Package eu.isas.reporter.calculation

Class Deisotoper

java.lang.Object

eu.isas.reporter.calculation.Deisotoper

public class Deisotoper
extends Object

This class takes care of the deisotoping of reporter ion intensities.

Author:

Marc Vaudel, Harald Barsnes

Constructor Summary

Constructors

Constructor	Description
Deisotoper(com.compomics.util.experiment.quantification.reporterion.ReporterMethod method, double tolerance)	Constructor.

Method Summary

Modifier and Type	Method	Description
HashMap<String,Double>	deisotope(HashMap<String,com.compomics.util.experiment.identification.matches.IonMatch> ionMatches, com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum spectrum, double mzTolerance, boolean mostAccurate)	This method returns deisotoped intensities.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

Deisotoper

public Deisotoper(com.compomics.util.experiment.quantification.reporterion.ReporterMethod method,
 double tolerance)

Constructor.

Parameters:

method - the reporter method used

tolerance - the tolerance to use for reporter ions detection

Method Details

deisotope

public HashMap<String,Double> deisotope(HashMap<String,com.compomics.util.experiment.identification.matches.IonMatch> ionMatches,
 com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum spectrum,
 double mzTolerance,
 boolean mostAccurate)

This method returns deisotoped intensities.

Parameters:

ionMatches - the ion matches to deisotope

spectrum - the spectrum to search the isotopic intensities in

mzTolerance - the MS2 m/z tolerance

mostAccurate - boolean indicating whether the most accurate ion should be selected

Returns:

a map of the deisotoped intensities (ion index > intensity)