java.lang.Object
com.compomics.util.experiment.identification.modification.scores.PhosphoRS

public class PhosphoRS
extends Object
This class estimates the PhosphoRS score as described in https://www.ncbi.nlm.nih.gov/pubmed/22073976. Warning: the calculation in its present form is very slow for multiply modified peptides, peptides with many modification sites, and noisy spectra. Typically, avoid scoring deamidation sites.
Author:
Marc Vaudel
  • Field Details

  • Constructor Details

    • PhosphoRS

      public PhosphoRS()
      Empty default constructor
  • Method Details

    • getSequenceProbabilities

      public static HashMap<Integer,​Double> getSequenceProbabilities​(Peptide peptide, ArrayList<Modification> modifications, ModificationParameters modificationParameters, Spectrum spectrum, SequenceProvider sequenceProvider, AnnotationParameters annotationParameters, SpecificAnnotationParameters specificAnnotationSettings, boolean accountNeutralLosses, SequenceMatchingParameters sequenceMatchingParameters, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator spectrumAnnotator)
      Returns the PhosphoRS sequence probabilities for the modification possible locations. 1 is the first amino acid. The N-terminus is indexed 0 and the C-terminus with the peptide length+1. Modifications of same mass should be scored together and given in the modifications list. Neutral losses of mass equal to the mass of the modification will be ignored. Neutral losses to be accounted for should be given in the SpecificAnnotationSettings and will be ignored if accountNeutralLosses is false.
      Parameters:
      peptide - the peptide of interest
      modifications - the modifications to score, for instance different phosphorylations (the modifications are considered as indistinguishable, i.e. of same mass)
      modificationParameters - the modification parameters
      spectrum - the corresponding spectrum
      sequenceProvider - a provider for the protein sequences
      annotationParameters - the global annotation parameters
      specificAnnotationSettings - the annotation settings specific to this peptide and spectrum
      accountNeutralLosses - a boolean indicating whether or not the calculation shall account for neutral losses.
      sequenceMatchingParameters - the sequence matching preferences for peptide to protein mapping
      modificationSequenceMatchingParameters - the sequence matching preferences for modification to peptide mapping
      spectrumAnnotator - the peptide spectrum annotator to use for spectrum annotation, can be null
      Returns:
      a map site > phosphoRS site probability