com.compomics.util.experiment.identification.spectrum_annotators

Class PeptideSpectrumAnnotator

java.lang.Object

com.compomics.util.experiment.identification.SpectrumAnnotator

com.compomics.util.experiment.identification.spectrum_annotators.PeptideSpectrumAnnotator

public class PeptideSpectrumAnnotator
extends SpectrumAnnotator

Annotates a spectrum with peptide fragments.

Author:

Marc Vaudel

Field Summary

Fields inherited from class com.compomics.util.experiment.identification.SpectrumAnnotator

fragmentFactory, intensityLimit, isPpm, massShift, massShiftCTerm, massShiftNTerm, mzTolerance, precursorCharge, spectrumAnnotation, subtractIsotope, theoreticalFragmentIons, unmatchedIons

Constructor Summary

Constructors

Constructor and Description
PeptideSpectrumAnnotator() Constructor.

Method Summary

Methods

Modifier and Type	Method and Description
java.util.HashMap<java.lang.Integer,java.util.ArrayList<IonMatch>>	getCoveredAminoAcids(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, NeutralLossesMap neutralLosses, java.util.ArrayList<java.lang.Integer> charges, int precursorCharge, MSnSpectrum spectrum, Peptide peptide, double intensityLimit, double mzTolerance, boolean isPpm) Returns the ion matches corresponding to fragment ions indexed by amino acid number in the sequence.
java.util.ArrayList<IonMatch>	getCurrentAnnotation(MSnSpectrum spectrum, java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, NeutralLossesMap neutralLosses, java.util.ArrayList<java.lang.Integer> charges) Returns the currently matched ions with the given settings.
Peptide	getCurrentlyLoadedPeptide() Returns the currently inspected peptide.
static NeutralLossesMap	getDefaultLosses(Peptide peptide, AminoAcidPattern.MatchingType matchingType, double mzTolerance) Returns the possible neutral losses expected by default for a given peptide.
java.util.HashMap<java.lang.Integer,java.util.ArrayList<Ion>>	getExpectedIons(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, NeutralLossesMap neutralLosses, java.util.ArrayList<java.lang.Integer> charges, int precursorCharge, Peptide peptide) Returns the expected ions in a map indexed by the possible charges.
java.util.ArrayList<IonMatch>	getSpectrumAnnotation(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, NeutralLossesMap neutralLosses, java.util.ArrayList<java.lang.Integer> charges, int precursorCharge, MSnSpectrum spectrum, Peptide peptide, double intensityLimit, double mzTolerance, boolean isPpm) Returns the spectrum annotations of a spectrum in a list of IonMatches.
java.util.ArrayList<IonMatch>	matchPeak(Peptide peptide, java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, java.util.ArrayList<java.lang.Integer> charges, int precursorCharge, NeutralLossesMap neutralLosses, Peak peak) This method matches the potential fragment ions of a given peptide with a given peak.
void	setPeptide(Peptide peptide, int precursorCharge) Sets a new peptide to match.

Methods inherited from class com.compomics.util.experiment.identification.SpectrumAnnotator

chargeValidated, getCurrentlyLoadedSpectrumKey, getDefaultLosses, getExpectedIons, getMassShift, getMassShiftCTerm, getMassShiftNTerm, getSpectrumAnnotation, isAccounted, lossesValidated, matchInSpectrum, matchPeak, matchReporterIon, setMassShift, setMassShifts, setMassTolerance, setSpectrum, setTerminalMassShifts

Methods inherited from class java.lang.Object

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

Constructor Detail

PeptideSpectrumAnnotator

public PeptideSpectrumAnnotator()

Constructor.

Method Detail

setPeptide

public void setPeptide(Peptide peptide,
              int precursorCharge)

Sets a new peptide to match.

Parameters:

peptide - the new peptide

precursorCharge - the new precursor charge

matchPeak

public java.util.ArrayList<IonMatch> matchPeak(Peptide peptide,
                                      java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
                                      java.util.ArrayList<java.lang.Integer> charges,
                                      int precursorCharge,
                                      NeutralLossesMap neutralLosses,
                                      Peak peak)

This method matches the potential fragment ions of a given peptide with a given peak.

Parameters:

peptide - The peptide

iontypes - The fragment ions selected

charges - The charges of the fragment to search for

precursorCharge - The precursor charge as deduced by the search engine

neutralLosses - Map of expected neutral losses: neutral loss -> maximal position in the sequence (first aa is 1). let null if neutral losses should not be considered.

peak - The peak to match

Returns:

A list of potential ion matches

getSpectrumAnnotation

public java.util.ArrayList<IonMatch> getSpectrumAnnotation(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
                                                  NeutralLossesMap neutralLosses,
                                                  java.util.ArrayList<java.lang.Integer> charges,
                                                  int precursorCharge,
                                                  MSnSpectrum spectrum,
                                                  Peptide peptide,
                                                  double intensityLimit,
                                                  double mzTolerance,
                                                  boolean isPpm)

Returns the spectrum annotations of a spectrum in a list of IonMatches. Note that, except for +1 precursors, fragments ions will be expected to have a charge strictly smaller than the precursor ion charge.

Parameters:

iontypes - The expected ions to look for

neutralLosses - Map of expected neutral losses: neutral loss -> first position in the sequence (first aa is 1). let null if neutral losses should not be considered.

charges - List of expected charges

precursorCharge - the precursor charge

spectrum - The spectrum to match

peptide - The peptide of interest

intensityLimit - The intensity limit to use

mzTolerance - The m/z tolerance to use

isPpm - a boolean indicating whether the mass tolerance is in ppm or in Da

Returns:

an ArrayList of IonMatch containing the ion matches with the given settings

getCoveredAminoAcids

public java.util.HashMap<java.lang.Integer,java.util.ArrayList<IonMatch>> getCoveredAminoAcids(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
                                                                                      NeutralLossesMap neutralLosses,
                                                                                      java.util.ArrayList<java.lang.Integer> charges,
                                                                                      int precursorCharge,
                                                                                      MSnSpectrum spectrum,
                                                                                      Peptide peptide,
                                                                                      double intensityLimit,
                                                                                      double mzTolerance,
                                                                                      boolean isPpm)

Returns the ion matches corresponding to fragment ions indexed by amino acid number in the sequence. 1 is first amino acid.

Parameters:

iontypes - The expected ions to look for

neutralLosses - Map of expected neutral losses: neutral loss -> first position in the sequence (first aa is 1). let null if neutral losses should not be considered.

charges - List of expected charges

precursorCharge - the precursor charge

spectrum - The spectrum to match

peptide - The peptide of interest

intensityLimit - The intensity limit to use

mzTolerance - The m/z tolerance to use

isPpm - a boolean indicating whether the mass tolerance is in ppm or in Da

Returns:

the ion matches corresponding to fragment ions indexed by amino acid number in the sequence

getExpectedIons

public java.util.HashMap<java.lang.Integer,java.util.ArrayList<Ion>> getExpectedIons(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
                                                                            NeutralLossesMap neutralLosses,
                                                                            java.util.ArrayList<java.lang.Integer> charges,
                                                                            int precursorCharge,
                                                                            Peptide peptide)

Returns the expected ions in a map indexed by the possible charges. Note that, except for +1 precursors, fragments ions will be expected to have a charge strictly smaller than the precursor ion charge.

Parameters:

iontypes - The expected ions to look for

neutralLosses - Map of expected neutral losses: neutral loss -> first position in the sequence (first aa is 1). let null if neutral losses should not be considered.

charges - List of expected charges

peptide - The peptide of interest

precursorCharge - The precursor charge

Returns:

an ArrayList of IonMatch containing the ion matches with the given settings

getCurrentAnnotation

public java.util.ArrayList<IonMatch> getCurrentAnnotation(MSnSpectrum spectrum,
                                                 java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
                                                 NeutralLossesMap neutralLosses,
                                                 java.util.ArrayList<java.lang.Integer> charges)

Description copied from class: SpectrumAnnotator

Returns the currently matched ions with the given settings.

Specified by:

getCurrentAnnotation in class SpectrumAnnotator

Parameters:

spectrum - the spectrum of interest

iontypes - The expected fragment ions to look for

neutralLosses - Map of expected neutral losses: neutral loss -> first position in the sequence (first aa is 1). let null if neutral losses should not be considered.

charges - List of expected charges

Returns:

the currently matched ions with the given settings

getDefaultLosses

public static NeutralLossesMap getDefaultLosses(Peptide peptide,
                                AminoAcidPattern.MatchingType matchingType,
                                double mzTolerance)
                                         throws java.io.IOException,
                                                java.lang.IllegalArgumentException,
                                                java.lang.InterruptedException,
                                                java.io.FileNotFoundException,
                                                java.lang.ClassNotFoundException,
                                                java.sql.SQLException

Returns the possible neutral losses expected by default for a given peptide. /!\ this method will work only if the PTM found in the peptide are in the PTMFactory.

Parameters:

peptide - the peptide of interest

matchingType - the matching type to map ptms on the peptide sequence

mzTolerance - the ms2 m/z tolerance to use

Returns:

the expected possible neutral losses

Throws:

java.io.IOException

java.lang.IllegalArgumentException

java.lang.InterruptedException

java.io.FileNotFoundException

java.lang.ClassNotFoundException

java.sql.SQLException

getCurrentlyLoadedPeptide

public Peptide getCurrentlyLoadedPeptide()

Returns the currently inspected peptide.

Returns:

the currently inspected peptide