# Real time optimization of electron-based fragmentation for middle and top-down proteomics in mass spectrometry

> **NIH NIH R43** · E-MSION, INC. · 2020 · $212,830

## Abstract

The identification and quantification of biological macromolecules remains challenging despite major
advances in the speed, resolution and mass accuracy of modern mass spectrometers. A key weakness with
current instrumentation lies in the methods used to induce fragmentation. The reliance in particular on
collision-induced dissociation (CID) has limited such analyses to bottom-up workflows of trypsin-digested
peptides of 10-30 residues. At e-MSion, we have developed an efficient electron-fragmentation technology
called ExD for large proteins and are now co-marketed our ExD Option with Agilent, and soon will be with
Thermo and Waters instruments. What has really captured the interest of the biopharma and top-down
communities in the past year is the exceptional sequence coverage of native proteins we obtain with the same
ExD cell. The resulting spectra are less congested than those obtained with currently available
ETD/UVPD/CID fragmentation methodologies. We have shown that our technology works faster and gives
cleaner spectra with more complete dissociation with larger macromolecular protein complexes than has
ever been possible before, while still preserving labile post translational modifications. In addition,
fragmentation with higher energy electrons can be used to provide complementary data to improve protein
and glycan identification. The challenge now has become how to optimally collect and process these data to
maximize the utility of ExD fragmentation. Last summer, Xilinx released its Versal Adaptive Compute
Acceleration Platform (ACAP), a massively parallel processor with 50 billion transistors targeted to
transform digital signal processing, handling of big data and artificial intelligence. This ACAP technology has
already accelerated Illumina DNA sequence assembly by 90-fold. Our feasibility question asks how to
effectively harness this new highly parallelized technology to preprocess complex top-down mass spectra on-
the-fly. This will allow us to actively optimize data acquisition by enabling adaptive operation of the ExD cell
and mass spectrometer. The objective is to maximize both fragmentation and dissociation of native proteins,
enabling faster and comprehensive characterization of challenging proteoforms important to the
biopharmaceutical industry and biomedical researchers.
 Success will offer an extremely fast, cost-effective solution to characterize complexes of
macromolecules under native conditions with increased accuracy, speed, and fewer misidentifications. Our
ExD technology with the Versal ACAP can be both retrofitted into existing mass spectrometers as well as
being available in new generations of mass spectrometers at a price below other less-effective alternative
fragmentation technologies like ETD and UVPD. Thus, it will provide new abilities for many NIH
investigators to advance basic research, probe disease mechanisms and permit more sophisticated searches
for both diagnostic and therapeutic biomarkers.

## Key facts

- **NIH application ID:** 10081127
- **Project number:** 1R43GM139467-01
- **Recipient organization:** E-MSION, INC.
- **Principal Investigator:** Valery G. Voinov
- **Activity code:** R43 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $212,830
- **Award type:** 1
- **Project period:** 2020-07-01 → 2021-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10081127

## Citation

> US National Institutes of Health, RePORTER application 10081127, Real time optimization of electron-based fragmentation for middle and top-down proteomics in mass spectrometry (1R43GM139467-01). Retrieved via AI Analytics 2026-05-27 from https://api.ai-analytics.org/grant/nih/10081127. Licensed CC0.

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