com.compomics.util.experiment.identification.psm_scoring.psm_scores

Class AAMS2MzFidelityScore

java.lang.Object

com.compomics.util.experiment.identification.psm_scoring.psm_scores.AAMS2MzFidelityScore

public class AAMS2MzFidelityScore
extends Object

The m/z fidelity sub-score as adapted from the DirecTag paper where the minimal value per amino-scid is retained (http://www.ncbi.nlm.nih.gov/pubmed/18630943).

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
AAMS2MzFidelityScore()

Method Summary

Modifier and Type	Method and Description
static double	getScore(Peptide peptide, MSnSpectrum spectrum, AnnotationSettings annotationPreferences, SpecificAnnotationSettings specificAnnotationPreferences) Scores the match between the given peptide and spectrum using an m/z fidelity score.
static double	getScore(Peptide peptide, MSnSpectrum spectrum, AnnotationSettings annotationPreferences, SpecificAnnotationSettings specificAnnotationPreferences, PeptideSpectrumAnnotator peptideSpectrumAnnotator) Scores the match between the given peptide and spectrum using an m/z fidelity score.

Methods inherited from class java.lang.Object

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

Constructor Detail

AAMS2MzFidelityScore

public AAMS2MzFidelityScore()

Method Detail

getScore

public static double getScore(Peptide peptide,
                              MSnSpectrum spectrum,
                              AnnotationSettings annotationPreferences,
                              SpecificAnnotationSettings specificAnnotationPreferences)

Scores the match between the given peptide and spectrum using an m/z fidelity score. Returns the average over the peptide sequence of the minimal mass error of the ions annotating an amino acid.

Parameters:

peptide - the peptide of interest

spectrum - the spectrum of interest

annotationPreferences - the general spectrum annotation preferences

specificAnnotationPreferences - the annotation preferences specific to this psm

Returns:

the score of the match

getScore

public static double getScore(Peptide peptide,
                              MSnSpectrum spectrum,
                              AnnotationSettings annotationPreferences,
                              SpecificAnnotationSettings specificAnnotationPreferences,
                              PeptideSpectrumAnnotator peptideSpectrumAnnotator)

Scores the match between the given peptide and spectrum using an m/z fidelity score. Returns the average over the peptide sequence of the minimal mass error of the ions annotating an amino acid.

Parameters:

peptide - the peptide of interest

spectrum - the spectrum of interest

annotationPreferences - the general spectrum annotation preferences

specificAnnotationPreferences - the annotation preferences specific to this psm

peptideSpectrumAnnotator - an external annotator (if null an internal will be used)

Returns:

the score of the match