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

Class MS2MzFidelityScore

java.lang.Object

com.compomics.util.experiment.identification.psm_scoring.psm_scores.MS2MzFidelityScore

public class MS2MzFidelityScore
extends Object

The m/z fidelity sub-score as adapted from the DirecTag manuscript (http://www.ncbi.nlm.nih.gov/pubmed/18630943).

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
MS2MzFidelityScore()

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

MS2MzFidelityScore

public MS2MzFidelityScore()

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. The mass interquartile distance of the fragment ion mass error is used as m/z fidelity score.

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. The mass interquartile distance of the fragment ion mass error is used as m/z fidelity score.

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