useBRAIN {BRAIN} | R Documentation

## Function computing probabilities of aggregated isotopic variants and their center-masses using BRAIN algorithm.

### Description

Function computing probabilities of isotopic variants and their aggregated masses 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

    useBRAIN(aC, stopOption = "nrPeaks", nrPeaks, coverage, abundantEstim)

### 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` | one of the following strings: "nrPeaks" (default), "coverage", "abundantEstim"
`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.
`coverage` | Scalar indicating the value of the cumulative aggregated distribution. The calculations will be stopped after reaching this value.
`abundantEstim` | Integer indicating the number of consecutive isotopic variants to be calculated, starting from one after the most abundant one. All consecutive isotopic variants before the most abundant peak are also returned.

### Details

Function uses recursive formulae based on algebraic Newton-Girard identity (see [Clae]).

### Value

Named list with the following fields:

- isoDistrProbabilities of aggregated isotopic variants (numeric vector)

- massesAggregated masses for isotopic variants (numeric vector)

- monoisotopicMassMonoisotopic mass (numeric)

- avgMassAverage mass - weighted average of the isotopic variants contributing to the most abundant aggregated variant (numeric)

### 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

[Clae] Claesen J., Dittwald P., Burzykowski T. and Valkenborg D. An efficient method to calculate the aggregated isotopic distribution and exact center-masses. JASMS, 2012, doi:10.1007/s13361-011-0326-2

### See Also

`calculateIsotopicProbabilities`

### Examples

      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)

[Package BRAIN version 1.40.0 Index]