Active Research Funding

NIH Funding

Seattle Quant: A Resource for the Skyline Software Ecosystem

This grant is an NIGMS resource to support the Skyline Software Ecosystem. Development on Skyline started in 2008 to fill a critical need for a software tool to enable targeted proteomics experiments. The development of Skyline grew into an entire ecosystem of tools and has since expanded beyond targeted proteomics. The Skyline software ecosystem is one of the most widely used software platforms in all of mass spectrometry. The current software and its thriving community create exciting new opportunities for quantitative mass spectrometry. These tools support >14,000 registered users in their basic science, pre-clinical, and translational research. Specifically, our proposal has four aims. 1) Expand our test infrastructure to improve the robustness, stress test the software, confirm compatibility across computer systems, and track performance over time. 2) Improve support for both proteomics and non- proteomics workflows. 3) Improve the collection, sharing, annotation and dissemination of mass spectrometry data and Skyline documents. 4) Provide continued support and training for the Skyline ecosystem.

Quantifying proteins in plasma do democratize personalized medicine for patients with type 1 diabetes

This grant is part of the Targeted Mass Spectrometry Assays for Diabetes and Obesity Research (TaMADOR) program. This proposal aims to generate and validate novel transferable protein assays that harness the power of mass spectrometry. We aim to leverage a new method for the enrichment of extracellular vesicles and new de novo proteins for affinity enrichment, called minibinders, to help with sensitivity of the methods.

Nathan Shock Centers of Excellence in Basic Biology of Aging

UW Nathan Shock Center of Excellence in the Basic Biology of Aging provides leadership and resources to support the Geroscience community locally, nationally, and internationally. Services are provided through our Resource Cores and funds are available annually to support pilot projects by external investigators. Aging-related studies involving Proteomics, Metabolomics, Invertebrate Model Organisms, and Bioinformatics/Artificial Intelligence are supported. The MacCoss lab has played a roll in the Protein Phenotypes of Aging Core for the last 20 years.

Next Generation Translational Proteomics of Alzheimer’s Disease

We propose to enable precision medicine for AD by developing a cooperative research program that will unite a unique research team with the specific goal of vastly improving the molecular characterization of CSF as predictors of cognitive decline and AD pathophysiology. The efforts of this program will complement existing efforts to accelerate the identification and validation of clinically relevant therapeutic targets. Our U19 research program consists of four projects and four cores that are synergistic to our mission. This U19 harnesses the collective expertise of multiple fields, combined with the financial resources sufficient to extend and apply next generation proteomics technologies to clinical specimens that have been extensively annotated with longitudinal, consensus clinical diagnostic and neuropsychological test data. We are creating new assays with the goal of deployment to the clinical lab. We will create unique and sustainable reagents that will facilitate dissemination and deployment of these methods worldwide. The application of new technologies, development of novel reagents, creation of new clinical assays, and dissemination of data and protocols will accelerate neuroscience in a way not feasible under traditional NIH mechanisms.

Department of Energy (DOE)

Quantitative Protein Signatures of Low Dose Radiation Exposure

  • Grant Number: DE-SC0025368

Our overarching goal is to develop the capabilities to assess individual tissue specific response from low dose radiation using quantitative proteomics data from plasma extracellular vesicles (EVs).

Intelligence Advanced Research Projects Activity (IARPA)

TEI-REX Program – Biodosimetry: Quantitation of radiation induced protein adducts using mass spectrometry

Biodosimetry is an evolving technology that uses an individual’s own biomolecules to detect and differentiate exposure to an ionizing radiation source or event. Ideally, biodosimetry would enable an accurate estimation of dose, type, and time since exposure from a single sample, obtained by non-invasive methods. The goals of the TEI-REX program are to discover, validate, and define a set of biomarkers that can be effectively used to build classifiers for biodosimetry. This project will use the unique expertise of the research team assembled from the University of Washington Departments of Genome Sciences and Radiation Oncology and Spectragen Informatics, including mass spectrometry, biochemistry, radiation oncology, machine learning, and the development of software tools for the analysis of mass spectrometry data. The biomarker discovery phase of the project will identify protein adducts resulting from exposure to ionizing radiation in human dermal cell lines and mouse models, and the classifier discovery phase will test the biomarkers in clinical specimens collected from oncology patients undergoing radiotherapy. Biodosimetry classifiers will be determined using machine learning and applied to assess TEI-REX T&E samples.

Foundations

American Heart Association

Blood-based biomarker discovery for acute ischemic stroke

  • Grant Number: 24CSA1054804

Acute ischemic stroke (AIS) is a major public health problem, and its treatment is time-dependent. We will use an novel proteomics method to study patients undergoing elective aortic arch surgery, in which the intraoperative AIS rate is ~70%. By obtaining blood immediately prior to and after such surgery, we can measure the change in protein concentration within each patient in the pre- and post-stroke condition, determining which proteins change only in relation to the presence and extent of intraoperative AIS.

Industry

Support for Skyline, Panorama, and Proteowizard

Support of Agilent Mass Spectrometers

  • Industry Gift from Agilent
  • 5/1/2012 – 12/31/2025 We are continuing to extend our analytical software tools to support Agilent mass spectrometers.

Support of Bruker Mass Spectrometers

  • Software Engineering Contract from Bruker
  • 8/1/2012 – 1/31/2026 We are continuing to extend our analytical software tools to support Bruker mass spectrometers.

Support of Shimadzu Mass Spectrometers

  • Software Engineering Contract from Shimadzu
  • 1/15/2014 – 1/14/2026 We are continuing to extend our analytical software tools to support Shimadzu mass spectrometers.

Support of Thermo Fisher Mass Spectrometers

  • Software Engineering Contract from Thermo Fisher
  • 3/1/2014 – 2/28/2028 We are continuing to extend our analytical software tools to support Thermo Fisher mass spectrometers.

Support of Waters Mass Spectrometers

  • Software Engineering Contract from Waters
  • 9/1/2013 – 12/31/2027 We are continuing to extend our analytical software tools to support Waters mass spectrometers.

Support for Mass Spectrometry Technology Development

ThermoFisher Sponsored Search Agreement

  • Data Acquisition and Analysis Strategies for Improving the Analysis of Peptide Mixtures Using Thermo Fisher Mass Spectrometers
  • 3/27/2017 - 6/15/2026

Pharma/Biotech Service Agreements

The MacCoss lab has regular short and medium term agreements to work on projects with Pharma collaboratively.