Speaker: Hui Zhang, Johns Hopkins University

Topic: Glycoproteomics: methods and applications in clinical proteomics

Date: May 20, 2024

Time: 6:15 pm Dinner, 7:15 pm Presentation

Location: Shimadzu Scientific Instrument, Inc. Training Center 7100 Riverwood Drive, Columbia, MD 21046 (Directions)

Dinner: Please RSVP to Jonathan Ferguson (jonathan.ferguson33@gmail.com) by Friday, May 17 if you will be attending the dinner.

Abstract: The integration of proteomic technologies into clinical practice indeed holds significant promise for revolutionizing disease diagnosis, prognosis, and treatment. By delving into the intricate world of proteins and their modifications, particularly protein glycosylation, researchers aim to unravel the complexities underlying various diseases.
Glycoproteomics, a specialized field within proteomics and glycomics, focuses on the comprehensive characterization of glycoproteins. In recent years, mass spectrometry-based technologies have emerged as the cornerstone of advancements in glycoproteomics. One of the main challenges in glycoproteomics lies in the heterogeneity of glycosylation of glycoproteins, including variations in glycan types, sites of glycosylation, and the specific glycans attached to each glycosylation site. To overcome these challenges, we have developed various methodologies in glycoprotein glycopeptide enrichment, liquid chromatography, mass spectrometry, and software tools, for precise site-specific glycan assignments.
The developed glycoproteomic techniques offer unprecedented opportunities to investigate the interplay between genomic, environmental factors, and protein modifications. By employing these advanced technologies to investigate tumors, we have gained invaluable insights into cancer biology, particularly pertaining to protein modifications such as glycosylation.
In summary, the integration of glycoproteomic approaches into biomedical research has the potential to significantly advance our understanding of cancer and pave the way for more personalized and effective clinical interventions.
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lightning talk
Ying Hao, Ph.D. (NIH/NIA/IRP)

Speaker: Fabio P. Gomes, Virginia Commonwealth University

Topic: Native Top-Down Characterization of Proteins and their Complexes in Breast Cancer Cells

Date: April 15, 2024

Time: 6:15 pm Dinner, 7:15 pm Presentation

Location: Shimadzu Scientific Instrument, Inc. Training Center 7100 Riverwood Drive, Columbia, MD 21046 (Directions)

Dinner: Please RSVP to Jonathan Ferguson (jonathan.ferguson33@gmail.com) by Friday, April 12 if you will be attending the dinner.

Abstract: Oligomerization of proteins and their modified forms (proteoforms) produces functional protein complexes. Complexoforms are complexes that consist of the same set of proteins with different proteoforms. The ability to characterize these assemblies within cells is critical to understanding the molecular mechanisms involved in disease and to designing effective drugs. An outstanding biological question is how proteoforms drive function and oligomerization of complexoforms. However, tools to define endogenous proteoform-proteoform/ligand interactions are scarce. I will present a native top-down proteomics (nTDP) strategy that combines size-exclusion chromatography, nano direct infusion, field asymmetric ion mobility spectrometry, and multistage mass spectrometry to identify protein assemblies (≤70 kDa) in breast cancer cells and in cells that overexpress EGFR, which serves as a resistance model of estrogen receptor-α (ER-α) targeted therapies. This nTDP approach was able to identify ~104 complexoforms from 17 protein complexes, which revealed several molecular features of the breast cancer proteome, including EGFR-induced dissociation of nuclear transport factor 2 (NUTF2) assemblies that modulate ER activity. We found that the K4 and K55 posttranslational modification sites discovered with nTDP differentially impact the effects of NUTF2 on the inhibition of the ER signaling pathway.
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lightning talks
Bay Xu, PhD (JHU)
Doeun Kim, PhD (NIAID/NIH)

Speaker: Bob Ernst, University of Maryland, Baltimore

Topic: Bacterial Lipids – Advances in Structural Analysis and Function using MALDI Mass Spectrometry

Date: March 18, 2024

Time: 6:15 pm Dinner, 7:15 pm Presentation

Location: Shimadzu Scientific Instrument, Inc. Training Center 7100 Riverwood Drive, Columbia, MD 21046 (Directions)

Dinner: Please RSVP to Jonathan Ferguson (jonathan.ferguson33@gmail.com) by Friday, March 15 if you will be attending the dinner.

Abstract: Microbial membranes are specialized structures with a specific arrangement of complex lipids and proteins. Depending on the microbe (bacterial, spirochete, fungi), each tends to have a distinct and characteristic lipid composition that resides on or is embedded in the outer membrane. As lipids are a large, diverse group of molecules, it is not easy to generalize lipid composition, which in many cases may be unique to particular genera, such as Gram-positive and Gram-negative bacterial species. Membrane lipids are crucial not only for integrity but also for signaling, responding to environmental stresses, propagation, antibiotic resistance, speciation, and pathogenesis. The characteristics, structure, and specific mechanisms leading to bacterial lipid synthesis and regulation represent long-standing questions that require the latest technologies to improve the resolution of microbial lipidomics. Analytical methodologies for the analysis of bacterial lipids have gradually become more sophisticated due to both advancements in instrumentation and extraction procedures leading to greater adoption of state-of-the-art techniques. Using MALDI-based MS analysis, we can now directly identify bacteria from complex biological samples without the need for ex vivo growth, engineer bacterial lipids to elicit specific host innate immune responses for vaccine adjuvant development, and map host-influenced de novo lipid A, the membrane anchor of lipopolysaccharide (LPS), modifications during Gram-negative bacterial infection, advance our understanding of the host-pathogen interactions.
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lightning talks
Jongmin Woo (JHU)
Amit Dey (NIH)

Speaker: Joshua Coon, University of Wisconsin-Madison

Topic: From Systems to Structural Biology – new MS technology to drive discovery

Date: Wednesday February 28, 2024

Time: 6:15 pm Dinner, 7:15 pm Presentation

Location: University of Maryland (Lecture Hall CHM 1402 Directions)

Dinner: Please RSVP to Jonathan Ferguson (jonathan.ferguson33@gmail.com) by Monday, February 26 if you will be attending the dinner.

Abstract: In this presentation I will provide several examples of how MS technology can drive biological discovery. First, we use a high-throughput proteomic, metabolomic, and lipidomic methodology to profile nearly 1,000 human cell lines that each are missing a mitochondrial gene. Then, using computation and informatics, we combine this dataset to discovery the functions of several genes, linking two of them directly to human disease. Next, we use multiple proteases and extensive MS to provide the deepest coverage and analysis of the human proteome to date – confirming that the majority of spliced RNA molecules do indeed get converted into proteins. Next, we describe use of the Orbitrap Astral hybrid to profile human proteomes in under one hour, profile human plasma at a depth of nearly 7,000 proteins, and measure protein phosphorylation at unprecedented depth and speed. Finally, we present on a modified Orbitrap mass spectrometer that is used to prepared samples for cryoEM. Briefly, protein-protein complexes are ionized using native ESI and then either mass analyzed or landed onto a cryogenically cool EM grid within the MS system. Water vapor is introduced to cover the landed particles with amorphous ice. Following landing, the samples are removed from vacuum and placed in a cryoEM instrument for direct imaging.

Speaker: Keenan Walker, National institute on Aging, NIH

Topic: Biomarkers and Peripheral Drivers of Dementia Identified Using Plasma Proteomics

Date: January 22, 2024

Time: 6:15 pm Dinner, 7:15 pm Presentation

Location: Shimadzu Scientific Instrument, Inc. Training Center 7100 Riverwood Drive, Columbia, MD 21046 (Directions)

Dinner: Please RSVP to Jonathan Ferguson (jonathan.ferguson33@gmail.com) by Friday, January 19 if you will be attending the dinner.

Abstract: Recent advances in high-throughput technology for the characterization of the human proteome have enabled the simultaneous assessment of thousands of circulating proteins at scale. Using this technology to examine plasma proteomic changes that precede the onset of dementia and Alzheimer’s disease may provide a window into the underlying disease biology and nominate new biomarkers and targets for intervention. By applying SomaLogic’s SomaScan Assay to conduct a large-scale prospective analysis of the plasma proteome in cognitively normal individuals who later progress to dementia, we take a data-driven approach to discovery of early-stage blood-based biomarkers for Alzheimer’s disease, dementia, and cerebral small vessel disease. Through multi-cohort efforts which leverage network-based proteomics, genetics, brain imaging, and cerebral spinal fluid (CSF) biomarkers, we have identified a novel set of proteins, protein networks, and related biological pathways that may play a mechanistic role in age-related neurodegenerative conditions, including Alzheimer’s disease and vascular cognitive impairment.
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lightning talks
Noah Smeriglio (George Washington University)
Yingwei Hu (Johns Hopkins University)