Precursor purity or noise estimation. More...

#include <OpenMS/ANALYSIS/ID/PrecursorPurity.h>

Classes
struct	PurityScores

Static Public Member Functions
static std::map< String, PurityScores >	computePrecursorPurities (const PeakMap &spectra, double precursor_mass_tolerance, bool precursor_mass_tolerance_unit_ppm, bool ignore_missing_precursor_spectra=false)
	compute precursor purity metrics for each MS2 spectrum in a PeakMap This is the main function of this class. See class description. Note: Spectra annotated with charge 0 will be treated as charge 1. More...

static PurityScores	computePrecursorPurity (const PeakSpectrum &ms1, const Precursor &pre, const double precursor_mass_tolerance, const bool precursor_mass_tolerance_unit_ppm)
	compute precursor purity metrics for one MS2 precursor More...

Static Private Member Functions
static PurityScores	combinePrecursorPurities (const PrecursorPurity::PurityScores &score1, const PrecursorPurity::PurityScores &score2)

Detailed Description

Precursor purity or noise estimation.

This class computes metrics for precursor isolation window purity (or noise). The function extracts the peaks from an isolation window targeted for fragmentation and determines which peaks are isotopes of the target and which come from other sources. The intensities of the assumed target peaks are summed up as the target intensity. Using this information it calculates an intensity ratio for the relative intensity of the target compared to other sources. These metrics are combined over the previous and the next MS1 spectrum.

Note: : If an MS1 spectrum does not contain the target peak within the given tolerance, all values are returned as 0.

Class Documentation

◆ OpenMS::PrecursorPurity::PurityScores

struct OpenMS::PrecursorPurity::PurityScores

Collaboration diagram for PrecursorPurity::PurityScores:

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Class Members
Size	interfering_peak_count
PeakSpectrum	interfering_peaks
double	signal_proportion
double	target_intensity
Size	target_peak_count
double	total_intensity

Member Function Documentation

◆ combinePrecursorPurities()

static PurityScores combinePrecursorPurities	(	const PrecursorPurity::PurityScores &	score1,
		const PrecursorPurity::PurityScores &	score2
	)

staticprivate

◆ computePrecursorPurities()

static std::map<String, PurityScores> computePrecursorPurities	(	const PeakMap &	spectra,
		double	precursor_mass_tolerance,
		bool	precursor_mass_tolerance_unit_ppm,
		bool	ignore_missing_precursor_spectra = `false`
	)

static

compute precursor purity metrics for each MS2 spectrum in a PeakMap This is the main function of this class. See class description. Note: Spectra annotated with charge 0 will be treated as charge 1.

Parameters

spectra	A PeakMap containing MS1 and MS2 spectra in order of acquisition or measurement. The first spectrum must be an MS1.
precursor_mass_tolerance	The precursor tolerance. Is used for determining the targeted peak and deisotoping.
precursor_mass_tolerance_unit_ppm	The unit of the precursor tolerance
ignore_missing_precursor_spectra	Allow MS2 spectra without a MS1 precursor spectrum (PurityScores for these spectra will be 0).

◆ computePrecursorPurity()

static PurityScores computePrecursorPurity	(	const PeakSpectrum &	ms1,
		const Precursor &	pre,
		const double	precursor_mass_tolerance,
		const bool	precursor_mass_tolerance_unit_ppm
	)

static

compute precursor purity metrics for one MS2 precursor

Note: This function is implemented in a general way and can also be used for e.g. MS3 precursor isolation windows in MS2 spectra. Spectra annotated with charge 0 will be treated as charge 1.