Deisotoper Class Reference

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

Public Member Functions
	Deisotoper ()
	Deisotoper (CentroidData &)
virtual	~Deisotoper ()
std::list< DeconvPeak > &	getDeconvPeaks ()
void	go (CentroidData &)
void	cleanDeconvPeaks ()
int	getMinPeakGroupSize ()
double	getTheta ()
int	getScanNumber ()
bool	getShortReportFlag ()
void	setMinPeakGroupSize (int pMinPeakGroupSize)
void	setTheta (double pTheta)
void	setScanNumber (int pScanNumber)
void	setShortReportFlag (bool pShortReportFlag)

Static Public Member Functions
static void	deisotopeAndSingleCharge (MSSpectrum &spectrum, double fragment_tolerance, bool fragment_unit_ppm, int min_charge=1, int max_charge=3, bool keep_only_deisotoped=false, unsigned int min_isopeaks=3, unsigned int max_isopeaks=10, bool make_single_charged=true, bool annotate_charge=false, bool annotate_iso_peak_count=false, bool use_decreasing_model=true, unsigned int start_intensity_check=2, bool add_up_intensity=false)
	Detect isotopic clusters in a mass spectrum. More...

Protected Attributes
std::list< DeconvPeak >	fDeconvPeaks
int	fMinPeakGroupSize
double	fTheta
int	fScanNumber
bool	fShortReportFlag

Constructor & Destructor Documentation

Deisotoper() [1/2]

Deisotoper

(

)

Deisotoper() [2/2]

Deisotoper

(

CentroidData &

)

~Deisotoper()

virtual ~Deisotoper ( )

virtual

Member Function Documentation

cleanDeconvPeaks()

void cleanDeconvPeaks

(

)

deisotopeAndSingleCharge()

static void deisotopeAndSingleCharge ( MSSpectrum &  spectrum, double  fragment_tolerance, bool  fragment_unit_ppm, int  min_charge = 1, int  max_charge = 3, bool  keep_only_deisotoped = false, unsigned int  min_isopeaks = 3, unsigned int  max_isopeaks = 10, bool  make_single_charged = true, bool  annotate_charge = false, bool  annotate_iso_peak_count = false, bool  use_decreasing_model = true, unsigned int  start_intensity_check = 2, bool  add_up_intensity = false  )

static

Detect isotopic clusters in a mass spectrum.

Deisotoping is based on C13 abundance and will try to identify a simple model based on the C12-C13 distance and charge state. This is often a good approximation for peptide fragment ion spectra but may not work well for other spectra. The algorithm will consider each peak (starting from the right of a spectrum) and, for each peak, attempt to add isotopic peaks to its envelope until either no peak is found, the maximum number of isotopic peaks is reached or (only when using use_decreasing_model) the intensity of the peak is higher than the previous peak.

Deisotoping is done in-place and if annotate_charge is true, an additional IntegerDataArray "charge" will be appended. If annotate_iso_peak_count is true, an additional IntegerDataArray "iso_peak_count" containing the number of isotopic peaks will be appended. Existing DataArrays are kept and shrunken to the peaks which remain in the spectrum.

Parameters

[spectra]	Input spectra (sorted by m/z)
[fragment_tolerance]	The tolerance used to match isotopic peaks
[fragment_unit_ppm]	Whether ppm or m/z is used as tolerance
[min_charge]	The minimum charge considered
[max_charge]	The maximum charge considered
[keep_only_deisotoped]	Only monoisotopic peaks of fragments with isotopic pattern are retained
[min_isopeaks]	The minimum number of isotopic peaks (at least 2) required for an isotopic cluster
[max_isopeaks]	The maximum number of isotopic peaks (at least 2) considered for an isotopic cluster
[make_single_charged]	Convert deisotoped monoisotopic peak to single charge
[annotate_charge]	Annotate the charge to the peaks in the IntegerDataArray: "charge" (0 for unknown charge)
[annotate_iso_peak_count]	Annotate the number of isotopic peaks in a pattern for each monoisotopic peak in the IntegerDataArray: "iso_peak_count"
[use_decreasing_model]	Use a simple averagine model that expects heavier isotopes to have less intensity. If false, no intensity checks are applied.
[start_intensity_check]	Number of the isotopic peak from which the decreasing model should be applied. <= 1 will force the monoisotopic peak to be the most intense. 2 will allow the monoisotopic peak to be less intense than the second peak. 3 will allow the monoisotopic and the second peak to be less intense than the third, etc. A number higher than max_isopeaks will effectively disable use_decreasing_model completely.
[add_up_intensity]	Sum up the total intensity of each isotopic pattern into the intensity of the reported monoisotopic peak

Note: If make_single_charged is selected, the original charge (>=1) gets annotated.

getDeconvPeaks()

std::list<DeconvPeak>& getDeconvPeaks ( )

inline

getMinPeakGroupSize()

int getMinPeakGroupSize ( )

inline

getScanNumber()

int getScanNumber ( )

inline

getShortReportFlag()

bool getShortReportFlag ( )

inline

getTheta()

double getTheta ( )

inline

go()

void go

(

CentroidData &

)

setMinPeakGroupSize()

void setMinPeakGroupSize ( int  pMinPeakGroupSize )

inline

setScanNumber()

void setScanNumber ( int  pScanNumber )

inline

setShortReportFlag()

void setShortReportFlag ( bool  pShortReportFlag )

inline

setTheta()

void setTheta ( double  pTheta )

inline

Member Data Documentation

fDeconvPeaks

std::list<DeconvPeak> fDeconvPeaks

protected

fMinPeakGroupSize

int fMinPeakGroupSize

protected

fScanNumber

int fScanNumber

protected

fShortReportFlag

bool fShortReportFlag

protected

fTheta

double fTheta

protected