| OpenMS 2.5.0

Public Member Functions | Static Public Member Functions | Private Types | List of all members
IonMobilityScoring Class Reference

A class that calls the ion mobility scoring routines. More...

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

## Public Member Functions

| IonMobilityScoring ()
| Constructor. More...
| ~IonMobilityScoring ()
| Destructor. More...

## Static Public Member Functions

static void | driftScoring (OpenSwath::SpectrumPtr spectrum, const std::vector< TransitionType > &transitions, OpenSwath_Scores &scores, const double drift_lower, const double drift_upper, const double drift_target, const double dia_extraction_window_, const bool dia_extraction_ppm_, const bool use_spline, const double drift_extra)
| Performs scoring of the ion mobility dimension in MS2. More...
static void | driftScoringMS1 (OpenSwath::SpectrumPtr spectrum, const std::vector< TransitionType > &transitions, OpenSwath_Scores &scores, const double drift_lower, const double drift_upper, const double drift_target, const double dia_extract_window_, const bool dia_extraction_ppm_, const bool use_spline, const double drift_extra)
| Performs scoring of the ion mobility dimension in MS1. More...
static void | driftScoringMS1Contrast (OpenSwath::SpectrumPtr spectrum, OpenSwath::SpectrumPtr ms1spectrum, const std::vector< TransitionType > &transitions, OpenSwath_Scores &scores, const double drift_lower, const double drift_upper, const double dia_extract_window_, const bool dia_extraction_ppm_, const double drift_extra)
| Performs scoring of the ion mobility dimension in MS1 and MS2 (contrast) More...

## Private Types

typedef OpenSwath::LightCompound | CompoundType
typedef OpenSwath::LightTransition | TransitionType

## Detailed Description

A class that calls the ion mobility scoring routines.

Use this class to invoke the individual OpenSWATH ion mobility scoring routines.

## Member Typedef Documentation

## ◆ CompoundType

typedef OpenSwath::LightCompound CompoundType

private

## ◆ TransitionType

typedef OpenSwath::LightTransition TransitionType

private

## Constructor & Destructor Documentation

## ◆ IonMobilityScoring()

IonMobilityScoring | ( |  | ) |

Constructor.

## ◆ ~IonMobilityScoring()

~IonMobilityScoring | ( |  | ) |

Destructor.

## Member Function Documentation

## ◆ driftScoring()

static void driftScoring | ( | OpenSwath::SpectrumPtr | spectrum,
|  | const std::vector< TransitionType > & | transitions,
|  | OpenSwath_Scores & | scores,
|  | const double | drift_lower,
|  | const double | drift_upper,
|  | const double | drift_target,
|  | const double | dia_extraction_window_,
|  | const bool | dia_extraction_ppm_,
|  | const bool | use_spline,
|  | const double | drift_extra
| ) |  |

static

Performs scoring of the ion mobility dimension in MS2.

Parameters

  spectrum | The DIA MS2 spectrum found at the peak apex
  transitions | The transitions used for scoring
  scores | The output scores
  drift_lower | Ion Mobility extraction start
  drift_upper | Ion Mobility extraction end
  drift_target | Ion Mobility extraction target
  dia_extraction_window_ | m/z extraction width
  dia_extraction_ppm_ | Whether m/z extraction width is in ppm
  use_spline | Whether to use spline for fitting
  drift_extra | Extend the extraction window to gain a larger field of view beyond drift_upper - drift_lower (in percent)

Returns
  Populates additional scores in the `scores` object

## ◆ driftScoringMS1()

static void driftScoringMS1 | ( | OpenSwath::SpectrumPtr | spectrum,
|  | const std::vector< TransitionType > & | transitions,
|  | OpenSwath_Scores & | scores,
|  | const double | drift_lower,
|  | const double | drift_upper,
|  | const double | drift_target,
|  | const double | dia_extract_window_,
|  | const bool | dia_extraction_ppm_,
|  | const bool | use_spline,
|  | const double | drift_extra
| ) |  |

static

Performs scoring of the ion mobility dimension in MS1.

Parameters

  spectrum | The DIA MS1 spectrum found at the peak apex
  transitions | The transitions used for scoring
  scores | The output scores
  drift_lower | Ion Mobility extraction start
  drift_upper | Ion Mobility extraction end
  drift_target | Ion Mobility extraction target
  dia_extraction_window_ | m/z extraction width
  dia_extraction_ppm_ | Whether m/z extraction width is in ppm
  use_spline | Whether to use spline for fitting
  drift_extra | Extra extraction to use for drift time (in percent)

Returns
  Populates additional scores in the `scores` object

## ◆ driftScoringMS1Contrast()

static void driftScoringMS1Contrast | ( | OpenSwath::SpectrumPtr | spectrum,
|  | OpenSwath::SpectrumPtr | ms1spectrum,
|  | const std::vector< TransitionType > & | transitions,
|  | OpenSwath_Scores & | scores,
|  | const double | drift_lower,
|  | const double | drift_upper,
|  | const double | dia_extract_window_,
|  | const bool | dia_extraction_ppm_,
|  | const double | drift_extra
| ) |  |

static

Performs scoring of the ion mobility dimension in MS1 and MS2 (contrast)

Parameters

  spectrum | The DIA MS2 spectrum found at the peak apex
  ms1spectrum | The DIA MS1 spectrum found at the peak apex
  transitions | The transitions used for scoring
  scores | The output scores
  drift_lower | Ion Mobility extraction start
  drift_upper | Ion Mobility extraction end
  drift_target | Ion Mobility extraction target
  dia_extraction_window_ | m/z extraction width
  dia_extraction_ppm_ | Whether m/z extraction width is in ppm
  use_spline | Whether to use spline for fitting
  drift_extra | Extra extraction to use for drift time (in percent)

Returns
  Populates additional scores in the `scores` object