I have an xcmsSet (centWave peak-picked, orbiwarp RT-corrected, grouped, and peaks filled) where two peak groups have a very low m/z difference around 0.0441 and same peak shapes but different abundances and apeces:
I am playing around with getEIC on xcmsRaw objects and do not really understand the step parameter.
In the beginning I ignored this parameter completely and let it set to its default (0.1). But then I realized that although I provided mz ranges with a width of about 10-35 ppm, getEIC extracted mass traces within a much broader range. So I lowered the step parameter to 0.0001. However, now I get again strange results as indicated by the three ion chromatograms:
So my question is, what happend to the second and third EIC (30ppm/35ppm, step = 0.0001) and why? To which value should I set the step size? Would be something like 0.1*(mzmax - mzmin) a robust value?
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:
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?
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:
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?
