DecomposeMass: Calculates possible sum formulas from a list of fragment...

In pasturm/TofDaqR: R Interface to the TOFWERK TofDaq API

Calculates possible sum formulas from a list of fragment masses.

Description

DecomposeMass calculates possible sum formulas from a list of fragment masses.

Usage

DecomposeMass(
  targetMass,
  tolerance,
  atomMass,
  atomLabel,
  elementIndex1,
  elementIndex2,
  filterMinVal,
  filterMaxVal
)

Arguments

targetMass	Target mass.
tolerance	Tolerance of target mass.
atomMass	Numeric vector with fragment masses.
atomLabel	String Vector of fragment labels.
elementIndex1	Element index for count filters, first element index for ratio filters.
elementIndex2	-1 for count filters, second element for ratio filters.
filterMinVal	Counts or ratios that are smaller than this value are filtered out.
filterMaxVal	Counts or ratios that are larger than this value are filtered out.

Details

Calculates possible sum formulas that amount to target mass +/- tolerance given a target mass, mass tolerance and a list of fragment masses. Filters specifying min/max values for absolute counts of a fragment or for ratios between fragments can be specified in order to reduce the amount of results and restrict hits to chemically reasonable sum formulae. Typically atomMass and atomLabels are the masses/labels of elements but you are free to use whatever you like (isotopes, amino acids, common fragments etc.).

Value

List with sum formula strings and the mass and mass errors of the sum formulas.

See Also

Other Chemistry functions: DecomposeMass2(), GetIsotopePattern2(), GetIsotopePattern(), GetMoleculeMass()

Examples

targetMass = 314
tolerance = 0.5
atomLabel = c("C", "H", "O")
n = length(atomLabel)
atomMass = rep(0, n)
for (i in 1:n) {
 atomMass[i] = GetMoleculeMass(atomLabel[i])
}
elementIndex1 = seq(along.with = atomLabel)-1
elementIndex2 = rep(-1, n)
filterMinVal = c(20, 20, 0)
filterMaxVal = c(22, 40, 5)
DecomposeMass(targetMass, tolerance, atomMass, atomLabel, elementIndex1,
              elementIndex2, filterMinVal, filterMaxVal)

pasturm/TofDaqR documentation built on March 29, 2024, 12:10 a.m.