useBRAIN2: Function computing probabilities of aggregated isotopic...

Description Usage Arguments Details Value Note Author(s) References See Also Examples

View source: R/iso.and.masses.R

Description

Function computing probabilities of isotopic variants using heuristics, for chemical components composed of carbon, hydrogen, oxygen, nitrogen and sulfur (e.g. peptides). Additionally the function returns also the monoisotopic mass and the average mass of given chemical component.

Usage

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useBRAIN2(aC, stopOption = "nrPeaks", nrPeaks, approxStart = 1, approxParam = NULL))

Arguments

aC

List with fields C, H, N, O, S of integer non-negative values (if any field is ommited, then its value is set to 0).

stopOption

only option "nrPeaks" allowed

nrPeaks

Integer indicating the number of consecutive isotopic variants to be calculated, starting from the monoisotopic one. This value can always be provided, even if <stop.option> is not a default setting. In the latter case it is a hard stopping criterion.

approxStart

Integer indicating the number of first isotopic peak to be calculated

approxParam

Integer indicating the length of recurrence (see RCL in [Ditt2])

Details

Function uses RCL and LSP heuristics from [Ditt2].

Value

Named list with the following fields:

Note

Remember that the isotopic variants starts from monoisotopic one. For large chemical molecules, first masses may have very low abundances. So sufficient number of peaks should be calculated to reach most abundant isotopic variant.

If only isotopic probabilities are needed, then the function calculateIsotopicProbabilities should be used.

Author(s)

Piotr Dittwald <piotr.dittwald@mimuw.edu.pl>

References

[Ditt2] Dittwald P., Valkenborg D. BRAIN 2.0: time and memory complexity improvements in the algorithm for calculating the isotope distribution. JASMS, 2014, doi: 10.1007/s13361-013-0796-5.

See Also

calculateIsotopicProbabilities

Examples

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  nrPeaks = 1000  
  aC <-  list(C=23832, H=37816, N=6528, O=7031, S=170)  # Human dynein heavy chain  
  res <-  useBRAIN(aC = aC, stopOption="nrPeaks", nrPeaks = nrPeaks)
  res2 <-  useBRAIN2(aC = aC, stopOption="nrPeaks", nrPeaks = nrPeaks, approxStart = 10)
  old = res$iso[10:109]/res$iso[11:110]
  new  = res2$iso[1:100]/res2$iso[2:101]
  max(old - new)
  max((old - new)/old)
  res3 <-  useBRAIN2(aC = aC, stopOption="nrPeaks", nrPeaks = nrPeaks, approx=TRUE, approxParam = 10)
  max(res3$iso - res$iso)

ditti2/BRAIN documentation built on Feb. 10, 2020, 5:43 a.m.