Deisotoper Class Reference

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

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...

Member Function Documentation

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.