SBIR-STTR Award

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.

Public Health Relevance Statement:
Even with all of the scientific progress made to date, the complexity of disease-affected tissues still challenges our ability to probe what makes people sick. The goal of this Phase I SBIR project is to develop a powerful computer technology to aid in characterizing biological molecules that will improve the diagnosis and treatment of diseases ranging from arthritis, cancer, diabetes to heart disease and neurodegeneration.

Project Terms:
Acceleration; Affect; Arthritis; arthritic; Artificial Intelligence; AI system; Computer Reasoning; Machine Intelligence; Automobile Driving; driving; Biological Products; Biologic Products; Biological Agent; biopharmaceutical; biotherapeutic agent; Biological Response Modifier Therapy; Biologic Therapy; Biological Therapy; biological therapeutic; biological treatment; biotherapeutics; biotherapy; Malignant Neoplasms; Cancers; Malignant Tumor; malignancy; neoplasm/cancer; Cells; Cell Body; Communities; Computers; Data Analyses; Data Analysis; data interpretation; Data Collection; Diabetes Mellitus; diabetes; Diagnosis; Digital Signal Processing; Disease; Disorder; Electronics; electronic device; Electrons; Negative Beta Particle; Negatrons; Engineering; Face; faces; facial; Family; Feasibility Studies; Goals; Grant; Health; Heart Diseases; Cardiac Diseases; Cardiac Disorders; heart disorder; Industrialization; Industry; instrumentation; Ions; Isoleucine; Laboratories; Leucine; Maps; Methods; Methodology; Modernization; United States National Institutes of Health; NIH; National Institutes of Health; Nerve Degeneration; Neuron Degeneration; neural degeneration; neurodegeneration; neurodegenerative; neurological degeneration; neuronal degeneration; Noise; Optics; optical; Peptides; Periodicity; Cyclicity; Rhythmicity; Polysaccharides; Glycans; Post-Translational Protein Processing; Post-Translational Modification Protein/Amino Acid Biochemistry; Post-Translational Modifications; Post-Translational Protein Modification; Posttranslational Modifications; Posttranslational Protein Processing; Protein Modification; Proteins; Reading; Research Personnel; Investigators; Researchers; Signal Transduction; Cell Communication and Signaling; Cell Signaling; Intracellular Communication and Signaling; Signal Transduction Systems; Signaling; biological signal transduction; Computer software; Software; Mass Spectrum Analysis; Mass Photometry/Spectrum Analysis; Mass Spectrometry; Mass Spectroscopy; Mass Spectrum; Mass Spectrum Analyses; Technology; Time; Tissues; Body Tissues; Transistors; Trypsin; Tripcellim; Vendor; Water; Hydrogen Oxide; Work; Generations; Price; pricing; Businesses; Dissociation; fragment X; DNA Sequence; base; macromolecule; improved; Phase; Biological; Individual; instrument; programs; Complex; Continuous Infusion; Techniques; interest; meetings; disulfide bond; experience; success; Speed; Structure; Basic Research; Basic Science; Macromolecular Complexes; Macromolecular Protein Complexes; Multiprotein Complexes; Proteomics; data processing; computerized data processing; protein complex; Protein Fragment; Data; Protein Analysis; Resolution; Collection; SBIR; Small Business Innovation Research; Small Business Innovation Research Grant; Process; mass spectrometer; cost effective; blind; data acquisition; encryption; operation; signal processing; BigData; Big Data; electron energy; diagnostic marker; diagnostic biomarker; therapeutic marker; therapeutic biomarker; preservation; computing platform; computational platform

Despite two decades of advances in the speed, resolution and mass accuracy of modern mass spectrometers, the characterization and quantification of biological macromolecules remains a daunting challenge. The remaining weakness with current instrumentation lies in the methods used to fragment macromolecules, which e-MSion is addressing with an efficient electron-fragmentation technology called ExD. The exceptional sequence coverage of native proteins and preservation of labile post-translational modifications achieved with our technology is capturing the interest of the biopharma and top-down communities. Our ExD cell is the only electron-based method that can keep pace with ion mobility separations. The combination of ExD with IMS opens many opportunities to better probe protein structure and work with protein complexes. We now have strong comarketing arrangements with Agilent, Thermo and Waters for their high-end instruments and have been granted deep access to their electronics and internal data processing. Our phase I efforts focused on creating a software application called ExD Viewer that addressed user concerns about processing electron fragmentation spectra produced by our ExD technology. This software helps users to address unmet needs for probing cystine knot proteins, validating antibody sequences and characterizing proteoform more completely. One particularly well-received capability provided by ExD Viewer allows annotation of top-down spectra live from the instrument, which users use to optimize methods. We were unable to address the second of our feasibility questions because the pandemic held up delivery of our engineering sample of the Versal Adaptive Compute Acceleration Platform (ACAP) by a year. However, the Versal ACAP has become commercially available last summer. Versal is a major hardware advance that allows massive streams of real-time data to be processed at least 100-fold faster than with current CPU/GPU processors and with the potential to transform how proteomics is conducted. Our current ExD Viewer uses efficient modern programming frameworks to process complex spectra in minutes. For Phase II, we will port the backend core engine to run efficiently on the powerful Versal ACAP enabled- workstation. Accomplishing this objective will allow entire frames of ion mobility spectra (IMS-MS) to be continuously analyzed. The Versal ACAP will allow adaptive control the ExD cell and mass spectrometer to dynamically adjust data collection to more fully characterize macromolecules on the fly and to apply a broader range of tools. The commercial value comes from reducing both sample analysis time and the need for expert user input. Our primary outcome for phase II is to develop user-facing workflows that optimize the activation, fragmentation and dissociation of native proteins on the fly, enabling faster and more comprehensive characterization of challenging proteoforms important to biomedical researchers and the biopharmaceutical industry.

Public Health Relevance Statement:
The COVID pandemic has proved how important modern instruments are to probe rapidly evolving disease threats and rapidly evolve new treatments. This Phase II SBIR project will develop an advanced intelligent computer technology to aid in characterizing biological molecules that will improve the diagnosis and treatment of diseases beyond COVID ranging from arthritis, cancer, diabetes to heart disease and neurodegeneration.

Project Terms:
base; macromolecule; improved; Phase; Biological; biologic; Ensure; Boils; Furuncles; data quality; tool; instrument; programs; Complex; Stream; Techniques; interest; experience; success; parallel architecture; Speed; Structure; Macromolecular Complexes; Sampling; Readability; Proteomics; Intervention Strategies; interventional strategy; Intervention; beta-Aspartate; Isoaspartate; data processing; computerized data processing; protein complex; Address; protein structures; proteins structure; protein structure; Data; Resolution; Collection; Small Business Innovation Research Grant; SBIR; Small Business Innovation Research; Process; pandemic disease; pandemic; cost; mass spectrometer; ion mobility; design; designing; Visualization software; visualization tool; blind; innovation; innovate; innovative; user-friendly; open source; primary outcome; flexibility; flexible; operation; Complex Analysis; Algorithmic Analysis; Algorithmic Analyses; Analyses of Algorithms; Analysis of Algorithms; preservation; COVID-19 pandemic; COVID crisis; COVID epidemic; COVID pandemic; COVID-19 crisis; COVID-19 epidemic; COVID-19 global health crisis; COVID-19 global pandemic; COVID-19 health crisis; COVID-19 public health crisis; COVID19 crisis; COVID19 epidemic; COVID19 global health crisis; COVID19 global pandemic; COVID19 health crisis; COVID19 pandemic; COVID19 public health crisis; SARS-CoV-2 epidemic; SARS-CoV-2 global health crisis; SARS-CoV-2 global pandemic; SARS-CoV-2 pandemic; SARS-CoV2 epidemic; SARS-CoV2 pandemic; SARS-coronavirus-2 epidemic; SARS-coronavirus-2 pandemic; Severe Acute Respiratory Syndrome CoV 2 epidemic; Severe Acute Respiratory Syndrome CoV 2 pandemic; Severe acute respiratory syndrome coronavirus 2 epidemic; Severe acute respiratory syndrome coronavirus 2 pandemic; corona virus disease 2019 epidemic; corona virus disease 2019 pandemic; coronavirus disease 2019 crisis; coronavirus disease 2019 epidemic; coronavirus disease 2019 global health crisis; coronavirus disease 2019 global pandemic; coronavirus disease 2019 health crisis; coronavirus disease 2019 pandemic; coronavirus disease 2019 public health crisis; coronavirus disease crisis; coronavirus disease epidemic; coronavirus disease pandemic; coronavirus disease-19 global pandemic; coronavirus disease-19 pandemic; severe acute respiratory syndrome coronavirus 2 global health crisis; severe acute respiratory syndrome coronavirus 2 global pandemic; coronavirus disease; COVID; CoV disease; corona virus disease; biopharmaceutical industry; biopharmaceutical company; Acceleration; Antibodies; Arthritis; arthritic; Behavior; Biological Response Modifier Therapy; Biological Therapy; biological therapeutic; biological treatment; biologically based therapeutics; biotherapeutics; biotherapy; Malignant Neoplasms; Cancers; Malignant Tumor; malignancy; neoplasm/cancer; Cell Separation; Cell Isolation; Cell Segregation; Cell Separation Technology; cell sorting; Cells; Cell Body; Communities; Computers; Cystine; L-Cystine; Data Analyses; Data Analysis; data interpretation; Data Collection; Diabetes Mellitus; diabetes; Diagnosis; Disease; Disorder; Disulfides; Electronics; electronic device; Electrons; Negative Beta Particle; Negatrons; Engineering; Family; Goals; Grant; Heart Diseases; Cardiac Diseases; Cardiac Disorders; heart disorder; instrumentation; Intelligence; Ions; Isoleucine; Isotopes; Judgment; Leucine; Manuals; Methods; Modernization; Neuron Degeneration; neural degeneration; neurodegeneration; neurodegenerative; neurological degeneration; neuronal degeneration; Nerve Degeneration; Noise; optical; Optics; Peptides; Post-Translational Modification Protein/Amino Acid Biochemistry; Post-Translational Modifications; Post-Translational Protein Modification; Posttranslational Modifications; Posttranslational Protein Processing; Protein Modification; Post-Translational Protein Processing; Proteins; Reading; Investigators; Researchers; Research Personnel; Running; Safety; Cell Communication and Signaling; Cell Signaling; Intracellular Communication and Signaling; Signal Transduction Systems; Signaling; biological signal transduction; Signal Transduction; Software; Computer software; Mass Photometry/Spectrum Analysis; Mass Spectrometry; Mass Spectroscopy; Mass Spectrum; Mass Spectrum Analyses; Mass Spectrum Analysis; Technology; Time; Translating; Water; Hydrogen Oxide; Work; Dissociation