decomposeIsotopes: Mass Decomposition of Isotope Patterns

In sneumann/Rdisop: Decomposition of Isotopic Patterns

Mass Decomposition of Isotope Patterns

Description

Calculate the elementary compositions from an exact mass or isotope pattern, obtained e.g. by FTICR or TOF mass spectrometers.

Usage

decomposeIsotopes(
  masses,
  intensities,
  ppm = 2,
  mzabs = 1e-04,
  elements = NULL,
  filter = NULL,
  z = 0,
  maxisotopes = 10,
  minElements = "C0",
  maxElements = "C999999"
)

decomposeMass(
  mass,
  ppm = 2,
  mzabs = 1e-04,
  elements = NULL,
  filter = NULL,
  z = 0,
  maxisotopes = 10,
  minElements = "C0",
  maxElements = "C999999"
)

isotopeScore(molecule, masses, intensities)

Arguments

masses	A vector of masses (or m/z values) of an isotope cluster.
intensities	Absolute or relative intensities of the masses peaks.
ppm	Allowed deviation of hypotheses from given mass.
mzabs	Absolute deviation in Dalton (mzabs and ppm will be added).
elements	List of allowed chemical elements, defaults to CHNOPS. See initializeElements.
filter	NYI, will be a selection of DU, DBE and Nitrogen rules.
z	Charge z of m/z peaks for calculation of real mass, keep z=0 for auto-detection.
maxisotopes	Maximum number of isotopes shown in the resulting molecules.
minElements	Molecular formula, defining lower boundaries of allowed elements.
maxElements	Molecular formula, defining upper boundaries of allowed elements.
mass	A single mass (or m/z value).
molecule	An initialized molecule as returned by getMolecule() or the decomposeMass() and decomposeIsotopes() functions.

Details

Sum formulas are calculated which explain the given mass or isotope pattern.

Value

A list of molecules, which contain the sub-lists 'formulas' potential formulas, 'exactmass' exact mass of each hypothesis (not monoisotopic), 'score' calculated score, 'isotopes' a list of isotopes.

Author(s)

Steffen Neumann <[e-mail]>

References

For a description of the underlying IMS see citation("Rdisop")

Examples

# query some measurement values from a Glutamate peak which will return two
# suggested/potential sum formulas
m <- c(147.0529, 148.0563, 149.0612)
i <- c(0.91, 0.06, 0.01)
mol <- decomposeIsotopes(m, i, maxisotopes = 3)
getFormula(mol)

# Rdisop returns the scores (how well does the exact data match the measured 
# data) in a normalized fashion, but you can calculate the raw scores
getScore(mol)
isotopeScore(mol, m, i)

# using a 5 mDa window, the number of potential candidates is increased to 26
getFormula(decomposeIsotopes(m, i, mzabs = 0.005))

# elemental ranges can be specified to affect the result
# use maxElements to exclude all of the above suggestions containing more 
# than one S and/or one P.
getFormula(decomposeIsotopes(m, i, mzabs = 0.005, maxElements = "S1P1"))

sneumann/Rdisop documentation built on Nov. 19, 2024, 12:42 a.m.