IsotopeLabelingMDVs is a class to support and analyze isotopic labeling experiments (i.e. MDVs : Mass Distribution Vectors, also known as Mass Isotopomer Distribution (MID)) More...

#include <OpenMS/ANALYSIS/QUANTITATION/IsotopeLabelingMDVs.h>

Inheritance diagram for IsotopeLabelingMDVs:

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Collaboration diagram for IsotopeLabelingMDVs:

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Public Types
enum class	DerivatizationAgent { NOT_SELECTED , TBDMS , SIZE_OF_DERIVATIZATIONAGENT }

enum class	MassIntensityType { NORM_MAX , NORM_SUM , SIZE_OF_MASSINTENSITYTYPE }

Public Member Functions
	IsotopeLabelingMDVs ()
	Constructor. More...

	~IsotopeLabelingMDVs () override
	Destructor. More...

void	isotopicCorrection (const Feature &normalized_feature, Feature &corrected_feature, const Matrix< double > &correction_matrix, const DerivatizationAgent &correction_matrix_agent)
	This function performs an isotopic correction to account for unlabeled abundances coming from the derivatization agent (e.g., tBDMS) using correction matrix method and is calculated as follows: MDV_corrected = CM^-1 * MDV_normalized_feature The formula is obtained from "The importance of accurately correcting for the natural abundance of stable isotopes", Midani et al, doi:10.1016/j.ab.2016.12.011. More...

void	isotopicCorrections (const FeatureMap &normalized_featureMap, FeatureMap &corrected_featureMap, const Matrix< double > &correction_matrix, const DerivatizationAgent &correction_matrix_agent)
	This function performs an isotopic correction to account for unlabeled abundances coming from the derivatization agent (e.g., tBDMS) using correction matrix method and is calculated as follows: MDV_corrected = CM^-1 * MDV_normalized_feature The formula is obtained from "The importance of accurately correcting for the natural abundance of stable isotopes", Midani et al, doi:10.1016/j.ab.2016.12.011. More...

void	calculateIsotopicPurity (Feature &normalized_feature, const std::vector< double > &experiment_data, const std::string &isotopic_purity_name)
	This function calculates the isotopic purity of the MDV using the following formula: isotopic purity of tracer (atom % 13C) = n / [n + (M + n-1)/(M + n)], where n in M+n is represented as the index of the result. The formula is extracted from "High-resolution 13C metabolic flux analysis", Long et al, doi:10.1038/s41596-019-0204-0. More...

void	calculateIsotopicPurities (FeatureMap &normalized_featureMap, const std::vector< std::vector< double >> &experiment_data, const std::vector< std::string > &isotopic_purity_name)
	This function calculates the isotopic purity of the MDVs using the following formula: isotopic purity of tracer (atom % 13C) = n / [n + (M + n-1)/(M + n)], where n in M+n is represented as the index of the result. The formula is extracted from "High-resolution 13C metabolic flux analysis", Long et al, doi:10.1038/s41596-019-0204-0. More...

void	calculateMDVAccuracy (Feature &normalized_feature, const std::string &feature_name, const std::string &fragment_isotopomer_theoretical_formula)
	This function calculates the accuracy of the MDV as compared to the theoretical MDV (only for 12C quality control experiments) using average deviation to the mean. The result is mapped to the meta value "average_accuracy" in the updated Feature. More...

void	calculateMDVAccuracies (FeatureMap &normalized_featureMap, const std::string &feature_name, const std::map< std::string, std::string > &fragment_isotopomer_theoretical_formulas)
	This function calculates the accuracy of the MDVs as compared to the theoretical MDVs (only for 12C quality control experiments) using average deviation to the mean. More...

void	calculateMDV (const Feature &measured_feature, Feature &normalized_feature, const MassIntensityType &mass_intensity_type, const std::string &feature_name)
	This function calculates the mass distribution vector (MDV) either normalized to the highest mass intensity (norm_max) or normalized to the sum of all mass intensities (norm_sum) More...

void	calculateMDVs (const FeatureMap &measured_featureMap, FeatureMap &normalized_featureMap, const MassIntensityType &mass_intensity_type, const std::string &feature_name)
	This function calculates the mass distribution vector (MDV) either normalized to the highest mass intensity (norm_max) or normalized to the sum of all mass intensities (norm_sum) 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...

Static Public Attributes
static const std::string	NamesOfDerivatizationAgent [static_cast< int >(DerivatizationAgent::SIZE_OF_DERIVATIZATIONAGENT)]

static const std::string	NamesOfMassIntensityType [static_cast< int >(MassIntensityType::SIZE_OF_MASSINTENSITYTYPE)]

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

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

Additional Inherited Members
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 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

IsotopeLabelingMDVs is a class to support and analyze isotopic labeling experiments (i.e. MDVs : Mass Distribution Vectors, also known as Mass Isotopomer Distribution (MID))

Member Enumeration Documentation

◆ DerivatizationAgent

enum DerivatizationAgent

strong

Enumerator
NOT_SELECTED
TBDMS
SIZE_OF_DERIVATIZATIONAGENT

◆ MassIntensityType

enum MassIntensityType

strong

Enumerator
NORM_MAX
NORM_SUM
SIZE_OF_MASSINTENSITYTYPE

Constructor & Destructor Documentation

◆ IsotopeLabelingMDVs()

IsotopeLabelingMDVs ( )

Constructor.

◆ ~IsotopeLabelingMDVs()

~IsotopeLabelingMDVs ( )

override

Destructor.

Member Function Documentation

◆ calculateIsotopicPurities()

void calculateIsotopicPurities	(	FeatureMap &	normalized_featureMap,
		const std::vector< std::vector< double >> &	experiment_data,
		const std::vector< std::string > &	isotopic_purity_name
	)

This function calculates the isotopic purity of the MDVs using the following formula: isotopic purity of tracer (atom % 13C) = n / [n + (M + n-1)/(M + n)], where n in M+n is represented as the index of the result. The formula is extracted from "High-resolution 13C metabolic flux analysis", Long et al, doi:10.1038/s41596-019-0204-0.

Parameters

[in,out]	normalized_featureMap	FeatureMap with normalized values for each component and the number of heavy labeled e.g., carbons. Out is a FeatureMap with the calculated isotopic purity for the component group.
[in]	experiment_data	Vector of vectors of Experiment data in percent.
[in]	isotopic_purity_name	Vector of names of the isotopic purity tracer to be saved as a meta value.

◆ calculateIsotopicPurity()

void calculateIsotopicPurity	(	Feature &	normalized_feature,
		const std::vector< double > &	experiment_data,
		const std::string &	isotopic_purity_name
	)

This function calculates the isotopic purity of the MDV using the following formula: isotopic purity of tracer (atom % 13C) = n / [n + (M + n-1)/(M + n)], where n in M+n is represented as the index of the result. The formula is extracted from "High-resolution 13C metabolic flux analysis", Long et al, doi:10.1038/s41596-019-0204-0.

Parameters

[in,out]	normalized_feature	Feature with normalized values for each component and the number of heavy labeled e.g., carbons. Out is a Feature with the calculated isotopic purity for the component group.
[in]	experiment_data	Vector of experiment data in percent.
[in]	isotopic_purity_name	Name of the isotopic purity tracer to be saved as a meta value.

◆ calculateMDV()

void calculateMDV	(	const Feature &	measured_feature,
		Feature &	normalized_feature,
		const MassIntensityType &	mass_intensity_type,
		const std::string &	feature_name
	)

This function calculates the mass distribution vector (MDV) either normalized to the highest mass intensity (norm_max) or normalized to the sum of all mass intensities (norm_sum)

Parameters

[in]	mass_intensity_type	Mass intensity type (either norm_max or norm_sum).
[in]	feature_name	Feature name to determine which features are needed to apply calculations on.
[in]	measured_feature	Feature with measured intensity for each component.
[out]	normalized_feature	Feature with normalized values for each component.

◆ calculateMDVAccuracies()

void calculateMDVAccuracies	(	FeatureMap &	normalized_featureMap,
		const std::string &	feature_name,
		const std::map< std::string, std::string > &	fragment_isotopomer_theoretical_formulas
	)

This function calculates the accuracy of the MDVs as compared to the theoretical MDVs (only for 12C quality control experiments) using average deviation to the mean.

Parameters

[in]	normalized_featuremap	FeatureMap with normalized values for each component and the chemical formula of the component group. Out is a FeatureMap with the component group accuracy and accuracy for the error for each component.
[in]	fragment_isotopomer_measured	Measured scan values.
[in]	fragment_isotopomer_theoretical_formula	A map of ProteinName/peptideRef to Empirical formula from which the theoretical values will be generated.

◆ calculateMDVAccuracy()

void calculateMDVAccuracy	(	Feature &	normalized_feature,
		const std::string &	feature_name,
		const std::string &	fragment_isotopomer_theoretical_formula
	)

This function calculates the accuracy of the MDV as compared to the theoretical MDV (only for 12C quality control experiments) using average deviation to the mean. The result is mapped to the meta value "average_accuracy" in the updated Feature.

Parameters

[in,out]	normalized_feature	Feature with normalized values for each component and the chemical formula of the component group. Out is a Feature with the component group accuracy and accuracy for the error for each component.
[in]	fragment_isotopomer_measured	Measured scan values.
[in]	fragment_isotopomer_theoretical_formula	Empirical formula from which the theoretical values will be generated.

◆ calculateMDVs()

void calculateMDVs	(	const FeatureMap &	measured_featureMap,
		FeatureMap &	normalized_featureMap,
		const MassIntensityType &	mass_intensity_type,
		const std::string &	feature_name
	)

This function calculates the mass distribution vector (MDV) either normalized to the highest mass intensity (norm_max) or normalized to the sum of all mass intensities (norm_sum)

Parameters

[in]	mass_intensity_type	Mass intensity type (either norm_max or norm_sum).
[in]	feature_name	Feature name to determine which features are needed to apply calculations on.
[in]	measured_featuremap	FeatureMap with measured intensity for each component.
[out]	normalized_featuremap	FeatureMap with normalized values for each component.

◆ isotopicCorrection()

void isotopicCorrection	(	const Feature &	normalized_feature,
		Feature &	corrected_feature,
		const Matrix< double > &	correction_matrix,
		const DerivatizationAgent &	correction_matrix_agent
	)

This function performs an isotopic correction to account for unlabeled abundances coming from the derivatization agent (e.g., tBDMS) using correction matrix method and is calculated as follows: MDV_corrected = CM^-1 * MDV_normalized_feature The formula is obtained from "The importance of accurately correcting for the natural abundance of stable isotopes", Midani et al, doi:10.1016/j.ab.2016.12.011.

Parameters

normalized_feature	Feature with normalized values for each component and unlabeled chemical formula for each component group.
correction_matrix	Square matrix holding correction factors derived either experimentally or theoretically which describe how spectral peaks of naturally abundant 13C contribute to spectral peaks that overlap (or convolve) the spectral peaks of the corrected MDV of the derivatization agent.
correction_matrix_agent	name of the derivatization agent, the internally stored correction matrix if the name of the agent is supplied, only "TBDMS" is supported for now.

Returns: corrected_feature Feature with corrected values for each component.

◆ isotopicCorrections()

void isotopicCorrections	(	const FeatureMap &	normalized_featureMap,
		FeatureMap &	corrected_featureMap,
		const Matrix< double > &	correction_matrix,
		const DerivatizationAgent &	correction_matrix_agent
	)

This function performs an isotopic correction to account for unlabeled abundances coming from the derivatization agent (e.g., tBDMS) using correction matrix method and is calculated as follows: MDV_corrected = CM^-1 * MDV_normalized_feature The formula is obtained from "The importance of accurately correcting for the natural abundance of stable isotopes", Midani et al, doi:10.1016/j.ab.2016.12.011.

Parameters

normalized_featuremap	FeatureMap with normalized values for each component and unlabeled chemical formula for each component group.
correction_matrix	Square matrix holding correction factors derived either experimentally or theoretically which describe how spectral peaks of naturally abundant 13C contribute to spectral peaks that overlap (or convolve) the spectral peaks of the corrected MDV of the derivatization agent.
correction_matrix_agent	name of the derivatization agent, the internally stored correction matrix if the name of the agent is supplied, only "TBDMS" is supported for now.

Returns: corrected_featuremap FeatureMap with corrected values for each component.

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ NamesOfDerivatizationAgent

const std::string NamesOfDerivatizationAgent[static_cast< int >(DerivatizationAgent::SIZE_OF_DERIVATIZATIONAGENT)]

static

◆ NamesOfMassIntensityType

const std::string NamesOfMassIntensityType[static_cast< int >(MassIntensityType::SIZE_OF_MASSINTENSITYTYPE)]

static

Public Types

Public Member Functions

Static Public Attributes

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ DerivatizationAgent

◆ MassIntensityType

Constructor & Destructor Documentation

◆ IsotopeLabelingMDVs()

◆ ~IsotopeLabelingMDVs()

Member Function Documentation

◆ calculateIsotopicPurities()

◆ calculateIsotopicPurity()

◆ calculateMDV()

◆ calculateMDVAccuracies()

◆ calculateMDVAccuracy()

◆ calculateMDVs()

◆ isotopicCorrection()

◆ isotopicCorrections()

◆ updateMembers_()

Member Data Documentation

◆ NamesOfDerivatizationAgent

◆ NamesOfMassIntensityType