Functions

bool	integrateWindow (const OpenSwath::SpectrumPtr &spectrum, double &mz, double &im, double &intensity, const RangeMZ &mz_range, const RangeMobility &im_range, bool centroided=false)
	Helper functions for the DIA scoring of OpenSWATH. More...

bool	integrateWindow (const SpectrumSequence &spectrum, double &mz, double &im, double &intensity, const RangeMZ &mz_range, const RangeMobility &im_range, bool centroided=false)
	Integrate intensity in SpectrumSequence in range `mz_range` (and `im_range` if defined) returning the intensity-weighted m/z and im values as well as the total intensity. 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, std::vector< double > &integrated_windows_im, const RangeMobility &im_range, bool remove_zero=false)
	Integrate intensities in a spectrum in range `im_range` (if defined) for multiple windows. More...

void	integrateWindows (const SpectrumSequence &spectrum, const std::vector< double > &windows_center, double width, std::vector< double > &integrated_windows_intensity, std::vector< double > &integrated_windows_mz, std::vector< double > &integrated_windows_im, const RangeMobility &im_range, bool remove_zero=false)
	Integrate intensities of a SpectrumSequence in range `im_range` (if defined) for multiple windows. 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, int charge=1)
	compute the b and y series masses for a given AASequence More...

void	getTheorMasses (const AASequence &a, std::vector< double > &masses, TheoreticalSpectrumGenerator const *g, int charge=1)
	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 > > &isotopes_spec, const int 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 > &first_isotope_masses, std::vector< std::pair< double, double > > &isotope_masses, TheoreticalSpectrumGenerator const *g, int charge=1)
	simulate spectrum from AASequence More...

void	addPreisotopeWeights (const std::vector< double > &first_isotope_masses, std::vector< std::pair< double, double > > &isotope_spec, UInt nr_peaks=2, double pre_isotope_peaks_weight=-0.5, double mannmass=1.000482, int charge=1)
	add (potentially negative) pre-isotope weights to spectrum More...

void	addPreisotopeWeights (double mz, std::vector< std::pair< double, double > > &isotope_spec, UInt nr_peaks=2, double pre_isotope_peaks_weight=-0.5, double mannmass=1.000482, int 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 > > &isotope_masses, Size nr_isotopes, int charge=1)

void	addSinglePeakIsotopes2Spec (double mz, double ity, std::vector< std::pair< double, double > > &isotope_masses, Size nr_isotopes, int charge)

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...

RangeMZ	createMZRangePPM (double mz_ref, double dia_extraction_window, const bool ppm)
	optionally convert a DIA extraction window from ppm to m/z More...

void	integrateWindow_ (const OpenSwath::SpectrumPtr &spectrum, double &mz, double &im, double &intensity, const RangeMZ &mz_range, const RangeMobility &im_range, bool centroided)
	Helper function for integrating a spectrum. More...

Function Documentation

◆ addIsotopes2Spec()

void OpenMS::DIAHelpers::addIsotopes2Spec	(	const std::vector< std::pair< double, double > > &	spec,
		std::vector< std::pair< double, double > > &	isotope_masses,
		Size	nr_isotopes,
		int	charge = `1`
	)

given an experimental spectrum, add averagine isotope pattern for every peak. Old + new peaks are pushed to isotopeMasses

◆ addPreisotopeWeights() [1/2]

void OpenMS::DIAHelpers::addPreisotopeWeights	(	const std::vector< double > &	first_isotope_masses,
		std::vector< std::pair< double, double > > &	isotope_spec,
		UInt	nr_peaks = `2`,
		double	pre_isotope_peaks_weight = `-0.5`,
		double	mannmass = `1.000482`,
		int	charge = `1`
	)

add (potentially negative) pre-isotope weights to spectrum

◆ addPreisotopeWeights() [2/2]

void OpenMS::DIAHelpers::addPreisotopeWeights	(	double	mz,
		std::vector< std::pair< double, double > > &	isotope_spec,
		UInt	nr_peaks = `2`,
		double	pre_isotope_peaks_weight = `-0.5`,
		double	mannmass = `1.000482`,
		int	charge = `1`
	)

add negative pre-isotope weights to spectrum

◆ addSinglePeakIsotopes2Spec()

void OpenMS::DIAHelpers::addSinglePeakIsotopes2Spec	(	double	mz,
		double	ity,
		std::vector< std::pair< double, double > > &	isotope_masses,
		Size	nr_isotopes,
		int	charge
	)

given a peak of experimental mz and intensity, add averagine isotope pattern to a "spectrum". Old + new peaks are pushed to isotopeMasses

◆ 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.

◆ createMZRangePPM()

RangeMZ OpenMS::DIAHelpers::createMZRangePPM	(	double	mz_ref,
		double	dia_extraction_window,
		const bool	ppm
	)

optionally convert a DIA extraction window from ppm to m/z

Parameters

mz_ref	Extraction window center
dia_extraction_window	How wide the extraction window is total (can be in m/z or ppm)
ppm	Is extraction window is in ppm?

Returns: The extraction window in m/z

◆ 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 > > &	isotopes_spec,
		const int	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,
		int	charge = `1`
	)

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,
		int	charge = `1`
	)

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

◆ integrateWindow() [1/2]

bool OpenMS::DIAHelpers::integrateWindow	(	const OpenSwath::SpectrumPtr &	spectrum,
		double &	mz,
		double &	im,
		double &	intensity,
		const RangeMZ &	mz_range,
		const RangeMobility &	im_range,
		bool	centroided = `false`
	)

Helper functions for the DIA scoring of OpenSWATH.

Integrate intensity in a spectrum from in mz_range (and im_range if defined) returning the intensity-weighted m/z and im values as well as the total intensity.

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

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

◆ integrateWindow() [2/2]

bool OpenMS::DIAHelpers::integrateWindow	(	const SpectrumSequence &	spectrum,
		double &	mz,
		double &	im,
		double &	intensity,
		const RangeMZ &	mz_range,
		const RangeMobility &	im_range,
		bool	centroided = `false`
	)

Integrate intensity in SpectrumSequence in range mz_range (and im_range if defined) returning the intensity-weighted m/z and im values as well as the total intensity.

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

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

◆ integrateWindow_()

void OpenMS::DIAHelpers::integrateWindow_	(	const OpenSwath::SpectrumPtr &	spectrum,
		double &	mz,
		double &	im,
		double &	intensity,
		const RangeMZ &	mz_range,
		const RangeMobility &	im_range,
		bool	centroided
	)

Helper function for integrating a spectrum.

◆ integrateWindows() [1/2]

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,
		std::vector< double > &	integrated_windows_im,
		const RangeMobility &	im_range,
		bool	remove_zero = `false`
	)

Integrate intensities in a spectrum in range im_range (if defined) for multiple windows.

Parameters

	spectrum	Input spectrum
	windows_center	Center locations of the windows.
	width	Width of the windows across m/z
[out]	integrated_windows_intensity	Integrated intensity for each window
[out]	integrated_windows_mz	Integrated intensity-weighted m/z for each window
[out]	integrated_windows_im	Integrated intensity-weighted im for each window
	im_range	is the range of the IM dimension (if defined)
	remove_zero	Remove zero intensity windows?

◆ integrateWindows() [2/2]

void OpenMS::DIAHelpers::integrateWindows	(	const SpectrumSequence &	spectrum,
		const std::vector< double > &	windows_center,
		double	width,
		std::vector< double > &	integrated_windows_intensity,
		std::vector< double > &	integrated_windows_mz,
		std::vector< double > &	integrated_windows_im,
		const RangeMobility &	im_range,
		bool	remove_zero = `false`
	)

Integrate intensities of a SpectrumSequence in range im_range (if defined) for multiple windows.

Parameters

	spectrum	Input spectrum
	windows_center	Center locations of the windows.
	width	Width of the windows across m/z
[out]	integrated_windows_intensity	Integrated intensity for each window
[out]	integrated_windows_mz	Integrated intensity-weighted m/z for each window
[out]	integrated_windows_im	Integrated intensity-weighted im for each window
	im_range	is the range of the IM dimension (if defined)
	remove_zero	Remove zero intensity windows?

◆ simulateSpectrumFromAASequence()

void OpenMS::DIAHelpers::simulateSpectrumFromAASequence	(	const AASequence &	aa,
		std::vector< double > &	first_isotope_masses,
		std::vector< std::pair< double, double > > &	isotope_masses,
		TheoreticalSpectrumGenerator const *	g,
		int	charge = `1`
	)

simulate spectrum from AASequence

◆ sortByFirst()

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

sorts vector of pairs by first

Functions

Function Documentation

◆ addIsotopes2Spec()

◆ addPreisotopeWeights() [1/2]

◆ addPreisotopeWeights() [2/2]

◆ addSinglePeakIsotopes2Spec()

◆ adjustExtractionWindow()

◆ createMZRangePPM()

◆ extractFirst()

◆ extractSecond()

◆ getAveragineIsotopeDistribution()

◆ getBYSeries()

◆ getTheorMasses()

◆ integrateWindow() [1/2]

◆ integrateWindow() [2/2]

◆ integrateWindow_()

◆ integrateWindows() [1/2]

◆ integrateWindows() [2/2]

◆ simulateSpectrumFromAASequence()

◆ sortByFirst()