search

sneumann / CAMERA

This is the git repository matching the Bioconductor package CAMERA: Collection of annotation related methods for mass spectrometry data
11 stars 22 forks source link

Unexpected [M+2]+ isotope annotation #32

Open Tomnl opened 6 years ago

Tomnl commented 6 years ago

Hi,

I was wondering what the reason would be for the [M+2]+ isotope annotation to be so far outside of the tolerated mz ranges.

See below:

mzmed isotope_mz_diff isotopes adduct pcgroup
520.5083   [102][M]+ [M+H-COCH2]+ 561.512 1
521.5117 1.003390443 [102][M+1]+   1
524.5032 2.991508421 [102][M+2]+   1
525.5065 1.003271503 [102][M+3]+   1

I thought that the [M+2]+ would be between the tolerance in this matrix plus the ppm and absolute tolerances.

Sorry if I am missing something obvious. Any help would be appreciated

Version details

R version 3.3.1   (2016-06-21)
--
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601)   Service Pack 1

CAMERA_1.30.0

CAMERA workflow

xsa <- xsAnnotate(xset)
xsa <- groupFWHM(xsa)
xsa <- groupCorr(xsa)
xsa <- findIsotopes(xsa)
xsa <- findAdducts(xsa, polarity = 'positive')
Tomnl commented 6 years ago

Attached is the peaklist in case it might be useful to troubleshoot

check_for_github_issue.zip