Hi,
I may have got it a bit wrong, but annotation of isotopes using the "findIsotopes" or "annotate" functions, doesn't seem to consider the basic intensity rule stated in the CAMERA publication. To illustrate, I have run annotations of a standard chemical compound injected in our lab, m/z=206.0943, with a coeluting Sodium adduct at 229.0829 Da. The CAMERA package seem to relate it's peak to a co eluting peak with lower mass and lower intensity and annotates it as the 3rd isotope of that peak (see below). In addition, is doesn't tag it as an adduct at all (probably because the isotope annotation is preceding it).
Idx mz rt "into"
291 226.07296 2298.066 4752.99263 [17][M]+ [M+H]+ 225.06
298 227.08055 2298.066 413.19623 [17][M+1]+
300 228.07704 2298.066 214.97685 [17][M+2]+
305 229.08299 2298.066 25178.37619 [17][M+3]+
308 230.08809 2298.066 3942.42732 [17][M+4]+
310 231.09079 2298.066 558.35965 [17][M+4]+
Note that the Sodium adduct at 229.08299 is annotated as an isotope of a lower intensity signal, and not as an adduct... This is reproduced with several mass accuracy settings... Can anyone comment on that?
Cheers,
Nir
I am sure Carsten can shed some more light on this but here are a few pointers:
- Did you use latest version? There were some recent fixes to the isotope function (http://www.bioconductor.org/packages/de ... AMERA.html (http://www.bioconductor.org/packages/devel/bioc/html/CAMERA.html)). Something definitely seems wrong with multiple assignments to [17][M+4]+.
- Did you use groupFWHM first? If so you could post the data for the whole pseudospectra?
Hi Nir,
could you try the latest CAMERA version 1.13.1?
http://http://bioconductor.org/packages/2.11/bioc/html/CAMERA.html
I made some bugfixes to the isotopes annotation
that should solve the bug.
If not, could you report the output of this version.
Carsten