enviPat is an R package for calculating isotope patterns and theoretical mass spectrometry envelopes. It implements fast algorithms for isotope fine structure calculations and tools for subsequent envelope generation, centroidization, and adduct handling.
The stable release is available on CRAN:
install.packages("enviPat")Development versions can be installed from GitHub using devtools:
# install.packages("devtools")
devtools::install_github("blosloos/enviPat")The following code generates isotope patterns for several chemical formulas and then convolutes them into theoretical envelopes:
library(enviPat)
# load data sets bundled with the package
data(isotopes)
data(chemforms)
# calculate isotope patterns for a subset of formulas
pattern <- isopattern(
isotopes,
chemforms[1:5],
threshold = 0.1,
plotit = TRUE,
charge = FALSE,
algo = 2
)
# convert the patterns to envelopes at 1 million resolving power
profiles <- envelope(
pattern,
ppm = FALSE,
dmz = 0.0001,
frac = 1/4,
env = "Gaussian",
resolution = 1e6,
plotit = TRUE
)If you use enviPat in your work, please cite:
Loos, M.; Gerber, C.; Corona, F.; Hollender, J.; Singer, H. (2015). Accelerated isotope fine structure calculation using pruned transition trees, Analytical Chemistry, 87(11), 5738-5744. https://doi.org/10.1021/acs.analchem.5b00941