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Topic: Isotopes identification (Read 6851 times) previous topic - next topic

Isotopes identification

Hi,

I have a question about the findIsotopic function in CAMERA.

For two coeluting lipids differing by one double bond, the masses differ by 2. By using findIsotpic function, the first lipid is identified as M+. And the second lipid is sometimes identified as M+2, even when its intensity is much higher than M+1.

How can I tell findIsotopic function that these are two different lipids? Is there any way considering intensity during isotopes identification?

Similar problem is also mentioned in the last 3 replies in http://metabolomics-forum.com/viewtopic ... 7a85e#p223 .

Thanks.

Xinrui

Re: Isotopes identification

Reply #1 –
Seems you need to play around with the isotopeMatrix parameter:
Quote
isotopeMatrix: four column m/z-diff and ratio Matrix, for matching isotopic peaks.


It is not terribly well documented but the default appears to be:
Code: [Select]
  
isotopeMatrix <- matrix(NA, 8, 4);
colnames(isotopeMatrix) <- c("mzmin", "mzmax", "intmin", "intmax")
  
  isotopeMatrix[1, ] <- c(1.000, 1.0040, 1.0, 150)
  isotopeMatrix[2, ] <- c(0.997, 1.0040, 0.01, 200)
  isotopeMatrix[3, ] <- c(1.000, 1.0040, 0.001, 200)
  isotopeMatrix[4, ] <- c(1.000, 1.0040, 0.0001, 200)
  isotopeMatrix[5, ] <- c(1.000, 1.0040, 0.00001, 200)
  isotopeMatrix[6, ] <- c(1.000, 1.0040, 0.000001, 200)
  isotopeMatrix[7, ] <- c(1.000, 1.0040, 0.0000001, 200)
  isotopeMatrix[8, ] <- c(1.000, 1.0040, 0.00000001, 200)  
 

with the rows being for each isotope peak and:
Code: [Select]
  isotopeMatrix[1:maxiso, , drop=FALSE]
Blog: stanstrup.github.io

Re: Isotopes identification

Reply #2 –
Hi,

Thank you so much for your response. isotopeMatrix is what I need.

But what do intmin and intmax mean? For example, in

Quote
isotopeMatrix <- matrix(NA, 8, 4);
colnames(isotopeMatrix) <- c("mzmin", "mzmax", "intmin", "intmax")
 
  isotopeMatrix[1, ] <- c(1.000, 1.0040, 1.0, 150)
  isotopeMatrix[2, ] <- c(0.997, 1.0040, 0.01, 200)

isotopeMatrix[2, 4] = 200.

Does it mean that the (int[M] / int[M+2]) or (int[M+1] / int[M+2]) must be smaller than 200?

Many thanks.

Cheers,
Xinrui