The main research focus of the Lab of Pharmaceutical Biotechnology can be summarized as “Data-independent Acquisition (DIA) strategies for mining the histone code”. Both Ion-mobility-assisted DIA (HDMSE) and SWATH are routinely applied as described in more detail at ProGenTomics.
As the image of the epigenetic landscape is gradually sharpening, the position of histone posttranslational modifications (hPTM) herein becomes increasingly defined. With this improved view also comes the growing sense that it is the interplay between different biochemical changes that dictates the final biological outcome. However, studying the proverbial grammar emerging from the combination of hPTMs, the so-called “histone code”, still is extremely challenging from a technical point of view. With some adaptions towards a more peptide-centric workflow, both HDMSE and SWATH data-independent acquisition (DIA) LC-MS strategies have the potential of propagating the study of the histone code into a new era.
Rendering these DIA workflows peptide-centric and hPTM-compatible requires innovative adaptations both at the level of identification and quantification. The main considerations herein involve (i) stringent data processing, (ii) the implementation of prior knowledge for identification and curation of combinations of hPTM and (iii) deeper mining of hPTM combinations during quantification, as opposed to the single hPTM “relative abundance” measurements customary to current hPTM research. Finally, ion mobility (IM) separation used in HDMSE adds a complete new dimension to the MS data that gradually becomes accessible for future mining.
Both the acquisition and data analysis in (IM-assisted) DIA is intrinsically different from the conventional data-directed acquisition strategy and it is thus not surprising that their complementarity can greatly increase the information content in histone samples.
Feel free to contact Dr. Maarten Dhaenens with all your questions concerning DIA MS and/or Histone PTM analysis.
Lab of Pharamaceutical Biotechnology, Ghent University