README.md

In sneumann/Rdisop: Decomposition of Isotopic Patterns

Rdisop

In high resolution mass spectrometry (HR-MS), the measured masses can be decomposed into potential element combinations (chemical sum formulas). Where additional mass/intensity information of respective isotopic peaks is available, decomposition can take this information into account to better rank the potential candidate sum formulas. To compare measured mass/intensity information with the theoretical distribution of candidate sum formulas, the latter needs to be calculated. This package implements fast algorithms to address both tasks, the calculation of isotopic distributions for arbitrary sum formulas (assuming a HR-MS resolution of roughly 30,000), and the ranked list of sum formulas fitting an observed peak or isotopic peak set.

Installation

You can install the development version of Rdisop using:

# install.packages("devtools")
devtools::install_github("sneumann/Rdisop")

Example

The user can use built in sets of chemical elements or define such sets specifically and get informations on a specified sum formula, i.e. the isotopic distribution which would be observed in HR-MS.

ele <- initializeElements(c("C","H","N","O","Mg"))
chlorophyll <- getMolecule("C55H72MgN4O5H", elements = ele)
getIsotope(chlorophyll, 1:4)
#>             [,1]        [,2]       [,3]         [,4]
#> [1,] 893.5431390 894.5459934 895.546247 896.54752708
#> [2,]   0.4140648   0.3171228   0.178565   0.06773657

For individual masses, potential molecules can be calculated.

decomposeMass(mass = 46.042, ppm = 20, maxisotopes = 4)
#> $formula
#> [1] "C2H6O"
#> 
#> $score
#> [1] 1
#> 
#> $exactmass
#> [1] 46.04186
#> 
#> $charge
#> [1] 0
#> 
#> $parity
#> [1] "e"
#> 
#> $valid
#> [1] "Valid"
#> 
#> $DBE
#> [1] 0
#> 
#> $isotopes
#> $isotopes[[1]]
#>            [,1]        [,2]        [,3]         [,4]
#> [1,] 46.0418648 47.04534542 48.04631711 4.904960e+01
#> [2,]  0.9749152  0.02293559  0.00210353 4.540559e-05

This decomposition can also be performed for measurements containing several isotopes.

# glutamic acid (C5H9NO4)
mol <- decomposeIsotopes(masses = c(147.053, 148.056), intensities = c(93, 5.8))
data.frame(getFormula(mol), getScore(mol), getValid(mol))
#>   getFormula.mol. getScore.mol. getValid.mol.
#> 1         C5H9NO4  1.000000e+00         Valid
#> 2        C3H17P2S  1.935336e-09       Invalid

sneumann/Rdisop documentation built on Oct. 19, 2024, 2:39 p.m.