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

Class MDScore

java.lang.Object

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

public class MDScore
extends Object

This class estimates the MD score as described in http://www.ncbi.nlm.nih.gov/pubmed/21057138 Note: this implementation of the MD score is not restricted to phosphorylation.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
MDScore()

Method Summary

Methods

Modifier and Type	Method and Description
static Double	getMDScore(SpectrumMatch spectrumMatch, ArrayList<String> ptms, AminoAcidPattern.MatchingType matchingType, Double massTolerance) Returns the MD score for the best peptide in a spectrum match (the best peptide has to be set before).
static Double	getMDScore(SpectrumMatch spectrumMatch, Peptide peptideCandidate, ArrayList<String> ptms, AminoAcidPattern.MatchingType matchingType, Double massTolerance) Returns the MD score for the given peptide in a spectrum match.

Methods inherited from class java.lang.Object

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

Constructor Detail

MDScore

public MDScore()

Method Detail

getMDScore

public static Double getMDScore(SpectrumMatch spectrumMatch,
                ArrayList<String> ptms,
                AminoAcidPattern.MatchingType matchingType,
                Double massTolerance)

Returns the MD score for the best peptide in a spectrum match (the best peptide has to be set before). Null if not identified by Mascot. If the peptide is the not the best scoring for Mascot the score will be negative.

Parameters:

spectrumMatch - the spectrum match of interest

ptms - the names of the PTMs to score

matchingType - the amino acid matching type

massTolerance - the mass tolerance for matching type 'indistiguishibleAminoAcids'. Can be null otherwise

Returns:

the MD score

getMDScore

public static Double getMDScore(SpectrumMatch spectrumMatch,
                Peptide peptideCandidate,
                ArrayList<String> ptms,
                AminoAcidPattern.MatchingType matchingType,
                Double massTolerance)

Returns the MD score for the given peptide in a spectrum match. Null if not identified by Mascot. If the peptide is the not the best scoring for Mascot the score will be negative.

Parameters:

peptideCandidate - the peptide of interest

spectrumMatch - the spectrum match of interest

ptms - the names of the PTMs to score

matchingType - the amino acid matching type

massTolerance - the mass tolerance for matching type 'indistiguishibleAminoAcids'. Can be null otherwise

Returns:

the MD score