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Topic: Compounds containing Cl, Br or S (Read 8844 times) previous topic - next topic

Compounds containing Cl, Br or S

Hey there,

my question concerns the findIsotopes() function. I have analyzed a set of LC/MS qTOF samples containing only a few number of compounds. One of it is Diclofenac (C14H11Cl2NO2, accurate mass 295.0167). groupFWHM() finds its Pseudospectrum perfectly:
[attachment=0:3f8rglrr]diclofenac.png[/attachment:3f8rglrr]

However, since Diclofenac contains Cl there is a prominent [M+2] peak in all adducts, which fails to be annotated correctly by calling findIsotopes( xsa.grouped, ppm=5, mzabs=0, maxcharge=3, maxiso=4 ). Instead of one Isotope cluster, I'll get three:
Code: [Select]
mz	iso
---------------------------
296,0239	[301][M]+
297,0252	[301][M+1]+
298,0210	[302][M]+
299,0238	[302][M+1]+
300,0184	[303][M]+

As far as I understood, CAMERA applies a C12/C13-Model only. In turn, any isotopes of compounds containing Cl, Br and S, will not be clustered correctly. Are there any suggestions how to improve the annotation?

Many thanks!

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Re: Compounds containing Cl, Br or S

Reply #1 –
Compounds with heteroatoms like CL or Br are still difficult to handle, because of there influence on the pattern and the mass difference between the isotopes.
In one of the upcoming updates, it will be possible to adjusted the expected number of the common heteroatoms to achieve a better isotope recognition.

At the moment it could be that the mass differences of the second isotope peak is more then CAMERA expect.
But you should be able to retrieve one cluster, if you compensate that with a relaxation of the allowed error.

Carsten

Re: Compounds containing Cl, Br or S

Reply #2 –
Hi,
I'm using version CAMERA_1.14.0
What would be the best strategy to be able to cluster correctly the compounds containing S using findIsotopes?
I use currently
 findIsotopes(an, mzabs=0.005,ppm=5, maxiso=5,filter=FALSE,maxcharge=1)
Is the setting filter=FALSE going to help in finding isotope clusters of compounds containing S?
It is not clear to me what is the function of the isotopeMatrix argument and how can it be used? To what do the four columns of the m/z-diff and ratio Matrix correspond?

On the other hand, I also wonder if there is a way known in R to detect compounds that contain S based on their isotope pattern?

Cheers,
Rebecca