ON-DEMAND WEBINAR: Ion Mobility-Assisted DIA of the Histone Code - Opening up Peptide-Centric Data Mining

Library Number:
Content Type:
On Demand Webinar
Content Subtype:
Laboratory Informatics and Software




As the image of the epigenetic landscape is gradually sharpening, the position of histone post-translational modifications (hPTM) becomes increasingly defined. While ion mobility-assisted data-independent analysis (DIA) (HDMSE) is intrinsically protein-centric, it has the potential of seeing more of this landscape than conventional data directed analysis (DDA) approaches.

In this webinar, we'll demonstrate how a new data pipeline technology was used to derive maximum value from a proteomics experiment investigating histone biochemistry. Benefits came from several areas including:

  • Increased data processing stringency with newly accessible parameters which can help to maintain data quality throughout the pipeline
  • The ease with which resulting identifications can be coupled back to quantitative data after finding the right balance with other essential software tools such as Progenesis® QI for proteomics
  • The option for plugging in-house scripting into the pipeline to tackle experiment-specific challenges. More specifically, identifying peptides with complex modifications requires a dedicated workflow for which we introduce prior knowledge on hPTM to model the search space, allowing prioritization of hPTM combinations for sequential searching and to classify the final annotations

Adding Waters® Symphony™ Data Pipeline Software provided the increased flexibility that was necessary to build the data analysis routine to make the transition from protein-centric to peptide-centric proteomics in this experiment. Once in place, the workflow enabled very large quantities of data to be processed automatically, that otherwise would have been very challenging, and will save time in the future.


  1. The challenges and solutions for analyzing histone structure and PTM content
  2. How HDMSE DIA acquisitions are advantageous for investigation of complex proteome samples
  3. The capabilities and advantages of addingSymphony Data Pipeline Software to a proteomics experiment


  1. Proteomics researchers, bioinformaticians and laboratory heads
  2. Histone biologists
  3. Informaticians interested in automation of mass spectrometry data processing