Ryan W. Benz

Multiplexed Nanoparticle Protein Corona Enables Accurate and Precise Deep Plasma Proteomics

Ting C. Huang, Jian Wang, Alexey Stukalov, Simion D. Kreimer et autres

The Proteograph Product Suite, a multiplexed nanoparticle (NP) protein corona-based workflow, substantially improves the depth of detection of proteins by mass spectrometry (MS) by compressing the dynamic range of protein abundances. Here, we evaluate its quantitative performance and suitability for large-scale studies. …

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Deep Profiling of Plasma Proteoforms with Engineered Nanoparticles for Top-Down Proteomics

Che‐Fan Huang, Michael A. R. Hollas, Aniel Sánchez, Mrittika Bhattacharya et autres

The dynamic range challenge for the detection of proteins and their proteoforms in human plasma has been well documented. Here, we use the nanoparticle protein corona approach to enrich low-abundance proteins selectively and reproducibly from human plasma and use top-down proteomics to …

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A Scaled Proteomic Discovery Study for Prostate Cancer Diagnostic Markers Using ProteographTM and Trapped Ion Mobility Mass Spectrometry

Matthew E.K. Chang, Jane M Lange, Jessie May Cartier, Travis W. Moore et autres

There is a significant unmet need for clinical reflex tests that increase the specificity of prostate-specific antigen blood testing, the longstanding but imperfect tool for prostate cancer diagnosis. Towards this endpoint, we present the results from a discovery study that identifies new …

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Deep Profiling of Plasma Proteoforms with Engineered Nanoparticles for Top-down Proteomics

Che‐Fan Huang, Michael A. R. Hollas, Aniel Sánchez, Mrittika Bhattacharya et autres

ABSTRACT The dynamic range challenge for detection of proteins and their proteoforms in human plasma has been well documented. Here, we use the nanoparticle protein corona approach to enrich low-abundant proteins selectively and reproducibly from human plasma and use top-down proteomics to …

The Space Omics and Medical Atlas (SOMA) and international astronaut biobank

Eliah G. Overbey, JangKeun Kim, Braden T. Tierney, Jiwoon Park et autres

Abstract Spaceflight induces molecular, cellular and physiological shifts in astronauts and poses myriad biomedical challenges to the human body, which are becoming increasingly relevant as more humans venture into space 1–6 . Yet current frameworks for aerospace medicine are nascent and lag …

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Secretome profiling reveals acute changes in oxidative stress, brain homeostasis, and coagulation following short-duration spaceflight

Nadia Houerbi, JangKeun Kim, Eliah G. Overbey, Richa Batra et autres

As spaceflight becomes more common with commercial crews, blood-based measures of crew health can guide both astronaut biomedicine and countermeasures. By profiling plasma proteins, metabolites, and extracellular vesicles/particles (EVPs) from the SpaceX Inspiration4 crew, we generated "spaceflight secretome profiles," which showed significant …

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Abstract 7090: A scaled proteomic discovery study for prostate cancer diagnostic signatures using Proteograph workflow with trapped ion mobility mass spectrometry

Mark R. Flory, Matthew E.K. Chang, Jessie May Cartier, Jane M Lange et autres

Abstract Background and Aims: The low cancer specificity of serum Prostate-Specific Antigen (PSA), the principal biomarker for prostate cancer detection, leads to a high frequency of unwarranted prostate biopsies. To alleviate this deficit, we executed a proteomic discovery study seeking PSA reflex …

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Protein Coronas on Functionalized Nanoparticles Enable Quantitative and Precise Large-Scale Deep Plasma Proteomics

Ting Huang, Jian Wang, Alexey Stukalov, Margaret K. R. Donovan et autres

Background: The wide dynamic range of circulating proteins coupled with the diversity of proteoforms present in plasma has historically impeded comprehensive and quantitative characterization of the plasma proteome at scale. Automated nanoparticle (NP) protein corona-based proteomics workflows can efficiently compress the dynamic …

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Functionally distinct BMP1 isoforms show an opposite pattern of abundance in plasma from non-small cell lung cancer subjects and controls

Margaret K. R. Donovan, Yingxiang Huang, John E. Blume, Jian Wang et autres

Advancements in deep plasma proteomics are enabling high-resolution measurement of plasma proteoforms, which may reveal a rich source of novel biomarkers previously concealed by aggregated protein methods. Here, we analyze 188 plasma proteomes from non-small cell lung cancer subjects (NSCLC) and controls …

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Abstract 6340: Deep, unbiased and peptide-centric plasma proteomics with differential analysis of proteoforms enabling proteogenomic studies of NSCLC at scale

Margaret K. R. Donovan, Henry Darchon Huang, John H. Blume, Marwin Ko et autres

Abstract Introduction: Comprehensive assessment of the proteome remains elusive because of proteoforms arising from alternative splicing, allelic variation, and protein modifications. Characterization of the variable protein forms, or proteoforms will expand our understanding of the molecular mechanisms underlying diseases, however requires unbiased …

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Abstract 6339: Deep plasma proteomics at scale enabling proteogenomic analyses in a lung cancer (NSCLC) study

Mahdi Zamanighomi, Harendra Guturu, Jian Wang, Amir Alavi et autres

Abstract Our ~20,000 genes encode over one million protein variants, given alternative splice forms, allelic variation, and protein modification. Though large-scale genomics studies have expanded our understanding of biology, similarly, scaled deep and untargeted proteomics studies of biofluids have remained impractical due …

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Engineered nanoparticles enable deep proteomics studies at scale by leveraging tunable nano–bio interactions

Shadi Ferdosi, Behzad Tangeysh, Tristan R. Brown, Patrick A. Everley et autres

SignificanceDeep profiling of the plasma proteome at scale has been a challenge for traditional approaches. We achieve superior performance across the dimensions of precision, depth, and throughput using a panel of surface-functionalized superparamagnetic nanoparticles in comparison to conventional workflows for deep proteomics …

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