeconv::main_().

◆ calculateAveragine()

void calculateAveragine ( const 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

◆ clearExcludedMonoMasses()

void clearExcludedMonoMasses ( )

Referenced by TOPPFLASHDeconv::main_().

◆ 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

◆ filterPeakGroupsByIsotopeCosine_()

void filterPeakGroupsByIsotopeCosine_ ( const int current_max_mass_count )

private

Filter out masses with low isotope cosine scores, only retaining current_max_mass_count masses.

◆ generatePeakGroupsFromSpectrum_()

void generatePeakGroupsFromSpectrum_ ( )

private

Generate peak groups from the input spectrum.

◆ getAveragine()

const PrecalculatedAveragine& getAveragine ( )

get calculated averagine. This should be called after calculateAveragine is called.

◆ getBinNumber_()

static Size getBinNumber_	(	const double	value,
		const double	min_value,
		const double	bin_width
	)

staticprivate

static function that converts value to bin

Parameters

value	value
min_value	minimum value (corresponding to bin number = 0)
bin_width	bin width

Returns: bin corresponding to value

◆ getBinValue_()

static double getBinValue_	(	const Size	bin,
		const double	min_value,
		const double	bin_width
	)

staticprivate

static function that converts bin to value

Parameters

bin	bin number
min_value	minimum value (corresponding to bin number = 0)
bin_width	bin width

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
	)

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

◆ getDeconvolvedSpectrum()

DeconvolvedSpectrum& getDeconvolvedSpectrum ( )

return deconvolved spectrum

◆ getDecoyDeconvolvedSpectrum()

DeconvolvedSpectrum& getDecoyDeconvolvedSpectrum ( )

return decoy deconvolved spectrum

Referenced by TOPPFLASHDeconv::main_().

◆ getIsotopeCosineAndDetermineIsotopeIndex()

static float getIsotopeCosineAndDetermineIsotopeIndex	(	const double	mono_mass,
		const std::vector< float > &	per_isotope_intensities,
		int &	offset,
		int &	second_best_iso_offset,
		const PrecalculatedAveragine &	avg,
		int	window_width = `-1`,
		int	allowed_iso_error = `1`
	)

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	per isotope intensity - aggregated through charges
offset	output offset between input monoisotopic mono_mass and determined monoisotopic mono_mass
second_best_iso_offset	second best scoring isotope offset - for decoy calculation.
avg	precalculated averagine
window_width	isotope offset value range. If -1, set automatically.
allowed_iso_error	allowed isotope error to calculate qscure

Returns: calculated cosine similar score

◆ getNominalMass()

static int getNominalMass ( const double mass )

static

convert double to nominal mass

◆ operator=()

FLASHDeconvAlgorithm& operator= ( const FLASHDeconvAlgorithm & fd )

default

assignment operator

◆ performSpectrumDeconvolution()

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

main deconvolution function that generates the deconvolved and decoy deconvolved spectrum from 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 is provided from input spectrum to this function in most cases. But this parameter is used for real time deconvolution where scan number may be put separately.
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< double >>> &	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.

◆ removeHarmonicsPeakGroups_()

void removeHarmonicsPeakGroups_ ( DeconvolvedSpectrum & dpec )

private

◆ removeOverlappingPeakGroups_()

void removeOverlappingPeakGroups_	(	DeconvolvedSpectrum &	dpec,
		const double	tol,
		const int	iso_length = `1`
	)

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_().

◆ setDecoyFlag()

void setDecoyFlag ( int flag )

set decoy_flag_

Referenced by TOPPFLASHDeconv::main_().

◆ setFilters_()

void setFilters_ ( )

private

Make the universal pattern.

◆ setTargetMasses()

void setTargetMasses ( const std::vector< double > & masses )

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

◆ unionPrevMassBins_()

void unionPrevMassBins_ ( )

private

this function takes the previous deconvolution results (from ovelapped spectra) for sensitive deconvolution of the current spectrum

◆ 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_ ( const MSSpectrum * spec )

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_	(	const 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_offsets_

std::vector<int> bin_offsets_

private

This stores the "universal pattern" in binned dimension.

◆ bin_width_

DoubleList bin_width_

private

bin size for first stage of mass selection - for fast convolution, binning is used

◆ charge_decoy_

const int charge_decoy_ = 1

staticprivate

◆ 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_charge_

int current_min_charge_

private

current_min_charge_ charge: 1 for MSn n>1; otherwise just min_abs_charge_

◆ 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

deconvolved_spectrum_ stores the deconvolved mass peak groups

◆ decoy_deconvolved_spectrum_

DeconvolvedSpectrum decoy_deconvolved_spectrum_

private

decoy_deconvolved_spectrum_ stores the deconvolved decoy mass peak groups

◆ decoy_run_flag_

int decoy_run_flag_ = 0

private

max mass count per spectrum for each MS level

if it is set to 0, not a decoy run. If 1, the charge decoy run, If 2, the random noise decoy run

◆ excluded_mass_bins_

boost::dynamic_bitset excluded_mass_bins_

private

mass bins that are excluded for decoy

◆ excluded_masses_

std::vector<double> excluded_masses_

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_charges_

const std::vector<int> harmonic_charges_ {2, 3, 5, 7}

private

harmonic charge factors that will be considered for harmonic mass reduction. For example, 2 is for 1/2 charge harmonic component reduction

◆ 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.

◆ isotope_decoy_

const int isotope_decoy_ = 3

staticprivate

◆ log_mz_peaks_

std::vector<LogMzPeak> log_mz_peaks_

private

Stores log mz peaks.

◆ low_charge_

const int low_charge_ = 6

private

high and low charges are differently deconvolved. This value determines the (inclusive) threshold for low charge.

◆ 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_peak_count_

const int max_peak_count_ = 30000

private

allowed maximum peak count per spectrum - intensity based.

◆ 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 IntList min_support_peak_count_ = {3,3,3,3,3,3,3,3}

private

minimum number of peaks supporting a mass

◆ ms_level_

int 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

◆ mz_bins_for_edge_effect_

boost::dynamic_bitset mz_bins_for_edge_effect_

private

mz_bins_for_edge_effect_ stores the binned log mz peaks, considering edge effect

◆ noise_decoy_

const int noise_decoy_ = 2

staticprivate

◆ prev_mass_bins_ms1_

std::vector<std::vector<Size> > prev_mass_bins_ms1_

private

The data structures for spectra overlapping.

◆ prev_mass_bins_ms2_

std::vector<std::map<int, std::vector<Size> > > prev_mass_bins_ms2_

private

◆ prev_rts_ms1_

std::vector<double> prev_rts_ms1_

private

◆ prev_rts_ms2_

std::vector<double> prev_rts_ms2_

private

◆ target_mass_bins_

boost::dynamic_bitset target_mass_bins_

private

mass bins that are targeted for FLASHIda global targeting mode

◆ target_masses_

std::vector<double> target_masses_

private

◆ tolerance_

DoubleList tolerance_

private

tolerance in ppm for each MS level

◆ write_detail_

bool write_detail_ = false

private

to store detailed information

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]

Member Function Documentation

◆ addExcludedMonoMass()

◆ calculateAveragine()

◆ clearExcludedMonoMasses()

◆ filterMassBins_()

◆ filterPeakGroupsByIsotopeCosine_()

◆ generatePeakGroupsFromSpectrum_()

◆ getAveragine()

◆ getBinNumber_()

◆ getBinValue_()

◆ getCandidatePeakGroups_()

◆ getCosine()

◆ getDeconvolvedSpectrum()

◆ getDecoyDeconvolvedSpectrum()

◆ getIsotopeCosineAndDetermineIsotopeIndex()

◆ getNominalMass()

◆ operator=()

◆ performSpectrumDeconvolution()

◆ registerPrecursor()

◆ removeHarmonicsPeakGroups_()

◆ removeOverlappingPeakGroups_()

◆ scoreAndFilterPeakGroups_()

◆ setAveragine()

◆ setDecoyFlag()

◆ setFilters_()

◆ setTargetMasses()

◆ unionPrevMassBins_()

◆ updateCandidateMassBins_()

◆ updateLogMzPeaks_()

◆ updateMassBins_()

◆ updateMembers_()

◆ updateMzBins_()

Member Data Documentation

◆ allowed_iso_error_

◆ avg_

◆ bin_offsets_

◆ bin_width_

◆ charge_decoy_

◆ current_max_charge_

◆ current_max_mass_

◆ current_min_charge_

◆ current_min_mass_

◆ deconvolved_spectrum_

◆ decoy_deconvolved_spectrum_

◆ decoy_run_flag_

◆ excluded_mass_bins_

◆ excluded_masses_

◆ filter_

◆ harmonic_bin_offset_matrix_

◆ harmonic_charges_

◆ harmonic_filter_matrix_

◆ intensity_threshold_

◆ is_positive_

◆ iso_da_distance_

◆ isolation_window_size_

◆ isotope_decoy_

◆ log_mz_peaks_

◆ low_charge_

◆ mass_bin_min_value_

◆ mass_bins_

◆ max_abs_charge_

◆ max_mass_

◆ max_mz_