Package: peakPantheR
Authors: Arnaud Wolfer

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

1 Overview

peakPantheR implements functions to detect, integrate and report pre-defined features in MS files (e.g. compounds, fragments, adducts, …).

It is designed for:

  • Real time feature detection and integration (see Real Time Annotation)
    • process multiple compounds in one file at a time
  • Post-acquisition feature detection, integration and reporting (see Parallel Annotation)
    • process multiple compounds in multiple files in parallel, store results in a single object

peakPantheR can process LC/MS data files in NetCDF, mzML/mzXML and mzData format as data import is achieved using Bioconductor’s mzR package.

2 Installation

To install peakPantheR from Bioconductor:

if (!requireNamespace("BiocManager", quietly = TRUE))


Install the development version of peakPantheR directly from GitHub with:

# Install devtools
if(!require("devtools")) install.packages("devtools")

2.1 Getting Started

To get started peakPantheR’s graphical user interface implements all the functions to detect and integrate multiple compounds in multiple files in parallel and store results in a single object. It can be employed to integrate a large number of expected features across a dataset:


peakPantheR_start_GUI(browser = TRUE)
#  To exit press ESC in the command line