#include <NucleicAcidSearchEngine/include/RNADeisotoper.h>

Public Member Functions
	RNADeisotoper (double tolerance_ppm, int max_abs_charge, bool positive, double max_mass=1000.0, double min_cos=0.85, double min_snr=0.25)
	Configure FLASH RNA isotope detection.

void	filter (MSSpectrum &spectrum, int scan_number, bool decharge)
	Remove confidently assigned isotope samples while preserving observed intensities.

Private Attributes
SpectralDeconvolution	detector_

bool	positive_

int	max_abs_charge_

double	min_cos_

double	min_snr_

Detailed Description

FLASHDeconv isotope detection with RNA averagine; preserves observed peak intensities. Each worker must use its own instance. Input must be sorted MS2, in profile or centroided form.

Constructor & Destructor Documentation

◆ RNADeisotoper()

RNADeisotoper	(	double	tolerance_ppm,
		int	max_abs_charge,
		bool	positive,
		double	max_mass = `1000.0`,
		double	min_cos = `0.85`,
		double	min_snr = `0.25`
	)

Configure FLASH RNA isotope detection.

Parameters

[in]	tolerance_ppm	Fragment tolerance in ppm.
[in]	max_abs_charge	Largest charge magnitude to consider, used unchanged.
[in]	positive	Use positive ionization mode.
[in]	max_mass	Largest neutral mass in Da (default: 1000). Explicit limits are used unchanged.

Exceptions

Exception::IllegalArgument If tolerance_ppm is not finite and positive, max_abs_charge is invalid, min_cos or min_snr is non-finite, or max_mass is non-finite or below the FLASH minimum mass (50 Da).

Parameters

[in]	min_cos	Minimum charge-specific isotope cosine.
[in]	min_snr	Minimum charge-specific envelope SNR.

References SpectralDeconvolution::calculateAveragine(), RNADeisotoper::detector_, DefaultParamHandler::getParameters(), Param::getValue(), DefaultParamHandler::setParameters(), and Param::setValue().

Member Function Documentation

◆ filter()

void filter	(	MSSpectrum &	spectrum,
		int	scan_number,
		bool	decharge
	)

Remove confidently assigned isotope samples while preserving observed intensities.

Keep unassigned peaks and envelopes without an observed monoisotope. Retain every monoisotope profile sample once. Ambiguous charges are not decharged. Higher-charge competitors within configured bounds may veto assignments but are not emitted above assignment bounds. Harmonic screening cannot see charges beyond max_abs_charge.

Parameters

[in,out]	spectrum	Sorted profile or centroided MS2 spectrum.
[in]	scan_number	Scan index supplied to FLASH.
[in]	decharge	Convert uniquely assigned monoisotopes to single charge.

References RNADeisotoper::detector_, SpectralDeconvolution::getDeconvolvedSpectrum(), MSSpectrum::getIntegerDataArrays(), SpectrumSettings::getPrecursors(), RNADeisotoper::max_abs_charge_, RNADeisotoper::min_cos_, RNADeisotoper::min_snr_, SpectralDeconvolution::performSpectrumDeconvolution(), RNADeisotoper::positive_, OpenMS::Constants::PROTON_MASS_U, MSSpectrum::select(), MetaInfoInterface::setMetaValue(), MetaInfoDescription::setName(), DeconvolvedSpectrum::size(), and MSSpectrum::sortByPosition().