OpenMS
2.8.0
|
Isotope pattern generator for coarse isotope distributions. More...
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/CoarseIsotopePatternGenerator.h>
Public Member Functions | |
CoarseIsotopePatternGenerator (const Size max_isotope=0, const bool round_masses=false) | |
~CoarseIsotopePatternGenerator () override | |
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) const |
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) const |
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... | |
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 () |
Static Public Member Functions | |
static IsotopeDistribution | approximateFromPeptideWeight (double mass, UInt num_peaks=20, UInt charge=1) |
roughly approximate peptide IsotopeDistribution from monoisotopic weight using Poisson distribution. m/z values approximated by adding one neutron mass (divided by charge) for every peak, starting at the given monoisotopic weight. Foundation from: Bellew et al, https://dx.doi.org/10.1093/bioinformatics/btl276 More... | |
static std::vector< double > | approximateIntensities (double mass, UInt num_peaks=20) |
roughly approximate intensity distribution of peptidic isotope patterns from monoisotopic weight using Poisson distribution. Foundation from: Bellew et al, https://dx.doi.org/10.1093/bioinformatics/btl276 More... | |
Protected Member Functions | |
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... | |
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_ |
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. In case you need fine resolution, please consider using FineIsotopePatternGenerator.
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 setting this option 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:
while accurate mass will produce:
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.
See also method run()
CoarseIsotopePatternGenerator | ( | const Size | max_isotope = 0 , |
const bool | round_masses = false |
||
) |
|
override |
|
static |
roughly approximate peptide IsotopeDistribution from monoisotopic weight using Poisson distribution. m/z values approximated by adding one neutron mass (divided by charge) for every peak, starting at the given monoisotopic weight. Foundation from: Bellew et al, https://dx.doi.org/10.1093/bioinformatics/btl276
This method is around 50 times faster than estimateFromPeptideWeight, but only an approximation. The following are the intensities of the first 6 peaks generated for a monoisotopic mass of 1000:
estimateFromPeptideWeight: 0.571133000;0.306181000;0.095811100;0.022036900;0.004092170;0.000644568 approximateFromPeptideWeight: 0.573753000;0.318752000;0.088542200;0.016396700;0.002277320;0.000253036
KL divergences of the first 20 intensities of estimateFromPeptideWeight and this approximation range from 4.97E-5 for a monoisotopic mass of 20 to 0.0144 for a mass of 2500. For comparison, when comparing an observed pattern with a theoretical ground truth, the observed pattern is said to be an isotopic pattern if the KL between the two is below 0.05 for 2 peaks and below 0.6 for >=6 peaks by Guo Ci Teo et al.
average_weight | m/z of monoisotopic peak (with charge = 1) to approximate the distribution of intensities for |
num_peaks | How many peaks should be generated (independent of this->max_isotope) |
|
static |
roughly approximate intensity distribution of peptidic isotope patterns from monoisotopic weight using Poisson distribution. Foundation from: Bellew et al, https://dx.doi.org/10.1093/bioinformatics/btl276
This method is around 100 times faster than estimateFromPeptideWeight, but only an approximation of the intensities. It does not return IsotopeDistribution but a vector of intensities. For an assessment of accuracy, see approximateFromPeptideWeight.
average_weight | m/z of monoisotopic peak (with charge = 1) to approximate the distribution of intensities for |
num_peaks | How many peaks should be generated (independent of this->max_isotope) |
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.
Equations come from Rockwood, AL; Kushnir, MA; Nelson, GJ. in "Dissociation of Individual Isotopic Peaks: Predicting Isotopic Distributions of Product Ions in MSn"
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. |
|
protected |
calculates the fragment distribution for a fragment molecule and stores it in result
.
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. |
IsotopeDistribution::ContainerType convolve | ( | const IsotopeDistribution::ContainerType & | left, |
const IsotopeDistribution::ContainerType & | right | ||
) | const |
convolves the distributions left
and right
and stores the result in result
|
protected |
convolves the distribution input
factor
times and stores the result in result
|
protected |
convolves the distribution input
with itself and stores the result in result
|
protected |
converts the masses of distribution input
from atomic numbers to accurate masses
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.
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. |
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.
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. |
IsotopeDistribution estimateForFragmentFromPeptideWeightAndS | ( | double | average_weight_precursor, |
UInt | S_precursor, | ||
double | average_weight_fragment, | ||
UInt | S_fragment, | ||
const std::set< UInt > & | precursor_isotopes | ||
) | const |
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.
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 |
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.
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. |
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 | ||
) | const |
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.
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 |
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.".
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().
IsotopeDistribution estimateFromPeptideWeightAndS | ( | double | average_weight, |
UInt | S | ||
) |
Estimate peptide IsotopeDistribution from average weight and exact number of sulfurs.
average_weight | Average weight to estimate an EmpiricalFormula for |
S | The exact number of Sulfurs in this molecule |
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."
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.
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.
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 |
|
protected |
fill a gapped isotope pattern (i.e. certain masses are missing), with zero probability masses
Size getMaxIsotope | ( | ) | const |
returns the currently set maximum isotope
bool getRoundMasses | ( | ) | const |
returns the current value of the flag to return expected masses (true) or atomic numbers (false).
CoarseIsotopePatternGenerator& operator= | ( | const CoarseIsotopePatternGenerator & | iso | ) |
|
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.
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
void setRoundMasses | ( | const bool | round_masses | ) |
sets the round_masses_ flag to round masses to integer values (true) or return accurate masses (false)
|
protected |
maximal isotopes which is used to calculate the distribution
|
protected |
flag to determine whether masses should be rounded or not