| OpenMS 2.5.0

OpenMS::DIAHelpers Namespace Reference

## Functions

bool | integrateWindow (const OpenSwath::SpectrumPtr spectrum, double mz_start, double mz_end, double &mz, double &intensity, bool centroided=false)
| Helper functions for the DIA scoring of OpenSWATH. More...
void | integrateWindows (const OpenSwath::SpectrumPtr spectrum, const std::vector< double > &windows_center, double width, std::vector< double > &integrated_windows_intensity, std::vector< double > &integrated_windows_mz, bool remove_zero=false)
| Integrate intensities in a spectrum from start to end. More...
void | integrateDriftSpectrum (OpenSwath::SpectrumPtr spectrum, double mz_start, double mz_end, double &im, double &intensity, double drift_start, double drift_end)
| Integrate intensity in an ion mobility spectrum from start to end. More...
void | adjustExtractionWindow (double &right, double &left, const double &mz_extract_window, const bool &mz_extraction_ppm)
| Adjust left/right window based on window and whether its ppm or not. More...
void | getBYSeries (const AASequence &a, std::vector< double > &bseries, std::vector< double > &yseries, TheoreticalSpectrumGenerator const *g, UInt charge=1u)
| compute the b and y series masses for a given AASequence More...
void | getTheorMasses (const AASequence &a, std::vector< double > &masses, TheoreticalSpectrumGenerator const *g, UInt charge=1u)
| for SWATH – get the theoretical b and y series masses for a sequence More...
void | getAveragineIsotopeDistribution (const double product_mz, std::vector< std::pair< double, double > > &isotopesSpec, const double charge=1., const int nr_isotopes=4, const double mannmass=1.00048)
| get averagine distribution given mass More...
void | simulateSpectrumFromAASequence (const AASequence &aa, std::vector< double > &firstIsotopeMasses, std::vector< std::pair< double, double > > &isotopeMasses, TheoreticalSpectrumGenerator const *g, double charge=1.)
| simulate spectrum from AASequence More...
void | modifyMassesByCharge (const std::vector< std::pair< double, double > > &masses, std::vector< std::pair< double, double > > &modmass, double charge=1.)
| modify masses by charge More...
void | addPreisotopeWeights (const std::vector< double > &firstIsotopeMasses, std::vector< std::pair< double, double > > &isotopeSpec, UInt nrpeaks=2, double preIsotopePeaksWeight=-0.5, double mannmass=1.000482, double charge=1.)
| add negative pre-isotope weights to spectrum More...
void | addIsotopes2Spec (const std::vector< std::pair< double, double > > &spec, std::vector< std::pair< double, double > > &isotopeMasses, double charge=1.)
| given an experimental spectrum add isotope pattern. More...
void | sortByFirst (std::vector< std::pair< double, double > > &tmp)
| sorts vector of pairs by first More...
void | extractFirst (const std::vector< std::pair< double, double > > &peaks, std::vector< double > &mass)
| extract first from vector of pairs More...
void | extractSecond (const std::vector< std::pair< double, double > > &peaks, std::vector< double > &mass)
| extract second from vector of pairs More...

## Function Documentation

## ◆ addIsotopes2Spec()

void OpenMS::DIAHelpers::addIsotopes2Spec | ( | const std::vector< std::pair< double, double > > & | spec,
|  | std::vector< std::pair< double, double > > & | isotopeMasses,
|  | double | charge = `1.`
| ) |  |

given an experimental spectrum add isotope pattern.

## ◆ addPreisotopeWeights()

void OpenMS::DIAHelpers::addPreisotopeWeights | ( | const std::vector< double > & | firstIsotopeMasses,
|  | std::vector< std::pair< double, double > > & | isotopeSpec,
|  | UInt | nrpeaks = `2`,
|  | double | preIsotopePeaksWeight = `-0.5`,
|  | double | mannmass = `1.000482`,
|  | double | charge = `1.`
| ) |  |

add negative pre-isotope weights to spectrum

## ◆ adjustExtractionWindow()

void OpenMS::DIAHelpers::adjustExtractionWindow | ( | double & | right,
|  | double & | left,
|  | const double & | mz_extract_window,
|  | const bool & | mz_extraction_ppm
| ) |  |

Adjust left/right window based on window and whether its ppm or not.

## ◆ extractFirst()

void OpenMS::DIAHelpers::extractFirst | ( | const std::vector< std::pair< double, double > > & | peaks,
|  | std::vector< double > & | mass
| ) |  |

extract first from vector of pairs

## ◆ extractSecond()

void OpenMS::DIAHelpers::extractSecond | ( | const std::vector< std::pair< double, double > > & | peaks,
|  | std::vector< double > & | mass
| ) |  |

extract second from vector of pairs

## ◆ getAveragineIsotopeDistribution()

void OpenMS::DIAHelpers::getAveragineIsotopeDistribution | ( | const double | product_mz,
|  | std::vector< std::pair< double, double > > & | isotopesSpec,
|  | const double | charge = `1.`,
|  | const int | nr_isotopes = `4`,
|  | const double | mannmass = `1.00048`
| ) |  |

get averagine distribution given mass

## ◆ getBYSeries()

void OpenMS::DIAHelpers::getBYSeries | ( | const AASequence & | a,
|  | std::vector< double > & | bseries,
|  | std::vector< double > & | yseries,
|  | TheoreticalSpectrumGenerator const * | g,
|  | UInt | charge = `1u`
| ) |  |

compute the b and y series masses for a given AASequence

## ◆ getTheorMasses()

void OpenMS::DIAHelpers::getTheorMasses | ( | const AASequence & | a,
|  | std::vector< double > & | masses,
|  | TheoreticalSpectrumGenerator const * | g,
|  | UInt | charge = `1u`
| ) |  |

for SWATH – get the theoretical b and y series masses for a sequence

## ◆ integrateDriftSpectrum()

void OpenMS::DIAHelpers::integrateDriftSpectrum | ( | OpenSwath::SpectrumPtr | spectrum,
|  | double | mz_start,
|  | double | mz_end,
|  | double & | im,
|  | double & | intensity,
|  | double | drift_start,
|  | double | drift_end
| ) |  |

Integrate intensity in an ion mobility spectrum from start to end.

This function will integrate the intensity in a spectrum between mz_start and mz_end, returning the total intensity and an intensity-weighted drift time value.

Note
  If there is no signal, mz will be set to -1 and intensity to 0

## ◆ integrateWindow()

bool OpenMS::DIAHelpers::integrateWindow | ( | const OpenSwath::SpectrumPtr | spectrum,
|  | double | mz_start,
|  | double | mz_end,
|  | double & | mz,
|  | double & | intensity,
|  | bool | centroided = `false`
| ) |  |

Helper functions for the DIA scoring of OpenSWATH.

Integrate intensity in a spectrum from start to end

This function will integrate the intensity in a spectrum between mz_start and mz_end, returning the total intensity and an intensity-weighted m/z value.

Note
  If there is no signal, mz will be set to -1 and intensity to 0

Returns
  Returns true if a signal was found (and false if no signal was found)

## ◆ integrateWindows()

void OpenMS::DIAHelpers::integrateWindows | ( | const OpenSwath::SpectrumPtr | spectrum,
|  | const std::vector< double > & | windows_center,
|  | double | width,
|  | std::vector< double > & | integrated_windows_intensity,
|  | std::vector< double > & | integrated_windows_mz,
|  | bool | remove_zero = `false`
| ) |  |

Integrate intensities in a spectrum from start to end.

Parameters

  [in] | spectrum | Spectrum
  [in] | windows_center | center location

## ◆ modifyMassesByCharge()

void OpenMS::DIAHelpers::modifyMassesByCharge | ( | const std::vector< std::pair< double, double > > & | masses,
|  | std::vector< std::pair< double, double > > & | modmass,
|  | double | charge = `1.`
| ) |  |

modify masses by charge

Parameters

  [in] | modmass | [out]

## ◆ simulateSpectrumFromAASequence()

void OpenMS::DIAHelpers::simulateSpectrumFromAASequence | ( | const AASequence & | aa,
|  | std::vector< double > & | firstIsotopeMasses,
|  | std::vector< std::pair< double, double > > & | isotopeMasses,
|  | TheoreticalSpectrumGenerator const * | g,
|  | double | charge = `1.`
| ) |  |

simulate spectrum from AASequence

## ◆ sortByFirst()

void OpenMS::DIAHelpers::sortByFirst | ( | std::vector< std::pair< double, double > > & | tmp | ) |

sorts vector of pairs by first