Correct MS2 precursor m/z from FLASH RNA envelopes in the parent MS1 scan. More...

#include <NucleicAcidSearchEngine/include/RNAPrecursorCorrector.h>

Classes
struct	Result

Public Member Functions
	RNAPrecursorCorrector (double tolerance_ppm, int min_abs_charge, int max_abs_charge, bool positive, double max_mass=1000.0, double min_cos=0.85, double min_snr=0.25)
	Configure MS1-supported RNA precursor correction.

Result	match (const DeconvolvedSpectrum &groups, const Precursor &precursor) const
	Select a unique envelope independently of RNA sequence matches or scores.

std::vector< Result >	correct (MSExperiment &experiment)
	Correct selected-ion values without moving acquisition isolation windows.

Static Public Member Functions
static void	storeReport (const std::string &filename, const std::vector< Result > &results)
	Write one tab-delimited audit row per MS2, including unresolved scans.

Private Attributes
RNADirectedDeconvolution	detector_

double	tolerance_ppm_

double	min_cos_

double	min_snr_

int	min_abs_charge_

int	max_abs_charge_

bool	positive_

Detailed Description

Correct MS2 precursor m/z from FLASH RNA envelopes in the parent MS1 scan.

Construct precursor-related FLASH envelopes using the complete parent MS1. Match the selected ion to an observed isotope at the reported charge. Unknown charges can be inferred from a unique envelope. Missing monoisotopes are allowed. FLASH supplies the isotope index; subtract its mass shift from the instrument's selected-ion m/z to preserve the original mass precision. Ambiguous or unmatched precursors retain their original m/z and charge. Accepted corrections preserve the input charge sign convention.

Constructor & Destructor Documentation

◆ RNAPrecursorCorrector()

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

Configure MS1-supported RNA precursor correction.

Parameters

[in]	tolerance_ppm	Selected-ion and envelope tolerance in ppm.
[in]	min_abs_charge	Smallest charge magnitude to consider.
[in]	max_abs_charge	Largest charge magnitude to consider.
[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, charge magnitudes are 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(), RNAPrecursorCorrector::detector_, DefaultParamHandler::getParameters(), Param::getValue(), DefaultParamHandler::setParameters(), and Param::setValue().

Member Function Documentation

◆ correct()

std::vector< RNAPrecursorCorrector::Result > correct ( MSExperiment & experiment )

Correct selected-ion values without moving acquisition isolation windows.

Batch all selected ions sharing a parent MS1 and deconvolve that parent once. Retain correction results only, without caching raw MS1 copies or envelopes. MS1 peaks may be unsorted; any sorting uses a copy and preserves the original scan. Prefer spectrum_ref; invalid references fall back to the preceding MS1 and are reported. Replace earlier FLASH annotations; unresolved results omit accepted-only fields.

Parameters

[in,out] experiment Original MS1/MS2 experiment in acquisition order.