Metabolomics Society Forum

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 (http://metabolomics-forum.com/viewtopic.php?f=24&t=118&p=223&hilit=isotopic&sid=f5331421a3d07ccb2158a006bfe7a85e#p223) .

Thanks.

Xinrui

Seems you need to play around with the isotopeMatrix parameter:


It is not terribly well documented but the default appears to be:

  
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:

  isotopeMatrix[1:maxiso, , drop=FALSE]

Hi,

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

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


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