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

java.lang.Object
  extended by 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
MDScore()
           
 
Method Summary
static Double getMDScore(SpectrumMatch spectrumMatch, ArrayList<String> ptms)
          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)
          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)
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
Returns:
the MD score

getMDScore

public static Double getMDScore(SpectrumMatch spectrumMatch,
                                Peptide peptideCandidate,
                                ArrayList<String> ptms)
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
Returns:
the MD score


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