Electron Activated Dissociation for Protein Post-Translational Modifications

In a new study published in the Journal of the American Society for Mass Spectrometry, scientists have revealed proteomic technique that could change the way researchers analyze protein post-translational modifications (PTMs), opening new avenues for understanding cellular processes and signaling at the molecular level.

Proteins are the workhorses of the cell, and their functions are often regulated through PTMs, which involve chemical modifications to proteins after they are synthesized. These modifications can influence a protein's activity and localization, making them a focal point of research in fields such as cell biology, biochemistry, and medicine. However, studying PTMs has proven to be a formidable challenge due to their dynamic nature and complexity.

Traditionally, collision-induced dissociation (CID) has been the go-to method for characterizing PTMs. CID involves applying collision energy to the analyte, causing it to fragment and provide information about its structure. However, this approach has limitations, including the potential for neutral losses and incomplete sequencing of labile PTM groups.

In the study, researchers introduced an alternative: electron activated dissociation (EAD). The team assessed the performance of EAD in comparison to CID using a fast-scanning quadrupole time-of-flight (QTOF) mass spectrometer. Their findings demonstrated the potential of EAD to overcome the challenges associated with PTM analysis.

One of the key advantages of EAD is its ability to preserve labile modifications, such as malonyl groups, preventing neutral losses. EAD also provided superior peptide sequence coverage and delivered strong fragment ions for PTM-site localization. This makes it an ideal candidate for precise characterization of PTMs, even in complex protein mixtures.

The study introduced a novel trap-and-release technology that significantly improved the duty cycle of the spectrometer. This translated into substantial gains in MS/MS sensitivity, with an average increase of 6 to 11-fold for EAD analyses. The enhanced sensitivity and data quality are expected to be a game-changer for proteomic researchers seeking to identify and quantify PTMs with high precision.

The evaluation of quantitative EAD workflows, specifically parallel reaction monitoring (PRM) assays, showcased high reproducibility, with coefficients of variation of approximately 2–7%. The technique also exhibited excellent linearity and quantification accuracy. This means that researchers can rely on EAD for precise and reliable PTM quantification, an essential aspect of proteomic research.

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Reference

Bons, J.; Hunter, C. L.; Chupalov, R.; Causon, J.; Antonoplis, A.; Rose, J.; MacLean, B.; Schilling, B. Localization and Quantification of Post-Translational Modifications of Proteins Using Electron Activated Dissociation Fragmentation on a Fast-Acquisition Time-of-Flight Mass Spectrometer. Journal of the American Society for Mass Spectrometry 2023, 34, 10, 2199–2210. DOI:10.1021/jasms.3c00144.