6 Sets workflows

In LC-HRMS screening workflows it is typically desired to be able to detect a broad range of chemicals. For this reason, the samples are often measured twice: with positive and negative ionization. Most data processing steps are only suitable for data with the same polarity, for instance, due to the fact that the m/z values in mass spectra are inherently different (e.g. [M+H]+ vs [M-H]-) and MS/MS fragmentation occurs differently. As a result, the screening workflow has to be done twice, which generally requires more time and complicates comparing and interpretation of the complete (positive and negative) dataset.

In patRoon version 2.0 the sets workflow is introduced. This allows you to perform a single non-target screening workflow from different sets of analyses files. Most commonly, each set represents a polarity, hence, there is a positive and negative set. However, more than two sets are supported, and other distinctions between sets are also possible, for instance, samples that were measured with different MS/MS techniques. Another important advantage of the sets workflow is that MS/MS data from different sets can be combined to provide more comprehensive annotations of features. The most important limitation is that (currently) the chromatographic method that was used when analyzing the samples from each set needs to be equal, since retention times are used to group features among the sets.

Performing a sets workflow usually only requires small modifications compared to a ‘regular’ patRoon workflow. This chapter outlines how to perform such workflows and how to use its unique functionality for data processing. It is assumed that the reader is already familiar with performing ‘regular’ workflows, which were discussed in the previous chapters.