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

#include <OpenMS/SIMULATION/RawMSSignalSimulation.h>

Inheritance diagram for RawMSSignalSimulation:

Classes
struct	ContaminantInfo
Public Member Functions
RawMSSignalSimulation &	operator= (const RawMSSignalSimulation &source)
void	loadContaminants ()
void	generateRawSignals (FeatureMapSim &features, MSSimExperiment &experiment, MSSimExperiment &experiment_ct, FeatureMapSim &contaminants)
	fill experiment with signals and noise
Constructors and Destructors

	RawMSSignalSimulation (const SimRandomNumberGenerator &rng)
	Constructor taking a random generator.
	RawMSSignalSimulation (const RawMSSignalSimulation &source)
	Copy constructor.
virtual	~RawMSSignalSimulation ()
	Destructor.
Protected Types
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 }
Protected Member Functions
	RawMSSignalSimulation ()
	Default constructor.
void	updateMembers_ ()
	Synchronize members with param class.
void	setDefaultParams_ ()
	Set default parameters.
void	add1DSignal_ (Feature &feature, MSSimExperiment &experiment, MSSimExperiment &experiment_ct)
	Add a 1D signal for a single feature.
void	add2DSignal_ (Feature &feature, MSSimExperiment &experiment, MSSimExperiment &experiment_ct)
	Add a 2D signal for a single feature.
void	samplePeptideModel1D_ (const IsotopeModel &iso, const SimCoordinateType mz_start, const SimCoordinateType mz_end, MSSimExperiment &experiment, MSSimExperiment &experiment_ct, Feature &activeFeature)
	Samples signals for the given 1D model.
void	samplePeptideModel2D_ (const ProductModel< 2 > &pm, const SimCoordinateType mz_start, const SimCoordinateType mz_end, SimCoordinateType rt_start, SimCoordinateType rt_end, MSSimExperiment &experiment, MSSimExperiment &experiment_ct, Feature &activeFeature)
	Samples signals for the given 2D model.
void	chooseElutionProfile_ (EGHModel *const elutionmodel, Feature &feature, const double scale, const DoubleReal rt_sampling_rate, const MSSimExperiment &experiment)
	Add the correct Elution profile to the passed ProductModel.
void	createContaminants_ (FeatureMapSim &contaminants, MSSimExperiment &exp, MSSimExperiment &exp_ct)
	build contaminant feature map
void	addShotNoise_ (MSSimExperiment &experiment, SimCoordinateType minimal_mz_measurement_limit, SimCoordinateType maximal_mz_measurement_limit)
	Add shot noise to the experiment.
void	addWhiteNoise_ (MSSimExperiment &experiment)
	Add white noise to the experiment.
void	addDetectorNoise_ (MSSimExperiment &experiment)
	Add detector noise to the experiment.
void	addBaseLine_ (MSSimExperiment &experiment, SimCoordinateType minimal_mz_measurement_limit)
	Add a base line to the experiment.
void	getSamplingGrid_ (std::vector< SimCoordinateType > &grid, const SimCoordinateType mz_min, const SimCoordinateType mz_max, const Int step_Da)
	get the mz grid where all m/z values will be mapped to
void	compressSignals_ (MSSimExperiment &experiment)
	Compress signales in a single RT scan (to merge signals which were sampled overlapping).
SimIntensityType	getFeatureScaledIntensity_ (const SimIntensityType feature_intensity, const 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`.
DoubleReal	getResolution_ (const DoubleReal query_mz, const DoubleReal resolution, const RESOLUTIONMODEL model) const
	Compute resolution at a given m/z given a base resolution and how it degrades with increasing m/z.
DoubleReal	getPeakWidth_ (const DoubleReal mz, const bool is_gaussian) const
	compute the peak's SD (Gaussian) at a given m/z (internally the resolution model is used)
Protected Attributes
Int	sampling_points_per_FWHM_
	number of points sampled per peak's FWHM
SimCoordinateType	mz_error_mean_
	Mean of peak m/z error.
SimCoordinateType	mz_error_stddev_
	Standard deviation of peak m/z error.
SimIntensityType	intensity_scale_
	Scaling factor of peak intensities.
SimIntensityType	intensity_scale_stddev_
	Standard deviation of peak intensity scaling.
RESOLUTIONMODEL	res_model_
	model of how resolution behaves with increasing m/z
DoubleReal	res_base_
	base resolution at 400 Th
std::vector< SimCoordinateType >	grid_
	m/z sampling grid for all signals
SimRandomNumberGenerator const *	rnd_gen_
	Random number generator.
std::vector< ContaminantInfo >	contaminants_
std::vector< std::vector < double > >	threaded_random_numbers_
std::vector< Size >	threaded_random_numbers_index_
bool	contaminants_loaded_
Static Protected Attributes
static const Size	THREADED_RANDOM_NUMBER_POOL_SIZE_ = 500

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	min: 0	Scale of baseline. Set to 0 to disable simulation of baseline.
baseline:shape	float	0.5	min: 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	examples/simulation/contaminants.csv		Contaminants file with sum formula and absolute RT interval. See 'OpenMS/examples/simulation/contaminants.txt' for details.
variation:mz:error_stddev	float	0		Standard deviation for m/z errors. Set to 0 to disable simulation of m/z errors.
variation:mz:error_mean	float	0		Average systematic m/z error (Da)
variation:intensity:scale	float	100	min: 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	min: 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	min: 0	Poisson rate of shot noise per unit m/z. Set this to 0 to disable simulation of shot noise.
noise:shot:intensity-mean	float	1		Shot noise intensity mean (exponentially distributed with given mean).
noise:white:mean	float	0		Mean value of white noise being added to each measured signal.
noise:white:stddev	float	0		Standard deviation of white noise being added to each measured signal.
noise:detector:mean	float	0		Mean value of the detector noise being added to the complete measurement.
noise:detector:stddev	float	0		Standard deviation of the detector noise being added to the complete measurement.

Note:

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

Member Enumeration Documentation

enum IONIZATIONMETHOD [protected]

Enumerator:

IM_ESI
IM_MALDI
IM_ALL

enum PROFILESHAPE [protected]

Enumerator:

RT_RECTANGULAR
RT_GAUSSIAN

enum RESOLUTIONMODEL [protected]

Enumerator:

RES_CONSTANT
RES_LINEAR
RES_SQRT

Constructor & Destructor Documentation

RawMSSignalSimulation ( const SimRandomNumberGenerator & rng )

Constructor taking a random generator.

RawMSSignalSimulation ( const RawMSSignalSimulation & source )

Copy constructor.

virtual ~RawMSSignalSimulation ( ) [virtual]

Destructor.

RawMSSignalSimulation ( ) [protected]

Default constructor.

Member Function Documentation

void add1DSignal_	(	Feature &	feature,
		MSSimExperiment &	experiment,
		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

void add2DSignal_	(	Feature &	feature,
		MSSimExperiment &	experiment,
		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

void addBaseLine_	(	MSSimExperiment &	experiment,
		SimCoordinateType	minimal_mz_measurement_limit
	)			`[protected]`

Add a base line to the experiment.

void addDetectorNoise_ ( MSSimExperiment & experiment ) [protected]

Add detector noise to the experiment.

void addShotNoise_	(	MSSimExperiment &	experiment,
		SimCoordinateType	minimal_mz_measurement_limit,
		SimCoordinateType	maximal_mz_measurement_limit
	)			`[protected]`

Add shot noise to the experiment.

void addWhiteNoise_ ( MSSimExperiment & experiment ) [protected]

Add white noise to the experiment.

void chooseElutionProfile_	(	EGHModel *const	elutionmodel,
		Feature &	feature,
		const double	scale,
		const DoubleReal	rt_sampling_rate,
		const MSSimExperiment &	experiment
	)			`[protected]`

Add the correct Elution profile to the passed ProductModel.

void compressSignals_ ( MSSimExperiment & experiment ) [protected]

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

void createContaminants_	(	FeatureMapSim &	contaminants,
		MSSimExperiment &	exp,
		MSSimExperiment &	exp_ct
	)			`[protected]`

build contaminant feature map

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

fill experiment with signals and noise

SimIntensityType getFeatureScaledIntensity_	(	const SimIntensityType	feature_intensity,
		const 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.

DoubleReal getPeakWidth_	(	const DoubleReal	mz,
		const bool	is_gaussian
	)			const `[protected]`

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

DoubleReal getResolution_	(	const DoubleReal	query_mz,
		const DoubleReal	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)

void getSamplingGrid_	(	std::vector< SimCoordinateType > &	grid,
		const SimCoordinateType	mz_min,
		const SimCoordinateType	mz_max,
		const Int	step_Da
	)			`[protected]`

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

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

RawMSSignalSimulation& operator= ( const RawMSSignalSimulation & source )

void samplePeptideModel1D_	(	const IsotopeModel &	iso,
		const SimCoordinateType	mz_start,
		const SimCoordinateType	mz_end,
		MSSimExperiment &	experiment,
		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

void samplePeptideModel2D_	(	const ProductModel< 2 > &	pm,
		const SimCoordinateType	mz_start,
		const SimCoordinateType	mz_end,
		SimCoordinateType	rt_start,
		SimCoordinateType	rt_end,
		MSSimExperiment &	experiment,
		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