Deisotope the mass spectrum this mass spectrum is iterated over and according to a data point-based moving window progression does the following tests: More...

#include <filtertandemremovec13.h>

Inheritance diagram for pappso::FilterTandemDeisotope:

Public Member Functions
	FilterTandemDeisotope (double mz_range_max=0.95, double minimum_mz=200.0)
	FilterTandemDeisotope (const FilterTandemDeisotope &other)
MassSpectrum &	filter (MassSpectrum &data_points) const override
Public Member Functions inherited from pappso::MassSpectrumFilterInterface
virtual	~MassSpectrumFilterInterface ()

Private Attributes
double	m_arbitrary_range_between_isotopes = 0.95
double	m_arbitrary_minimum_mz = 200.0

Detailed Description

Deisotope the mass spectrum this mass spectrum is iterated over and according to a data point-based moving window progression does the following tests:

any data point having a x value (m/z value) less than 200 is conserved;
any data point having a x value greater than the previous data point's x value by at least 0.95 is conserved;

remove isotopes as in X!Tandem algorithm this method doesn't really remove isotopes: it cleans up multiple intensities within one Dalton of each other.

first tandem filter is 0.95 (remove_isotopes(_s);)
second tandem filter is 1.5 (clean_isotopes(_s);)

Definition at line 57 of file filtertandemremovec13.h.

Constructor & Destructor Documentation

◆ FilterTandemDeisotope() [1/2]

FilterTandemDeisotope::FilterTandemDeisotope	(	double	mz_range_max = 0.95,
		double	minimum_mz = 200.0 )

Definition at line 36 of file filtertandemremovec13.cpp.

{
  m_arbitrary_minimum_mz             = minimum_mz;
  m_arbitrary_range_between_isotopes = mz_range_max;
}

References m_arbitrary_minimum_mz, and m_arbitrary_range_between_isotopes.

Referenced by FilterTandemDeisotope().

◆ FilterTandemDeisotope() [2/2]

FilterTandemDeisotope::FilterTandemDeisotope ( const FilterTandemDeisotope & other )

Definition at line 43 of file filtertandemremovec13.cpp.

{
  m_arbitrary_minimum_mz             = other.m_arbitrary_minimum_mz;
  m_arbitrary_range_between_isotopes = other.m_arbitrary_range_between_isotopes;
}

References FilterTandemDeisotope(), m_arbitrary_minimum_mz, and m_arbitrary_range_between_isotopes.

Member Function Documentation

◆ filter()

MassSpectrum & FilterTandemDeisotope::filter ( MassSpectrum & data_points ) const

overridevirtual

Implements pappso::MassSpectrumFilterInterface.

Definition at line 50 of file filtertandemremovec13.cpp.

{
 
  MassSpectrum massSpectrum;
 
  if(data_points.size() > 0)
    {
      // auto it_write   = data_points.begin();
      auto it_read = data_points.begin() + 1;
      auto it_end  = data_points.end();
 
 
      DataPoint value_write = *data_points.begin();
      double last_mz        = value_write.x;
      while(it_read != it_end)
        {
          if((it_read->x - last_mz) >= m_arbitrary_range_between_isotopes ||
             it_read->x < m_arbitrary_minimum_mz)
            {
              massSpectrum.push_back(value_write);
              value_write = *it_read;
              last_mz     = value_write.x;
            }
          else if(it_read->y > value_write.y)
            {
              value_write = *it_read;
            }
          it_read++;
        }
      massSpectrum.push_back(value_write);
    }
 
  data_points = std::move(massSpectrum);
  return data_points;
}

References m_arbitrary_minimum_mz, m_arbitrary_range_between_isotopes, pappso::DataPoint::x, and pappso::DataPoint::y.

Member Data Documentation

◆ m_arbitrary_minimum_mz

double pappso::FilterTandemDeisotope::m_arbitrary_minimum_mz = 200.0

private

Definition at line 68 of file filtertandemremovec13.h.

Referenced by FilterTandemDeisotope(), FilterTandemDeisotope(), and filter().

◆ m_arbitrary_range_between_isotopes

double pappso::FilterTandemDeisotope::m_arbitrary_range_between_isotopes = 0.95