RNAPrecursorCorrector Class Reference

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
SpectralDeconvolution	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.

Match the reported selected ion to an observed isotope at the reported charge. Unknown charges can be inferred from a unique envelope. Missing monoisotopes are allowed when FLASH still assigns a unique high-quality envelope. Isotope shifts are subtracted from the instrument's selected-ion m/z. 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.

Correct every MS2 in acquisition order, deconvolving each referenced MS1 once. 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.

Returns

One audit result for each MS2, including unresolved scans.

References RNAPrecursorCorrector::Result::accepted(), RNAPrecursorCorrector::Result::charge, RNAPrecursorCorrector::Result::corrected_mz, RNAPrecursorCorrector::Result::cosine, RNAPrecursorCorrector::detector_, found, SpectralDeconvolution::getDeconvolvedSpectrum(), RNAPrecursorCorrector::Result::isotope, RNAPrecursorCorrector::match(), RNAPrecursorCorrector::Result::mono_mass, RNAPrecursorCorrector::Result::mono_observed, RNAPrecursorCorrector::Result::original_charge, RNAPrecursorCorrector::Result::original_mz, RNAPrecursorCorrector::Result::parent, RNAPrecursorCorrector::Result::parent_source, SpectralDeconvolution::performSpectrumDeconvolution(), DeconvolvedSpectrum::setOriginalSpectrum(), MSExperiment::size(), RNAPrecursorCorrector::Result::snr, RNAPrecursorCorrector::Result::spectrum, and RNAPrecursorCorrector::Result::status.

Referenced by NucleicAcidSearchEngine::main_().

match()

RNAPrecursorCorrector::Result match	(	const DeconvolvedSpectrum &	groups,
		const Precursor &	precursor
	)		const

Select a unique envelope independently of RNA sequence matches or scores.

Parameters

[in]	groups	RNA envelopes detected from complete parent MS1 evidence.
[in]	precursor	Original selected ion and reported charge.

Returns

Confident correction or an unresolved result preserving the input.

References OpenMS::Constants::C13C12_MASSDIFF_U, RNAPrecursorCorrector::Result::charge, RNAPrecursorCorrector::Result::corrected_mz, RNAPrecursorCorrector::Result::cosine, Precursor::getCharge(), Peak1D::getMZ(), RNAPrecursorCorrector::Result::isotope, RNAPrecursorCorrector::max_abs_charge_, RNAPrecursorCorrector::min_cos_, RNAPrecursorCorrector::min_snr_, RNAPrecursorCorrector::Result::mono_mass, RNAPrecursorCorrector::Result::mono_observed, RNAPrecursorCorrector::Result::original_charge, RNAPrecursorCorrector::Result::original_mz, RNAPrecursorCorrector::positive_, OpenMS::Constants::PROTON_MASS_U, RNAPrecursorCorrector::Result::selected_error_ppm, RNAPrecursorCorrector::Result::snr, RNAPrecursorCorrector::Result::status, and RNAPrecursorCorrector::tolerance_ppm_.

Referenced by RNAPrecursorCorrector::correct().

storeReport()

void storeReport ( const std::string &  filename, const std::vector< Result > &  results  )

static

Write one tab-delimited audit row per MS2, including unresolved scans.

Parameters

[in]	filename	Audit output path.
[in]	results	Correction results in acquisition order.

References TextFile::addLine(), TextFile::store(), and OpenMS::StringUtils::toStr().

Referenced by NucleicAcidSearchEngine::main_().

Member Data Documentation

detector_

SpectralDeconvolution detector_

private

Referenced by RNAPrecursorCorrector::correct(), and RNAPrecursorCorrector::RNAPrecursorCorrector().

max_abs_charge_

int max_abs_charge_

private

Referenced by RNAPrecursorCorrector::match().

min_abs_charge_

int min_abs_charge_

private

min_cos_

double min_cos_

private

Referenced by RNAPrecursorCorrector::match().

min_snr_

double min_snr_

private

Referenced by RNAPrecursorCorrector::match().

positive_

bool positive_

private

Referenced by RNAPrecursorCorrector::match().

tolerance_ppm_

double tolerance_ppm_

private

Referenced by RNAPrecursorCorrector::match().