7 Transformation product screening

This chapter describes the various functionality for screening of transformation products (TPs), which are introduced since patRoon 2.0. Screening for TPs, i.e. chemicals that are formed from a parent chemical by e.g. chemical or biological processes, has broad applications. For this reason, the TP screening related functionality is designed to be flexible, thus allowing one to use a workflow that is best suited for a particular study.

Regardless, the TP screening workflow in patRoon can be roughly summarized as follows:

  • Parent screening During this step a common patRoon workflow is used to screen for the parent chemicals of interest. This could be a full non-target analysis with compound annotation or a relative simple suspect or target screening.
  • Obtaining TPs Data is obtained of potential TPs for the parents of interest. The TPs may originate from a library or predicted in-silico. Note that in some workflows this step is omitted (discussed later).
  • TP screening A suspect screening is performed to find the TPs in the analysis data.
  • Linking parents and TPs In the step the parent features are linked with the TP features. Several post-processing functionality exists to improve and prioritize the data.

The next sections will outline more details on these steps are performed and configured. The last section in this chapter outlines several example workflows.

NOTE The newProject tool can be used to easily generate a workflow with transformation product screening.