This class can select appropriate fragment ions of an MS/MS spectrum of a peptide. More...

#include <OpenMS/ANALYSIS/MRM/MRMFragmentSelection.h>

Inheritance diagram for MRMFragmentSelection:

Public Member Functions
MRMFragmentSelection &	operator= (const MRMFragmentSelection &rhs)
	assignment operator More...

void	selectFragments (std::vector< Peak1D > &selected_peaks, const PeakSpectrum &spec)
	selects accordingly to the parameters the best peaks of spec and writes them into selected_peaks More...

Constructors and destructors
	MRMFragmentSelection ()
	default constructor More...

	MRMFragmentSelection (const MRMFragmentSelection &rhs)
	copy constructor More...

	~MRMFragmentSelection () override
	destructor 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...

Protected Member Functions
bool	peakselectionIsAllowed_ (const String &name, const int charge)
	returns true if the selection of peak is allowed, according to the parameters set and the ion name More...

Protected Member Functions inherited from DefaultParamHandler
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...

void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. 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

This class can select appropriate fragment ions of an MS/MS spectrum of a peptide.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
num_top_peaks	int	4		Number of most intense peak to pick
min_pos_precursor_percentage	float	80		Minimal ion position the ion should have, relative to the precursor position
min_mz	float	400		Minimal m/z value that is allowed for selection.
max_mz	float	1200		Maximal m/z value that is allowed for selection.
consider_names	string	true	true, false	Should names be considered when selecting ions?
allow_loss_ions	string	false	true, false	Should loss ions allowed to be selected?
allowed_ion_types	string list	[y]		The one-character-typenames of the ion types allowed
allowed_charges	string list	[1]		List of allowed charge states for selection.

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Several user choices can influence the selection of the ions from the MS/MS spectrum. These choices can be done using the parameters as described on the parameters page (see below). Basically there are two different ways of selecting suitable ions. One, using standardized names, e.g. given in the meta value "IonName" of each peaks of the spectrum (this can be written from TheoreticalSpectrumGenerator, PILISModel...). The second one is simply using the most abundant peaks in a specified m/z range.

Constructor & Destructor Documentation

◆ MRMFragmentSelection() [1/2]

MRMFragmentSelection ( )

default constructor

◆ MRMFragmentSelection() [2/2]

MRMFragmentSelection ( const MRMFragmentSelection & rhs )

copy constructor

◆ ~MRMFragmentSelection()

~MRMFragmentSelection ( )

override

destructor

Member Function Documentation

◆ operator=()

MRMFragmentSelection& operator= ( const MRMFragmentSelection & rhs )

assignment operator

◆ peakselectionIsAllowed_()

bool peakselectionIsAllowed_	(	const String &	name,
		const int	charge
	)

protected

returns true if the selection of peak is allowed, according to the parameters set and the ion name

◆ selectFragments()

void selectFragments	(	std::vector< Peak1D > &	selected_peaks,
		const PeakSpectrum &	spec
	)

selects accordingly to the parameters the best peaks of spec and writes them into selected_peaks

Public Member Functions

Protected Member Functions

Additional Inherited Members