| OpenMS 2.5.0

Public Member Functions | Private Attributes | List of all members
MultiplexFilteredPeak Class Reference

data structure storing a single peak that passed all filters More...

`#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexFilteredPeak.h>`

## Public Member Functions

| MultiplexFilteredPeak (double mz, float rt, size_t mz_idx, size_t rt_idx)
| constructor More...
double | getMZ () const
| returns m/z of the peak More...
float | getRT () const
| returns RT of the peak More...
size_t | getMZidx () const
| returns the index of the peak in the spectrum More...
size_t | getRTidx () const
| returns the index of the corresponding spectrum in the MS experiment More...
void | addSatellite (size_t rt_idx, size_t mz_idx, size_t pattern_idx)
| add a satellite peak More...
void | addSatellite (const MultiplexSatelliteCentroided &satellite, size_t pattern_idx)
void | addSatelliteProfile (float rt, double mz, float intensity, size_t pattern_idx)
| add a satellite data point More...
void | addSatelliteProfile (const MultiplexSatelliteProfile &satellite, size_t pattern_idx)
bool | checkSatellite (size_t rt_idx, size_t mz_idx) const
| check if the peak (rt_idx, mz_idx) is already in the set of satellite peaks More...
const std::multimap< size_t, MultiplexSatelliteCentroided > & | getSatellites () const
| return all satellite peaks More...
const std::multimap< size_t, MultiplexSatelliteProfile > & | getSatellitesProfile () const
| return all satellite data points More...
size_t | size () const
| return number of satellite peaks More...
size_t | sizeProfile () const
| return number of satellite data points More...

## Private Attributes

double | mz_
| position of the primary peak More...
float | rt_
size_t | mz_idx_
| indices of the primary peak position in the centroided experiment More...
size_t | rt_idx_
std::multimap< size_t, MultiplexSatelliteCentroided > | satellites_
| set of satellites More...
std::multimap< size_t, MultiplexSatelliteProfile > | satellites_profile_
| set of profile satellites (used on profile data only) More...

## Detailed Description

data structure storing a single peak that passed all filters

Each filter result corresponds to a successful search for a particular peak pattern in the centroided data. The actual m/z shifts seen in the filter result might differ from the theoretical shifts listed in the peak pattern.

Each MultiplexFilteredPeak consists of a primary peak and a set of satellite peaks. The primary peak is a peak in the mono-isotopic masstrace of the lightest peptide in the multiplet. The satellite peaks are peaks that form the m/z shift pattern relative to the primary peak within a retention time range rt_band_. They are the evidence on which grounds a peak may pass the filters.

Note that in both centroid and profile mode, centroided data are filtered. (One of the first steps in the profile mode algorithm is the peak picking of the profile data.) Consequently in both modes, centroided peaks make up a final filtered peak.

See also
  size(). In profile mode, we additional store the profile data points that make up these peak.
  sizeProfile().
  MultiplexPeakPattern

## Constructor & Destructor Documentation

## ◆ MultiplexFilteredPeak()

MultiplexFilteredPeak | ( | double | mz,
|  | float | rt,
|  | size_t | mz_idx,
|  | size_t | rt_idx
| ) |  |

constructor

## Member Function Documentation

## ◆ addSatellite() [1/2]

void addSatellite | ( | size_t | rt_idx,
|  | size_t | mz_idx,
|  | size_t | pattern_idx
| ) |  |

add a satellite peak

## ◆ addSatellite() [2/2]

void addSatellite | ( | const MultiplexSatelliteCentroided & | satellite,
|  | size_t | pattern_idx
| ) |  |

## ◆ addSatelliteProfile() [1/2]

void addSatelliteProfile | ( | float | rt,
|  | double | mz,
|  | float | intensity,
|  | size_t | pattern_idx
| ) |  |

add a satellite data point

## ◆ addSatelliteProfile() [2/2]

void addSatelliteProfile | ( | const MultiplexSatelliteProfile & | satellite,
|  | size_t | pattern_idx
| ) |  |

## ◆ checkSatellite()

bool checkSatellite | ( | size_t | rt_idx,
|  | size_t | mz_idx
| ) |  | const

check if the peak (rt_idx, mz_idx) is already in the set of satellite peaks

## ◆ getMZ()

double getMZ | ( |  | ) | const

returns m/z of the peak

## ◆ getMZidx()

size_t getMZidx | ( |  | ) | const

returns the index of the peak in the spectrum

## ◆ getRT()

float getRT | ( |  | ) | const

returns RT of the peak

## ◆ getRTidx()

size_t getRTidx | ( |  | ) | const

returns the index of the corresponding spectrum in the MS experiment

## ◆ getSatellites()

const std::multimap<size_t, MultiplexSatelliteCentroided >& getSatellites | ( |  | ) | const

return all satellite peaks

See also
  also <satellites_>

## ◆ getSatellitesProfile()

const std::multimap<size_t, MultiplexSatelliteProfile >& getSatellitesProfile | ( |  | ) | const

return all satellite data points

See also
  also <satellites_profile_>

## ◆ size()

size_t size | ( |  | ) | const

return number of satellite peaks

## ◆ sizeProfile()

size_t sizeProfile | ( |  | ) | const

return number of satellite data points

## Member Data Documentation

## ◆ mz_

double mz_

private

position of the primary peak

Position of the primary peak in the m/z-RT plane in [Th, sec]. It is the input for the subsequent clustering step.

## ◆ mz_idx_

size_t mz_idx_

private

indices of the primary peak position in the centroided experiment

Spectral index and peak index within the spectrum of the primary peak. The indices are used to check the blacklist.

## ◆ rt_

float rt_

private

## ◆ rt_idx_

size_t rt_idx_

private

## ◆ satellites_

std::multimap<size_t, MultiplexSatelliteCentroided > satellites_

private

set of satellites

Mapping from a pattern index i.e. a specific mass trace to all peaks forming the pattern. The primary peak is part of the satellite peak set.

pattern_idx -> (rt_idx, mz_idx)

Typically peaks of the same mass trace show up in neighbouring spectra. The algorithm considers spectra in the RT range <rt_band>. Consequently, the same <pattern_idx> key will have multiple associated satellites, and a multimap is required.

Note that we store only indices, not iterators or pointers. We filter 'white' experiments, but all indices refer to the original experiment. White experiments are temporary (for each pattern), but the original <exp_picked_> experiment is permanent.

## ◆ satellites_profile_

std::multimap<size_t, MultiplexSatelliteProfile > satellites_profile_

private

set of profile satellites (used on profile data only)

Mapping from a pattern index i.e. a specific mass trace to all spline-interpolated data points forming the pattern. Basically, when profile data are available as input, we scan over the profile of each satellite peak (see MultiplexSatelliteCentroided above) and decide if it passes the filters or not.

pattern_idx -> (rt, mz, intensity)

Typically peaks of the same mass trace show up in neighbouring spectra. The algorithm considers spectra in the RT range <rt_band>. Consequently, the same <pattern_idx> key will have multiple associated satellites, and a multimap is required.