References SIPPeptide::accessions, SIPPeptide::accumulated, TextFile::addLine(), MSExperiment::areaBeginConst(), MSExperiment::areaEndConst(), PeptideIdentification::assignRanks(), TextFile::begin(), MetaProSIPDecomposition::calculateDecompositionWeightsIsotopicPatterns(), MetaProSIPDecomposition::calculateIsotopePatternsFor13CRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor13CRangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor15NRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor15NRangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor18ORange(), MetaProSIPDecomposition::calculateIsotopePatternsFor18ORangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor2HRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor2HRangeOfAveraginePeptide(), SIPPeptide::charge, MSExperiment::clear(), MetaProSIPClustering::clusterSIPPeptides(), SIPPeptide::correlation_map, SIPPeptide::correlation_maxima, MetaProSIPReporting::createCSVReport(), MetaProSIPReporting::createPeptideCentricCSVReport(), MetaProSIPReporting::createQualityReport(), SIPPeptide::decomposition_map, MSExperiment::empty(), TextFile::end(), CoarseIsotopePatternGenerator::estimateFromPeptideWeight(), SIPPeptide::explained_TIC_fraction, PeptideHit::extractProteinAccessionsSet(), MetaProSIPXICExtraction::extractXICsOfIsotopeTraces(), SIPPeptide::feature_mz, SIPPeptide::feature_rt, SIPPeptide::feature_type, ThresholdMower::filterPeakMap(), seqan::find(), AASequence::fromString(), Residue::Full, PeptideHit::getCharge(), IsotopeDistribution::getContainer(), AASequence::getFormula(), MetaProSIPInterpolation::getHighPoints(), PeptideIdentification::getHits(), MSExperiment::getMaxRT(), MSExperiment::getMinRT(), AASequence::getMonoWeight(), MetaProSIPDecomposition::getNumberOfLabelingElements(), MzMLFile::getOptions(), MetaProSIPClustering::getRIAClusterCenter(), AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >::getRT(), PeptideHit::getScore(), PeptideHit::getSequence(), File::getTempDirectory(), FeatureMap::getUnassignedPeptideIdentifications(), SIPPeptide::global_LR, SIPPeptide::incorporations, PeptideIdentification::insertHit(), OpenMS::Constants::k, MzMLFile::load(), FeatureXMLFile::load(), FASTAFile::load(), main(), SIPPeptide::mass_diff, SIPPeptide::mass_theo, DIntervalBase< D >::maxPosition(), DIntervalBase< D >::minPosition(), SIPPeptide::mz_theo, MSSpectrum::MZBegin(), MSSpectrum::MZEnd(), SIPPeptide::non_zero_decomposition_coefficients, String::number(), OPENMS_LOG_DEBUG, OPENMS_LOG_ERROR, OPENMS_LOG_INFO, OPENMS_LOG_WARN, SIPPeptide::patterns, OpenMS::Math::pearsonCorrelationCoefficient(), OpenMS::Constants::PROTON_MASS_U, String::random(), SIPIncorporation::rate, OpenMS::Internal::ClassTest::ratio, SIPPeptide::reconstruction_monoistopic, SIPPeptide::RR, MSExperiment::RTBegin(), SIPPeptide::score, SIPPeptide::sequence, PeptideHit::setCharge(), PeptideIdentification::setHigherScoreBetter(), PeptideIdentification::setHits(), Peak1D::setIntensity(), Peak2D::setIntensity(), MetaInfoInterface::setMetaValue(), MSSpectrum::setMSLevel(), PeakFileOptions::setMSLevels(), Peak1D::setMZ(), Peak2D::setMZ(), DefaultParamHandler::setParameters(), BaseFeature::setPeptideIdentifications(), Peak2D::setRT(), PeptideHit::setSequence(), Param::setValue(), MSExperiment::size(), MSSpectrum::sortByPosition(), MSExperiment::sortSpectra(), TextFile::store(), String::substitute(), OpenMS::Math::sum(), String::toQString(), AASequence::toString(), String::toUpper(), String::trim(), SIPPeptide::unique, FeatureMap::updateRanges(), and MSExperiment::updateRanges().