| OpenMS 2.5.0

Public Member Functions | Private Attributes | List of all members
SwathMapMassCorrection Class Reference

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

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

Inheritance diagram for SwathMapMassCorrection:

## Public Member Functions

void | updateMembers_ () override
| Synchronize members with param class. More...
void | correctMZ (const std::map< String, OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType *> &transition_group_map, std::vector< OpenSwath::SwathMap > &swath_maps, const OpenSwath::LightTargetedExperiment &targeted_exp)
| 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 std::vector< OpenSwath::SwathMap > &swath_maps, TransformationDescription &im_trafo, const OpenSwath::LightTargetedExperiment &targeted_exp)
| Correct the ion mobility values of a SWATH map based on the RT-normalization peptides. More...
| SwathMapMassCorrection ()
| Constructor. More...
| ~SwathMapMassCorrection ()=default
| Destructor. 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...
virtual 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

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 | ( |  | ) |

default

Destructor.

## Member Function Documentation

## ◆ correctIM()

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

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.

Parameters

  transition_group_map | A MRMFeatureFinderScoring result map
  swath_maps | The raw swath maps from the current run
  im_trafo | The resulting map containing the transformation

## ◆ correctMZ()

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

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
  swath_maps | The raw swath maps from the current run

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

override virtual

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