org.expasy.mzjava.proteomics.ms.fragment

Class PeptideNeutralLossPeakGenerator

java.lang.Object

org.expasy.mzjava.proteomics.ms.fragment.PeptideNeutralLossPeakGenerator

All Implemented Interfaces:

PeptidePeakGenerator<PepFragAnnotation>

public class PeptideNeutralLossPeakGenerator
extends Object
implements PeptidePeakGenerator<PepFragAnnotation>

Generates a neutral loss for a peptide fragment if the modificationPredicate accepts the fragment.

There are convenience constructors for generating neutral losses depending on the presence of a set of amino acids. To create a neutral loss generator that depends on the presence of a modified amino acid, such as a phosphorylated serine, the ModifiedAaPresencePredicate can be used

There are also static methods to generate neutral losses that are common. Such as water, ammonia and phosphate loss

Version:

1.0

Author:

Oliver Horlacher

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PeptideNeutralLossPeakGenerator.ModifiedAaPresencePredicate Accepts a PeptideFragment if the fragment contains an amino acid in aminoAcids that has a modification which is equal to the mass of one modification in modifications.

Constructor Summary

Constructors

Constructor and Description
PeptideNeutralLossPeakGenerator(Mass massShift, com.google.common.base.Predicate<PeptideFragment> modificationPredicate, Set<IonType> ionTypes, double peakIntensity)
PeptideNeutralLossPeakGenerator(Mass massShift, Set<AminoAcid> affectedAA, Set<IonType> ionTypes, double peakIntensity)

Method Summary

Methods

Modifier and Type	Method and Description
List<AnnotatedPeak<PepFragAnnotation>>	generatePeaks(Peptide precursor, PeptideFragment fragment, int[] charges, List<AnnotatedPeak<PepFragAnnotation>> peaks) Generate peaks that are observed for the fragment at the supplied charge states.
Set<FragmentType>	getFragmentTypes()
static PeptideNeutralLossPeakGenerator	newAmmoniaLossGenerator(Set<IonType> ionTypes, double peakIntensity)
static PeptideNeutralLossPeakGenerator	newModificationLossGenerator(Mass loss, Set<AminoAcid> aminoAcids, Set<Modification> modifications, Set<ModAttachment> modAttachments, Set<IonType> ionTypes, double peakIntensity)
static PeptideNeutralLossPeakGenerator	newPhosphateLossGenerator(Set<IonType> ionTypes, double peakIntensity)
static PeptideNeutralLossPeakGenerator	newPhosphoricAcidLossGenerator(Set<IonType> ionTypes, double peakIntensity)
static PeptideNeutralLossPeakGenerator	newWaterLossGenerator(Set<IonType> ionTypes, double peakIntensity)

Methods inherited from class java.lang.Object

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

Constructor Detail

PeptideNeutralLossPeakGenerator

public PeptideNeutralLossPeakGenerator(Mass massShift,
                               Set<AminoAcid> affectedAA,
                               Set<IonType> ionTypes,
                               double peakIntensity)

PeptideNeutralLossPeakGenerator

public PeptideNeutralLossPeakGenerator(Mass massShift,
                               com.google.common.base.Predicate<PeptideFragment> modificationPredicate,
                               Set<IonType> ionTypes,
                               double peakIntensity)

Method Detail

newWaterLossGenerator

public static PeptideNeutralLossPeakGenerator newWaterLossGenerator(Set<IonType> ionTypes,
                                                    double peakIntensity)

newAmmoniaLossGenerator

public static PeptideNeutralLossPeakGenerator newAmmoniaLossGenerator(Set<IonType> ionTypes,
                                                      double peakIntensity)

newModificationLossGenerator

public static PeptideNeutralLossPeakGenerator newModificationLossGenerator(Mass loss,
                                                           Set<AminoAcid> aminoAcids,
                                                           Set<Modification> modifications,
                                                           Set<ModAttachment> modAttachments,
                                                           Set<IonType> ionTypes,
                                                           double peakIntensity)

newPhosphateLossGenerator

public static PeptideNeutralLossPeakGenerator newPhosphateLossGenerator(Set<IonType> ionTypes,
                                                        double peakIntensity)

newPhosphoricAcidLossGenerator

public static PeptideNeutralLossPeakGenerator newPhosphoricAcidLossGenerator(Set<IonType> ionTypes,
                                                             double peakIntensity)

generatePeaks

public List<AnnotatedPeak<PepFragAnnotation>> generatePeaks(Peptide precursor,
                                                   PeptideFragment fragment,
                                                   int[] charges,
                                                   List<AnnotatedPeak<PepFragAnnotation>> peaks)

Description copied from interface: PeptidePeakGenerator

Generate peaks that are observed for the fragment at the supplied charge states. The generated peaks are to be added to peaks

Specified by:

generatePeaks in interface PeptidePeakGenerator<PepFragAnnotation>

Parameters:

precursor - the peptide that this fragment was derived from

fragment - the fragment

charges - the charges for which to generate peaks

peaks - the list of peaks

Returns:

the peaks list that was passed in

getFragmentTypes

public Set<FragmentType> getFragmentTypes()

Specified by:

getFragmentTypes in interface PeptidePeakGenerator<PepFragAnnotation>