1 Introduction

Nowadays there are various software tools available to process data from non-target analysis (NTA) experiments. Individual tools such as ProteoWizard, XCMS, OpenMS, MetFrag and mass spectrometry vendor tools are often combined to perform a complete data processing workflow. During this workflow, raw data files may undergo pre-treatment (e.g. conversion), chromatographic and mass spectral data are combined to extract so called features (or ‘peaks’) and finally annotation is performed to elucidate chemical identities. The aim of patRoon is to harmonize the many available tools in order to provide a consistent user interface without the need to know all the details of each individual software tool and remove the need for tedious conversion of data when multiple tools are used. The name is derived from a Dutch word that means pattern and may also be an acronym for hyPhenated mAss specTROmetry nOn-target aNalysis. The workflow of non-target analysis is typically highly dependent on several factors such as the analytical instrumentation used and requirements of the study. For this reason, patRoon does not enforce a certain workflow. Instead, most workflow steps are optional, are highly configurable and algorithms can easily be mixed or even combined. Furthermore, patRoon supplies a straightforward interface to easily inspect, select, visualize and report all data that is generated during the workflow.

The documentation of patRoon consists of three parts:

  1. A tutorial (accessible at here)
  2. This handbook
  3. The reference manual (accessible in R with ?`patRoon-package` or online here)

New users are highly recommended to start with the tutorial: this document provides an interactive introduction in performing a basic NTA processing workflow with patRoon. The handbook provides a more thorough overview of all concepts, functionalities and provides instructions and many examples on working with patRoon. Finally, the reference manual provides all the gritty details for all functionalities, and is meant if you want to know more details or need a quick reminder how a function should be used.