Isotope pattern generator for coarse isotope distributions. More...

#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/CoarseIsotopePatternGenerator.h>

Inheritance diagram for CoarseIsotopePatternGenerator:

Public Member Functions
	CoarseIsotopePatternGenerator ()

	CoarseIsotopePatternGenerator (const Size &max_isotope)

	CoarseIsotopePatternGenerator (const Size &max_isotope, const bool round_masses)

virtual	~CoarseIsotopePatternGenerator ()

IsotopeDistribution	run (const EmpiricalFormula &) const override
	Creates an isotope distribution from an empirical sum formula. More...

IsotopeDistribution	estimateFromPeptideWeight (double average_weight)
	Estimate Peptide Isotopedistribution from weight and number of isotopes that should be reported. More...

IsotopeDistribution	estimateFromPeptideWeightAndS (double average_weight, UInt S)
	Estimate peptide IsotopeDistribution from average weight and exact number of sulfurs. More...

IsotopeDistribution	estimateFromRNAWeight (double average_weight)
	Estimate Nucleotide Isotopedistribution from weight and number of isotopes that should be reported. More...

IsotopeDistribution	estimateFromDNAWeight (double average_weight)
	Estimate Nucleotide Isotopedistribution from weight and number of isotopes that should be reported averagine model from Zubarev, R. A.; Demirev, P. A. in "Isotope depletion of large biomolecules: Implications for molecular mass measurements.". More...

IsotopeDistribution	estimateFromWeightAndComp (double average_weight, double C, double H, double N, double O, double S, double P)
	Estimate Isotopedistribution from weight, average composition, and number of isotopes that should be reported. More...

IsotopeDistribution	estimateFromWeightAndCompAndS (double average_weight, UInt S, double C, double H, double N, double O, double P)
	Estimate IsotopeDistribution from weight, exact number of sulfurs, and average remaining composition. More...

IsotopeDistribution	estimateForFragmentFromPeptideWeight (double average_weight_precursor, double average_weight_fragment, const std::set< UInt > &precursor_isotopes)
	Estimate peptide fragment IsotopeDistribution from the precursor's average weight, fragment's average weight, and a list of isolated precursor isotopes. More...

IsotopeDistribution	estimateForFragmentFromPeptideWeightAndS (double average_weight_precursor, UInt S_precursor, double average_weight_fragment, UInt S_fragment, const std::set< UInt > &precursor_isotopes)
	Estimate peptide fragment IsotopeDistribution from the precursor's average weight, number of sulfurs in the precursor, fragment's average weight, number of sulfurs in the fragment, and a list of isolated precursor isotopes. More...

IsotopeDistribution	estimateForFragmentFromRNAWeight (double average_weight_precursor, double average_weight_fragment, const std::set< UInt > &precursor_isotopes)
	Estimate RNA fragment IsotopeDistribution from the precursor's average weight, fragment's average weight, and a list of isolated precursor isotopes. More...

IsotopeDistribution	estimateForFragmentFromDNAWeight (double average_weight_precursor, double average_weight_fragment, const std::set< UInt > &precursor_isotopes)
	Estimate DNA fragment IsotopeDistribution from the precursor's average weight, fragment's average weight, and a list of isolated precursor isotopes. More...

IsotopeDistribution	estimateForFragmentFromWeightAndComp (double average_weight_precursor, double average_weight_fragment, const std::set< UInt > &precursor_isotopes, double C, double H, double N, double O, double S, double P)
	Estimate fragment IsotopeDistribution from the precursor's average weight, fragment's average weight, a list of isolated precursor isotopes, and average composition. More...

IsotopeDistribution	calcFragmentIsotopeDist (const IsotopeDistribution &fragment_isotope_dist, const IsotopeDistribution &comp_fragment_isotope_dist, const std::set< UInt > &precursor_isotopes, const double fragment_mono_mass) const
	Calculate isotopic distribution for a fragment molecule. More...

CoarseIsotopePatternGenerator &	operator= (const CoarseIsotopePatternGenerator &iso)

IsotopeDistribution::ContainerType	convolve_ (const IsotopeDistribution::ContainerType &left, const IsotopeDistribution::ContainerType &right) const
	convolves the distributions `left` and `right` and stores the result in `result` More...

IsotopeDistribution::ContainerType	convolvePow_ (const IsotopeDistribution::ContainerType &input, Size factor) const
	convolves the distribution `input` `factor` times and stores the result in `result` More...

IsotopeDistribution::ContainerType	convolveSquare_ (const IsotopeDistribution::ContainerType &input) const
	convolves the distribution `input` with itself and stores the result in `result` More...

IsotopeDistribution::ContainerType	correctMass_ (const IsotopeDistribution::ContainerType &input, const double mono_weight) const
	converts the masses of distribution `input` from atomic numbers to accurate masses More...

Accessors
void	setMaxIsotope (const Size &max_isotope)
	sets the maximal isotope with `max_isotope` More...

void	setRoundMasses (const bool round_masses)
	sets the round_masses_ flag to round masses to integer values (true) or return accurate masses (false) More...

Size	getMaxIsotope () const
	returns the currently set maximum isotope More...

bool	getRoundMasses () const
	returns the current value of the flag to return expected masses (true) or atomic numbers (false). More...

Public Member Functions inherited from IsotopePatternGenerator
	IsotopePatternGenerator ()

	IsotopePatternGenerator (double probability_cutoff)

virtual	~IsotopePatternGenerator ()

Protected Member Functions
IsotopeDistribution	calcFragmentIsotopeDist_ (const IsotopeDistribution::ContainerType &fragment_isotope_dist, const IsotopeDistribution::ContainerType &comp_fragment_isotope_dist, const std::set< UInt > &precursor_isotopes) const
	calculates the fragment distribution for a fragment molecule and stores it in `result`. More...

IsotopeDistribution::ContainerType	fillGaps_ (const IsotopeDistribution::ContainerType &id) const
	fill a gapped isotope pattern (i.e. certain masses are missing), with zero probability masses More...

Protected Attributes
Size	max_isotope_
	maximal isotopes which is used to calculate the distribution More...

bool	round_masses_
	flag to determine whether masses should be rounded or not More...

Protected Attributes inherited from IsotopePatternGenerator
double	min_prob_

Detailed Description

Isotope pattern generator for coarse isotope distributions.

This algorithm generates theoretical pattern distributions for empirical formulas with resolution of 1Da. It assumes that every isotope has atomic mass that is rounded to the closest integer in Daltons, therefore it produces coarse distributions (it does not discriminate between 13C, N15 and O18 peaks). For example for (13)Carbon it assumes that the mass of the isotope is 13Da instead of 13.0033548378

The output is a list of pairs containing nominal isotope probabilities paired with a number that is either an accurate or rounded (integer) mass. The accurate masses assume the nominal isotopes are mostly due to (13)Carbon. To return accurate vs rounded masses, use setRoundMasses accordingly. The default is to return accurate masses (note that this will not influence the probabilities and still produce a coarse distributions spaced at ca 1Da). For example, using rounded mass, for a C100 molecule, you will get:

1200 : 0.341036528 1201 : 0.368855864 1202 : 0.197477505 1203 : 0.0697715357

while accurate mass will produce:

1200 : 0.341036528 1201.00335 : 0.368855864 1202.00671 : 0.197477505 1203.01006 : 0.0697715357

The other important value which needs to be set is the max isotope value. This value can be set using the setMaxIsotope method. It is an upper bound for the number of isotopes which are calculated If e.g., set to 3, only the first three isotopes, Monoisotopic mass, +1 and +2 are calculated. By default all possible isotopes are calculated, which leads to a large number of values, if the mass value is large!

Constructor & Destructor Documentation

◆ CoarseIsotopePatternGenerator() [1/3]

CoarseIsotopePatternGenerator ( )

◆ CoarseIsotopePatternGenerator() [2/3]

CoarseIsotopePatternGenerator ( const Size & max_isotope )

◆ CoarseIsotopePatternGenerator() [3/3]

CoarseIsotopePatternGenerator	(	const Size &	max_isotope,
		const bool	round_masses
	)

◆ ~CoarseIsotopePatternGenerator()

virtual ~CoarseIsotopePatternGenerator ( )

virtual

Member Function Documentation

◆ calcFragmentIsotopeDist()

IsotopeDistribution calcFragmentIsotopeDist	(	const IsotopeDistribution &	fragment_isotope_dist,
		const IsotopeDistribution &	comp_fragment_isotope_dist,
		const std::set< UInt > &	precursor_isotopes,
		const double	fragment_mono_mass
	)		const

Calculate isotopic distribution for a fragment molecule.

This calculates the isotopic distribution for a fragment molecule given the isotopic distribution of the fragment and complementary fragment (as if they were precursors), and which precursor isotopes were isolated.

Note: Do consider normalising the distribution afterwards to get conditional probabilities.

Equations come from Rockwood, AL; Kushnir, MA; Nelson, GJ. in "Dissociation of Individual Isotopic Peaks: Predicting Isotopic Distributions of Product Ions in MSn"

Parameters

fragment_isotope_dist	the isotopic distribution of the fragment (as if it was a precursor).
comp_fragment_isotope_dist	the isotopic distribution of the complementary fragment (as if it was a precursor).
precursor_isotopes	a list of which precursor isotopes were isolated. 0 corresponds to the mono-isotopic molecule (M0), 1->M1, etc.
fragment_mono_mass	the monoisotopic mass of the fragment.

Precondition: fragment_isotope_dist and comp_fragment_isotope_dist are gapless (no missing isotopes between the min/max isotopes of the dist)

◆ calcFragmentIsotopeDist_()

IsotopeDistribution calcFragmentIsotopeDist_	(	const IsotopeDistribution::ContainerType &	fragment_isotope_dist,
		const IsotopeDistribution::ContainerType &	comp_fragment_isotope_dist,
		const std::set< UInt > &	precursor_isotopes
	)		const

protected

calculates the fragment distribution for a fragment molecule and stores it in result.

Parameters

fragment_isotope_dist	the isotopic distribution of the fragment (as if it was a precursor).
comp_fragment_isotope_dist	the isotopic distribution of the complementary fragment (as if it was a precursor).
precursor_isotopes	which precursor isotopes were isolated. 0 corresponds to the mono-isotopic molecule (M0), 1->M1, etc.

◆ convolve_()

IsotopeDistribution::ContainerType convolve_	(	const IsotopeDistribution::ContainerType &	left,
		const IsotopeDistribution::ContainerType &	right
	)		const

convolves the distributions left and right and stores the result in result

◆ convolvePow_()

IsotopeDistribution::ContainerType convolvePow_	(	const IsotopeDistribution::ContainerType &	input,
		Size	factor
	)		const

convolves the distribution input factor times and stores the result in result

◆ convolveSquare_()

IsotopeDistribution::ContainerType convolveSquare_ ( const IsotopeDistribution::ContainerType & input ) const

convolves the distribution input with itself and stores the result in result

◆ correctMass_()

IsotopeDistribution::ContainerType correctMass_	(	const IsotopeDistribution::ContainerType &	input,
		const double	mono_weight
	)		const

converts the masses of distribution input from atomic numbers to accurate masses

◆ estimateForFragmentFromDNAWeight()

IsotopeDistribution estimateForFragmentFromDNAWeight	(	double	average_weight_precursor,
		double	average_weight_fragment,
		const std::set< UInt > &	precursor_isotopes
	)

Estimate DNA fragment IsotopeDistribution from the precursor's average weight, fragment's average weight, and a list of isolated precursor isotopes.

The max_depth of the isotopic distribution is set to max(precursor_isotopes)+1.

Parameters

average_weight_precursor	average weight of the precursor nucleotide
average_weight_fragment	average weight of the fragment
precursor_isotopes	the precursor isotopes that were isolated. 0 corresponds to the mono-isotopic molecule (M0), 1->M1, etc.

Precondition: average_weight_precursor >= average_weight_fragment; average_weight_precursor > 0; average_weight_fragment > 0; precursor_isotopes.size() > 0

◆ estimateForFragmentFromPeptideWeight()

IsotopeDistribution estimateForFragmentFromPeptideWeight	(	double	average_weight_precursor,
		double	average_weight_fragment,
		const std::set< UInt > &	precursor_isotopes
	)

Estimate peptide fragment IsotopeDistribution from the precursor's average weight, fragment's average weight, and a list of isolated precursor isotopes.

The max_depth of the isotopic distribution is set to max(precursor_isotopes)+1.

Parameters

average_weight_precursor	average weight of the precursor peptide
average_weight_fragment	average weight of the fragment
precursor_isotopes	the precursor isotopes that were isolated. 0 corresponds to the mono-isotopic molecule (M0), 1->M1, etc.

Precondition: average_weight_precursor >= average_weight_fragment; average_weight_fragment > 0; average_weight_precursor > 0; precursor_isotopes.size() > 0

◆ estimateForFragmentFromPeptideWeightAndS()

IsotopeDistribution estimateForFragmentFromPeptideWeightAndS	(	double	average_weight_precursor,
		UInt	S_precursor,
		double	average_weight_fragment,
		UInt	S_fragment,
		const std::set< UInt > &	precursor_isotopes
	)

Estimate peptide fragment IsotopeDistribution from the precursor's average weight, number of sulfurs in the precursor, fragment's average weight, number of sulfurs in the fragment, and a list of isolated precursor isotopes.

The max_depth of the isotopic distribution is set to max(precursor_isotopes)+1.

Parameters

average_weight_precursor	average weight of the precursor peptide
S_precursor	The exact number of Sulfurs in the precursor peptide
average_weight_fragment	average weight of the fragment
S_fragment	The exact number of Sulfurs in the fragment
precursor_isotopes	the precursor isotopes that were isolated

Precondition: S_fragment <= average_weight_fragment / average_weight(sulfur); S_precursor - S_fragment <= (average_weight_precursor - average_weight_fragment) / average_weight(sulfur); average_weight_precursor >= average_weight_fragment; average_weight_precursor > 0; average_weight_fragment > 0; precursor_isotopes.size() > 0

◆ estimateForFragmentFromRNAWeight()

IsotopeDistribution estimateForFragmentFromRNAWeight	(	double	average_weight_precursor,
		double	average_weight_fragment,
		const std::set< UInt > &	precursor_isotopes
	)

Estimate RNA fragment IsotopeDistribution from the precursor's average weight, fragment's average weight, and a list of isolated precursor isotopes.

The max_depth of the isotopic distribution is set to max(precursor_isotopes)+1.

Parameters

average_weight_precursor	average weight of the precursor nucleotide
average_weight_fragment	average weight of the fragment
precursor_isotopes	the precursor isotopes that were isolated. 0 corresponds to the mono-isotopic molecule (M0), 1->M1, etc.

Precondition: average_weight_precursor >= average_weight_fragment; average_weight_precursor > 0; average_weight_fragment > 0; precursor_isotopes.size() > 0

◆ estimateForFragmentFromWeightAndComp()

IsotopeDistribution estimateForFragmentFromWeightAndComp	(	double	average_weight_precursor,
		double	average_weight_fragment,
		const std::set< UInt > &	precursor_isotopes,
		double	C,
		double	H,
		double	N,
		double	O,
		double	S,
		double	P
	)

Estimate fragment IsotopeDistribution from the precursor's average weight, fragment's average weight, a list of isolated precursor isotopes, and average composition.

The max_depth of the isotopic distribution is set to max(precursor_isotopes)+1.

Parameters

average_weight_precursor	average weight of the precursor molecule
average_weight_fragment	average weight of the fragment molecule
precursor_isotopes	the precursor isotopes that were isolated. 0 corresponds to the mono-isotopic molecule (M0), 1->M1, etc.
C	The approximate relative stoichiometry of Carbons to other elements in this molecule
H	The approximate relative stoichiometry of Hydrogens to other elements in this molecule
N	The approximate relative stoichiometry of Nitrogens to other elements in this molecule
O	The approximate relative stoichiometry of Oxygens to other elements in this molecule
S	The approximate relative stoichiometry of Sulfurs to other elements in this molecule
P	The approximate relative stoichiometry of Phosphoruses to other elements in this molecule

Precondition: S, C, H, N, O, P >= 0; average_weight_precursor >= average_weight_fragment; average_weight_precursor > 0; average_weight_fragment > 0; precursor_isotopes.size() > 0

◆ estimateFromDNAWeight()

IsotopeDistribution estimateFromDNAWeight ( double average_weight )

Estimate Nucleotide Isotopedistribution from weight and number of isotopes that should be reported averagine model from Zubarev, R. A.; Demirev, P. A. in "Isotope depletion of large biomolecules: Implications for molecular mass measurements.".

◆ estimateFromPeptideWeight()

IsotopeDistribution estimateFromPeptideWeight ( double average_weight )

Estimate Peptide Isotopedistribution from weight and number of isotopes that should be reported.

Implementation using the averagine model proposed by Senko et al. in "Determination of Monoisotopic Masses and Ion Populations for Large Biomolecules from Resolved Isotopic Distributions"

Referenced by IsotopeMarker::apply(), TOPPMetaProSIP::calculateCorrelation(), MetaProSIPDecomposition::calculateIsotopePatternsFor13CRangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor15NRangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor18ORangeOfAveraginePeptide(), and MetaProSIPDecomposition::calculateIsotopePatternsFor2HRangeOfAveraginePeptide().

◆ estimateFromPeptideWeightAndS()

IsotopeDistribution estimateFromPeptideWeightAndS	(	double	average_weight,
		UInt	S
	)

Estimate peptide IsotopeDistribution from average weight and exact number of sulfurs.

Parameters

average_weight	Average weight to estimate an EmpiricalFormula for
S	The exact number of Sulfurs in this molecule

Precondition: S <= average_weight / average_weight(sulfur); average_weight >= 0

◆ estimateFromRNAWeight()

IsotopeDistribution estimateFromRNAWeight ( double average_weight )

Estimate Nucleotide Isotopedistribution from weight and number of isotopes that should be reported.

averagine model from Zubarev, R. A.; Demirev, P. A. in "Isotope depletion of large biomolecules: Implications for molecular mass measurements."

◆ estimateFromWeightAndComp()

IsotopeDistribution estimateFromWeightAndComp	(	double	average_weight,
		double	C,
		double	H,
		double	N,
		double	O,
		double	S,
		double	P
	)

Estimate Isotopedistribution from weight, average composition, and number of isotopes that should be reported.

◆ estimateFromWeightAndCompAndS()

IsotopeDistribution estimateFromWeightAndCompAndS	(	double	average_weight,
		UInt	S,
		double	C,
		double	H,
		double	N,
		double	O,
		double	P
	)

Estimate IsotopeDistribution from weight, exact number of sulfurs, and average remaining composition.

Parameters

average_weight	Average weight to estimate an IsotopeDistribution for
S	The exact numbers of Sulfurs in this molecule
C	The approximate relative stoichiometry of Carbons to other elements (excluding Sulfur) in this molecule
H	The approximate relative stoichiometry of Hydrogens to other elements (excluding Sulfur) in this molecule
N	The approximate relative stoichiometry of Nitrogens to other elements (excluding Sulfur) in this molecule
O	The approximate relative stoichiometry of Oxygens to other elements (excluding Sulfur) in this molecule
P	The approximate relative stoichiometry of Phosphoruses to other elements (excluding Sulfur) in this molecule

Precondition: S, C, H, N, O, P >= 0; average_weight >= 0

◆ fillGaps_()

IsotopeDistribution::ContainerType fillGaps_ ( const IsotopeDistribution::ContainerType & id ) const

protected

fill a gapped isotope pattern (i.e. certain masses are missing), with zero probability masses

◆ getMaxIsotope()

Size getMaxIsotope ( ) const

returns the currently set maximum isotope

◆ getRoundMasses()

bool getRoundMasses ( ) const

returns the current value of the flag to return expected masses (true) or atomic numbers (false).

◆ operator=()

CoarseIsotopePatternGenerator& operator= ( const CoarseIsotopePatternGenerator & iso )

◆ run()

IsotopeDistribution run ( const EmpiricalFormula & ) const

overridevirtual

Creates an isotope distribution from an empirical sum formula.

Iterates through all elements, convolves them according to the number of atoms from that element and sums up the result.

Implements IsotopePatternGenerator.

◆ setMaxIsotope()

void setMaxIsotope ( const Size & max_isotope )

sets the maximal isotope with max_isotope

sets the maximal isotope which is included in the distribution and used to limit the calculations. This is useful as distributions with numerous isotopes tend to have a lot of numerical zeros at the end

◆ setRoundMasses()

void setRoundMasses ( const bool round_masses )

sets the round_masses_ flag to round masses to integer values (true) or return accurate masses (false)

Member Data Documentation

◆ max_isotope_

Size max_isotope_

protected

maximal isotopes which is used to calculate the distribution

◆ round_masses_

bool round_masses_

protected

flag to determine whether masses should be rounded or not

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ CoarseIsotopePatternGenerator() [1/3]

◆ CoarseIsotopePatternGenerator() [2/3]

◆ CoarseIsotopePatternGenerator() [3/3]

◆ ~CoarseIsotopePatternGenerator()

Member Function Documentation

◆ calcFragmentIsotopeDist()

◆ calcFragmentIsotopeDist_()

◆ convolve_()

◆ convolvePow_()

◆ convolveSquare_()

◆ correctMass_()

◆ estimateForFragmentFromDNAWeight()

◆ estimateForFragmentFromPeptideWeight()

◆ estimateForFragmentFromPeptideWeightAndS()

◆ estimateForFragmentFromRNAWeight()

◆ estimateForFragmentFromWeightAndComp()

◆ estimateFromDNAWeight()

◆ estimateFromPeptideWeight()

◆ estimateFromPeptideWeightAndS()

◆ estimateFromRNAWeight()

◆ estimateFromWeightAndComp()

◆ estimateFromWeightAndCompAndS()

◆ fillGaps_()

◆ getMaxIsotope()

◆ getRoundMasses()

◆ operator=()

◆ run()

◆ setMaxIsotope()

◆ setRoundMasses()

Member Data Documentation

◆ max_isotope_

◆ round_masses_