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

#include <OpenMS/SIMULATION/RawMSSignalSimulation.h>

Inheritance diagram for RawMSSignalSimulation:

Collaboration diagram for RawMSSignalSimulation:

Classes
struct	ContaminantInfo

Constructors and Destructors
enum	IONIZATIONMETHOD { IM_ESI = 0 , IM_MALDI = 1 , IM_ALL = 2 }

enum	PROFILESHAPE { RT_RECTANGULAR , RT_GAUSSIAN }

enum	RESOLUTIONMODEL { RES_CONSTANT , RES_LINEAR , RES_SQRT }

Int	sampling_points_per_FWHM_
	number of points sampled per peak's FWHM More...

SimTypes::SimCoordinateType	mz_error_mean_
	Mean of peak m/z error. More...

SimTypes::SimCoordinateType	mz_error_stddev_
	Standard deviation of peak m/z error. More...

SimTypes::SimIntensityType	intensity_scale_
	Scaling factor of peak intensities. More...

SimTypes::SimIntensityType	intensity_scale_stddev_
	Standard deviation of peak intensity scaling. More...

RESOLUTIONMODEL	res_model_
	model of how resolution behaves with increasing m/z More...

double	res_base_
	base resolution at 400 Th More...

std::vector< SimTypes::SimCoordinateType >	grid_
	m/z sampling grid for all signals More...

SimTypes::MutableSimRandomNumberGeneratorPtr	rnd_gen_
	Random number generator. More...

std::vector< ContaminantInfo >	contaminants_

std::vector< std::vector< double > >	threaded_random_numbers_

std::vector< Size >	threaded_random_numbers_index_

bool	contaminants_loaded_

static const Size	THREADED_RANDOM_NUMBER_POOL_SIZE_ = 500

	RawMSSignalSimulation ()
	Default constructor. More...

	RawMSSignalSimulation (SimTypes::MutableSimRandomNumberGeneratorPtr rng)
	Constructor taking a random generator. More...

	RawMSSignalSimulation (const RawMSSignalSimulation &source)
	Copy constructor. More...

	~RawMSSignalSimulation () override
	Destructor. More...

RawMSSignalSimulation &	operator= (const RawMSSignalSimulation &source)

void	loadContaminants ()

void	generateRawSignals (SimTypes::FeatureMapSim &features, SimTypes::MSSimExperiment &experiment, SimTypes::MSSimExperiment &experiment_ct, SimTypes::FeatureMapSim &contaminants)
	fill experiment with signals and noise More...

void	updateMembers_ () override
	Synchronize members with param class. More...

void	setDefaultParams_ ()
	Set default parameters. More...

void	add1DSignal_ (Feature &feature, SimTypes::MSSimExperiment &experiment, SimTypes::MSSimExperiment &experiment_ct)
	Add a 1D signal for a single feature. More...

void	add2DSignal_ (Feature &feature, SimTypes::MSSimExperiment &experiment, SimTypes::MSSimExperiment &experiment_ct)
	Add a 2D signal for a single feature. More...

void	samplePeptideModel1D_ (const IsotopeModel &iso, const SimTypes::SimCoordinateType mz_start, const SimTypes::SimCoordinateType mz_end, SimTypes::MSSimExperiment &experiment, SimTypes::MSSimExperiment &experiment_ct, Feature &activeFeature)
	Samples signals for the given 1D model. More...

void	samplePeptideModel2D_ (const ProductModel< 2 > &pm, const SimTypes::SimCoordinateType mz_start, const SimTypes::SimCoordinateType mz_end, SimTypes::SimCoordinateType rt_start, SimTypes::SimCoordinateType rt_end, SimTypes::MSSimExperiment &experiment, SimTypes::MSSimExperiment &experiment_ct, Feature &activeFeature)
	Samples signals for the given 2D model. More...

void	chooseElutionProfile_ (EGHModel *const elutionmodel, Feature &feature, const double scale, const double rt_sampling_rate, const SimTypes::MSSimExperiment &experiment)
	Add the correct Elution profile to the passed ProductModel. More...

void	createContaminants_ (SimTypes::FeatureMapSim &contaminants, SimTypes::MSSimExperiment &exp, SimTypes::MSSimExperiment &exp_ct)
	build contaminant feature map More...

void	addShotNoise_ (SimTypes::MSSimExperiment &experiment, SimTypes::SimCoordinateType minimal_mz_measurement_limit, SimTypes::SimCoordinateType maximal_mz_measurement_limit)
	Add shot noise to the experiment. More...

void	addWhiteNoise_ (SimTypes::MSSimExperiment &experiment)
	Add white noise to the experiment. More...

void	addDetectorNoise_ (SimTypes::MSSimExperiment &experiment)
	Add detector noise to the experiment. More...

void	addBaseLine_ (SimTypes::MSSimExperiment &experiment, SimTypes::SimCoordinateType minimal_mz_measurement_limit)
	Add a base line to the experiment. More...

void	getSamplingGrid_ (std::vector< SimTypes::SimCoordinateType > &grid, const SimTypes::SimCoordinateType mz_min, const SimTypes::SimCoordinateType mz_max, const Int step_Da)
	get the mz grid where all m/z values will be mapped to More...

void	compressSignals_ (SimTypes::MSSimExperiment &experiment)
	Compress signals in a single RT scan (to merge signals which were sampled overlapping) More...

SimTypes::SimIntensityType	getFeatureScaledIntensity_ (const SimTypes::SimIntensityType feature_intensity, const SimTypes::SimIntensityType natural_scaling_factor)
	Computes a rescaled feature intensity based on the set parameters for feature intensity scaling and the passed parameter `natural_scaling_factor`. More...

double	getResolution_ (const double query_mz, const double resolution, const RESOLUTIONMODEL model) const
	Compute resolution at a given m/z given a base resolution and how it degrades with increasing m/z. More...

double	getPeakWidth_ (const double mz, const bool is_gaussian) const
	compute the peak's SD (Gaussian) at a given m/z (internally the resolution model is used) More...

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. 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...

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...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

virtual	~ProgressLogger ()
	Destructor. More...

	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...

LogType	getLogType () const
	Returns the type of progress log being used. More...

void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...

void	setProgress (SignedSize value) const
	Sets the current progress. More...

void	endProgress () const
	Ends the progress display. More...

void	nextProgress () const
	increment progress by 1 (according to range begin-end) 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...

Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. 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...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

Simulates MS signals for a given set of peptides.

Simulates 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
enabled	string	true	true, false	Enable RAW signal simulation? (select 'false' if you only need feature-maps)
ionization_type	string	ESI	MALDI, ESI	Type of Ionization (MALDI or ESI)
peak_shape	string	Gaussian	Gaussian, Lorentzian	Peak Shape used around each isotope peak (be aware that the area under the curve is constant for both types, but the maximal height will differ (~ 2:3 = Lorentz:Gaussian) due to the wider base of the Lorentzian
resolution:value	int	50000		Instrument resolution at 400 Th
resolution:type	string	linear	constant, linear, sqrt	How does resolution change with increasing m/z?! QTOFs usually show 'constant' behavior, FTs have linear degradation, and on Orbitraps the resolution decreases with square root of mass
baseline:scaling	float	0.0	min: 0.0	Scale of baseline. Set to 0 to disable simulation of baseline
baseline:shape	float	0.5	min: 0.0	The baseline is modeled by an exponential probability density function (pdf) with f(x) = shapee^(- shapex)
mz:sampling_points	int	3	min: 2	Number of raw data points per FWHM of the peak
contaminants:file	string	SIMULATION/contaminants.csv		Contaminants file with sum formula and absolute RT interval. See 'share/OpenMS/SIMULATION/contaminants.txt' for details
variation:mz:error_mean	float	0.0		Average systematic m/z error (in Da)
variation:mz:error_stddev	float	0.0		Standard deviation for m/z errors. Set to 0 to disable simulation of m/z errors
variation:intensity:scale	float	100.0	min: 0.0	Constant scale factor of the feature intensity. Set to 1.0 to get the real intensity values provided in the FASTA file
variation:intensity:scale_stddev	float	0.0	min: 0.0	Standard deviation of peak intensity (relative to the scaled peak height). Set to 0 to get simple rescaled intensities
noise:shot:rate	float	0.0	min: 0.0	Poisson rate of shot noise per unit m/z (random peaks in m/z, where the number of peaks per unit m/z follows a Poisson distribution). Set this to 0 to disable simulation of shot noise
noise:shot:intensity-mean	float	1.0		Shot noise intensity mean (exponentially distributed with given mean)
noise:white:mean	float	0.0		Mean value of white noise (Gaussian) being added to each measured signal intensity
noise:white:stddev	float	0.0		Standard deviation of white noise being added to each measured signal intensity
noise:detector:mean	float	0.0		Mean intensity value of the detector noise (Gaussian distribution)
noise:detector:stddev	float	0.0		Standard deviation of the detector noise (Gaussian distribution)

Note:

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

Class Documentation

◆ OpenMS::RawMSSignalSimulation::ContaminantInfo

struct OpenMS::RawMSSignalSimulation::ContaminantInfo

Collaboration diagram for RawMSSignalSimulation::ContaminantInfo:

[legend]

Class Members
IONIZATIONMETHOD	im
double	intensity
String	name
Int	q
double	rt_end
double	rt_start
EmpiricalFormula	sf
PROFILESHAPE	shape

Member Enumeration Documentation

◆ IONIZATIONMETHOD

enum IONIZATIONMETHOD

protected

Enumerator
IM_ESI
IM_MALDI
IM_ALL

◆ PROFILESHAPE

enum PROFILESHAPE

protected

Enumerator
RT_RECTANGULAR
RT_GAUSSIAN

◆ RESOLUTIONMODEL

enum RESOLUTIONMODEL

protected

Enumerator
RES_CONSTANT
RES_LINEAR
RES_SQRT

Constructor & Destructor Documentation

◆ RawMSSignalSimulation() [1/3]

RawMSSignalSimulation ( )

Default constructor.

◆ RawMSSignalSimulation() [2/3]

RawMSSignalSimulation ( SimTypes::MutableSimRandomNumberGeneratorPtr rng )

explicit

Constructor taking a random generator.

◆ RawMSSignalSimulation() [3/3]

RawMSSignalSimulation ( const RawMSSignalSimulation & source )

Copy constructor.

◆ ~RawMSSignalSimulation()

~RawMSSignalSimulation ( )

override

Destructor.

Member Function Documentation

◆ add1DSignal_()

void add1DSignal_	(	Feature &	feature,
		SimTypes::MSSimExperiment &	experiment,
		SimTypes::MSSimExperiment &	experiment_ct
	)

protected

Add a 1D signal for a single feature.

Parameters

feature	The feature which should be simulated
experiment	The experiment to which the simulated signals should be added
experiment_ct	Ground truth for picked peaks

◆ add2DSignal_()

void add2DSignal_	(	Feature &	feature,
		SimTypes::MSSimExperiment &	experiment,
		SimTypes::MSSimExperiment &	experiment_ct
	)

protected

Add a 2D signal for a single feature.

Parameters

feature	The feature which should be simulated
experiment	The experiment to which the simulated signals should be added
experiment_ct	Ground truth for picked peaks

◆ addBaseLine_()

void addBaseLine_	(	SimTypes::MSSimExperiment &	experiment,
		SimTypes::SimCoordinateType	minimal_mz_measurement_limit
	)

protected

Add a base line to the experiment.

◆ addDetectorNoise_()

void addDetectorNoise_ ( SimTypes::MSSimExperiment & experiment )

protected

Add detector noise to the experiment.

◆ addShotNoise_()

void addShotNoise_	(	SimTypes::MSSimExperiment &	experiment,
		SimTypes::SimCoordinateType	minimal_mz_measurement_limit,
		SimTypes::SimCoordinateType	maximal_mz_measurement_limit
	)

protected

Add shot noise to the experiment.

◆ addWhiteNoise_()

void addWhiteNoise_ ( SimTypes::MSSimExperiment & experiment )

protected

Add white noise to the experiment.

◆ chooseElutionProfile_()

void chooseElutionProfile_	(	EGHModel *const	elutionmodel,
		Feature &	feature,
		const double	scale,
		const double	rt_sampling_rate,
		const SimTypes::MSSimExperiment &	experiment
	)

protected

Add the correct Elution profile to the passed ProductModel.

◆ compressSignals_()

void compressSignals_ ( SimTypes::MSSimExperiment & experiment )

protected

Compress signals in a single RT scan (to merge signals which were sampled overlapping)

◆ createContaminants_()

void createContaminants_	(	SimTypes::FeatureMapSim &	contaminants,
		SimTypes::MSSimExperiment &	exp,
		SimTypes::MSSimExperiment &	exp_ct
	)

protected

build contaminant feature map

◆ generateRawSignals()

void generateRawSignals	(	SimTypes::FeatureMapSim &	features,
		SimTypes::MSSimExperiment &	experiment,
		SimTypes::MSSimExperiment &	experiment_ct,
		SimTypes::FeatureMapSim &	contaminants
	)

fill experiment with signals and noise

◆ getFeatureScaledIntensity_()

SimTypes::SimIntensityType getFeatureScaledIntensity_	(	const SimTypes::SimIntensityType	feature_intensity,
		const SimTypes::SimIntensityType	natural_scaling_factor
	)

protected

Computes a rescaled feature intensity based on the set parameters for feature intensity scaling and the passed parameter natural_scaling_factor.

Parameters

feature_intensity	Intensity of the current feature.
natural_scaling_factor	Additional scaling factor used by some of the sampling models.

Returns: Rescaled feature intensity.

◆ getPeakWidth_()

double getPeakWidth_	(	const double	mz,
		const bool	is_gaussian
	)		const

protected

compute the peak's SD (Gaussian) at a given m/z (internally the resolution model is used)

◆ getResolution_()

double getResolution_	(	const double	query_mz,
		const double	resolution,
		const RESOLUTIONMODEL	model
	)		const

protected

Compute resolution at a given m/z given a base resolution and how it degrades with increasing m/z.

Parameters

query_mz	The m/z value where the resolution should be estimated
resolution	The resolution at 400 Th
model	The model describing how resolution behaves, i.e. RES_CONSTANT: resolution does not change with m/z (this will just return `resolution`) RES_LINEAR: resolution decreases linear with m/z, i.e. at 800 Th, it will have 50% of original RES_SQRT: the resolution decreases with square root of mass, i.e. at 1600 Th, it will have 50% of original (sqrt(400) = sqrt(1600)*0.5)

◆ getSamplingGrid_()

void getSamplingGrid_	(	std::vector< SimTypes::SimCoordinateType > &	grid,
		const SimTypes::SimCoordinateType	mz_min,
		const SimTypes::SimCoordinateType	mz_max,
		const Int	step_Da
	)

protected

get the mz grid where all m/z values will be mapped to

◆ loadContaminants()

void loadContaminants ( )

load the contaminants from contaminants:file param You do not have to call this function before calling generateRawSignals(), but it might be useful to check if the contaminant file is valid

◆ operator=()

RawMSSignalSimulation& operator= ( const RawMSSignalSimulation & source )

◆ samplePeptideModel1D_()

void samplePeptideModel1D_	(	const IsotopeModel &	iso,
		const SimTypes::SimCoordinateType	mz_start,
		const SimTypes::SimCoordinateType	mz_end,
		SimTypes::MSSimExperiment &	experiment,
		SimTypes::MSSimExperiment &	experiment_ct,
		Feature &	activeFeature
	)

protected

Samples signals for the given 1D model.

Parameters

iso	The isotope model from which the signals will be sampled
mz_start	Start coordinate (in m/z dimension) of the region where the signals will be sampled
mz_end	End coordinate (in m/z dimension) of the region where the signals will be sampled
experiment	Experiment to which the sampled signals will be added
experiment_ct	Experiment to which the centroided Ground Truth sampled signals will be added
activeFeature	The current feature that is simulated

◆ samplePeptideModel2D_()

void samplePeptideModel2D_	(	const ProductModel< 2 > &	pm,
		const SimTypes::SimCoordinateType	mz_start,
		const SimTypes::SimCoordinateType	mz_end,
		SimTypes::SimCoordinateType	rt_start,
		SimTypes::SimCoordinateType	rt_end,
		SimTypes::MSSimExperiment &	experiment,
		SimTypes::MSSimExperiment &	experiment_ct,
		Feature &	activeFeature
	)

protected

Samples signals for the given 2D model.

Parameters

pm	The product model from which the signals will be sampled
mz_start	Start coordinate (in m/z dimension) of the region where the signals will be sampled
mz_end	End coordinate (in m/z dimension) of the region where the signals will be sampled
rt_start	Start coordinate (in rt dimension) of the region where the signals will be sampled
rt_end	End coordinate (in rt dimension) of the region where the signals will be sampled
experiment	Experiment to which the sampled signals will be added
experiment_ct	Experiment to which the centroided Ground Truth sampled signals will be added
activeFeature	The current feature that is simulated

◆ setDefaultParams_()

void setDefaultParams_ ( )

protected

Set default parameters.

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ contaminants_

std::vector<ContaminantInfo> contaminants_

protected

◆ contaminants_loaded_

bool contaminants_loaded_

protected

◆ grid_

std::vector<SimTypes::SimCoordinateType> grid_

protected

m/z sampling grid for all signals

◆ intensity_scale_

SimTypes::SimIntensityType intensity_scale_

protected

Scaling factor of peak intensities.

◆ intensity_scale_stddev_

SimTypes::SimIntensityType intensity_scale_stddev_

protected

Standard deviation of peak intensity scaling.

◆ mz_error_mean_

SimTypes::SimCoordinateType mz_error_mean_

protected

Mean of peak m/z error.

◆ mz_error_stddev_

SimTypes::SimCoordinateType mz_error_stddev_

protected

Standard deviation of peak m/z error.

◆ res_base_

double res_base_

protected

base resolution at 400 Th

◆ res_model_

RESOLUTIONMODEL res_model_

protected

model of how resolution behaves with increasing m/z

◆ rnd_gen_

SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen_

protected

Random number generator.

◆ sampling_points_per_FWHM_

Int sampling_points_per_FWHM_

protected

number of points sampled per peak's FWHM

◆ THREADED_RANDOM_NUMBER_POOL_SIZE_

const Size THREADED_RANDOM_NUMBER_POOL_SIZE_ = 500

staticprotected

◆ threaded_random_numbers_

std::vector<std::vector<double> > threaded_random_numbers_

protected

threaded_random_numbers keeps a set of random numbers for each thread simulating a feature.

◆ threaded_random_numbers_index_

std::vector<Size> threaded_random_numbers_index_

protected

Indicates which random numbers each thread has used already and if the random number pool should be rebuild.

Classes

Constructors and Destructors

Additional Inherited Members

Detailed Description

Class Documentation

◆ OpenMS::RawMSSignalSimulation::ContaminantInfo

Member Enumeration Documentation

◆ IONIZATIONMETHOD

◆ PROFILESHAPE

◆ RESOLUTIONMODEL

Constructor & Destructor Documentation

◆ RawMSSignalSimulation() [1/3]

◆ RawMSSignalSimulation() [2/3]

◆ RawMSSignalSimulation() [3/3]

◆ ~RawMSSignalSimulation()

Member Function Documentation

◆ add1DSignal_()

◆ add2DSignal_()

◆ addBaseLine_()

◆ addDetectorNoise_()

◆ addShotNoise_()

◆ addWhiteNoise_()

◆ chooseElutionProfile_()

◆ compressSignals_()

◆ createContaminants_()

◆ generateRawSignals()

◆ getFeatureScaledIntensity_()

◆ getPeakWidth_()

◆ getResolution_()

◆ getSamplingGrid_()

◆ loadContaminants()

◆ operator=()

◆ samplePeptideModel1D_()

◆ samplePeptideModel2D_()

◆ setDefaultParams_()

◆ updateMembers_()

Member Data Documentation

◆ contaminants_

◆ contaminants_loaded_

◆ grid_

◆ intensity_scale_

◆ intensity_scale_stddev_

◆ mz_error_mean_

◆ mz_error_stddev_

◆ res_base_

◆ res_model_

◆ rnd_gen_

◆ sampling_points_per_FWHM_

◆ THREADED_RANDOM_NUMBER_POOL_SIZE_

◆ threaded_random_numbers_

◆ threaded_random_numbers_index_