OpenMS
SwathMapMassCorrection Class Reference

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

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

Inheritance diagram for SwathMapMassCorrection:
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Collaboration diagram for SwathMapMassCorrection:
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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::SwathMapfindSwathMapsPasef (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...
 
DefaultParamHandleroperator= (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 ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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< Stringsubsections_
 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()

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_mapA MRMFeatureFinderScoring result map
swath_mapsThe raw swath maps from the current run
targeted_expThe corresponding spectral library (required for extraction coordinates)
pasefwhether 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_trafoThe 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_mapA MRMFeatureFinderScoring result map
targeted_expThe corresponding spectral library (required for extraction coordinates)
swath_mapsThe raw swath maps from the current run, will be modified (replaced with a corrected version)
pasefWhether 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_groupA MRMTransitionGroup for which the SwathMap is assigned to
[out]swath_mapsA 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