This vignette briefly recaps the main concepts of QFeatures on which scp relies. More in depth information is to be found in the QFeatures vignettes.

1 The QFeatures class

The QFeatures class (Gatto and Vanderaa (2023)) is based on the MultiAssayExperiment class that holds a collection of SummarizedExperiment (or other classes that inherits from it) objects termed assays. The assays in a QFeatures object have a hierarchical relation: proteins are composed of peptides, themselves produced by spectra, as depicted in figure below.

A more technical representation is shown below, highlighting that each assay is a SummarizedExperiment (containing the quantitative data, row and column annotations for each individual assay), as well as a global sample annotation table, that annotates cells across all assays.