An interactive mass spectrometry atlas of histone posttranslational modifications in T-cell acute leukemia

Abstract

The holistic nature of omics studies makes them ideally suited to generate hypotheses on health and disease. Sequencing-based genomics and mass spectrometry (MS)-based proteomics are linked through epigenetic regulation mechanisms. However, epigenomics is currently mainly focused on DNA methylation status using sequencing technologies, while studying histone posttranslational modifications (hPTMs) using MS is lagging, partly because reuse of raw data is impractical. Yet, targeting hPTMs using epidrugs is an established promising research avenue in cancer treatment. Therefore, we here present the most comprehensive MS-based preprocessed hPTM atlas to date, including 21 T-cell acute lymphoblastic leukemia (T-ALL) cell lines. We present the data in an intuitive and browsable single licensed Progenesis QIP project and provide all essential quality metrics, allowing users to assess the quality of the data, edit individual peptides, try novel annotation algorithms and export both peptide and protein data for downstream analyses, exemplified by the PeptidoformViz tool. This data resource sets the stage for generalizing MS-based histone analysis and provides the first reusable histone dataset for epidrug development.

Epigenetic analytical approaches in ecotoxicological aquatic research

“…Mass spectrometry (MS)-based methods allow qualitative and quantitative characterization of protein composition of complex sample lysates. These methods also allow to identify and map posttranslational modification (PTM) of for example histone enriched protein samples (De Clerck et al, 2021;Provez et al, 2022). The modification or non-modification of an amino acid is identified by its molecular weight changing once it presents a PTM.…”