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

Class PhosphoRS

java.lang.Object

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

public class PhosphoRS
extends java.lang.Object

This class estimates the PhosphoRS score as described in http://www.ncbi.nlm.nih.gov/pubmed/22073976. Warining: still under testing

Author:

Marc Vaudel

Field Summary

Fields

Modifier and Type	Field and Description
static int	maxDepth The maximal depth to use per window (8 in the original paper).

Constructor Summary

Constructors

Constructor and Description
PhosphoRS()

Method Summary

Methods

Modifier and Type

Method and Description

static java.util.HashMap<java.lang.Integer,java.lang.Double>

getSequenceProbabilities(Peptide peptide, java.util.ArrayList<PTM> ptms, MSnSpectrum spectrum, java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, NeutralLossesMap neutralLosses, java.util.ArrayList<java.lang.Integer> charges, int precursorCharge, double mzTolerance, boolean accountNeutralLosses, AminoAcidPattern.MatchingType matchingType) Returns the PhosphoRS sequence probabilities for the PTM possible locations.

Methods inherited from class java.lang.Object

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

Field Detail

maxDepth

public static final int maxDepth

The maximal depth to use per window (8 in the original paper).

See Also:

Constant Field Values

Constructor Detail

PhosphoRS

public PhosphoRS()

Method Detail

getSequenceProbabilities

public static java.util.HashMap<java.lang.Integer,java.lang.Double> getSequenceProbabilities(Peptide peptide,
                                                                             java.util.ArrayList<PTM> ptms,
                                                                             MSnSpectrum spectrum,
                                                                             java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
                                                                             NeutralLossesMap neutralLosses,
                                                                             java.util.ArrayList<java.lang.Integer> charges,
                                                                             int precursorCharge,
                                                                             double mzTolerance,
                                                                             boolean accountNeutralLosses,
                                                                             AminoAcidPattern.MatchingType matchingType)
                                                                                      throws java.io.IOException,
                                                                                             java.lang.IllegalArgumentException,
                                                                                             java.lang.InterruptedException,
                                                                                             java.io.FileNotFoundException,
                                                                                             java.lang.ClassNotFoundException,
                                                                                             java.sql.SQLException

Returns the PhosphoRS sequence probabilities for the PTM possible locations. 0 is the first amino acid. Note that PTMs found on peptides must be loaded in the PTM factory.

Parameters:

peptide - The peptide of interest

ptms - The PTMs to score, for instance different phosphorylations. These PTMs are considered as indistinguishable, i.e. of same mass.

spectrum - The corresponding spectrum

iontypes - The fragment ions to look for

neutralLosses - The neutral losses to look for

charges - The fragment ions charges to look for

precursorCharge - The precursor charge

mzTolerance - The m/z tolerance to use

accountNeutralLosses - a boolean indicating whether or not the calculation shall account for neutral losses.

matchingType - the amino acid matching type to use to map PTMs on peptides

Returns:

a map site -> phosphoRS site probability

Throws:

java.io.IOException - exception thrown whenever an error occurred while reading a protein sequence

java.lang.IllegalArgumentException - exception thrown whenever an error occurred while reading a protein sequence

java.lang.InterruptedException - exception thrown whenever an error occurred while reading a protein sequence

java.io.FileNotFoundException

java.lang.ClassNotFoundException

java.sql.SQLException