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. Note that the single swath_map returned is in a vector so that this function is compatible with SONAR functions

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