decomposeMass: Mass Decomposition of Isotope Patterns

In Rdisop: Decomposition of Isotopic Patterns

Description

Calculate the elementary compositions from an exact Mass or Isotope Pattern, obtained e.g.\ by FTICR or TOF mass spectrometers

Usage

decomposeMass(mass, ppm=2.0, mzabs=0.0001, elements=NULL, filter=NULL,
z=0, maxisotopes = 10, minElements="C0", maxElements="C999999")
decomposeIsotopes(masses, intensities, ppm=2.0, mzabs=0.0001,
elements=NULL, filter=NULL,  z=0, maxisotopes = 10, minElements="C0", maxElements="C999999")
isotopeScore(molecule, masses, intensities, elements = NULL, filter = NULL, z = 0)

Arguments

mass	A single exact mass (or m/z value)
masses	A vector of masses (or m/z values) of an isotope cluster
intensities	Abolute 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)
z	charge z of m/z peaks for calculation of real mass. 0 is for auto-detection
maxisotopes	maximum number of isotopes shown in the resulting molecules
elements	list of allowed chemical elements, defaults to CHNOPS
minElements, maxElements	Molecular formulas, which contain lower and upper boundaries of allowed formula respectively
filter	NYI, will be a selection of DU, DBE and Nitrogen rules
molecule	a molecule as obtained from getMolecule() or decomposeMass / decomposeIsotopes

Details

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

Value

A list of molecules, which contain the sub-lists

formula	potential formulae
mass	exact monoisotopic mass of hypothesis
score	calculated score
isotopes	a list of isotopes

Author(s)

Steffen Neumann <[e-mail]>

References

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

See Also

decomposeMass

Examples

# For Glutamate: 
decomposeIsotopes(c(147.0529,148.0563), c(100.0,5.561173))

Example output

Loading required package: RcppClassic
$formula
[1] "C5H9NO4"  "C3H17P2S"

$score
[1] 9.999982e-01 1.797145e-06

$exactmass
[1] 147.0532 147.0526

$charge
[1] 0

$parity
[1] "e" "o"

$valid
[1] "Valid"   "Invalid"

$DBE
[1]  2.0 -3.5

$isotopes
$isotopes[[1]]
           [,1]        [,2]         [,3]         [,4]         [,5]         [,6]
[1,] 147.053158 148.0562238 1.490577e+02 150.06053662 1.510623e+02 1.520649e+02
[2,]   0.932531   0.0579652 8.984518e-03   0.00048312 3.456494e-05 1.546502e-06
             [,7]         [,8]         [,9]        [,10]
[1,] 1.530669e+02 1.540693e+02 1.550716e+02 1.560739e+02
[2,] 6.665258e-08 2.322723e-09 6.531604e-11 1.557911e-12

$isotopes[[2]]
            [,1]         [,2]         [,3]         [,4]         [,5]
[1,] 147.0526203 148.05543051 149.04857845 1.500520e+02 1.510483e+02
[2,]   0.9168459   0.04016747   0.04130321 1.464593e-03 2.116584e-04
             [,6]         [,7]         [,8]         [,9]        [,10]
[1,] 1.520513e+02 1.530549e+02 1.540591e+02 1.550648e+02 1.560708e+02
[2,] 7.029951e-06 8.882343e-08 4.685368e-10 9.115655e-13 9.851081e-16

Rdisop documentation built on Nov. 8, 2020, 5:40 p.m.