SwathMapMassCorrection Class Reference

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

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

Inheritance diagram for SwathMapMassCorrection:

Collaboration diagram for SwathMapMassCorrection:

Public Member Functions
	SwathMapMassCorrection ()
	Constructor. More...
	~SwathMapMassCorrection () override=default
	Destructor. More...
void	updateMembers_ () override
	Synchronize members with param class. More...
void	correctMZ (const std::map< 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. More...
void	correctIM (const std::map< 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. More...
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. 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...

Private Attributes
double	mz_extraction_window_
bool	mz_extraction_window_ppm_
bool	ms1_im_
double	im_extraction_window_
String	mz_correction_function_
String	im_correction_function_
String	debug_im_file_
String	debug_mz_file_

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

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< 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.

Parameters

transition_group_map	A MRMFeatureFinderScoring result map
swath_maps	The raw swath maps from the current run
targeted_exp	The corresponding spectral library (required for extraction coordinates)
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.
im_trafo	The resulting map containing the transformation

correctMZ()

void correctMZ	(	const std::map< 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

transition_group_map	A MRMFeatureFinderScoring result map
targeted_exp	The corresponding spectral library (required for extraction coordinates)
swath_maps	The raw swath maps from the current run, will be modified (replaced with a corrected version)
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.

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

updateMembers_()

void updateMembers_ ( )

overridevirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

Member Data Documentation

debug_im_file_

String debug_im_file_

private

debug_mz_file_

String debug_mz_file_

private

im_correction_function_

String im_correction_function_

private

im_extraction_window_

double im_extraction_window_

private

ms1_im_

bool ms1_im_

private

mz_correction_function_

String mz_correction_function_

private

mz_extraction_window_

double mz_extraction_window_

private

mz_extraction_window_ppm_

bool mz_extraction_window_ppm_

private