| OpenMS 2.5.0

Classes | Static Public Member Functions | Static Private Member Functions | List of all members
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, PurityScores > | computePrecursorPurities (const PeakMap &spectra, double precursor_mass_tolerance, bool precursor_mass_tolerance_unit_ppm)
| compute precursor purity metrics for each MS2 spectrum in a PeakMap This is the main function of this class. See class description. 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

Class Members
Size | residual_peak_count |
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
| ) |  |

static private

## ◆ computePrecursorPurities()

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

static

compute precursor purity metrics for each MS2 spectrum in a PeakMap This is the main function of this class. See class description.

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

## ◆ 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

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