Getting Started with the peakPantheR package

Arnaud Wolfer



Package for Peak Picking and ANnoTation of High resolution Experiments in R, implemented in R and Shiny


peakPantheR implements functions to detect, integrate and report pre-defined features in MS files. It is designed for:


Install the development version of the package directly from GitHub with:

If the dependencies mzR and MSnbase are not successfully installed, Bioconductor must be added to the default repositories with:

Input Data

Both real time and parallel compound integration require a common set of information:

The faahKO package provides with a set of MS spectra that we can use for peakPantheR annotation and is installed as follow:

#> [1] "C:/R/R-3.5.0/library/faahKO/cdf/KO/ko15.CDF"
#> [2] "C:/R/R-3.5.0/library/faahKO/cdf/KO/ko16.CDF"
#> [3] "C:/R/R-3.5.0/library/faahKO/cdf/KO/ko18.CDF"

A table of targeted features contains as column:

cpdID cpdName rtMin rt rtMax mzMin mz mzMax
1 Cpd 1 3310 3344.888 3390 522.194778 522.2 522.205222
2 Cpd 2 3280 3385.577 3440 496.195038 496.2 496.204962

See Also