libopenms-dev 1.11.1-5 / usr / include / OpenMS / SIMULATION / LABELING / ITRAQLabeler.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
// --------------------------------------------------------------------------

#ifndef OPENMS_SIMULATION_LABELING_ITRAQLABELER_H
#define OPENMS_SIMULATION_LABELING_ITRAQLABELER_H

#include <OpenMS/SIMULATION/LABELING/BaseLabeler.h>
#include <OpenMS/SIMULATION/SimTypes.h>

namespace OpenMS
{

  /**
    @brief Simulate iTRAQ experiments

    Adds reporter ion intensities to MS/MS scans.
    Supports custom channel allocation and isotope matrices.

        @htmlinclude OpenMS_ITRAQLabeler.parameters
  */
  class OPENMS_DLLAPI ITRAQLabeler :
    public BaseLabeler
  {
public:

    typedef ItraqConstants::ChannelInfo ChannelInfo;
    typedef ItraqConstants::ChannelMapType ChannelMapType;
    typedef ItraqConstants::IsotopeMatrices IsotopeMatrices;

    /// default constructor
    ITRAQLabeler();

    /// destructor
    virtual ~ITRAQLabeler();

    /// create new object (needed by Factory)
    static BaseLabeler * create()
    {
      return new ITRAQLabeler();
    }

    /// name of the model (needed by Factory)
    static const String getProductName()
    {
      return "itraq";
    }

    // redeclaration of virtual methods
    void preCheck(Param & param) const;

    void setUpHook(FeatureMapSimVector & /* channels */);

    void postDigestHook(FeatureMapSimVector & /* features_to_simulate */);

    void postRTHook(FeatureMapSimVector & /* features_to_simulate */);

    void postDetectabilityHook(FeatureMapSimVector & /* features_to_simulate */);

    void postIonizationHook(FeatureMapSimVector & /* features_to_simulate */);

    void postRawMSHook(FeatureMapSimVector & /* features_to_simulate */);

    void postRawTandemMSHook(FeatureMapSimVector & /* features_to_simulate */, MSSimExperiment & /* simulated map */);

protected:

    /**
      @brief Modify the first peptide hit of the feature with a modification at @p pos

    */
    void addModificationToPeptideHit_(Feature & feature, const String & modification, const Size & pos) const;

    /**
      @brief tag a feature with iTRAQ modifications

      This might produce several features, due to incomplete labeling of "Y" residues.
      The resulting features are exact copies, except for their intensity and modification state.

    */
    void labelPeptide_(const Feature & feature, FeatureMapSim & result) const;

    Feature mergeFeatures_(Feature & labeled_channel_feature, const AASequence & unmodified_sequence, std::map<AASequence, Feature> & unlabeled_features_index) const;

    /// Synchronize members with param class
    void updateMembers_();

    // get the closest RT profile factor of a feature for a given RT
    DoubleReal getRTProfileIntensity_(const Feature & f, const DoubleReal MS2_RT_time) const;

    /// convert meta information from feature into intensity values for iTRAQ
    Matrix<SimIntensityType> getItraqIntensity_(const Feature & f, const DoubleReal MS2_RT_time) const;


    // Members:

    /// set to either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX
    Int itraq_type_;

    /// map the channel-name (e.g. 114) onto its description and the centroid mass
    /// the channel-name is also the id-string in the mapList section of the ConsensusMap
    ChannelMapType channel_map_;

    /// Matrices with isotope correction values (one for each plex-type)
    IsotopeMatrices isotope_corrections_;

    /// efficiency of "Y" labeling
    DoubleReal y_labeling_efficiency_;

  };
} // namespace OpenMS

#endif //#ifndef OPENMS_SIMULATION_LABELING_ITRAQLabeler_H