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Topic: Rdisop: Isotope patterns of labeled compounds (Read 4831 times) previous topic - next topic

Rdisop: Isotope patterns of labeled compounds

Hey there,

hopefully this question is placed correctly on this board. I am programming a targeted analysis for 13C-labeled metabolites using xcms. For the calculation of the accurate masses to look for I wanted to use Rdisop. However, since this library considers only natural isotope distributions, the accurate masses of labeled compounds occurring naturally at very low abundances are not calculated. A short example calculating the accurate mass of a fully 13C-labeled Glucose demonstrates this:

Code: [Select]
> library( "Rdisop" )
> getIsotope( getMolecule( "C6H12O6" ), 7 )
[1] 186.0774    2.678176e-07

H1  <- 1.007825032
C13 <- 13.00335484
O16 <- 15.99491462

6*C13 + 12 * H1 + 6 * O16
[1] 186.0835

Obviously, the mass should be 186.0835u and not 186.0774u (difference around 30ppm). I assume, that the calculated mass results from a mix of naturally occurring 12C/13C + 16O/18O since the calculated abundance (2.7e-07) is also magnitudes larger than the one of a naturally occurring [13C]6[1H]12[16O]6 which should be 6.4e-10.

My question is if anyone can give me a hint how to calculate the accurate masses for isotopic labeled compounds using Rdisop? The isotope distribution seams to be hard coded in initializePSE(). Is there any hook, to which I could provide an alternative isotope distribution?

Many thanks in advance
Isam

Re: Rdisop: Isotope patterns of labeled compounds

Reply #1
Try:
?initializeElements
You should be able to define your own elements here.

Try initializeCHNOPSMgKCaFe() to see how the list of elements should be build.


Hope it helps.
Blog: stanstrup.github.io

Re: Rdisop: Isotope patterns of labeled compounds

Reply #2
Hey,

thanks for your reply.

[quote author="Jan Stanstrup"]
Try initializeCHNOPSMgKCaFe() to see how the list of elements should be build.[/quote]

Thats how I started. However, initializeElements just calls Rdisop:::.getElement which again calls initializePSE. From my understanding the initialize methods only allow for the selection of relevant elements but not for the adjustment of isotope distributions.

EDIT:

OK sorry, this was the pointer I needed. I can write my own initialize13C() method, let it call initializePSE, adjust the 13C distribution.
Code: [Select]
getMolecule("C6H12O6", elements = initialize13C() )
should finally do the trick.

Many thanks!
Isam

Re: Rdisop: Isotope patterns of labeled compounds

Reply #3
initializeCHNOPSMgKCaFe() was just to show you how to build the list of elements you should use with initializeElements.


Quote
new=list()

new[[1]]=initializeCHNOPSMgKCaFe()[[1]]
new[[1]]$mass=13
new[[1]]$isotope$mass=new[[1]]$isotope$mass[2:3]
new[[1]]$isotope$abundance=new[[1]]$isotope$abundance[1:2]


new[[2]]=initializeCHNOPSMgKCaFe()[[2]]


new[[3]]=initializeCHNOPSMgKCaFe()[[4]]


getMass(getMolecule( "C6H12O6" ,elements=new))


EDIT: dang... too slow... and I guess initializeElements is not needed if you use my example.
Blog: stanstrup.github.io

Re: Rdisop: Isotope patterns of labeled compounds

Reply #4
Just for the completeness, this solution works pretty well:

Code: [Select]
initialize13C <- function( a12C13C14C = c( 0.1, 0.9, 0 ) ) {
  require("Rdisop")
  elements <- initializePSE()
  elements <- lapply( elements, function(x){
    if(x$name == "C" ){
      x$isotope$abundance <- a12C13C14C
    }
    return( x )
  })
  return(elements)
}

H1  <- 1.007825032
C12 <– 12
C13 <- 13.00335484
O16 <- 15.99491462

all.equal(
  sapply( 0:6, FUN=function(x) { x * C13 + (6-x) * C12 + 12 * H1 + 6 * O16 } ),
  getIsotope( getMolecule( "C6H12O6", elements=initialize13C() ) )[ 1,1:7 ]
)
[1] TRUE

Thanks again for pointing me to the right direction. I simply missed the "elements" parameter in getMolecule().
Isam