A class representing a deconvolved spectrum. DeconvolvedSpectrum consists of PeakGroups representing masses. For MSn n>1, a PeakGroup representing the precursor mass is also added in this class. Properly assigning a precursor mass from the original precursor peak and its deconvolution result is very important in top down proteomics. This assignment is performed here for conventional datasets. But for FLASHIda acquired datasets, the assignment is already done by FLASHIda. So this class simply use the results from FLASHIda log file for assignment. The parsing of FLASHIda log file is done in FLASHDeconv tool class. More...

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

Collaboration diagram for DeconvolvedSpectrum:

[legend]

Public Types
typedef FLASHDeconvHelperStructs::LogMzPeak	LogMzPeak

Public Member Functions
	DeconvolvedSpectrum ()=default
	default constructor More...

	DeconvolvedSpectrum (const MSSpectrum &spectrum, const int scan_number)
	Constructor for DeconvolvedSpectrum. Takes the spectrum and scan number calculated from outside. More...

	~DeconvolvedSpectrum ()=default
	default destructor More...

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

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

DeconvolvedSpectrum &	operator= (const DeconvolvedSpectrum &deconvolved_spectrum)=default
	assignment operator More...

MSSpectrum	toSpectrum (const int to_charge, bool retain_undeconvolved=false)

const MSSpectrum &	getOriginalSpectrum () const
	original spectrum getter More...

const PeakGroup &	getPrecursorPeakGroup () const
	get precursor peak group for MSn (n>1) spectrum. It returns an empty peak group if no peak group is registered (by registerPrecursor) More...

int	getPrecursorCharge () const
	precursor charge getter (set in registerPrecursor) More...

const Precursor &	getPrecursor () const
	get precursor peak More...

void	setPrecursorPeakGroupQvalue (const double qvalue_with_iso_decoy_only, const double qvalue_with_noise_decoy_only, const double qvalue_with_charge_decoy_only)
	set qvalue of precursor peak More...

double	getCurrentMaxMass (const double max_mass) const

double	getCurrentMinMass (const double min_mass) const

int	getCurrentMaxAbsCharge (const int max_abs_charge) const

int	getScanNumber () const
	get scan number of the original spectrum More...

int	getPrecursorScanNumber () const
	get precursor scan number - only if it is registered. Otherwise return 0 More...

const String &	getActivationMethod () const
	get activation method More...

void	setPrecursor (const Precursor &precursor)
	set max isotope index More...

void	setPrecursorIntensity (const double i)
	set precursor peak intensity More...

void	setPrecursorScanNumber (const int scan_number)
	set max isotope index More...

void	setActivationMethod (const String &method)
	set activation method More...

void	setPrecursorPeakGroup (const PeakGroup &pg)
	set precusor peakGroup More...

std::vector< PeakGroup >::const_iterator	begin () const noexcept

std::vector< PeakGroup >::const_iterator	end () const noexcept

std::vector< PeakGroup >::iterator	begin () noexcept

std::vector< PeakGroup >::iterator	end () noexcept

const PeakGroup &	operator[] (Size i) const

void	push_back (const PeakGroup &pg)

Size	size () const noexcept

void	clear ()

void	reserve (Size n)

bool	empty () const

void	swap (std::vector< PeakGroup > &x)

void	sort ()

void	sortByQScore ()

Static Public Member Functions
static void	updatePeakGroupQvalues (std::vector< DeconvolvedSpectrum > &deconvolved_spectra, std::vector< DeconvolvedSpectrum > &deconvolved_decoy_spectra)

Private Attributes
std::vector< PeakGroup >	peak_groups
	peak groups (deconvolved masses) More...

MSSpectrum	spec_
	the original raw spectrum (not deconvolved) More...

PeakGroup	precursor_peak_group_
	precursor peakGroup (or mass) More...

Precursor	precursor_peak_
	precursor raw peak (not deconvolved one) More...

String	activation_method_
	activation method for file output More...

int	scan_number_ = 0
	scan number and precursor scan number More...

int	precursor_scan_number_ = 0

Detailed Description

A class representing a deconvolved spectrum. DeconvolvedSpectrum consists of PeakGroups representing masses. For MSn n>1, a PeakGroup representing the precursor mass is also added in this class. Properly assigning a precursor mass from the original precursor peak and its deconvolution result is very important in top down proteomics. This assignment is performed here for conventional datasets. But for FLASHIda acquired datasets, the assignment is already done by FLASHIda. So this class simply use the results from FLASHIda log file for assignment. The parsing of FLASHIda log file is done in FLASHDeconv tool class.

Member Typedef Documentation

◆ LogMzPeak

typedef FLASHDeconvHelperStructs::LogMzPeak LogMzPeak

Constructor & Destructor Documentation

◆ DeconvolvedSpectrum() [1/4]

DeconvolvedSpectrum ( )

default

default constructor

◆ DeconvolvedSpectrum() [2/4]

DeconvolvedSpectrum	(	const MSSpectrum &	spectrum,
		const int	scan_number
	)

Constructor for DeconvolvedSpectrum. Takes the spectrum and scan number calculated from outside.

Parameters

spectrum	spectrum for which the deconvolution will be performed
scan_number	scan number of the spectrum: this argument is put here for real time case where scan number should be input separately.

◆ ~DeconvolvedSpectrum()

~DeconvolvedSpectrum ( )

default

default destructor

◆ DeconvolvedSpectrum() [3/4]

DeconvolvedSpectrum ( const DeconvolvedSpectrum & )

default

copy constructor

◆ DeconvolvedSpectrum() [4/4]

DeconvolvedSpectrum ( DeconvolvedSpectrum && other )

default

move constructor

Member Function Documentation

◆ begin() [1/2]

std::vector<PeakGroup>::const_iterator begin ( ) const

noexcept

◆ begin() [2/2]

std::vector<PeakGroup>::iterator begin ( )

noexcept

◆ clear()

void clear ( )

◆ empty()

bool empty ( ) const

◆ end() [1/2]

std::vector<PeakGroup>::const_iterator end ( ) const

noexcept

◆ end() [2/2]

std::vector<PeakGroup>::iterator end ( )

noexcept

◆ getActivationMethod()

const String& getActivationMethod ( ) const

get activation method

◆ getCurrentMaxAbsCharge()

int getCurrentMaxAbsCharge ( const int max_abs_charge ) const

get possible max charge of the deconvolved masses - for MS1, max charge specified by user for MSn, min value between max charge specified by the user and precursor charge

Parameters

max_abs_charge the max absolute value of the charge specified by the user

◆ getCurrentMaxMass()

double getCurrentMaxMass ( const double max_mass ) const

get possible max mass of the deconvolved masses - for MS1, max mass specified by user for MSn, min value between max mass specified by the user and precursor mass

Parameters

max_mass the max mass specified by the user

◆ getCurrentMinMass()

double getCurrentMinMass ( const double min_mass ) const

get possible min mass of the deconvolved masses - for MS1, min mass specified by user for MSn, 50.0

Parameters

min_mass the min mass specified by the user

◆ getOriginalSpectrum()

const MSSpectrum& getOriginalSpectrum ( ) const

original spectrum getter

◆ getPrecursor()

const Precursor& getPrecursor ( ) const

get precursor peak

◆ getPrecursorCharge()

int getPrecursorCharge ( ) const

precursor charge getter (set in registerPrecursor)

◆ getPrecursorPeakGroup()

const PeakGroup& getPrecursorPeakGroup ( ) const

get precursor peak group for MSn (n>1) spectrum. It returns an empty peak group if no peak group is registered (by registerPrecursor)

◆ getPrecursorScanNumber()

int getPrecursorScanNumber ( ) const

get precursor scan number - only if it is registered. Otherwise return 0

◆ getScanNumber()

int getScanNumber ( ) const

get scan number of the original spectrum

◆ operator=()

DeconvolvedSpectrum& operator= ( const DeconvolvedSpectrum & deconvolved_spectrum )

default

assignment operator

◆ operator[]()

const PeakGroup& operator[] ( Size i ) const

◆ push_back()

void push_back ( const PeakGroup & pg )

◆ reserve()

void reserve ( Size n )

◆ setActivationMethod()

void setActivationMethod ( const String & method )

set activation method

◆ setPrecursor()

void setPrecursor ( const Precursor & precursor )

set max isotope index

◆ setPrecursorIntensity()

void setPrecursorIntensity ( const double i )

set precursor peak intensity

◆ setPrecursorPeakGroup()

void setPrecursorPeakGroup ( const PeakGroup & pg )

set precusor peakGroup

◆ setPrecursorPeakGroupQvalue()

void setPrecursorPeakGroupQvalue	(	const double	qvalue_with_iso_decoy_only,
		const double	qvalue_with_noise_decoy_only,
		const double	qvalue_with_charge_decoy_only
	)

set qvalue of precursor peak

◆ setPrecursorScanNumber()

void setPrecursorScanNumber ( const int scan_number )

set max isotope index

◆ size()

Size size ( ) const

noexcept

Referenced by TOPPFLASHDeconv::main_().

◆ sort()

void sort ( )

◆ sortByQScore()

void sortByQScore ( )

◆ swap()

void swap ( std::vector< PeakGroup > & x )

◆ toSpectrum()

MSSpectrum toSpectrum	(	const int	to_charge,
		bool	retain_undeconvolved = `false`
	)

Convert DeconvolvedSpectrum to MSSpectrum (e.g., used to store in mzML format).

Parameters

to_charge	the charge of each peak in mzml output.
retain_undeconvolved	if set, undeconvolved peaks in the original peaks are output (assuming their abs charge == 1 and m/zs are adjusted with the to_charge parameter)

◆ updatePeakGroupQvalues()

static void updatePeakGroupQvalues	(	std::vector< DeconvolvedSpectrum > &	deconvolved_spectra,
		std::vector< DeconvolvedSpectrum > &	deconvolved_decoy_spectra
	)

static

Referenced by TOPPFLASHDeconv::main_().

Member Data Documentation

◆ activation_method_

String activation_method_

private

activation method for file output

◆ peak_groups

std::vector<PeakGroup> peak_groups

private

peak groups (deconvolved masses)

◆ precursor_peak_

Precursor precursor_peak_

private

precursor raw peak (not deconvolved one)

◆ precursor_peak_group_

PeakGroup precursor_peak_group_

private

precursor peakGroup (or mass)

◆ precursor_scan_number_

int precursor_scan_number_ = 0

private

◆ scan_number_

int scan_number_ = 0

private

scan number and precursor scan number

◆ spec_

MSSpectrum spec_

private

the original raw spectrum (not deconvolved)

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ LogMzPeak

Constructor & Destructor Documentation

◆ DeconvolvedSpectrum() [1/4]

◆ DeconvolvedSpectrum() [2/4]

◆ ~DeconvolvedSpectrum()

◆ DeconvolvedSpectrum() [3/4]

◆ DeconvolvedSpectrum() [4/4]

Member Function Documentation

◆ begin() [1/2]

◆ begin() [2/2]

◆ clear()

◆ empty()

◆ end() [1/2]

◆ end() [2/2]

◆ getActivationMethod()

◆ getCurrentMaxAbsCharge()

◆ getCurrentMaxMass()

◆ getCurrentMinMass()

◆ getOriginalSpectrum()

◆ getPrecursor()

◆ getPrecursorCharge()

◆ getPrecursorPeakGroup()

◆ getPrecursorScanNumber()

◆ getScanNumber()

◆ operator=()

◆ operator[]()

◆ push_back()

◆ reserve()

◆ setActivationMethod()

◆ setPrecursor()

◆ setPrecursorIntensity()

◆ setPrecursorPeakGroup()

◆ setPrecursorPeakGroupQvalue()

◆ setPrecursorScanNumber()

◆ size()

◆ sort()

◆ sortByQScore()

◆ swap()

◆ toSpectrum()

◆ updatePeakGroupQvalues()

Member Data Documentation

◆ activation_method_

◆ peak_groups

◆ precursor_peak_

◆ precursor_peak_group_

◆ precursor_scan_number_

◆ scan_number_

◆ spec_