eu.isas.peptideshaker.recalibration

Class RunMzDeviation

java.lang.Object

eu.isas.peptideshaker.recalibration.RunMzDeviation

public class RunMzDeviation
extends Object

This class computes the mz deviations for a a given run (i.e. file).

Author:

Marc Vaudel

Field Summary

Fields

Modifier and Type	Field and Description
static int	mzBinSize The bin size in m/z in number of MS/MS spectra.
static int	rtBinSize The bin size in retention time in number of MS/MS spectra.

Constructor Summary

Constructors

Constructor and Description

RunMzDeviation(String spectrumFileNameWithoutExtension, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.waiting.WaitingHandler waitingHandler) Creates a map of m/z deviations for a given run.

Method Summary

Modifier and Type	Method and Description
double	getFragmentMzError(double precursorRT, double fragmentMZ) Returns the fragment error at the given retention time and fragment m/z.
ArrayList<Double>	getFragmentMZList(double precursorRT) Returns the list for fragment ion m/z bins at a given retention time point.
double	getOffset(double rtBin) Returns the precursor m/z deviation offset at a given retention time point.
double	getPrecursorMzCorrection(double precursorMz, double precursorRT) Returns an interpolation of the median error in the bins surrounding the given precursor m/z when recalibrating with m/z only.
ArrayList<Double>	getPrecursorRTList() Returns the list of precursor retention time bins.
double	getSlope(double rtBin) Returns the precursor m/z deviation slope at a given retention time point.
double[]	recalibrateFragmentMz(double precursorRT, double[] originalMz) Recalibrate an m/z array.

Methods inherited from class java.lang.Object

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

Field Detail

rtBinSize

public static final int rtBinSize

The bin size in retention time in number of MS/MS spectra.

See Also:

Constant Field Values

mzBinSize

public static final int mzBinSize

The bin size in m/z in number of MS/MS spectra.

See Also:

Constant Field Values

Constructor Detail

RunMzDeviation

public RunMzDeviation(String spectrumFileNameWithoutExtension,
                      com.compomics.util.experiment.identification.Identification identification,
                      com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                      com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                      com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                      com.compomics.util.waiting.WaitingHandler waitingHandler)

Creates a map of m/z deviations for a given run.

Parameters:

spectrumFileNameWithoutExtension - the name of the file of the run

identification - the corresponding identification

sequenceProvider - the protein sequence provider

spectrumProvider - the spectrum provider

identificationParameters - the identification parameters

waitingHandler - a waiting handler displaying the progress and allowing the user to cancel the process. Can be null

Method Detail

getPrecursorRTList

public ArrayList<Double> getPrecursorRTList()

Returns the list of precursor retention time bins.

Returns:

the list of precursor retention time bins

getFragmentMZList

public ArrayList<Double> getFragmentMZList(double precursorRT)

Returns the list for fragment ion m/z bins at a given retention time point.

Parameters:

precursorRT - the precursor retention time

Returns:

the list for fragment ion m/z bins

getSlope

public double getSlope(double rtBin)

Returns the precursor m/z deviation slope at a given retention time point.

Parameters:

rtBin - the retention time bin

Returns:

the precursor m/z deviation slope

getOffset

public double getOffset(double rtBin)

Returns the precursor m/z deviation offset at a given retention time point.

Parameters:

rtBin - the retention time bin

Returns:

the precursor m/z deviation offset

getPrecursorMzCorrection

public double getPrecursorMzCorrection(double precursorMz,
                                       double precursorRT)

Returns an interpolation of the median error in the bins surrounding the given precursor m/z when recalibrating with m/z only.

Parameters:

precursorMz - the precursor m/z

precursorRT - the precursor retention time

Returns:

the median error

getFragmentMzError

public double getFragmentMzError(double precursorRT,
                                 double fragmentMZ)

Returns the fragment error at the given retention time and fragment m/z.

Parameters:

precursorRT - the precursor retention time

fragmentMZ - the fragment m/z

Returns:

the error found

recalibrateFragmentMz

public double[] recalibrateFragmentMz(double precursorRT,
                                      double[] originalMz)

Recalibrate an m/z array.

Parameters:

precursorRT - the precursor retention time

originalMz - the original m/z

Returns:

the recalibrated m/z