Performs isotope impurity correction on intensities extracted from isobaric labeling experiments. More...

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

Static Public Member Functions
static IsobaricQuantifierStatistics	correctIsotopicImpurities (const ConsensusMap &consensus_map_in, ConsensusMap &consensus_map_out, const IsobaricQuantitationMethod *quant_method)
	Apply isotope correction to the given input map and store the corrected values in the output map. More...

static void	correctIsotopicImpurities (std::vector< double > &intensities, const IsobaricQuantitationMethod *quant_method)
	Apply isotope correction to a vector of channel intensities. More...

Static Private Member Functions
static void	fillInputVector_ (Eigen::VectorXd &b, Matrix< double > &m_b, const ConsensusFeature &cf, const ConsensusMap &cm)
	Fills the input vector for the Eigen/NNLS step given the ConsensusFeature. More...

static std::vector< double >	getIntensities_ (const IsobaricQuantitationMethod *quant_method, const ConsensusFeature &cf, const ConsensusMap &cm)
	Extract channel intensities from a ConsensusFeature. More...

static void	solveNNLS_ (const Matrix< double > &correction_matrix, const Matrix< double > &m_b, Matrix< double > &m_x)
	Solve the non-negative least squares problem using OpenMS matrices. More...

static void	solveNNLS_ (Matrix< double >::EigenMatrixType &correction_matrix, std::vector< double > &b, std::vector< double > &x)
	Solve the non-negative least squares problem using Eigen matrices. More...

static void	computeStats_ (const std::vector< double > &m_x, const Eigen::MatrixXd &x, const float cf_intensity, const IsobaricQuantitationMethod *quant_method, IsobaricQuantifierStatistics &stats)

static void	computeStats_ (const Matrix< double > &m_x, const Eigen::MatrixXd &x, const float cf_intensity, const IsobaricQuantitationMethod *quant_method, IsobaricQuantifierStatistics &stats)
	Compute statistics for the correction process using OpenMS matrices. More...

static float	updateOutputMap_ (const ConsensusMap &consensus_map_in, ConsensusMap &consensus_map_out, Size current_cf, const std::vector< double > &m_x)
	Update the output consensus map with corrected intensities using std::vector. More...

static float	updateOutputMap_ (const ConsensusMap &consensus_map_in, ConsensusMap &consensus_map_out, Size current_cf, const Matrix< double > &m_x)
	Update the output consensus map with corrected intensities using OpenMS Matrix. More...

Detailed Description

Performs isotope impurity correction on intensities extracted from isobaric labeling experiments.

This class implements algorithms for correcting isotope impurities in quantitative proteomics data obtained from isobaric labeling experiments such as iTRAQ or TMT. Isotope impurities arise from the fact that the reagents used for labeling are not 100% pure and contain isotopic variants that can contribute to the signal in neighboring channels.

The correction is performed using a non-negative least squares (NNLS) approach, which solves the linear system Ax = b, where:

A is the correction matrix derived from the isotope impurity information provided by the reagent manufacturer
b is the vector of observed intensities in each channel
x is the vector of corrected intensities

The NNLS approach ensures that the corrected intensities remain non-negative, which is physically meaningful for mass spectrometry data.

See also: IsobaricQuantitationMethod; IsobaricQuantifierStatistics

Member Function Documentation

◆ computeStats_() [1/2]

static void computeStats_	(	const Matrix< double > &	m_x,
		const Eigen::MatrixXd &	x,
		const float	cf_intensity,
		const IsobaricQuantitationMethod *	quant_method,
		IsobaricQuantifierStatistics &	stats
	)

staticprivate

Compute statistics for the correction process using OpenMS matrices.

Calculates various statistics about the correction process, such as the sum of corrected intensities, and updates the statistics object.

Parameters

m_x	The vector of corrected intensities as OpenMS matrix
x	The vector of corrected intensities as Eigen matrix
cf_intensity	The original intensity of the consensus feature
quant_method	The isobaric quantitation method
stats	The statistics object to update

◆ computeStats_() [2/2]

static void computeStats_	(	const std::vector< double > &	m_x,
		const Eigen::MatrixXd &	x,
		const float	cf_intensity,
		const IsobaricQuantitationMethod *	quant_method,
		IsobaricQuantifierStatistics &	stats
	)

staticprivate

◆ correctIsotopicImpurities() [1/2]

static IsobaricQuantifierStatistics correctIsotopicImpurities	(	const ConsensusMap &	consensus_map_in,
		ConsensusMap &	consensus_map_out,
		const IsobaricQuantitationMethod *	quant_method
	)

static

Apply isotope correction to the given input map and store the corrected values in the output map.

Parameters

consensus_map_in	The map containing the values that should be corrected.
consensus_map_out	The map where the corrected values should be stored.
quant_method	IsobaricQuantitationMethod (e.g., iTRAQ 4 plex)

Exceptions

Exception::FailedAPICall	If the least-squares fit fails.
Exception::InvalidParameter	If the given correction matrix is invalid.

◆ correctIsotopicImpurities() [2/2]

static void correctIsotopicImpurities	(	std::vector< double > &	intensities,
		const IsobaricQuantitationMethod *	quant_method
	)

static

Apply isotope correction to a vector of channel intensities.

This method applies the isotope correction directly to a vector of intensities representing the different isobaric channels. The vector is modified in-place to contain the corrected values.

Parameters

intensities	Vector of channel intensities to be corrected (modified in-place)
quant_method	IsobaricQuantitationMethod providing the correction matrix (e.g., iTRAQ 4 plex)

Exceptions

Exception::FailedAPICall	If the least-squares fit fails.
Exception::InvalidParameter	If the given correction matrix is invalid.

Note: The size of the intensities vector must match the number of channels in the quantitation method.

◆ fillInputVector_()

static void fillInputVector_	(	Eigen::VectorXd &	b,
		Matrix< double > &	m_b,
		const ConsensusFeature &	cf,
		const ConsensusMap &	cm
	)

staticprivate

Fills the input vector for the Eigen/NNLS step given the ConsensusFeature.

Warning, assumes that the consensusMap and its ConsensusFeatures have exactly the same cardinality as the number of channels as in the quantitation method and are in the same order as the channels.

I.e. for a TMT16plex, although the whole ConsensusMap has 160 potential map_index values because we had 10 files, every ConsensusFeature is only allowed to have exactly 16 map_index values (one for each channel) and they are in the same order as the channels in the quantitation method.

Parameters

[out]	b	Eigen vector to be filled with intensities
[out]	m_b	OpenMS matrix to be filled with intensities (alternative representation)
[in]	cf	ConsensusFeature containing the channel intensities
[in]	cm	ConsensusMap containing the feature

Precondition: The ConsensusFeature must contain exactly the same number of elements as there are channels in the quantitation method

◆ getIntensities_()

static std::vector<double> getIntensities_	(	const IsobaricQuantitationMethod *	quant_method,
		const ConsensusFeature &	cf,
		const ConsensusMap &	cm
	)

staticprivate

Extract channel intensities from a ConsensusFeature.

Extracts the intensities for each channel from the given ConsensusFeature.

Parameters

quant_method	The isobaric quantitation method defining the channels
cf	ConsensusFeature containing the channel intensities
cm	ConsensusMap containing the feature

Returns: Vector of intensities, one for each channel

◆ solveNNLS_() [1/2]

static void solveNNLS_	(	const Matrix< double > &	correction_matrix,
		const Matrix< double > &	m_b,
		Matrix< double > &	m_x
	)

staticprivate

Solve the non-negative least squares problem using OpenMS matrices.

Solves the NNLS problem Ax = b, where A is the correction matrix and b is the vector of observed intensities. This version uses OpenMS Matrix objects for the computation.

Parameters

correction_matrix	The isotope correction matrix (A)
m_b	The vector of observed intensities (b)
m_x	The output vector of corrected intensities (x)

Exceptions

Exception::FailedAPICall If the NNLS solver fails

◆ solveNNLS_() [2/2]

static void solveNNLS_	(	Matrix< double >::EigenMatrixType &	correction_matrix,
		std::vector< double > &	b,
		std::vector< double > &	x
	)

staticprivate

Solve the non-negative least squares problem using Eigen matrices.

Solves the NNLS problem Ax = b, where A is the correction matrix and b is the vector of observed intensities. This version uses Eigen matrices and std::vector for the computation.

Parameters

correction_matrix	The isotope correction matrix (A) as Eigen matrix
b	The vector of observed intensities (b)
x	The output vector of corrected intensities (x)

◆ updateOutputMap_() [1/2]

static float updateOutputMap_	(	const ConsensusMap &	consensus_map_in,
		ConsensusMap &	consensus_map_out,
		Size	current_cf,
		const Matrix< double > &	m_x
	)

staticprivate

Update the output consensus map with corrected intensities using OpenMS Matrix.

Copies the consensus feature from the input map to the output map and updates its intensities with the corrected values.

Parameters

consensus_map_in	The input consensus map
consensus_map_out	The output consensus map to be updated
current_cf	Index of the current consensus feature
m_x	Matrix of corrected intensities

Returns: The sum of corrected intensities

◆ updateOutputMap_() [2/2]

static float updateOutputMap_	(	const ConsensusMap &	consensus_map_in,
		ConsensusMap &	consensus_map_out,
		Size	current_cf,
		const std::vector< double > &	m_x
	)

staticprivate

Update the output consensus map with corrected intensities using std::vector.

Copies the consensus feature from the input map to the output map and updates its intensities with the corrected values.

Parameters

consensus_map_in	The input consensus map
consensus_map_out	The output consensus map to be updated
current_cf	Index of the current consensus feature
m_x	Vector of corrected intensities

Returns: The sum of corrected intensities

Static Public Member Functions

Static Private Member Functions

Detailed Description

Member Function Documentation

◆ computeStats_() [1/2]

◆ computeStats_() [2/2]

◆ correctIsotopicImpurities() [1/2]

◆ correctIsotopicImpurities() [2/2]

◆ fillInputVector_()

◆ getIntensities_()

◆ solveNNLS_() [1/2]

◆ solveNNLS_() [2/2]

◆ updateOutputMap_() [1/2]

◆ updateOutputMap_() [2/2]