A class representing a deconvolved spectrum. DeconvolvedSpectrum consists of PeakGroup instances 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 acquired 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 FLASHHelperClasses::LogMzPeak	LogMzPeak

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

	DeconvolvedSpectrum (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) noexcept=default
	move constructor More...

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

MSSpectrum	toSpectrum (int to_charge, double tol=10.0, 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...

double	getCurrentMaxMass (double max_mass) const

double	getCurrentMinMass (double min_mass) const

int	getCurrentMaxAbsCharge (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 Precursor::ActivationMethod &	getActivationMethod () const
	get activation method More...

FLASHHelperClasses::IsobaricQuantities	getQuantities () const
	return isobaric quantities More...

void	setQuantities (const FLASHHelperClasses::IsobaricQuantities &quantities)
	set isobaric quantities More...

void	setPrecursor (const Precursor &precursor)
	set precursor for MSn for n>1 More...

void	setPrecursorScanNumber (int scan_number)
	set precursor scan number More...

void	setActivationMethod (const Precursor::ActivationMethod &method)
	set activation method More...

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

void	setOriginalSpectrum (const MSSpectrum &spec)
	original spectrum setter More...

void	setPeakGroups (std::vector< PeakGroup > &x)
	set peak groups in this spectrum More...

std::vector< PeakGroup >::const_iterator	begin () const noexcept
	iterators and vector operators for std::vector<PeakGroup> peak_groups_ in this spectrum More...

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
	PeakGroup vector functions and operators. More...

PeakGroup &	operator[] (Size i)

void	push_back (const PeakGroup &pg)

void	emplace_back (const PeakGroup &pg)

void	pop_back ()

PeakGroup &	back ()

Size	size () const noexcept

void	clear ()

void	reserve (Size n)

bool	empty () const

bool	isDecoy () const

void	sort ()
	sort by deconvolved monoisotopic masses More...

void	sortByQscore ()
	sort by Qscore of peakGroups More...

bool	operator< (const DeconvolvedSpectrum &a) const
	comparison operators More...

bool	operator> (const DeconvolvedSpectrum &a) const

bool	operator== (const DeconvolvedSpectrum &a) const

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...

Precursor::ActivationMethod	activation_method_ = Precursor::ActivationMethod::CID
	activation method for file output More...

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

int	precursor_scan_number_ = 0

FLASHHelperClasses::IsobaricQuantities	quantities_
	isobaric quantities More...

Detailed Description

A class representing a deconvolved spectrum. DeconvolvedSpectrum consists of PeakGroup instances 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 acquired 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 FLASHHelperClasses::LogMzPeak LogMzPeak

Constructor & Destructor Documentation

◆ DeconvolvedSpectrum() [1/4]

DeconvolvedSpectrum ( )

default

default constructor

◆ DeconvolvedSpectrum() [2/4]

DeconvolvedSpectrum ( int scan_number )

explicit

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

Parameters

scan_number scan number of the spectrum

◆ ~DeconvolvedSpectrum()

~DeconvolvedSpectrum ( )

default

default destructor

◆ DeconvolvedSpectrum() [3/4]

DeconvolvedSpectrum ( const DeconvolvedSpectrum & )

default

copy constructor

◆ DeconvolvedSpectrum() [4/4]

DeconvolvedSpectrum ( DeconvolvedSpectrum && other )

defaultnoexcept

move constructor

Member Function Documentation

◆ back()

PeakGroup& back ( )

◆ begin() [1/2]

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

noexcept

iterators and vector operators for std::vector<PeakGroup> peak_groups_ in this spectrum

◆ begin() [2/2]

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

noexcept

◆ clear()

void clear ( )

◆ emplace_back()

void emplace_back ( const PeakGroup & pg )

◆ 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 Precursor::ActivationMethod& getActivationMethod ( ) const

get activation method

◆ getCurrentMaxAbsCharge()

int getCurrentMaxAbsCharge ( 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 ( 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 ( 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

◆ getQuantities()

FLASHHelperClasses::IsobaricQuantities getQuantities ( ) const

return isobaric quantities

◆ getScanNumber()

int getScanNumber ( ) const

get scan number of the original spectrum

◆ isDecoy()

bool isDecoy ( ) const

◆ operator<()

bool operator< ( const DeconvolvedSpectrum & a ) const

comparison operators

◆ operator=()

DeconvolvedSpectrum& operator= ( const DeconvolvedSpectrum & deconvolved_spectrum )

default

assignment operator

◆ operator==()

bool operator== ( const DeconvolvedSpectrum & a ) const

◆ operator>()

bool operator> ( const DeconvolvedSpectrum & a ) const

◆ operator[]() [1/2]

PeakGroup& operator[] ( Size i )

◆ operator[]() [2/2]

const PeakGroup& operator[] ( Size i ) const

PeakGroup vector functions and operators.

◆ pop_back()

void pop_back ( )

◆ push_back()

void push_back ( const PeakGroup & pg )

◆ reserve()

void reserve ( Size n )

◆ setActivationMethod()

void setActivationMethod ( const Precursor::ActivationMethod & method )

set activation method

◆ setOriginalSpectrum()

void setOriginalSpectrum ( const MSSpectrum & spec )

original spectrum setter

◆ setPeakGroups()

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

set peak groups in this spectrum

◆ setPrecursor()

void setPrecursor ( const Precursor & precursor )

set precursor for MSn for n>1

◆ setPrecursorPeakGroup()

void setPrecursorPeakGroup ( const PeakGroup & pg )

set precursor peakGroup

◆ setPrecursorScanNumber()

void setPrecursorScanNumber ( int scan_number )

set precursor scan number

◆ setQuantities()

void setQuantities ( const FLASHHelperClasses::IsobaricQuantities & quantities )

set isobaric quantities

◆ size()

Size size ( ) const

noexcept

◆ sort()

void sort ( )

sort by deconvolved monoisotopic masses

◆ sortByQscore()

void sortByQscore ( )

sort by Qscore of peakGroups

◆ toSpectrum()

MSSpectrum toSpectrum	(	int	to_charge,
		double	tol = `10.0`,
		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.
tol	the ppm tolerance
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)

Member Data Documentation

◆ activation_method_

Precursor::ActivationMethod activation_method_ = Precursor::ActivationMethod::CID

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

◆ quantities_

FLASHHelperClasses::IsobaricQuantities quantities_

private

isobaric quantities

◆ 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

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

◆ back()

◆ begin() [1/2]

◆ begin() [2/2]

◆ clear()

◆ emplace_back()

◆ empty()

◆ end() [1/2]

◆ end() [2/2]

◆ getActivationMethod()

◆ getCurrentMaxAbsCharge()

◆ getCurrentMaxMass()

◆ getCurrentMinMass()

◆ getOriginalSpectrum()

◆ getPrecursor()

◆ getPrecursorCharge()

◆ getPrecursorPeakGroup()

◆ getPrecursorScanNumber()

◆ getQuantities()

◆ getScanNumber()

◆ isDecoy()

◆ operator<()

◆ operator=()

◆ operator==()

◆ operator>()

◆ operator[]() [1/2]

◆ operator[]() [2/2]

◆ pop_back()

◆ push_back()

◆ reserve()

◆ setActivationMethod()

◆ setOriginalSpectrum()

◆ setPeakGroups()

◆ setPrecursor()

◆ setPrecursorPeakGroup()

◆ setPrecursorScanNumber()

◆ setQuantities()

◆ size()

◆ sort()

◆ sortByQscore()

◆ toSpectrum()

Member Data Documentation

◆ activation_method_

◆ peak_groups_

◆ precursor_peak_

◆ precursor_peak_group_

◆ precursor_scan_number_

◆ quantities_

◆ scan_number_

◆ spec_