A mass trace extraction method that gathers peaks similar in m/z and moving along retention time. More...

#include <OpenMS/FILTERING/DATAREDUCTION/MassTraceDetection.h>

Inheritance diagram for MassTraceDetection:

Public Member Functions
	MassTraceDetection ()
	Default constructor.
virtual	~MassTraceDetection ()
	Default destructor.
Helper methods

void	updateIterativeWeightedMeanMZ (const DoubleReal &, const DoubleReal &, DoubleReal &, DoubleReal &, DoubleReal &)
	Allows the iterative computation of the intensity-weighted mean of a mass trace's centroid m/z.
Main computation methods
Computes a rough estimate of the average peak width of the experiment (median) and an estimate of a lower and upper bound for the peak width (+/-2*MAD, median of absolute deviances).
DoubleReal	mass_error_ppm_
DoubleReal	noise_threshold_int_
DoubleReal	chrom_peak_snr_
DoubleReal	min_sample_rate_
DoubleReal	min_trace_length_
bool	reestimate_mt_sd_
void	run (const MSExperiment< Peak1D > &, std::vector< MassTrace > &)
	Main method of MassTraceDetection. Extracts mass traces of a MSExperiment and gathers them into a vector container.
void	run (MSExperiment< Peak1D >::ConstAreaIterator &begin, MSExperiment< Peak1D >::ConstAreaIterator &end, std::vector< MassTrace > &found_masstraces)
	Invokes the run method (see above) on merely a subregion of a MSExperiment map.
virtual void	updateMembers_ ()

Detailed Description

A mass trace extraction method that gathers peaks similar in m/z and moving along retention time.

Peaks of a MSExperiment are sorted by their intensity and stored in a list of potential chromatographic apex positions. Starting with these, mass traces are extended in- and decreasingly in retention time. During this extension phase, the centroid m/z is computed on-line as an intensity-weighted mean of peaks. The extension phase ends when the frequency of gathered peaks drops below a threshold (min_sample_rate, see MassTraceDetection parameters).

Constructor & Destructor Documentation

MassTraceDetection ( )

Default constructor.

virtual ~MassTraceDetection ( ) [virtual]

Default destructor.

Member Function Documentation

void run	(	const MSExperiment< Peak1D > &	,
		std::vector< MassTrace > &
	)

Main method of MassTraceDetection. Extracts mass traces of a MSExperiment and gathers them into a vector container.

void run	(	MSExperiment< Peak1D >::ConstAreaIterator &	begin,
		MSExperiment< Peak1D >::ConstAreaIterator &	end,
		std::vector< MassTrace > &	found_masstraces
	)