Simulates/Predicts retention times for peptides or peptide separation. More...

#include <OpenMS/SIMULATION/RTSimulation.h>

Inheritance diagram for RTSimulation:

Public Member Functions
RTSimulation &	operator= (const RTSimulation &source)
	Assignment operator.
void	predictRT (FeatureMapSim &features)
	Predict retention times for given peptide features based for HPLC or CE.
void	predictContaminantsRT (FeatureMapSim &)
	Set retention times randomly for given contaminants.
bool	isRTColumnOn () const
	Returns true if a RT column was simulated.
void	wrapSVM (std::vector< AASequence > &peptide_sequences, std::vector< DoubleReal > &predicted_retention_times)
	Wrapper for the SVM RT Prediction (HPLC) using AASequences.
SimCoordinateType	getGradientTime () const
void	createExperiment (MSSimExperiment &experiment)
	Size experiment and assign retention time grid.
Constructors and Destructors

	RTSimulation (const SimRandomNumberGenerator &random_generator)
	Constructor taking a random generator.
	RTSimulation (const RTSimulation &source)
	Copy constructor.
virtual	~RTSimulation ()
	Destructor.
Protected Member Functions
void	updateMembers_ ()
	Synchronize members with param class.
Protected Attributes
SimRandomNumberGenerator const *	rnd_gen_
	Random number generator.
Private Member Functions
	RTSimulation ()
	Default constructor.
void	setDefaultParams_ ()
	Set default parameters.
void	noRTColumn_ (FeatureMapSim &)
	Simply set all retention times to -1.
void	smoothRTDistortion_ (MSSimExperiment &experiment)
	smoothes the simulated distortion for the elution profiles with a moving average filter of size 3
void	calculateMT_ (FeatureMapSim &features, std::vector< DoubleReal > &predicted_retention_times)
void	getChargeContribution_ (Map< String, double > &q_cterm, Map< String, double > &q_nterm, Map< String, double > &q_aa_basic, Map< String, double > &q_aa_acidic)
Private Attributes
OpenMS::String	rt_model_file_
SimCoordinateType	total_gradient_time_
	Total gradient time.
SimCoordinateType	gradient_min_
	gradient ranges
SimCoordinateType	gradient_max_
	Maximal observed gradient time.
SimCoordinateType	rt_sampling_rate_
	bin size in rt dimension
DoubleReal	egh_tau_location_
	EGH tau value.
DoubleReal	egh_tau_scale_
	EGH tau scale parameter of the lorentzian variation.
DoubleReal	egh_variance_location_
	EGH sigma value.
DoubleReal	egh_variance_scale_
	EGH sigma scale parameter of the lorentzian variation.

Detailed Description

Simulates/Predicts retention times for peptides or peptide separation.

The retention times for the different peptides are determined based on a SVM model or are all set to -1 in case of simulations without a HPLC column.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
rt_column	string	HPLC	none, HPLC, CE	Modelling of an RT or CE column
auto_scale	string	true	true, false	Scale predicted RT's/MT's to given 'total_gradient_time'? If 'true', for CE this means that 'CE:lenght_d', 'CE:length_total', 'CE:voltage' have no influence.
total_gradient_time	float	2500	min: 1e-05	The duration [s] of the gradient.
sampling_rate	float	2	min: 0.01 max: 60	Time interval [s] between consecutive scans
scan_window:min	float	500	min: 0	Start of RT Scan Window [s]
scan_window:max	float	1500	min: 1	End of RT Scan Window [s]
variation:feature_stddev	int	3		Standard deviation of shift in retention time [s] from predicted model (applied to every single feature independently)
variation:affine_offset	int	0		Global offset in retention time [s] from predicted model
variation:affine_scale	int	1		Global scaling in retention time from predicted model
column_condition:distortion	int	0	min: 0 max: 10	Distortion of the elution profiles. Good presets are 0 for a perfect elution profile, 1 for a slightly distorted elution profile etc... For trapping instruments (e.g. Orbitrap) distortion should be >4.
profile_shape:width:value	float	9	min: 0	Width of the Exponential Gaussian Hybrid distribution shape of the elution profile. This does not correspond directly to the width in [s].
profile_shape:width:variance	float	1.6	min: 0	Random component of the width (set to 0 to disable randomness), i.e. scale parameter for the lorentzian variation of the variance (Note: The scale parameter has to be >= 0).
profile_shape:skewness:value	float	0.1		Asymmetric component of the EGH. Higher absolute(!) values lead to more skewness (negative values cause fronting, positive values cause tailing). Tau parameter of the EGH, i.e. time constant of the exponential decay of the Exponential Gaussian Hybrid distribution shape of the elution profile.
profile_shape:skewness:variance	float	0.3	min: 0	Random component of skewness (set to 0 to disable randomness), i.e. scale parameter for the lorentzian variation of the time constant (Note: The scale parameter has to be > 0).
HPLC:model_file	string	examples/simulation/RTPredict.model		SVM model for retention time prediction
CE:pH	float	3	min: 0 max: 14	pH of buffer
CE:alpha	float	0.5	min: 0 max: 1	Exponent Alpha used to calculate mobility
CE:mu_eo	float	0	min: 0 max: 5	Electroosmotic flow
CE:lenght_d	float	70	min: 0 max: 1000	Length of capillary [cm] from injection site to MS
CE:length_total	float	75	min: 0 max: 1000	Total length of capillary [cm]
CE:voltage	float	1000	min: 0	Voltage applied to capillary

Note:

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

Constructor & Destructor Documentation

RTSimulation ( const SimRandomNumberGenerator & random_generator )

Constructor taking a random generator.

RTSimulation ( const RTSimulation & source )

Copy constructor.

virtual ~RTSimulation ( ) [virtual]

Destructor.

RTSimulation ( ) [private]

Default constructor.

Member Function Documentation

void calculateMT_	(	FeatureMapSim &	features,
		std::vector< DoubleReal > &	predicted_retention_times
	)			`[private]`

Wrapper for the Migration time calculation (CE)

Parameters:

	features	will get modified with metavalue "RT_CE_width_factor", describing widening of MT shape.
	predicted_retention_times	will contain afterwards the predicted retention times.

void createExperiment ( MSSimExperiment & experiment )

Size experiment and assign retention time grid.

void getChargeContribution_	(	Map< String, double > &	q_cterm,
		Map< String, double > &	q_nterm,
		Map< String, double > &	q_aa_basic,
		Map< String, double > &	q_aa_acidic
	)			`[private]`