Biomedical Engineering Reference
In-Depth Information
mass. With this library, users are able to generate possible formulas from
an input mass value and output this data via the command decomposeMass
as shown below.
#-------------------------
# Install Package
#-------------------------
install.packages('Rdisop')
library (Rdisop)
#-------------------------
# Install Package
#-------------------------
install.packages('Rdisop')
library (Rdisop)
molecules <- decomposeMass(89.99531, ppm = 10)
molecules <- decomposeMass(89.99531, ppm = 10)
#----------------------------------------------------------------------
# The output shows the formula, exact mass, score probability, charge,
# validity (adherence to the Nitrogen rule), and a list of isotopes and
# abundances. (Note only the fi rst 5 isotopes are listed for clarity)
#----------------------------------------------------------------------
molecules
#----------------------------------------------------------------------
# The output shows the formula, exact mass, score probability, charge,
# validity (adherence to the Nitrogen rule), and a list of isotopes and
# abundances. (Note only the fi rst 5 isotopes are listed for clarity)
#----------------------------------------------------------------------
molecules
$formula
[1] 'C2H2O4'
$score
[1] 1
$exactmass
[1] 89.99529
$charge
[1] 0
$parity
[1] 'o'
$valid
[1] 'Valid'
$DBE
[1] 2
$isotopes
$isotopes[[1]]
[,1] [,2] [,3] [,4] [,5]
[1,] 89.99529 90.99873554 91.99959798 9.30E+01 9.40E+01
[2,] 0.968356 0.02350477 0.007928286 1.86E-04 2.46E-05
$formula
[1] 'C2H2O4'
$score
[1] 1
$exactmass
[1] 89.99529
$charge
[1] 0
$parity
[1] 'o'
$valid
[1] 'Valid'
$DBE
[1] 2
$isotopes
$isotopes[[1]]
[,1] [,2] [,3] [,4] [,5]
[1,] 89.99529 90.99873554 91.99959798 9.30E+01 9.40E+01
[2,] 0.968356 0.02350477 0.007928286 1.86E-04 2.46E-05
￿ ￿ ￿ ￿ ￿
Subsequently, a formula can be selected and the isotopic distribution
calculated using the getMolecule command. Plotting as a graph produces
the output shown in Figure 4.1, representing the composition cystine
with two sulphur atoms that have four isotopes 32 S (95.02%), 33 S (0.75%),
34 S (4.21%) and 36 S (0.02%).
cystine<-getMolecule('C6H12N2O4S2')
spectrum<-matrix(unlist(cystine$isotopes), nr=2)
cystine<-getMolecule('C6H12N2O4S2')
spectrum<-matrix(unlist(cystine$isotopes), nr=2)
plot(spectrum[1,], spectrum[2,], type='h', main='Isotope Pattern',
ylab='Abundence', xlab='m/z')
plot(spectrum[1,], spectrum[2,], type='h', main='Isotope Pattern',
ylab='Abundence', xlab='m/z')
 
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