RawTandemMSSignalSimulation Class Reference

Simulates tandem MS signals for a given set of peptides. More...

#include <OpenMS/SIMULATION/RawTandemMSSignalSimulation.h>

Inheritance diagram for RawTandemMSSignalSimulation:

Collaboration diagram for RawTandemMSSignalSimulation:

Constructors and Destructors
SimTypes::MutableSimRandomNumberGeneratorPtr	rnd_gen_
	Random number generator. More...
	RawTandemMSSignalSimulation ()
	Default constructor (hidden) More...
	RawTandemMSSignalSimulation (SimTypes::MutableSimRandomNumberGeneratorPtr rng)
	Constructor taking a random generator. More...
	RawTandemMSSignalSimulation (const RawTandemMSSignalSimulation &source)
	Copy constructor. More...
	~RawTandemMSSignalSimulation () override
	Destructor. More...
RawTandemMSSignalSimulation &	operator= (const RawTandemMSSignalSimulation &source)
void	generateRawTandemSignals (const SimTypes::FeatureMapSim &, SimTypes::MSSimExperiment &, SimTypes::MSSimExperiment &)
void	initParam_ ()
	initialize param_ class More...
void	generateMSESpectra_ (const SimTypes::FeatureMapSim &features, const SimTypes::MSSimExperiment &experiment, SimTypes::MSSimExperiment &ms2)
void	generatePrecursorSpectra_ (const SimTypes::FeatureMapSim &features, const SimTypes::MSSimExperiment &experiment, SimTypes::MSSimExperiment &ms2)

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...
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...
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
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...
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

Simulates tandem MS signals for a given set of peptides.

Simulates tandem MS signals for a given set of peptides, with charge annotation, given detectabilities, predicted retention times and charge values.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
status	string	disabled	disabled, precursor, MS^E	Create Tandem-MS scans?
tandem_mode	int	0	min: 0 max: 2	Algorithm to generate the tandem-MS spectra. 0 - fixed intensities, 1 - SVC prediction (abundant/missing), 2 - SVR prediction of peak intensity
svm_model_set_file	string	SIMULATION/SvmModelSet.model		File containing the filenames of SVM Models for different charge variants
ionization_type	string	ESI	MALDI, ESI	Type of Ionization (MALDI or ESI)
Precursor:ms2_spectra_per_rt_bin	int	5	min: 1	Number of allowed MS/MS spectra in a retention time bin.
Precursor:min_mz_peak_distance	float	2.0	min: 1.0e-04	The minimal distance (in Th) between two peaks for concurrent selection for fragmentation. Also used to define the m/z width of an exclusion window (distance +/- from m/z of precursor). If you set this lower than the isotopic envelope of a peptide, you might get multiple fragment spectra pointing to the same precursor.
Precursor:mz_isolation_window	float	2.0	min: 0.0	All peaks within a mass window (in Th) of a selected peak are also selected for fragmentation.
Precursor:exclude_overlapping_peaks	string	false	true, false	If true, overlapping or nearby peaks (within 'min_mz_peak_distance') are excluded for selection.
Precursor:charge_filter	int list	[2, 3]	min: 1 max: 5	Charges considered for MS2 fragmentation.
Precursor:Exclusion:use_dynamic_exclusion	string	false	true, false	If true dynamic exclusion is applied.
Precursor:Exclusion:exclusion_time	float	100.0	min: 0.0	The time (in seconds) a feature is excluded.
Precursor:ProteinBasedInclusion:max_list_size	int	1000	min: 1	The maximal number of precursors in the inclusion list.
Precursor:ProteinBasedInclusion:rt:min_rt	float	960.0	min: 0.0	Minimal rt in seconds.
Precursor:ProteinBasedInclusion:rt:max_rt	float	3840.0	min: 0.0	Maximal rt in seconds.
Precursor:ProteinBasedInclusion:rt:rt_step_size	float	30.0	min: 1.0	rt step size in seconds.
Precursor:ProteinBasedInclusion:rt:rt_window_size	int	100	min: 1	rt window size in seconds.
Precursor:ProteinBasedInclusion:thresholds:min_protein_id_probability	float	0.95	min: 0.0 max: 1.0	Minimal protein probability for a protein to be considered identified.
Precursor:ProteinBasedInclusion:thresholds:min_pt_weight	float	0.5	min: 0.0 max: 1.0	Minimal pt weight of a precursor
Precursor:ProteinBasedInclusion:thresholds:min_mz	float	500.0	min: 0.0	Minimal mz to be considered in protein based LP formulation.
Precursor:ProteinBasedInclusion:thresholds:max_mz	float	5000.0	min: 0.0	Minimal mz to be considered in protein based LP formulation.
Precursor:ProteinBasedInclusion:thresholds:use_peptide_rule	string	false	true, false	Use peptide rule instead of minimal protein id probability
Precursor:ProteinBasedInclusion:thresholds:min_peptide_ids	int	2	min: 1	If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id
Precursor:ProteinBasedInclusion:thresholds:min_peptide_probability	float	0.95	min: 0.0 max: 1.0	If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified
MS_E:add_single_spectra	string	false	true, false	If true, the MS2 spectra for each peptide signal are included in the output (might be a lot). They will have a meta value 'MSE_DebugSpectrum' attached, so they can be filtered out. Native MS_E spectra will have 'MSE_Spectrum' instead.
TandemSim:Simple:isotope_model	string	none	none, coarse, fine	Model to use for isotopic peaks ('none' means no isotopic peaks are added, 'coarse' adds isotopic peaks in unit mass distance, 'fine' uses the hyperfine isotopic generator to add accurate isotopic peaks. Note that adding isotopic peaks is very slow.
TandemSim:Simple:max_isotope	int	2		Defines the maximal isotopic peak which is added if 'isotope_model' is 'coarse'
TandemSim:Simple:max_isotope_probability	float	0.05		Defines the maximal isotopic probability to cover if 'isotope_model' is 'fine'
TandemSim:Simple:add_metainfo	string	false	true, false	Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++
TandemSim:Simple:add_losses	string	false	true, false	Adds common losses to those ion expect to have them, only water and ammonia loss is considered
TandemSim:Simple:sort_by_position	string	true	true, false	Sort output by position
TandemSim:Simple:add_precursor_peaks	string	false	true, false	Adds peaks of the unfragmented precursor ion to the spectrum
TandemSim:Simple:add_all_precursor_charges	string	false	true, false	Adds precursor peaks with all charges in the given range
TandemSim:Simple:add_abundant_immonium_ions	string	false	true, false	Add most abundant immonium ions (for Proline, Cystein, Iso/Leucine, Histidin, Phenylalanin, Tyrosine, Tryptophan)
TandemSim:Simple:add_first_prefix_ion	string	false	true, false	If set to true e.g. b1 ions are added
TandemSim:Simple:add_y_ions	string	true	true, false	Add peaks of y-ions to the spectrum
TandemSim:Simple:add_b_ions	string	true	true, false	Add peaks of b-ions to the spectrum
TandemSim:Simple:add_a_ions	string	false	true, false	Add peaks of a-ions to the spectrum
TandemSim:Simple:add_c_ions	string	false	true, false	Add peaks of c-ions to the spectrum
TandemSim:Simple:add_x_ions	string	false	true, false	Add peaks of x-ions to the spectrum
TandemSim:Simple:add_z_ions	string	false	true, false	Add peaks of z-ions to the spectrum
TandemSim:Simple:y_intensity	float	1.0	min: 0.0	Intensity of the y-ions
TandemSim:Simple:b_intensity	float	1.0	min: 0.0	Intensity of the b-ions
TandemSim:Simple:a_intensity	float	1.0	min: 0.0	Intensity of the a-ions
TandemSim:Simple:c_intensity	float	1.0	min: 0.0	Intensity of the c-ions
TandemSim:Simple:x_intensity	float	1.0	min: 0.0	Intensity of the x-ions
TandemSim:Simple:z_intensity	float	1.0	min: 0.0	Intensity of the z-ions
TandemSim:Simple:relative_loss_intensity	float	0.1	min: 0.0 max: 1.0	Intensity of loss ions, in relation to the intact ion intensity
TandemSim:Simple:precursor_intensity	float	1.0	min: 0.0	Intensity of the precursor peak
TandemSim:Simple:precursor_H2O_intensity	float	1.0	min: 0.0	Intensity of the H2O loss peak of the precursor
TandemSim:Simple:precursor_NH3_intensity	float	1.0	min: 0.0	Intensity of the NH3 loss peak of the precursor
TandemSim:SVM:add_isotopes	string	false	true, false	If set to 1 isotope peaks of the product ion peaks are added
TandemSim:SVM:max_isotope	int	2		Defines the maximal isotopic peak which is added, add_isotopes must be set to 1
TandemSim:SVM:add_metainfo	string	false	true, false	Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++
TandemSim:SVM:add_first_prefix_ion	string	false	true, false	If set to true e.g. b1 ions are added
TandemSim:SVM:hide_y_ions	string	false	true, false	Add peaks of y-ions to the spectrum
TandemSim:SVM:hide_y2_ions	string	false	true, false	Add peaks of y-ions to the spectrum
TandemSim:SVM:hide_b_ions	string	false	true, false	Add peaks of b-ions to the spectrum
TandemSim:SVM:hide_b2_ions	string	false	true, false	Add peaks of b-ions to the spectrum
TandemSim:SVM:hide_a_ions	string	false	true, false	Add peaks of a-ions to the spectrum
TandemSim:SVM:hide_c_ions	string	false	true, false	Add peaks of c-ions to the spectrum
TandemSim:SVM:hide_x_ions	string	false	true, false	Add peaks of x-ions to the spectrum
TandemSim:SVM:hide_z_ions	string	false	true, false	Add peaks of z-ions to the spectrum
TandemSim:SVM:hide_losses	string	false	true, false	Adds common losses to those ion expect to have them, only water and ammonia loss is considered
TandemSim:SVM:y_intensity	float	1.0		Intensity of the y-ions
TandemSim:SVM:b_intensity	float	1.0		Intensity of the b-ions
TandemSim:SVM:a_intensity	float	1.0		Intensity of the a-ions
TandemSim:SVM:c_intensity	float	1.0		Intensity of the c-ions
TandemSim:SVM:x_intensity	float	1.0		Intensity of the x-ions
TandemSim:SVM:z_intensity	float	1.0		Intensity of the z-ions
TandemSim:SVM:relative_loss_intensity	float	0.1		Intensity of loss ions, in relation to the intact ion intensity

Note:

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

Constructor & Destructor Documentation

RawTandemMSSignalSimulation() [1/3]

RawTandemMSSignalSimulation

(

)

Default constructor (hidden)

RawTandemMSSignalSimulation() [2/3]

RawTandemMSSignalSimulation ( SimTypes::MutableSimRandomNumberGeneratorPtr  rng )

explicit

Constructor taking a random generator.

RawTandemMSSignalSimulation() [3/3]

RawTandemMSSignalSimulation

(

const RawTandemMSSignalSimulation &

source

)

Copy constructor.

~RawTandemMSSignalSimulation()

~RawTandemMSSignalSimulation ( )

override

Destructor.

Member Function Documentation

generateMSESpectra_()

void generateMSESpectra_ ( const SimTypes::FeatureMapSim &  features, const SimTypes::MSSimExperiment &  experiment, SimTypes::MSSimExperiment &  ms2  )

protected

generatePrecursorSpectra_()

void generatePrecursorSpectra_ ( const SimTypes::FeatureMapSim &  features, const SimTypes::MSSimExperiment &  experiment, SimTypes::MSSimExperiment &  ms2  )

protected

generateRawTandemSignals()

void generateRawTandemSignals	(	const SimTypes::FeatureMapSim &	,
		SimTypes::MSSimExperiment &	,
		SimTypes::MSSimExperiment &
	)

initParam_()

void initParam_ ( )

protected

initialize param_ class

operator=()

RawTandemMSSignalSimulation& operator=

(

const RawTandemMSSignalSimulation &

source

)

Member Data Documentation

rnd_gen_

SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen_

protected

Random number generator.