Document text
Principal Investigator: Aaron T Timperman
Organization: UNIVERSITY OF PENNSYLVANIA
Fiscal Year: 2024
Award: $202,368
Funding agency: National Institute of Allergy and Infectious Diseases
Project Summary/Abstract
The long-term goal of this project is to develop of a rapid, inexpensive, and sensitive screening
diagnostic based on an innovative broad proteomic approach to improve our ability to diagnose
infectious disease, monitor changes in the microbiome, measure the state of the host immune system,
and identify disease specific biomarkers. Specifically, the initiative will provide proof of principle for a
method to achieve simultaneous multi-pathogen detection and deep proteomic microbiome
characterization. We will work to detect the presence of several hundred pathogens while also
identifying thousands of microbes at clinically relevant levels. The short amino acid sequences or
peptides from the proteins will provide markers that range from the virus variant level, such as SARS-
CoV-2 variants of concern, to the family level, such as coronaviridae. In developing this diagnostic, a key
challenge is to maximize the sensitivity of peptide marker detection while analyzing for many clinically
relevant viruses and bacteria. We will therefore compare the performance of (a) a data-dependent
acquisition method that searches a custom database and (b) a data-independent acquisition method
that can identify thousands of proteins. The proposed study will begin with the analysis of
approximately twenty model pathogens before proceeding to the more ambitious analysis of more than
230 oro-respiratory samples. We will assess the primary factors that determine the performance of each
method and use our milestones to select one approach for further development. In the end, this
research will demonstrate the feasibility of a broad protein-based screening diagnostic that can detect
numerous pathogens and provide microbiome profiling to ultimately improve the diagnosis of disease
and assessment of human health. The project team includes researchers with diverse expertise from
Penn Engineering, Microbiology, and Penn Medicine.
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2><SARSCoV2><Saliva><Sampling><Scanning><Severe Acute Respiratory Coronavirus 2><Severe Acute Respiratory Distress Syndrome CoV 2><Severe Acute Respiratory Distress Syndrome Corona Virus 2><Severe Acute Respiratory Distress Syndrome Coronavirus 2><Severe Acute Respiratory Syndrome CoV 2><Severe Acute Respiratory Syndrome-associated coronavirus 2><Severe Acute Respiratory Syndrome-related coronavirus 2><Severe acute respiratory syndrome associated corona virus 2><Severe acute respiratory syndrome coronavirus 2><Severe acute respiratory syndrome related corona virus 2><Speed><Stable Isotope Labeling><System><Technology><Testing><Universities><Validation><Variant><Variation><Viral><Viral Burden><Viral Gene Products><Viral Gene Proteins><Viral Load><Viral Load result><Viral Proteins><Virus><Work><Wuhan coronavirus><airway microbiome><ancestry analysis><bacteria pathogen><bacterial pathogen><bio-engineered><bio-engineers><bio-markers><bioengineering><biologic><biologic marker><biological 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forms><severe acute respiratory syndrome coronavirus 2 variant strains><specific biomarkers><tailored approach><validations><variants of concern><viral detection><viral pathogen><virology><virus detection><virus pathogen><virus protein><µfluidic>