findIsotopes and ppm

September 07, 2011, 02:10:16 PM

Hello,

I am trying to use the findIsotopes function within CAMERA. I am pretty excited to use this function as it will certainly help decide which features I will focus on for my downstream analysis.

However, I am wondering about the implementation of the 'ppm' variable. Following the syntax on the help page, I am doing the following:

xsaFI <-findIsotopes(xsaF,ppm=1)

The first set of isotopes are:
293.1617 [1][M]+
294.1755 [1][M+1]+

I interpret this as the 294.1755 is the 13C match to the 12C compound that is 293.1617.

However, if you change one of the carbons in the 12C compound to be 13C, the calculated mass would be 294.1650. By my math, the difference (in ppm) between 294.1650 and 294.1755 is 35.7 ppm, which is way more than the 'ppm=1' I requested.

The question is, is the error actually defined somewhere else in the processing? Or, what am I missing?

Thanks,
Krista

Re: findIsotopes and ppm

Reply #1 – September 07, 2011, 02:55:24 PM

It uses a combination of relative (mass dependent, ppm) and absolute (mass independent, mzabs) error.

findIsotopes(.., ppm=5, mzabs=0.01, ...)

If you set mzabs to 0 (or just something very small like 0.0001), you should get the result that you expected.

Re: findIsotopes and ppm

Reply #2 – September 07, 2011, 03:42:24 PM

OK - I obviously missed the need to present both errors.
Thanks,
Krista