com.compomics.util.experiment.identification.ptm.ptmscores

Class AScore

java.lang.Object

com.compomics.util.experiment.identification.ptm.ptmscores.AScore

public class AScore
extends Object

This class estimates the A-score as described in http://www.ncbi.nlm.nih.gov/pubmed/16964243 Note: Here the window size is adapted to mz tolerance and the score is not restricted to phosphorylation.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
AScore()

Method Summary

Modifier and Type	Method and Description
static HashMap<Integer,Double>	getAScore(Peptide peptide, ArrayList<PTM> ptms, MSnSpectrum spectrum, AnnotationSettings annotationPreferences, SpecificAnnotationSettings specificAnnotationPreferences, boolean accountNeutralLosses, SequenceMatchingPreferences sequenceMatchingPreferences, SequenceMatchingPreferences ptmSequenceMatchingPreferences, PeptideSpectrumAnnotator spectrumAnnotator) Returns the A-score for the best PTM location.
static HashMap<Double,ArrayList<Integer>>	getPeptideScoreToPositionMap(HashMap<Integer,HashMap<Integer,Double>> positionToScoreMap) Estimates the peptide score for every modification localization and returns a map score > localization.
static HashMap<Integer,HashMap<Integer,Double>>	getPositionToScoreMap(Peptide peptide, Peptide noModPeptide, ArrayList<Integer> possibleSites, MSnSpectrum spectrum, HashMap<Integer,MSnSpectrum> spectrumMap, AnnotationSettings annotationPreferences, SpecificAnnotationSettings specificAnnotationPreferences, PeptideSpectrumAnnotator spectrumAnnotator, PTM refPTM) Returns a map PTM localization > score.
static HashMap<Integer,MSnSpectrum>	getReducedSpectra(MSnSpectrum baseSpectrum, double mzTolerance) Generates a map containing the spectra filtered on intensity with a basis of 20*m/z tolerance indexed by the depth used.
static HashMap<Integer,MSnSpectrum>	getReducedSpectra(MSnSpectrum baseSpectrum, double mzTolerance, int depthMax) Generates a map containing the spectra filtered on intensity with a basis of 20*m/z tolerance indexed by the depth used.

Methods inherited from class java.lang.Object

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

Constructor Detail

AScore

public AScore()

Method Detail

getAScore

public static HashMap<Integer,Double> getAScore(Peptide peptide,
                                                ArrayList<PTM> ptms,
                                                MSnSpectrum spectrum,
                                                AnnotationSettings annotationPreferences,
                                                SpecificAnnotationSettings specificAnnotationPreferences,
                                                boolean accountNeutralLosses,
                                                SequenceMatchingPreferences sequenceMatchingPreferences,
                                                SequenceMatchingPreferences ptmSequenceMatchingPreferences,
                                                PeptideSpectrumAnnotator spectrumAnnotator)
                                         throws IOException,
                                                InterruptedException,
                                                ClassNotFoundException,
                                                SQLException,
                                                org.apache.commons.math.MathException

Returns the A-score for the best PTM location. In case the two best locations score the same they are both given with the score of 0. 1 is the first amino acid. The N-terminus is indexed 0 and the C-terminus with the peptide length+1. Note that PTMs found on peptides must be loaded in the PTM factory (com.compomics.util.experiment.biology.PTMFactory), and if the scoring involves protein terminal PTMs, the protein sequences must be loaded in the sequence factory (com.compomics.util.experiment.identification.SequenceFactory) and indexed using the protein tree (see getDefaultProteinTree in SequenceFactory). PTMs of same mass should be scored together and given in the PTMs list. Neutral losses of mass equal to the mass of the PTM will be ignored. Neutral losses to be accounted for should be given in the SpecificAnnotationPreferences and will be ignored if accountNeutralLosses is false.

Parameters:

peptide - the peptide of interest

ptms - the PTMs to score, for instance different phosphorylations (the PTMs are considered as indistinguishable, i.e. of same mass).

spectrum - the corresponding spectrum

annotationPreferences - the global annotation preferences

specificAnnotationPreferences - the annotation preferences specific to this peptide and spectrum

accountNeutralLosses - if false, neutral losses available in the specific annotation preferences will be ignored

sequenceMatchingPreferences - the sequence matching preferences for peptide to protein mapping

ptmSequenceMatchingPreferences - the sequence matching preferences for PTM to peptide mapping

spectrumAnnotator - a spectrum annotator to annotate the spectra

Returns:

a map containing the best or two best PTM location(s) and the corresponding A-score

Throws:

IOException - exception thrown whenever an error occurred while reading or writing a file

InterruptedException - exception thrown whenever a threading issue occurred while scoring the PTM

ClassNotFoundException - exception thrown whenever an error occurred while deserializing an object from the protein tree (the protein sequence index)

SQLException - exception thrown whenever an error occurred while interacting with the protein tree

org.apache.commons.math.MathException - exception thrown whenever a math error occurred while computing the score.

getPeptideScoreToPositionMap

public static HashMap<Double,ArrayList<Integer>> getPeptideScoreToPositionMap(HashMap<Integer,HashMap<Integer,Double>> positionToScoreMap)

Estimates the peptide score for every modification localization and returns a map score > localization.

Parameters:

positionToScoreMap - the position to score map

Returns:

a score to position map

getPositionToScoreMap

public static HashMap<Integer,HashMap<Integer,Double>> getPositionToScoreMap(Peptide peptide,
                                                                             Peptide noModPeptide,
                                                                             ArrayList<Integer> possibleSites,
                                                                             MSnSpectrum spectrum,
                                                                             HashMap<Integer,MSnSpectrum> spectrumMap,
                                                                             AnnotationSettings annotationPreferences,
                                                                             SpecificAnnotationSettings specificAnnotationPreferences,
                                                                             PeptideSpectrumAnnotator spectrumAnnotator,
                                                                             PTM refPTM)
                                                                      throws org.apache.commons.math.MathException

Returns a map PTM localization > score.

Parameters:

peptide - the peptide of interest

noModPeptide - the peptide without the variable modification of interest

refPTM - the PTM of interest

annotationPreferences - the global annotation preferences

specificAnnotationPreferences - the annotation preferences specific to this peptide and spectrum

spectrumAnnotator - the spectrum annotator which should be used to annotate the spectrum

spectrum - the spectrum of interest

spectrumMap - the map of the extracted spectra: depth > extracted spectrum

possibleSites - the possible modification sites

Returns:

a map PTM localization > score

Throws:

org.apache.commons.math.MathException - exception thrown whenever a math error occurred while computing the score.

getReducedSpectra

public static HashMap<Integer,MSnSpectrum> getReducedSpectra(MSnSpectrum baseSpectrum,
                                                             double mzTolerance)

Generates a map containing the spectra filtered on intensity with a basis of 20*m/z tolerance indexed by the depth used. (see A-score paper for more details).

Parameters:

baseSpectrum - the base spectrum

mzTolerance - the m/z tolerance

Returns:

a map containing the spectra filtered indexed by peak depth.

getReducedSpectra

public static HashMap<Integer,MSnSpectrum> getReducedSpectra(MSnSpectrum baseSpectrum,
                                                             double mzTolerance,
                                                             int depthMax)

Generates a map containing the spectra filtered on intensity with a basis of 20*m/z tolerance indexed by the depth used.

Parameters:

baseSpectrum - the base spectrum

mzTolerance - the m/z tolerance

depthMax - the depth to look into (10 for A-score). If -1 the maximal depth will be used

Returns:

a map containing the spectra filtered indexed by peak depth.