OpenMS
PrecursorPurity Class Reference

Precursor purity or noise estimation. More...

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

Classes

struct  PurityScores
 

Static Public Member Functions

static std::map< String, PurityScorescomputePrecursorPurities (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:
[legend]
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
spectraA PeakMap containing MS1 and MS2 spectra in order of acquisition or measurement. The first spectrum must be an MS1.
precursor_mass_toleranceThe precursor tolerance. Is used for determining the targeted peak and deisotoping.
precursor_mass_tolerance_unit_ppmThe unit of the precursor tolerance
ignore_missing_precursor_spectraAllow 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
ms1The Spectrum containing the isolation window
preThe precursor containing the definition the isolation window
precursor_mass_toleranceThe precursor tolerance. Is used for determining the targeted peak and deisotoping.
precursor_mass_tolerance_unit_ppmThe unit of the precursor tolerance