PIs: Galit Lahav PhD and Jeremy Gunawardena PhD, Harvard Medical School. Proteoform analyses of p53, a complex regulator of cellular stress. This project strongly drives TR&D 1 — resolving complex proteoform profiles and TR&D 6 — targeted top-down proteomics.
Tracking Allograft Outcomes Using High-throughput Whole Protein Analysis
PIs: Joshua Levitsky MD, Northwestern University. Proteoform biomarkers for early detection and prediction of acute allograft rejection. This project strongly drives TR&D 5 — reduction to practice of methods for analysis of patient samples.
PI: Kevin Haigis, PhD, Harvard Medical School. This DBP will generate robust instrumentation (TR&D 5), bioinformatics tools, and standardized enrichment protocols for high-throughput targeted characterization of KRAS oncoproteoforms from cell lines, mouse models, and primary patient tumors (TR&D 6).
PIs: Amanda Saratsis, MD and Javad Nazarian, PhD, Lurie Children’s Hospital and University Children’s Hospital Zurich. This DBP will afford the ability to detect and characterize complex patterns of post-translational modification on histones and other proteins in sample-limited contexts (TR&D 7). Glioma tissue is difficult to acquire and the collaboration with Dr. Saratsis, pediatric neurosurgeon at Lurie Children’s Hospital will allow deep phenotyping of a rare cancer that affects hundreds of children per year.
ESKAPE Pathogen Proteoform Remodeling During Metal Acquisition by Top-Down
PI: Eric Skaar PhD MPH. Top-down proteomics methods to identify glycosylated and acylated proteoforms from antibiotic-resistant pathogens. Novel drug and antibody proteoform targets (and validated assays to monitor them from TR&D 6) during ESKAPE pathogen infection. LCM methods (TR&D 7) will be applied to characterize proteoforms from mosaic tissues composed of host and pathogen.
PI: Viviane Labrie, PhD. Robust top-down instrumentation (TR&D 5), bioinformatics tools, and enrichment technologies (TR&D 6) to identify proteoforms and targeted isolation approaches to analyze proteoforms from alpha-synuclein aggregates in the appendix and intestine (TR&D 7).
Proteoforms in Alzheimer’s Disease Proteinopathies
PIs: Bill DeGrado PhD and Carlo Condello, PhD. Aligned sample handling, liquid chromatography, high-resolving power mass spectrometry and bioinformatics resources (TR&D 5) for confident assertion of isolated proteoforms (TR&D 6) unique to discrete amyloid conformers isolated from discrete brain regions. The use of technologies developed in TR&D 7 will allow detection of proteoforms in neurodegenerative plaques using LCM- and PIRL-based sampling.
PI: Dan Rader, MD. New software that streamlines the transition of proteoform discovery to develop, perform and export targeted proteoform assays that scale favorably into hybrid mass spectrometers (TR&D 5). Infrastructure (hardware and software) required to perform large-scale quantitative assays on low-abundance proteoforms on the scale of hundreds of participant samples (e.g., in the CARDIA cohort) (TR&D 6. Methods for micro-sampling of proteoforms with reduced bias and sample degradation (TR&D 7).