SummarizedExperiment, but for MS data.
QFeatures is a Bioconductor package that provides infrastructure enabling the management and processing of quantitative features for high-throughput mass spectrometry assays. It provides a familiar Bioconductor user experience to manages quantitative data across different assay levels (such as peptide spectrum matches, peptides and proteins) in a coherent and tractable format.
QFeatures class is used to manage and process quantitative features for high-throughput mass spectrometry assays. See the QFeatures introduction to get started and the Processing quantitative proteomics data with QFeatures vignette for a real-life application.