A class containing correction functions for Swath MS maps. More...

#include <OpenMS/ANALYSIS/OPENSWATH/SwathMapMassCorrection.h>

Inheritance diagram for SwathMapMassCorrection:

Public Member Functions
	SwathMapMassCorrection ()
	Constructor.

	~SwathMapMassCorrection () override=default
	Destructor.

void	updateMembers_ () override
	Synchronize members with param class.

void	correctMZ (const std::map< std::string, OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType * > &transition_group_map, const OpenSwath::LightTargetedExperiment &targeted_exp, std::vector< OpenSwath::SwathMap > &swath_maps, const bool pasef)
	Correct the m/z values of a SWATH map based on the RT-normalization peptides.

void	correctIM (const std::map< std::string, OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType * > &transition_group_map, const OpenSwath::LightTargetedExperiment &targeted_exp, const std::vector< OpenSwath::SwathMap > &swath_maps, const bool pasef, TransformationDescription &im_trafo)
	Correct the ion mobility values of a SWATH map based on the RT-normalization peptides.

std::vector< OpenSwath::SwathMap >	findSwathMapsPasef (const OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType &transition_group, const std::vector< OpenSwath::SwathMap > &swath_maps)
	Computes the SwathMaps for PASEF data in which windows can have the same m/z but differ by ion mobility.

double	getFragmentMzWindow () const
	Retrieve the estimated fragment m/z extraction window (ppm)

void	setFragmentMzWindow (double fragmentMzWindow)
	Set the estimated fragment m/z extraction window (ppm_.

double	getFragmentImWindow () const
	Retrieve the estimated fragment ion mobility extraction window.

void	setFragmentImWindow (double fragmentImWindow)
	Set the estimated fragment ion mobility extraction window.

double	getPrecursorMzWindow () const
	Retrieve the estimated precursor m/z extraction window (ppm)

void	setPrecursorMzWindow (double precursorMzWindow)
	Set the estimated precursor m/z extraction window (ppm)

double	getPrecursorImWindow () const
	Retrieve the estimated precursor ion mobility extraction window.

void	setPrecursorImWindow (double precursorImWindow)
	Set the estimated precursor ion mobility extraction window.

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const std::string &name)
	Constructor with name that is displayed in error messages.

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor.

virtual	~DefaultParamHandler ()
	Destructor.

DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator.

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator.

void	setParameters (const Param &param)
	Sets the parameters.

const Param &	getParameters () const
	Non-mutable access to the parameters.

const Param &	getDefaults () const
	Non-mutable access to the default parameters.

const std::string &	getName () const
	Non-mutable access to the name.

void	setName (const std::string &name)
	Mutable access to the name.

const std::vector< std::string > &	getSubsections () const
	Non-mutable access to the registered subsections.

Static Public Member Functions
static double	estimateWindow (std::vector< double > residuals, double quantile=0.99, bool full_width=true, double padding_factor=1.0)
	Estimate an extraction window from absolute residuals.

Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const std::string &key_prefix="")
	Writes all parameters to meta values.

Private Attributes
double	mz_extraction_window_

bool	mz_extraction_window_ppm_

bool	ms1_im_

double	im_extraction_window_

std::string	mz_correction_function_

std::string	im_correction_function_

std::string	debug_im_file_

std::string	debug_mz_file_

double	mz_estimation_padding_factor_ = 1.0
	fields for estimated mz and ion mobility windows

double	im_estimation_padding_factor_ = 1.0

double	mz_estimation_percentile_ = 99.0

double	im_estimation_percentile_ = 99.0

double	fragment_mz_window_ = -1

double	fragment_im_window_ = -1

double	precursor_mz_window_ = -1

double	precursor_im_window_ = -1

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

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters.

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes!

std::vector< std::string >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes!

std::string	error_name_
	Name that is displayed in error messages during the parameter checking.

bool	check_defaults_
	If this member is set to false no checking if parameters in done;.

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;.

Detailed Description

A class containing correction functions for Swath MS maps.

This class can use a set of pre-determined points in a Swath-MS map to correct all maps according to the m/z shift found in those fixed points.

Constructor & Destructor Documentation

◆ SwathMapMassCorrection()

SwathMapMassCorrection ( )

Constructor.

◆ ~SwathMapMassCorrection()

~SwathMapMassCorrection ( )

overridedefault

Destructor.

Member Function Documentation

◆ correctIM()

void correctIM	(	const std::map< std::string, OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType * > &	transition_group_map,
		const OpenSwath::LightTargetedExperiment &	targeted_exp,
		const std::vector< OpenSwath::SwathMap > &	swath_maps,
		const bool	pasef,
		TransformationDescription &	im_trafo
	)

Correct the ion mobility values of a SWATH map based on the RT-normalization peptides.

This extracts the full spectra at the most likely elution time of the calibrant peptides and fits a linear regression curve to correct for a possible ion mobility (drift time) shift of the empirical drift time vs the theoretically expected drift time. The resulting linear transformation is stored using a TransformationDescription object. Transitions with peptide references absent from targeted_exp are skipped for both calibration and auxiliary MS1 window estimation. Non-finite experimental/theoretical pairs are discarded before fitting and window estimation. Remaining pairs are ordered together deterministically. If correction is disabled or the extraction window is negative, the transformation and estimated windows are left unchanged.

Exceptions

Exception::UnableToFit if correction is enabled but no finite calibration pairs remain. The transformation and estimated windows are left unchanged.

Parameters

[out]	transition_group_map	A MRMFeatureFinderScoring result map
[in,out]	swath_maps	The raw swath maps from the current run
[in]	targeted_exp	The corresponding spectral library (required for extraction coordinates)
[in]	pasef	whether the data is PASEF data with possible overlapping m/z windows (with different ion mobility). In this case, the "best" SWATH window (with precursor cetntered around IM) is chosen.
[out]	im_trafo	The resulting map containing the transformation

◆ correctMZ()

void correctMZ	(	const std::map< std::string, OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType * > &	transition_group_map,
		const OpenSwath::LightTargetedExperiment &	targeted_exp,
		std::vector< OpenSwath::SwathMap > &	swath_maps,
		const bool	pasef
	)

Correct the m/z values of a SWATH map based on the RT-normalization peptides.

This extracts the full spectra at the most likely elution time of the calibrant peptides and fits a regression curve to correct for a possible mass shift of the empirical masses vs the theoretically expected masses. Several types of regressions are available (see below corr_type parameter).

The function will replace the pointers stored in swath_maps with a transforming map that will contain corrected m/z values.

Parameters

[out]	transition_group_map	A MRMFeatureFinderScoring result map
[in]	targeted_exp	The corresponding spectral library (required for extraction coordinates)
[in]	swath_maps	The raw swath maps from the current run, will be modified (replaced with a corrected version)
[in]	pasef	Whether the data is PASEF data with possible overlapping m/z windows (with different ion mobility). In this case, the "best" SWATH window (with precursor cetntered around IM) is chosen.

◆ estimateWindow()

static double estimateWindow	(	std::vector< double >	residuals,
		double	quantile = `0.99`,
		bool	full_width = `true`,
		double	padding_factor = `1.0`
	)

static

Estimate an extraction window from absolute residuals.

Treats the input residuals as absolute errors (e.g., |delta ppm| for m/z). We compute an adaptive half-width using OpenMS::Math::adaptiveQuantile (Tukey k=1.5; blend raw vs winsorized by tail density), and return either the half-width or the full width (2×half).

Notes:

Empty input yields 0.0.
Ensure residuals contain absolute values; non-absolute inputs will be converted via std::abs internally.

Parameters

[in]	residuals	Absolute residuals (e.g., \|delta ppm\|).
[in]	quantile	Quantile of the half-width distribution to use (default 0.99).
[in]	full_width	If true, return 2×half-width; if false, return half-width.
[in]	padding_factor	A padding factor to add to the estimated window.

Returns: Estimated window (same units as residuals; 0.0 if empty).

◆ findSwathMapsPasef()

std::vector< OpenSwath::SwathMap > findSwathMapsPasef	(	const OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType &	transition_group,
		const std::vector< OpenSwath::SwathMap > &	swath_maps
	)

Computes the SwathMaps for PASEF data in which windows can have the same m/z but differ by ion mobility.

For each precursor, the SwathMap is chosen based on library m/z and ion mobility. If two or more SwathMaps isolate the same precursor the SwathMap in which the precursor is more centered across ion mobility is chosen.

Parameters

[in]	transition_group	A MRMTransitionGroup for which the SwathMap is assigned to
[out]	swath_maps	A vector containing the a single entry, the swath map which the MRMFeature is assigned to

◆ getFragmentImWindow()

double getFragmentImWindow ( ) const

Retrieve the estimated fragment ion mobility extraction window.

◆ getFragmentMzWindow()

double getFragmentMzWindow ( ) const

Retrieve the estimated fragment m/z extraction window (ppm)

◆ getPrecursorImWindow()

double getPrecursorImWindow ( ) const

Retrieve the estimated precursor ion mobility extraction window.

◆ getPrecursorMzWindow()

double getPrecursorMzWindow ( ) const

Retrieve the estimated precursor m/z extraction window (ppm)

◆ setFragmentImWindow()

void setFragmentImWindow ( double fragmentImWindow )

Set the estimated fragment ion mobility extraction window.

◆ setFragmentMzWindow()

void setFragmentMzWindow ( double fragmentMzWindow )

Set the estimated fragment m/z extraction window (ppm_.

◆ setPrecursorImWindow()

void setPrecursorImWindow ( double precursorImWindow )

Set the estimated precursor ion mobility extraction window.

◆ setPrecursorMzWindow()

void setPrecursorMzWindow ( double precursorMzWindow )

Set the estimated precursor m/z extraction window (ppm)

◆ updateMembers_()

void updateMembers_ ( )

overridevirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ debug_im_file_

std::string debug_im_file_

private

◆ debug_mz_file_

std::string debug_mz_file_

private

◆ fragment_im_window_

double fragment_im_window_ = -1

private

◆ fragment_mz_window_

double fragment_mz_window_ = -1

private

◆ im_correction_function_

std::string im_correction_function_

private

◆ im_estimation_padding_factor_

double im_estimation_padding_factor_ = 1.0

private

◆ im_estimation_percentile_

double im_estimation_percentile_ = 99.0

private

◆ im_extraction_window_

double im_extraction_window_

private

◆ ms1_im_

bool ms1_im_

private

◆ mz_correction_function_

std::string mz_correction_function_

private

◆ mz_estimation_padding_factor_

double mz_estimation_padding_factor_ = 1.0

private

fields for estimated mz and ion mobility windows

◆ mz_estimation_percentile_

double mz_estimation_percentile_ = 99.0

private

◆ mz_extraction_window_

double mz_extraction_window_

private

◆ mz_extraction_window_ppm_

bool mz_extraction_window_ppm_

private

◆ precursor_im_window_

double precursor_im_window_ = -1

private

◆ precursor_mz_window_

double precursor_mz_window_ = -1

private

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SwathMapMassCorrection()

◆ ~SwathMapMassCorrection()

Member Function Documentation

◆ correctIM()

◆ correctMZ()

◆ estimateWindow()

◆ findSwathMapsPasef()

◆ getFragmentImWindow()

◆ getFragmentMzWindow()

◆ getPrecursorImWindow()

◆ getPrecursorMzWindow()

◆ setFragmentImWindow()

◆ setFragmentMzWindow()

◆ setPrecursorImWindow()

◆ setPrecursorMzWindow()

◆ updateMembers_()

Member Data Documentation

◆ debug_im_file_

◆ debug_mz_file_

◆ fragment_im_window_

◆ fragment_mz_window_

◆ im_correction_function_

◆ im_estimation_padding_factor_

◆ im_estimation_percentile_

◆ im_extraction_window_

◆ ms1_im_

◆ mz_correction_function_

◆ mz_estimation_padding_factor_

◆ mz_estimation_percentile_

◆ mz_extraction_window_

◆ mz_extraction_window_ppm_

◆ precursor_im_window_

◆ precursor_mz_window_