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 std::vector< double >	computeSingleScanPrecursorPurities (int ms2_spec_idx, int precursor_spec_idx, const MSExperiment &exp, double max_precursor_isotope_deviation)
	Computes a simple purity score aggregate for all Precursors (and their windows) of spectrum at `ms2_spec_idx` in the precursor spectrum at `precursor_spec_idx`. More...

static std::vector< double >	computeInterpolatedPrecursorPurity (int ms2_spec_idx, int precursor_spec_idx, int next_ms1_spec_idx, const MSExperiment &exp, double max_precursor_isotope_deviation)
	Computes a simple purity score aggregate for all Precursors (and their windows) of spectrum at `ms2_spec_idx` interpolated between precursor spectrum at `precursor_spec_idx` and the next parent type spectrum at `next_ms1_spec_idx`. 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

◆ computeInterpolatedPrecursorPurity()

static std::vector<double> computeInterpolatedPrecursorPurity	(	int	ms2_spec_idx,
		int	precursor_spec_idx,
		int	next_ms1_spec_idx,
		const MSExperiment &	exp,
		double	max_precursor_isotope_deviation
	)

static

Computes a simple purity score aggregate for all Precursors (and their windows) of spectrum at ms2_spec_idx interpolated between precursor spectrum at precursor_spec_idx and the next parent type spectrum at next_ms1_spec_idx.

Interpolates by RT distances of ms2_spec_idx to the precursor_spec_idx and next_ms1_spec_idx. Extracts with fuzzy boundaries around expected isotopes where it only considers 50% of the intensity of the peak as belonging to the target. Warning: Does neither check if the relationship between those spectra make sense nor that all precursors windows in ms2_spec_idx even come from the same spectrum.

Note: If next_ms1_spec_idx is out of range, does not refer to an MS1 spectrum, or the RT denominator is zero/invalid, the function will fall back to returning the early scan purity (from precursor_spec_idx) without interpolation.

Parameters

ms2_spec_idx	index for the spectrum holding the precursor information
precursor_spec_idx	index for the precursor spectrum to extract the intensities from
next_ms1_spec_idx	index for the next parent type spectrum to extract the intensities from
exp	the MSExperiment holding the spectra to look them up
max_precursor_isotope_deviation	the maximum allowed deviation for the precursor isotopes in ppm

Returns: std::vector<double> precursor intensity vs. total intensity for every precursor window in ms2_spec_idx

◆ 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.

Parameters

ms1	The Spectrum containing the isolation window
pre	The precursor containing the definition the isolation window
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

◆ computeSingleScanPrecursorPurities()

static std::vector<double> computeSingleScanPrecursorPurities	(	int	ms2_spec_idx,
		int	precursor_spec_idx,
		const MSExperiment &	exp,
		double	max_precursor_isotope_deviation
	)

static

Computes a simple purity score aggregate for all Precursors (and their windows) of spectrum at ms2_spec_idx in the precursor spectrum at precursor_spec_idx.

Extracts with fuzzy boundaries around expected isotopes where it only considers 50% of the intensity of the peak as belonging to the target. Warning: Does neither check if the relationship between those spectra make sense nor that all precursors windows in ms2_spec_idx even come from the same spectrum.

Parameters

ms2_spec_idx	index for the spectrum holding the precursor information
precursor_spec_idx	index for the precursor spectrum to extract the intensities from
exp	the MSExperiment holding the spectra to look them up
max_precursor_isotope_deviation	the maximum allowed deviation for the precursor isotopes in ppm

Returns: std::vector<double> precursor intensity vs. total intensity for every precursor window in ms2_spec_idx

Classes

Static Public Member Functions

Static Private Member Functions

Detailed Description

Class Documentation

◆ OpenMS::PrecursorPurity::PurityScores

Member Function Documentation

◆ combinePrecursorPurities()

◆ computeInterpolatedPrecursorPurity()

◆ computePrecursorPurities()

◆ computePrecursorPurity()

◆ computeSingleScanPrecursorPurities()