Generates theoretical spectra for cross-linked peptides. More...

#include <OpenMS/CHEMISTRY/SimpleTSGXLMS.h>

Inheritance diagram for SimpleTSGXLMS:

Collaboration diagram for SimpleTSGXLMS:

Classes
struct	LossIndex

struct	SimplePeak
	A simple struct to represent peaks with mz and charge and sort them easily. More...

struct	SimplePeakComparator
	Comparator to sort SimplePeaks by mz. More...

Constructors and Destructors
bool	add_b_ions_

bool	add_y_ions_

bool	add_a_ions_

bool	add_c_ions_

bool	add_x_ions_

bool	add_z_ions_

bool	add_first_prefix_ion_

bool	add_losses_

bool	add_charges_

bool	add_isotopes_

bool	add_precursor_peaks_

bool	add_abundant_immonium_ions_

Int	max_isotope_

double	pre_int_

double	pre_int_H2O_

double	pre_int_NH3_

bool	add_k_linked_ions_

std::map< String, LossIndex >	loss_db_

double	loss_H2O_ = 0

double	loss_NH3_ = 0

	SimpleTSGXLMS ()
	default constructor More...

	SimpleTSGXLMS (const SimpleTSGXLMS &source)
	copy constructor More...

	~SimpleTSGXLMS () override
	destructor More...

SimpleTSGXLMS &	operator= (const SimpleTSGXLMS &tsg)
	assignment operator More...

virtual void	getLinearIonSpectrum (std::vector< SimplePeak > &spectrum, AASequence &peptide, Size link_pos, int charge=1, Size link_pos_2=0) const
	Generates fragment ions not containing the cross-linker for one peptide. More...

virtual void	getXLinkIonSpectrum (std::vector< SimplePeak > &spectrum, AASequence &peptide, Size link_pos, double precursor_mass, int min_charge, int max_charge, Size link_pos_2=0) const
	Generates fragment ions containing the cross-linker for one peptide. More...

virtual void	getXLinkIonSpectrum (std::vector< SimplePeak > &spectrum, OPXLDataStructs::ProteinProteinCrossLink &crosslink, bool frag_alpha, int min_charge, int max_charge) const
	Generates fragment ions containing the cross-linker for a pair of peptides. More...

void	updateMembers_ () override
	overwrite More...

virtual void	addLinearPeaks_ (std::vector< SimplePeak > &spectrum, AASequence &peptide, Size link_pos, Residue::ResidueType res_type, std::vector< LossIndex > &forward_losses, std::vector< LossIndex > &backward_losses, int charge=1, Size link_pos_2=0) const
	Adds cross-link-less ions of a specific ion type and charge to a spectrum. More...

virtual void	addPrecursorPeaks_ (std::vector< SimplePeak > &spectrum, double precursor_mass, int charge) const
	Adds precursor masses including neutral losses for the given charge. More...

virtual void	addLosses_ (std::vector< SimplePeak > &spectrum, double mono_weight, int charge, LossIndex &losses) const
	Adds neutral losses for an ion to a spectrum. More...

virtual void	addKLinkedIonPeaks_ (std::vector< SimplePeak > &spectrum, AASequence &peptide, Size link_pos, double precursor_mass, int charge) const
	Adds one-residue-linked ion peaks, that are specific to XLMS. More...

virtual void	addXLinkIonPeaks_ (std::vector< SimplePeak > &spectrum, AASequence &peptide, Size link_pos, double precursor_mass, Residue::ResidueType res_type, std::vector< LossIndex > &forward_losses, std::vector< LossIndex > &backward_losses, int charge, Size link_pos_2=0) const
	Adds cross-linked ions of a specific ion type and charge to a spectrum. More...

virtual void	addXLinkIonPeaks_ (std::vector< SimplePeak > &spectrum, OPXLDataStructs::ProteinProteinCrossLink &crosslink, bool frag_alpha, Residue::ResidueType res_type, std::vector< LossIndex > &forward_losses, std::vector< LossIndex > &backward_losses, LossIndex &losses_peptide2, int charge) const
	Adds cross-linked ions of a specific ion type and charge to a spectrum. More...

std::vector< LossIndex >	getForwardLosses_ (AASequence &peptide) const
	Calculates sets of possible neutral losses for each position in the given peptide. More...

std::vector< LossIndex >	getBackwardLosses_ (AASequence &peptide) const
	Calculates sets of possible neutral losses for each position in the given peptide. More...

Additional Inherited Members
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...

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

Detailed Description

Generates theoretical spectra for cross-linked peptides.

The spectra this class generates are vectors of SimplePeaks. This class generates the same peak types as TheoreticalSpectrumGeneratorXLMS and the interface is very similar, but it is simpler and faster. SimplePeak only contains an mz value and a charge. No intensity values or String annotations or other additional DataArrays are generated.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
add_isotopes	string	false	true, false	If set to 1 isotope peaks of the product ion peaks are added
max_isotope	int	2		Defines the maximal isotopic peak which is added, add_isotopes must be set to 1
add_losses	string	false	true, false	Adds common losses to those ion expect to have them, only water and ammonia loss is considered
add_precursor_peaks	string	true	true, false	Adds peaks of the precursor to the spectrum, which happen to occur sometimes
add_abundant_immonium_ions	string	false	true, false	Add most abundant immonium ions
add_k_linked_ions	string	true	true, false	Add RES-Linked ions, which are specific to XLMS
add_first_prefix_ion	string	true	true, false	If set to true e.g. b1 ions are added
add_y_ions	string	true	true, false	Add peaks of y-ions to the spectrum
add_b_ions	string	true	true, false	Add peaks of b-ions to the spectrum
add_a_ions	string	true	true, false	Add peaks of a-ions to the spectrum
add_c_ions	string	false	true, false	Add peaks of c-ions to the spectrum
add_x_ions	string	false	true, false	Add peaks of x-ions to the spectrum
add_z_ions	string	false	true, false	Add peaks of z-ions to the spectrum

Note:

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

Class Documentation

◆ OpenMS::SimpleTSGXLMS::LossIndex

struct OpenMS::SimpleTSGXLMS::LossIndex

Collaboration diagram for SimpleTSGXLMS::LossIndex:

[legend]

Class Members
bool	has_H2O_loss
bool	has_NH3_loss

Constructor & Destructor Documentation

◆ SimpleTSGXLMS() [1/2]

SimpleTSGXLMS ( )

default constructor

◆ SimpleTSGXLMS() [2/2]

SimpleTSGXLMS ( const SimpleTSGXLMS & source )

copy constructor

◆ ~SimpleTSGXLMS()

~SimpleTSGXLMS ( )

override

destructor

Member Function Documentation

◆ addKLinkedIonPeaks_()

virtual void addKLinkedIonPeaks_	(	std::vector< SimplePeak > &	spectrum,
		AASequence &	peptide,
		Size	link_pos,
		double	precursor_mass,
		int	charge
	)		const

protectedvirtual

Adds one-residue-linked ion peaks, that are specific to XLMS.

These fragments consist of one whole peptide, the cross-linker and a part of the linked residue from the second peptide. The residue fragment on the linker is an internal ion from a y- and an a-fragmentation with the length of one residue. The function is called KLinked for now, but instead of K it is whatever residue the linker is bound to.

Parameters

spectrum	The spectrum to which the peaks are added
peptide	The fragmented peptide
link_pos	position of the linker on the fragmented peptide
precursor_mass	The mass of the whole cross-link candidate or the precursor mass of the experimental MS2 spectrum.
charge	The charge of the ion

◆ addLinearPeaks_()

virtual void addLinearPeaks_	(	std::vector< SimplePeak > &	spectrum,
		AASequence &	peptide,
		Size	link_pos,
		Residue::ResidueType	res_type,
		std::vector< LossIndex > &	forward_losses,
		std::vector< LossIndex > &	backward_losses,
		int	charge = `1`,
		Size	link_pos_2 = `0`
	)		const

protectedvirtual

Adds cross-link-less ions of a specific ion type and charge to a spectrum.

Parameters

spectrum	The spectrum to which the new peaks are added. Does not have to be empty, the generated peaks will be pushed onto it.
peptide	The peptide to fragment
link_pos	The position of the cross-linker on the given peptide
res_type	The ion type of the added peaks
forward_losses	vector of LossIndex generated by getForwardLosses_
backward_losses	vector of LossIndex generated by getBackwardLosses_
charge	The charge of the added peaks
link_pos_2	A second position for the linker, in case it is a loop link

◆ addLosses_()

virtual void addLosses_	(	std::vector< SimplePeak > &	spectrum,
		double	mono_weight,
		int	charge,
		LossIndex &	losses
	)		const

protectedvirtual

Adds neutral losses for an ion to a spectrum.

Parameters

spectrum	The spectrum to which the new peak is added
mono_weight	monoisotopic mass of the current ion
charge	The charge of the ion
losses	a LossIndex with which to modify the current ion

◆ addPrecursorPeaks_()

virtual void addPrecursorPeaks_	(	std::vector< SimplePeak > &	spectrum,
		double	precursor_mass,
		int	charge
	)		const

protectedvirtual

Adds precursor masses including neutral losses for the given charge.

Parameters

spectrum	The spectrum to which the peaks are added
precursor_mass	The mass of the uncharged precursor
charge	The charge of the precursor

◆ addXLinkIonPeaks_() [1/2]

virtual void addXLinkIonPeaks_	(	std::vector< SimplePeak > &	spectrum,
		AASequence &	peptide,
		Size	link_pos,
		double	precursor_mass,
		Residue::ResidueType	res_type,
		std::vector< LossIndex > &	forward_losses,
		std::vector< LossIndex > &	backward_losses,
		int	charge,
		Size	link_pos_2 = `0`
	)		const

protectedvirtual

Adds cross-linked ions of a specific ion type and charge to a spectrum.

This version of the function is for mono-links and loop-links.

Parameters

spectrum	The spectrum to which the new peaks are added. Does not have to be empty, the generated peaks will be pushed onto it.
peptide	The peptide to fragment
link_pos	The position of the cross-linker on the given peptide
precursor_mass	The mass of the whole cross-link candidate or the precursor mass of the experimental MS2 spectrum.
res_type	The ion type of the added peaks
forward_losses	vector of LossIndex generated by getForwardLosses_
backward_losses	vector of LossIndex generated by getBackwardLosses_
charge	The charge of the added peaks
link_pos_2	A second position for the linker, in case it is a loop link

◆ addXLinkIonPeaks_() [2/2]

virtual void addXLinkIonPeaks_	(	std::vector< SimplePeak > &	spectrum,
		OPXLDataStructs::ProteinProteinCrossLink &	crosslink,
		bool	frag_alpha,
		Residue::ResidueType	res_type,
		std::vector< LossIndex > &	forward_losses,
		std::vector< LossIndex > &	backward_losses,
		LossIndex &	losses_peptide2,
		int	charge
	)		const

protectedvirtual

Adds cross-linked ions of a specific ion type and charge to a spectrum.

This version of the function is for cross-linked peptide pairs.

Parameters

spectrum	The spectrum to which the new peaks are added. Does not have to be empty, the generated peaks will be pushed onto it.
crosslink	The ProteinProteinCrossLink to be fragmented
frag_alpha	True, if the fragmented peptide is the Alpha peptide. Used for ion-name annotation.
res_type	The ion type of the added peaks
forward_losses	vector of LossIndex generated by getForwardLosses_ for the fragmented peptide
backward_losses	vector of LossIndex generated by getBackwardLosses_ for the fragmented peptide
losses_peptide2	set of losses for the second, not fragmented peptide, e.g. last set from getForwardLosses_ for the second peptide
charge	The charge of the added peaks

◆ getBackwardLosses_()

std::vector< LossIndex > getBackwardLosses_ ( AASequence & peptide ) const

protected

Calculates sets of possible neutral losses for each position in the given peptide.

This function generates a vector of sets. Each set contains the possible neutral losses for a specific suffix of the peptide.

Parameters

peptide The peptide or ion for which to collect possible losses

◆ getForwardLosses_()

std::vector< LossIndex > getForwardLosses_ ( AASequence & peptide ) const

protected

Calculates sets of possible neutral losses for each position in the given peptide.

This function generates a vector of sets. Each set contains the possible neutral losses for a specific prefix of the peptide.

Parameters

peptide The peptide or ion for which to collect possible losses

◆ getLinearIonSpectrum()

virtual void getLinearIonSpectrum	(	std::vector< SimplePeak > &	spectrum,
		AASequence &	peptide,
		Size	link_pos,
		int	charge = `1`,
		Size	link_pos_2 = `0`
	)		const

virtual

Generates fragment ions not containing the cross-linker for one peptide.

B-ions are generated from the beginning of the peptide up to the first linked position, y-ions are generated from the second linked position up the end of the peptide. If link_pos_2 is 0, a mono-link or cross-link is assumed and the second position is the same as the first position. For a loop-link two different positions can be set and link_pos_2 must be larger than link_pos. The generated ion types and other additional settings are determined by the tool parameters.

Parameters

spectrum	The spectrum to which the new peaks are added. Does not have to be empty, the generated peaks will be pushed onto it.
peptide	The peptide to fragment
link_pos	The position of the cross-linker on the given peptide
charge	The maximal charge of the ions
link_pos_2	A second position for the linker, in case it is a loop link

◆ getXLinkIonSpectrum() [1/2]

virtual void getXLinkIonSpectrum	(	std::vector< SimplePeak > &	spectrum,
		AASequence &	peptide,
		Size	link_pos,
		double	precursor_mass,
		int	min_charge,
		int	max_charge,
		Size	link_pos_2 = `0`
	)		const

virtual

Generates fragment ions containing the cross-linker for one peptide.

B-ions are generated from the first linked position up to the end of the peptide, y-ions are generated from the beginning of the peptide up to the second linked position. If link_pos_2 is 0, a mono-link or cross-link is assumed and the second position is the same as the first position. For a loop-link two different positions can be set and link_pos_2 must be larger than link_pos. Since in the case of a cross-link a whole second peptide is attached to the other side of the cross-link, a precursor mass for the two peptides and the linker is needed. In the case of a loop link the precursor mass is the mass of the only peptide and the linker. Although this function is more general, currently it is mainly used for loop-links and mono-links, because residues in the second, unknown peptide cannot be considered for possible neutral losses. The generated ion types and other additional settings are determined by the tool parameters.

Parameters

spectrum	The spectrum to which the new peaks are added. Does not have to be empty, the generated peaks will be pushed onto it.
peptide	The peptide to fragment
link_pos	The position of the cross-linker on the given peptide
precursor_mass	The mass of the whole cross-link candidate or the precursor mass of the experimental MS2 spectrum.
min_charge	The minimal charge of the ions
max_charge	The maximal charge of the ions, it should be the precursor charge and is used to generate precursor ion peaks
link_pos_2	A second position for the linker, in case it is a loop link

◆ getXLinkIonSpectrum() [2/2]

virtual void getXLinkIonSpectrum	(	std::vector< SimplePeak > &	spectrum,
		OPXLDataStructs::ProteinProteinCrossLink &	crosslink,
		bool	frag_alpha,
		int	min_charge,
		int	max_charge
	)		const

virtual

Generates fragment ions containing the cross-linker for a pair of peptides.

B-ions are generated from the first linked position up to the end of the peptide, y-ions are generated from the beginning of the peptide up to the second linked position. This function generates neutral loss ions by considering both linked peptides. Only one of the peptides, decided by frag_alpha, is fragmented. This simplifies the function, but it has to be called twice to get all fragments of a peptide pair. The generated ion types and other additional settings are determined by the tool parameters. This function is not suitable to generate fragments for mono-links or loop-links.

Parameters

spectrum	The spectrum to which the new peaks are added. Does not have to be empty, the generated peaks will be pushed onto it.
crosslink	ProteinProteinCrossLink to be fragmented
frag_alpha	True, if the fragmented peptide is the Alpha peptide.
min_charge	The minimal charge of the ions
max_charge	The maximal charge of the ions, it should be the precursor charge and is used to generate precursor ion peaks

◆ operator=()

SimpleTSGXLMS& operator= ( const SimpleTSGXLMS & tsg )

assignment operator

◆ updateMembers_()

void updateMembers_ ( )

overridevirtual

overwrite

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ add_a_ions_

bool add_a_ions_

protected

◆ add_abundant_immonium_ions_

bool add_abundant_immonium_ions_

protected

◆ add_b_ions_

bool add_b_ions_

protected

◆ add_c_ions_

bool add_c_ions_

protected

◆ add_charges_

bool add_charges_

protected

◆ add_first_prefix_ion_

bool add_first_prefix_ion_

protected

◆ add_isotopes_

bool add_isotopes_

protected

◆ add_k_linked_ions_

bool add_k_linked_ions_

protected

◆ add_losses_

bool add_losses_

protected

◆ add_precursor_peaks_

bool add_precursor_peaks_

protected

◆ add_x_ions_

bool add_x_ions_

protected

◆ add_y_ions_

bool add_y_ions_

protected

◆ add_z_ions_

bool add_z_ions_

protected

◆ loss_db_

std::map< String, LossIndex > loss_db_

protected

◆ loss_H2O_

double loss_H2O_ = 0

protected

◆ loss_NH3_

double loss_NH3_ = 0

protected

◆ max_isotope_

Int max_isotope_

protected

◆ pre_int_

double pre_int_

protected

◆ pre_int_H2O_

double pre_int_H2O_

protected

◆ pre_int_NH3_

double pre_int_NH3_

protected

Classes

Constructors and Destructors

Additional Inherited Members

Detailed Description

Class Documentation

◆ OpenMS::SimpleTSGXLMS::LossIndex

Constructor & Destructor Documentation

◆ SimpleTSGXLMS() [1/2]

◆ SimpleTSGXLMS() [2/2]

◆ ~SimpleTSGXLMS()

Member Function Documentation

◆ addKLinkedIonPeaks_()

◆ addLinearPeaks_()

◆ addLosses_()

◆ addPrecursorPeaks_()

◆ addXLinkIonPeaks_() [1/2]

◆ addXLinkIonPeaks_() [2/2]

◆ getBackwardLosses_()

◆ getForwardLosses_()

◆ getLinearIonSpectrum()

◆ getXLinkIonSpectrum() [1/2]

◆ getXLinkIonSpectrum() [2/2]

◆ operator=()

◆ updateMembers_()

Member Data Documentation

◆ add_a_ions_

◆ add_abundant_immonium_ions_

◆ add_b_ions_

◆ add_c_ions_

◆ add_charges_

◆ add_first_prefix_ion_

◆ add_isotopes_

◆ add_k_linked_ions_

◆ add_losses_

◆ add_precursor_peaks_

◆ add_x_ions_

◆ add_y_ions_

◆ add_z_ions_

◆ loss_db_

◆ loss_H2O_

◆ loss_NH3_

◆ max_isotope_

◆ pre_int_

◆ pre_int_H2O_

◆ pre_int_NH3_