MetaProSIPDecomposition Class Reference

Static Public Member Functions
static Int	calculateDecompositionWeightsIsotopicPatterns (Size n_bins, const vector< double > &isotopic_intensities, const IsotopePatterns &patterns, MapRateToScoreType &map_rate_to_decomposition_weight, SIPPeptide &sip_peptide)
	> Perform the decomposition More...
static IsotopePatterns	calculateIsotopePatternsFor13CRange (const AASequence &peptide, Size additional_isotopes=5)
static Size	getNumberOfLabelingElements (String labeling_element, const AASequence &peptide)
static IsotopePatterns	calculateIsotopePatternsFor15NRange (const AASequence &peptide, Size additional_isotopes=5)
static IsotopePatterns	calculateIsotopePatternsFor2HRange (const AASequence &peptide, Size additional_isotopes=5)
static IsotopePatterns	calculateIsotopePatternsFor18ORange (const AASequence &peptide, Size additional_isotopes=5)
static IsotopePatterns	calculateIsotopePatternsFor15NRangeOfAveraginePeptide (double mass)
static IsotopePatterns	calculateIsotopePatternsFor13CRangeOfAveraginePeptide (double mass)
static IsotopePatterns	calculateIsotopePatternsFor2HRangeOfAveraginePeptide (double mass)
static IsotopePatterns	calculateIsotopePatternsFor18ORangeOfAveraginePeptide (double mass)

Member Function Documentation

calculateDecompositionWeightsIsotopicPatterns()

static Int calculateDecompositionWeightsIsotopicPatterns ( Size  n_bins, const vector< double > &  isotopic_intensities, const IsotopePatterns &  patterns, MapRateToScoreType &  map_rate_to_decomposition_weight, SIPPeptide &  sip_peptide  )

inlinestatic

> Perform the decomposition

References SIPPeptide::charge, SIPPeptide::mass_diff, OpenMS::Math::mean(), SIPPeptide::mz_theo, SIPPeptide::reconstruction, SIPPeptide::reconstruction_monoistopic, SIPPeptide::RR, Peak1D::setIntensity(), Peak1D::setMZ(), and NonNegativeLeastSquaresSolver::solve().

Referenced by TOPPMetaProSIP::main_().

calculateIsotopePatternsFor13CRange()

static IsotopePatterns calculateIsotopePatternsFor13CRange ( const AASequence &  peptide, Size  additional_isotopes = 5  )

inlinestatic

> Given a peptide sequence calculate the theoretical isotopic patterns given all incorporations rate (13C Version) > extend isotopic patterns by additional_isotopes to collect other element higher isotopes at 100% incorporation

References AASequence::fromString(), IsotopeDistribution::getContainer(), ElementDB::getElement(), AASequence::getFormula(), ElementDB::getInstance(), EmpiricalFormula::getIsotopeDistribution(), EmpiricalFormula::getNumberOf(), IsotopeDistribution::set(), Element::setIsotopeDistribution(), and AASequence::toUnmodifiedString().

Referenced by TOPPMetaProSIP::main_().

calculateIsotopePatternsFor13CRangeOfAveraginePeptide()

static IsotopePatterns calculateIsotopePatternsFor13CRangeOfAveraginePeptide ( double  mass )

inlinestatic

References IsotopeDistribution::estimateFromPeptideWeight(), IsotopeDistribution::getContainer(), ElementDB::getElement(), ElementDB::getInstance(), IsotopeDistribution::set(), and Element::setIsotopeDistribution().

Referenced by TOPPMetaProSIP::main_().

calculateIsotopePatternsFor15NRange()

static IsotopePatterns calculateIsotopePatternsFor15NRange ( const AASequence &  peptide, Size  additional_isotopes = 5  )

inlinestatic

> Given a peptide sequence calculate the theoretical isotopic patterns given all incorporations rate (15C Version) > extend isotopic patterns by additional_isotopes to collect other element higher isotopes at 100% incorporation

References AASequence::fromString(), IsotopeDistribution::getContainer(), ElementDB::getElement(), AASequence::getFormula(), ElementDB::getInstance(), EmpiricalFormula::getIsotopeDistribution(), EmpiricalFormula::getNumberOf(), IsotopeDistribution::set(), Element::setIsotopeDistribution(), and AASequence::toUnmodifiedString().

Referenced by TOPPMetaProSIP::main_().

calculateIsotopePatternsFor15NRangeOfAveraginePeptide()

static IsotopePatterns calculateIsotopePatternsFor15NRangeOfAveraginePeptide ( double  mass )

inlinestatic

References IsotopeDistribution::estimateFromPeptideWeight(), IsotopeDistribution::getContainer(), ElementDB::getElement(), ElementDB::getInstance(), IsotopeDistribution::set(), and Element::setIsotopeDistribution().

Referenced by TOPPMetaProSIP::main_().

calculateIsotopePatternsFor18ORange()

static IsotopePatterns calculateIsotopePatternsFor18ORange ( const AASequence &  peptide, Size  additional_isotopes = 5  )

inlinestatic

References AASequence::fromString(), IsotopeDistribution::getContainer(), ElementDB::getElement(), AASequence::getFormula(), ElementDB::getInstance(), EmpiricalFormula::getIsotopeDistribution(), EmpiricalFormula::getNumberOf(), IsotopeDistribution::set(), Element::setIsotopeDistribution(), and AASequence::toUnmodifiedString().

Referenced by TOPPMetaProSIP::main_().

calculateIsotopePatternsFor18ORangeOfAveraginePeptide()

static IsotopePatterns calculateIsotopePatternsFor18ORangeOfAveraginePeptide ( double  mass )

inlinestatic

References IsotopeDistribution::estimateFromPeptideWeight(), IsotopeDistribution::getContainer(), ElementDB::getElement(), ElementDB::getInstance(), IsotopeDistribution::set(), and Element::setIsotopeDistribution().

Referenced by TOPPMetaProSIP::main_().

calculateIsotopePatternsFor2HRange()

static IsotopePatterns calculateIsotopePatternsFor2HRange ( const AASequence &  peptide, Size  additional_isotopes = 5  )

inlinestatic

References AASequence::fromString(), IsotopeDistribution::getContainer(), ElementDB::getElement(), AASequence::getFormula(), ElementDB::getInstance(), EmpiricalFormula::getIsotopeDistribution(), EmpiricalFormula::getNumberOf(), IsotopeDistribution::set(), Element::setIsotopeDistribution(), and AASequence::toUnmodifiedString().

Referenced by TOPPMetaProSIP::main_().

calculateIsotopePatternsFor2HRangeOfAveraginePeptide()

static IsotopePatterns calculateIsotopePatternsFor2HRangeOfAveraginePeptide ( double  mass )

inlinestatic

References IsotopeDistribution::estimateFromPeptideWeight(), IsotopeDistribution::getContainer(), ElementDB::getElement(), ElementDB::getInstance(), IsotopeDistribution::set(), and Element::setIsotopeDistribution().

Referenced by TOPPMetaProSIP::main_().

getNumberOfLabelingElements()

static Size getNumberOfLabelingElements ( String  labeling_element, const AASequence &  peptide  )

inlinestatic

References AASequence::fromString(), ElementDB::getElement(), AASequence::getFormula(), ElementDB::getInstance(), EmpiricalFormula::getNumberOf(), and AASequence::toUnmodifiedString().

Referenced by TOPPMetaProSIP::main_().