44 class IsobaricQuantitationMethod;
46 class ConsensusFeature;
126 void advanceFollowUp(
const double rt);
133 bool followUpValid(
const double rt);
167 void registerChannelsInOutputMap_(
ConsensusMap& consensus_map);
175 bool isValidPrecursor_(
const Precursor& precursor)
const;
221 void setDefaultParams_();
224 void updateMembers_()
override;
Peak2D::IntensityType min_precursor_intensity_
Minimum intensity of the precursor to be considered for quantitation.
Definition: IsobaricChannelExtractor.h:146
Small struct to capture the current state of the purity computation.
Definition: IsobaricChannelExtractor.h:102
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
PeakMap::ConstIterator followUpScan
Iterator pointing to the potential follow up MS1 scan.
Definition: IsobaricChannelExtractor.h:107
const IsobaricQuantitationMethod * quant_method_
The used quantitation method (itraq4plex, tmt6plex,..).
Definition: IsobaricChannelExtractor.h:137
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
PeakMap::ConstIterator precursorScan
Iterator pointing to the potential MS1 precursor scan.
Definition: IsobaricChannelExtractor.h:105
const PeakMap & baseExperiment
reference to the experiment to analyze
Definition: IsobaricChannelExtractor.h:112
bool hasFollowUpScan
Indicates if a follow up scan was found.
Definition: IsobaricChannelExtractor.h:110
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:113
Precursor meta information.
Definition: Precursor.h:57
String selected_activation_
Used to select only specific types of spectra for the channel extraction.
Definition: IsobaricChannelExtractor.h:140
Peak2D::CoordinateType reporter_mass_shift_
Allowed deviation between the expected and observed reporter ion m/z.
Definition: IsobaricChannelExtractor.h:143
Peak2D::IntensityType min_reporter_intensity_
Minimum reporter ion intensity to be considered for quantitation.
Definition: IsobaricChannelExtractor.h:152
Abstract base class describing an isobaric quantitation method in terms of the used channels and an i...
Definition: IsobaricQuantitationMethod.h:54
bool remove_low_intensity_quantifications_
Flag if complete quantification should be discarded if a single reporter ion has an intensity below t...
Definition: IsobaricChannelExtractor.h:155
double min_precursor_purity_
Minimum precursor purity to accept the spectrum for quantitation.
Definition: IsobaricChannelExtractor.h:158
bool interpolate_precursor_purity_
Flag if precursor purity will solely be computed based on the precursor scan (false), or interpolated between the precursor- and the following MS1 scan.
Definition: IsobaricChannelExtractor.h:164
Extracts individual channels from MS/MS spectra for isobaric labeling experiments.
Definition: IsobaricChannelExtractor.h:69
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
static const std::string NamesOfActivationMethod[SIZE_OF_ACTIVATIONMETHOD]
Names of activation methods.
Definition: Precursor.h:94
A more convenient string class.
Definition: String.h:58
bool keep_unannotated_precursor_
Flag if precursor with missing intensity value or missing precursor spectrum should be included or no...
Definition: IsobaricChannelExtractor.h:149
A container for consensus elements.
Definition: ConsensusMap.h:79
String getActivationMethod_(const PeakMap::SpectrumType &s) const
Get the first (of potentially many) activation methods (HCD,CID,...) of this spectrum.
Definition: IsobaricChannelExtractor.h:209
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
double max_precursor_isotope_deviation_
Max. allowed deviation between theoretical and observed isotopic peaks of the precursor peak in the i...
Definition: IsobaricChannelExtractor.h:161
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46