DecomposeMass2: 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

DecomposeMass2 calculates possible sum formulas from a list of fragment masses.

Usage

DecomposeMass2(
  targetMass,
  tolerance,
  atomMass,
  atomLabel,
  elementIndex1,
  elementIndex2,
  filterMinVal,
  filterMaxVal,
  maxHits,
  maxSearch
)

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.
maxHits	Maximum number of candidate hits to report.
maxSearch	Maximum number of candidate formula to search.

Details

Same as DecomposeMass but with additional parameters maxHits and maxSearch to better fine-tune when to abort a compomer search. 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: DecomposeMass(), 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)
maxHits = 10
maxSearch = 1000
DecomposeMass2(targetMass, tolerance, atomMass, atomLabel, elementIndex1,
              elementIndex2, filterMinVal, filterMaxVal, maxHits, maxSearch)

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