isoorbi

Overview

The goal of the isoorbi R package is to help you process isotopocule measurements from an Orbitrap Isotope Solutions mass spectrometer. It expects .isox files created by IsoX as input.

Installation

You can install the current CRAN version of isoorbi with:

install.packages("isoorbi")

To use the latest updates, you can install the development version of isoorbi from GitHub with:

if(!requireNamespace("pak", quietly = TRUE)) install.packages("pak")
pak::pak("isoverse/isoorbi")

Important: reading .raw files directly is made possible by the rawrr package, which wraps Thermo’s RawFileReader. The first time you read a .raw file, you will be asked to agree to Thermo’s license agreement to proceed.

Show me some code

library(isoorbi)

system.file(package = "isoorbi", "extdata", "testfile_flow.isox") |>
  orbi_read_isox() |>
  orbi_flag_satellite_peaks() |>
  orbi_define_basepeak(basepeak_def = "M0")|> 
  orbi_summarize_results(ratio_method = "sum") |>
  orbi_export_data_to_excel(file = "data_summary.xlsx")

Package structure

Getting help

If you encounter a bug, please file an issue with a minimal reproducible example on GitHub.

For questions and other discussion, please use the isoorbi slack workspace.