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 deisotoping - 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 Member Functions
	FLASHDeconvAlgorithm ()
	default constructor More...

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

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

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

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

	~FLASHDeconvAlgorithm () override=default
	destructor More...

std::vector< double >	getTolerances () const

void	run (MSExperiment &map, std::vector< DeconvolvedSpectrum > &deconvolved_spectra, std::vector< FLASHHelperClasses::MassFeature > &deconvolved_feature)
	Run FLASHDeconv algorithm for `map` and store `deconvolved_spectra` and `deconvolved_feature`. More...

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

const FLASHHelperClasses::PrecalculatedAveragine &	getDecoyAveragine ()
	get calculated decoy averagine. Call after calculateAveragine is called. More...

double	getNoiseDecoyWeight () const
	get noise decoy weight 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...

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...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

virtual	~ProgressLogger ()
	Destructor. More...

	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...

LogType	getLogType () const
	Returns the type of progress log being used. More...

void	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging. More...

void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...

void	setProgress (SignedSize value) const
	Sets the current progress. More...

void	endProgress (UInt64 bytes_processed=0) const

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Static Public Member Functions
static int	getScanNumber (const MSExperiment &map, Size index)
	get scan number of the spectrum in `index` -th in `map` 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	updateMSLevels_ (MSExperiment &map)
	read dataset to update ms level information More...

void	mergeSpectra_ (MSExperiment &map, uint ms_level)
	merge spectra More...

void	runSpectralDeconvolution_ (MSExperiment &map, std::vector< DeconvolvedSpectrum > &deconvolved_spectra)
	run spectral deconvolution More...

int	findPrecursorScanNumber_ (const MSExperiment &map, Size index, uint ms_level) const
	find precursor scan number when peak group is not found More...

void	appendDecoyPeakGroups_ (DeconvolvedSpectrum &deconvolved_spectrum, const MSSpectrum &spec, int scan_number, const PeakGroup &precursor_pg)
	append decoy peak groups to deconvolved spectrum More...

void	runFeatureFinding_ (std::vector< DeconvolvedSpectrum > &deconvolved_spectra, std::vector< FLASHHelperClasses::MassFeature > &deconvolved_features)
	run feature finding to get deconvolved features More...

void	findPrecursorPeakGroupsFormIdaLog_ (const MSExperiment &map, Size index, double start_mz, double end_mz)
	find precursor peak groups from FLASHIda log file More...

void	findPrecursorPeakGroupsForMSnSpectra_ (const MSExperiment &map, const std::vector< DeconvolvedSpectrum > &deconvolved_spectra, uint ms_level)
	register the precursor peak group (or mass) if possible for MSn (n>1) spectrum. More...

std::pair< int, int >	findScanNumberBounds_ (const MSExperiment &map, Size index, uint ms_level) const
	find scan number bounds for precursor search More...

std::vector< DeconvolvedSpectrum >	collectSurveyScans_ (const std::vector< DeconvolvedSpectrum > &deconvolved_spectra, int b_scan_number, int a_scan_number, uint ms_level) const
	collect survey scans within the given scan number bounds More...

std::pair< double, double >	getIsolationWindowMzRange_ (const MSSpectrum &spec) const
	get isolation window m/z range from precursors More...

PeakGroup	findBestPrecursorPeakGroup_ (const std::vector< DeconvolvedSpectrum > &survey_scans, double start_mz, double end_mz) const
	find the best precursor peak group from survey scans within the isolation window More...

void	determineTolerance_ (const MSExperiment &map, const Param &sd_param, const FLASHHelperClasses::PrecalculatedAveragine &avg, uint ms_level)
	determine tolerance More...

Static Private Member Functions
static void	updatePrecursorQScores_ (std::vector< DeconvolvedSpectrum > &deconvolved_spectra, int ms_level)
	with found deconvolved features, update QScores for masses that are contained in features. More...

static std::vector< int >	getHistogram_ (const std::vector< double > &data, double min_range, double max_range, double bin_size)
	get histogram More...

static void	filterLowPeaks_ (MSExperiment &map)
	filter low intensity peaks More...

Private Attributes
SpectralDeconvolution	sd_
	SpectralDeconvolution instances for spectral deconvolution for target and decoys. More...

SpectralDeconvolution	sd_noise_decoy_

SpectralDeconvolution	sd_signal_decoy_

int	merge_spec_ = 0
	to merge spectra. More...

int	forced_ms_level_ = 0
	forced MS level More...

UInt	max_ms_level_ = 4
	maximum MS level, which is 4. More...

UInt	current_max_ms_level_ = 0
	current maximum MS level - i.e., for MS2, this is the precursor charge More...

UInt	current_min_ms_level_ = 0
	current minimum MS level. More...

int	precursor_MS1_window_ = 0
	the number of preceding full scans from which MS2 precursor mass will be searched. More...

String	ida_log_file_
	FLASHIda log file name. More...

DoubleList	tols_
	mass tolerances, and minimum cosine scores per MS level More...

DoubleList	min_cos_

bool	use_RNA_averagine_ = false
	to use RNA averagine model More...

bool	report_decoy_ = false
	should decoy deconvolution be done? More...

double	isolation_window_size_ {3.0}
	default precursor isolation window size. More...

double	noise_decoy_weight_ = 1
	noise decoy weight determined with qvalue calcualtion. More...

std::map< int, std::vector< std::vector< float > > >	precursor_map_for_ida_
	FLASHIda parsing information is stored here: MS1 scan - information. More...

std::map< String, PeakGroup >	native_id_precursor_peak_group_map_
	a map from native ID to precursor peak group More...

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...

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...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

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 deisotoping - peak groups are defined here iii) scoring and filter out low scoring masses (i.e., peak groups)

Constructor & Destructor Documentation

◆ FLASHDeconvAlgorithm() [1/3]

FLASHDeconvAlgorithm ( )

default constructor

◆ FLASHDeconvAlgorithm() [2/3]

FLASHDeconvAlgorithm ( const FLASHDeconvAlgorithm & )

default

copy constructor

◆ FLASHDeconvAlgorithm() [3/3]

FLASHDeconvAlgorithm ( FLASHDeconvAlgorithm && other )

defaultnoexcept

move constructor

◆ ~FLASHDeconvAlgorithm()

~FLASHDeconvAlgorithm ( )

overridedefault

destructor

Member Function Documentation

◆ appendDecoyPeakGroups_()

void appendDecoyPeakGroups_	(	DeconvolvedSpectrum &	deconvolved_spectrum,
		const MSSpectrum &	spec,
		int	scan_number,
		const PeakGroup &	precursor_pg
	)

private

append decoy peak groups to deconvolved spectrum

◆ collectSurveyScans_()

std::vector<DeconvolvedSpectrum> collectSurveyScans_	(	const std::vector< DeconvolvedSpectrum > &	deconvolved_spectra,
		int	b_scan_number,
		int	a_scan_number,
		uint	ms_level
	)		const

private

collect survey scans within the given scan number bounds

◆ determineTolerance_()

void determineTolerance_	(	const MSExperiment &	map,
		const Param &	sd_param,
		const FLASHHelperClasses::PrecalculatedAveragine &	avg,
		uint	ms_level
	)

private

determine tolerance

◆ filterLowPeaks_()

static void filterLowPeaks_ ( MSExperiment & map )

staticprivate

filter low intensity peaks

◆ findBestPrecursorPeakGroup_()

PeakGroup findBestPrecursorPeakGroup_	(	const std::vector< DeconvolvedSpectrum > &	survey_scans,
		double	start_mz,
		double	end_mz
	)		const

private

find the best precursor peak group from survey scans within the isolation window

◆ findPrecursorPeakGroupsFormIdaLog_()

void findPrecursorPeakGroupsFormIdaLog_	(	const MSExperiment &	map,
		Size	index,
		double	start_mz,
		double	end_mz
	)

private

find precursor peak groups from FLASHIda log file

◆ findPrecursorPeakGroupsForMSnSpectra_()

void findPrecursorPeakGroupsForMSnSpectra_	(	const MSExperiment &	map,
		const std::vector< DeconvolvedSpectrum > &	deconvolved_spectra,
		uint	ms_level
	)

private

register the precursor peak group (or mass) if possible for MSn (n>1) spectrum.

◆ findPrecursorScanNumber_()

int findPrecursorScanNumber_	(	const MSExperiment &	map,
		Size	index,
		uint	ms_level
	)		const

private

find precursor scan number when peak group is not found

◆ findScanNumberBounds_()

std::pair<int, int> findScanNumberBounds_	(	const MSExperiment &	map,
		Size	index,
		uint	ms_level
	)		const

private

find scan number bounds for precursor search

◆ getAveragine()

const FLASHHelperClasses::PrecalculatedAveragine& getAveragine ( )

get calculated averagine. Call after calculateAveragine is called.

Referenced by TOPPFLASHDeconv::main_().

◆ getDecoyAveragine()

const FLASHHelperClasses::PrecalculatedAveragine& getDecoyAveragine ( )

get calculated decoy averagine. Call after calculateAveragine is called.

Referenced by TOPPFLASHDeconv::main_().

◆ getHistogram_()

static std::vector<int> getHistogram_	(	const std::vector< double > &	data,
		double	min_range,
		double	max_range,
		double	bin_size
	)

staticprivate

get histogram

◆ getIsolationWindowMzRange_()

std::pair<double, double> getIsolationWindowMzRange_ ( const MSSpectrum & spec ) const

private

get isolation window m/z range from precursors

◆ getNoiseDecoyWeight()

double getNoiseDecoyWeight ( ) const

inline

get noise decoy weight

Referenced by TOPPFLASHDeconv::main_().

◆ getScanNumber()

static int getScanNumber	(	const MSExperiment &	map,
		Size	index
	)

static

get scan number of the spectrum in index -th in map

◆ getTolerances()

std::vector<double> getTolerances ( ) const

Referenced by TOPPFLASHDeconv::main_().

◆ mergeSpectra_()

void mergeSpectra_	(	MSExperiment &	map,
		uint	ms_level
	)

private

merge spectra

◆ operator=() [1/2]

FLASHDeconvAlgorithm& operator= ( const FLASHDeconvAlgorithm & fd )

default

assignment operator

◆ operator=() [2/2]

FLASHDeconvAlgorithm& operator= ( FLASHDeconvAlgorithm && fd )

default

move assignment operator

◆ run()

void run	(	MSExperiment &	map,
		std::vector< DeconvolvedSpectrum > &	deconvolved_spectra,
		std::vector< FLASHHelperClasses::MassFeature > &	deconvolved_feature
	)

Run FLASHDeconv algorithm for map and store deconvolved_spectra and deconvolved_feature.

Parameters

map	the dataset
deconvolved_spectra	the deconvolved spectra will be stored in here
deconvolved_feature	the deconvolved features wll be strored in here

Referenced by TOPPFLASHDeconv::main_().

◆ runFeatureFinding_()

void runFeatureFinding_	(	std::vector< DeconvolvedSpectrum > &	deconvolved_spectra,
		std::vector< FLASHHelperClasses::MassFeature > &	deconvolved_features
	)

private

run feature finding to get deconvolved features

◆ runSpectralDeconvolution_()

void runSpectralDeconvolution_	(	MSExperiment &	map,
		std::vector< DeconvolvedSpectrum > &	deconvolved_spectra
	)

private

run spectral deconvolution

◆ 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.

◆ updateMSLevels_()

void updateMSLevels_ ( MSExperiment & map )

private

read dataset to update ms level information

◆ updatePrecursorQScores_()

static void updatePrecursorQScores_	(	std::vector< DeconvolvedSpectrum > &	deconvolved_spectra,
		int	ms_level
	)

staticprivate

with found deconvolved features, update QScores for masses that are contained in features.

Member Data Documentation

◆ current_max_ms_level_

UInt current_max_ms_level_ = 0

private

current maximum MS level - i.e., for MS2, this is the precursor charge

◆ current_min_ms_level_

UInt current_min_ms_level_ = 0

private

current minimum MS level.

◆ forced_ms_level_

int forced_ms_level_ = 0

private

forced MS level

◆ ida_log_file_

String ida_log_file_

private

FLASHIda log file name.

◆ isolation_window_size_

double isolation_window_size_ {3.0}

private

default precursor isolation window size.

◆ max_ms_level_

UInt max_ms_level_ = 4

private

maximum MS level, which is 4.

◆ merge_spec_

int merge_spec_ = 0

private

to merge spectra.

◆ min_cos_

DoubleList min_cos_

private

◆ native_id_precursor_peak_group_map_

std::map<String, PeakGroup> native_id_precursor_peak_group_map_

private

a map from native ID to precursor peak group

◆ noise_decoy_weight_

double noise_decoy_weight_ = 1

private

noise decoy weight determined with qvalue calcualtion.

◆ precursor_map_for_ida_

std::map<int, std::vector<std::vector<float> > > precursor_map_for_ida_

private

FLASHIda parsing information is stored here: MS1 scan - information.

◆ precursor_MS1_window_

int precursor_MS1_window_ = 0

private

the number of preceding full scans from which MS2 precursor mass will be searched.

◆ report_decoy_

bool report_decoy_ = false

private

should decoy deconvolution be done?

◆ sd_

SpectralDeconvolution sd_

private

SpectralDeconvolution instances for spectral deconvolution for target and decoys.

◆ sd_noise_decoy_

SpectralDeconvolution sd_noise_decoy_

private

◆ sd_signal_decoy_

SpectralDeconvolution sd_signal_decoy_

private

◆ tols_

DoubleList tols_

private

mass tolerances, and minimum cosine scores per MS level

◆ use_RNA_averagine_

bool use_RNA_averagine_ = false

private

to use RNA averagine model

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FLASHDeconvAlgorithm() [1/3]

◆ FLASHDeconvAlgorithm() [2/3]

◆ FLASHDeconvAlgorithm() [3/3]

◆ ~FLASHDeconvAlgorithm()

Member Function Documentation

◆ appendDecoyPeakGroups_()

◆ collectSurveyScans_()

◆ determineTolerance_()

◆ filterLowPeaks_()

◆ findBestPrecursorPeakGroup_()

◆ findPrecursorPeakGroupsFormIdaLog_()

◆ findPrecursorPeakGroupsForMSnSpectra_()

◆ findPrecursorScanNumber_()

◆ findScanNumberBounds_()

◆ getAveragine()

◆ getDecoyAveragine()

◆ getHistogram_()

◆ getIsolationWindowMzRange_()

◆ getNoiseDecoyWeight()

◆ getScanNumber()

◆ getTolerances()

◆ mergeSpectra_()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ run()

◆ runFeatureFinding_()

◆ runSpectralDeconvolution_()

◆ updateMembers_()

◆ updateMSLevels_()

◆ updatePrecursorQScores_()

Member Data Documentation

◆ current_max_ms_level_

◆ current_min_ms_level_

◆ forced_ms_level_

◆ ida_log_file_

◆ isolation_window_size_

◆ max_ms_level_

◆ merge_spec_

◆ min_cos_

◆ native_id_precursor_peak_group_map_

◆ noise_decoy_weight_

◆ precursor_map_for_ida_

◆ precursor_MS1_window_

◆ report_decoy_

◆ sd_

◆ sd_noise_decoy_

◆ sd_signal_decoy_

◆ tols_

◆ use_RNA_averagine_