Class PhosphoRS
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
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Field Summary
Fields Modifier and Type Field Description static int
MAX_DEPTH
The maximal depth to use per window.static int
MIN_DEPTH
The minimal depth to use per window.static double
WINDOW_SIZE
The window size in m/z. -
Constructor Summary
Constructors Constructor Description PhosphoRS()
Empty default constructor -
Method Summary
Modifier and Type Method Description 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.
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Field Details
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WINDOW_SIZE
public static final double WINDOW_SIZEThe window size in m/z.- See Also:
- Constant Field Values
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MAX_DEPTH
public static final int MAX_DEPTHThe maximal depth to use per window. 8 in the original paper, Must be greater than 1.- See Also:
- Constant Field Values
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MIN_DEPTH
public static final int MIN_DEPTHThe minimal depth to use per window.- See Also:
- Constant Field Values
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Constructor Details
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PhosphoRS
public PhosphoRS()Empty default constructor
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Method Details
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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 interestmodifications
- the modifications to score, for instance different phosphorylations (the modifications are considered as indistinguishable, i.e. of same mass)modificationParameters
- the modification parametersspectrum
- the corresponding spectrumsequenceProvider
- a provider for the protein sequencesannotationParameters
- the global annotation parametersspecificAnnotationSettings
- the annotation settings specific to this peptide and spectrumaccountNeutralLosses
- a boolean indicating whether or not the calculation shall account for neutral losses.sequenceMatchingParameters
- the sequence matching preferences for peptide to protein mappingmodificationSequenceMatchingParameters
- the sequence matching preferences for modification to peptide mappingspectrumAnnotator
- the peptide spectrum annotator to use for spectrum annotation, can be null- Returns:
- a map site > phosphoRS site probability
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