Speaker: Chan-Hyun Na, Johns Hopkins University

Topic: In situ cell-type-specific proteome analysis using antibody-mediated protein biotinylation

Date: Monday, January 12, 2026

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 Sheng Feng (SFeng@som.umaryland.edu) by Friday, January 9 if you will be attending the dinner.

Abstract: Decoding proteome changes is crucial for understanding biological phenomena. Traditional proteomic studies face challenges due to the complexity of tissue samples, where multiple cell types are intermingled. Existing cell-type-specific techniques require genetic modifications or dissection of individual cells, hampering their broad application. This study introduces a novel method, in situ cell-type-specific proteome analysis using antibody-mediated biotinylation (iCAB), leveraging immunohistochemistry and biotin-tyramide signal amplification to biotinylate proteins in target cells within tissue. Applied to mouse brain tissue, iCAB enriched proteins from neuronal cell bodies, astrocytes, and microglia, identifying approximately 8,400 proteins in enriched samples, revealing cell-type-specific differential expressions. Applied to neurodegenerative disease mouse models, the iCAB-enriched proteome showed 2-5 times more significantly differentially expressed proteins than the non-enriched proteome, revealing cell-type-specific pathways for respective cell types. We also expanded it to other brain cell types and post-translational modifications. iCAB offers a potent tool for a straightforward cell-type-specific proteomic analysis of animal or human tissues.

Lightning Talk
Development of an integrated high-throughput proteomics sample preparation platform for analysis of C. elegans
Valentine V. Courouble , Ph.D.
NCATS, NIH

Caenorhabditis elegans (C. elegans) have long served as a eukaryotic model organism for human biology by virtue of genetic conservation and experimental tractability but their application in high-throughput (HT) screening has been limited due to incompatibility of the labor-intensive handling and difficulty obtaining robust molecular level analyses. We developed an integrated platform for the automated, HT proteomics sample preparation and mass spectrometry (MS) analysis of C. elegans that incorporates novel Adaptive Focused Acoustics (AFA) technology to extract proteins from C. elegans samples. We are able to identify approximately 2,250 proteins with a relative standard deviation below 10% from samples consisting of only 3 worms each. Additionally, this platform reduces overall sample preparation time from two days to eight hours and allows simultaneous processing of 384 differential samples – a 30-fold improvement in throughput. Ultimately, this automated and HT platform will allow effective utilization of C. elegans as an orthologous phenotypic model within pre-clinical therapeutic development for a wide range of human diseases.

Speaker: Mazdak Taghioskoui, Trace Matters Scientific

Topic: Overcoming Fundamental Limits in Mass Spectrometry: SPion®, Super Mass Spectrometry, and the Delayed-ESI Technique

Date: Monday, December 15, 2025

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 Sheng Feng (SFeng@som.umaryland.edu) by Friday, December 12 if you will be attending the dinner.

Abstract: Despite decades of progress, modern mass spectrometry has advanced primarily through incremental refinements built on fundamentally unchanged architectures, and while these improvements have expanded capabilities, the underlying instrumentation has not kept pace with the increasing analytical demands of proteomics, biomedicine, in-situ chemical analysis, and other rapidly evolving fields. This persistent mismatch highlights the need for disruptive technologies that reconceptualize how ions are generated, transferred, and measured. Over the past several years, I have been developing such technologies, and in this seminar I will present three complementary innovations designed to directly address these long-standing limitations. I will first introduce SPion®, a NASA award–winning flexible ion-guide architecture that enables near-lossless ion transfer over extended distances and decouples the ion source from the instrument, thereby supporting handheld probes, robotic imaging platforms, and dendritic mass spectrometry, in which multiple instruments acquire data from a single ionization event. I will then discuss the conceptual and practical foundations of Super Mass Spectrometry, a distributed, cluster-based measurement framework that independently scales sensitivity and scan speed, mitigates the bandwidth mismatch between LC and MS, and provides a feasible path toward high-dynamic-range mass spectrometry. Within this broader framework, I will also highlight the Delayed-ESI technique, which creates compositionally identical but temporally staggered ion beams to enable deterministic re-measurement, extend dynamic range, and improve repeatability and quantitative fidelity in LCMS workflows. Collectively, these advances establish a new class of scalable mass-spectrometry architectures engineered to overcome severe ion losses, restricted intrinsic dynamic range, and raster-limited sampling—fundamental constraints that prevent conventional instruments from producing high-fidelity digital representations of complex biological samples—and together they outline a path toward the next generation of mass-spectrometry technologies aligned with the scientific and industrial challenges of the coming decades.

Lightning Talks
Integrative Blood Proteomics Reveals the HuBP Atlas of over 10,000 Proteins Informing Human Physiology and Disease
Zhenyu Sun, Ph.D.
Johns Hopkins University School of Medicine

Blood is a rich source of clinical information, yet no resource systematically maps protein detectability across sample types, workflows, and disease states. We developed the Human Blood Proteome (HuBP) database, integrating protein abundance, detectability, and reproducibility across plasma workflows and whole-blood disease cohorts. Using DIA with complementary enrichment strategies, we identified 9,965 proteins in healthy plasma and profiled PDAC, ccRCC, and LUAD whole blood, detecting 8,002–8,009 proteins and 498 disease-specific markers. In total, HuBP compiles 10,463 nonredundant proteins, providing a quantitative atlas that supports experimental optimization, biomarker discovery, and precision medicine applications.

Painting the Proteome: SPOTTER for High-Plex Spatial Protein Maps
Yuanwei (Bay) Xu, Ph.D.
Johns Hopkins University School of Medicine

Spatial proteomics aims to identify and quantify proteins and PTMs in situ with regional resolution, linking molecular states to tissue architecture and microenvironments. Dissecting molecular heterogeneity at relevant spatial scales is critical for understanding the biological and pathological roles of functional proteins. Current technologies include antibody-based imaging, which typically tracks a limited panel of markers, and LMD-based LC–MS workflows, which isolate and analyze a small number of regions separately. In contrast, SPOTTER directly labels tissue proteins with chemical tags across the entire section, generating arrays of ~100–200 µm microregions. A single SPOTTER experiment could report proteome-wide abundance distributions across all spots, enabling scalable, high-plex spatial maps using standard instruments and workflows.

Speaker: Zhicheng Jin, University of Wisconsin – Madison

Topic: Liquid Chromatography-Tandem Mass Spectrometry Method Development and Implementation in Clinical Laboratories

Date: Monday, November 17, 2025

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 Sheng Feng (SFeng@som.umaryland.edu) by Friday, November 14 if you will be attending the dinner.

Abstract: Clinical diagnostic assays developed on mass spectrometry are classified as laboratory developed test (LDT) and must meet stringent method validation requirements before implementation. Beyond regulatory compliance, laboratories should conduct operational assessments to evaluate the feasibility of bringing in-house a clinical test. Considerations include choice of instruments, anticipated test volume, turn-around time requirement, sample preparation, and staff training. Recently, our laboratory went live with total testosterone assay, antifungals panel, and urine drug confirmatory test on LC-MS/MS platform. This presentation will discuss challenges and solutions in the implementation of these three methods. The focus will be urine drug
confirmatory test in supporting prescription drug monitor and investigating acute drug poisoning. I will discuss urine drug tests available in our hospital, including high-throughput immunoassays and point-of-care tests. Details in the development and implementation of a large pain management drug panel on LC-MS/MS will be presented. Additionally, I will share examples of broad-spectrum drug testing on GC-MS and LC-QTOF instruments. Case studies highlighting the utilities of urine drug confirmatory tests and results interpretation will be presented.

Lightning Talk
Bioanalysis of Large Molecule Drugs in Pre-clinical Development using Intact and Reduced LC-MS Approaches
Jake Melby, Ph.D.
Senior Scientist, AstraZeneca

Speaker: Ronald L. Schnaar, Johns Hopkins University School of Medicine

Topic: Expanding the Molecular Horizon: Integrative Mass Spectrometry Strategies for Spatial Omics and Neurodegenerative Disease Research

Date: Monday, October 20, 2025

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

Location: Shimadzu Scientific Instrument, Inc. Training Center 7100 Riverwood Drive, Columbia, MD 21046 (Directions) This will be an in-person meeting.

Dinner: Please RSVP to Sheng Feng (SFeng@som.umaryland.edu) by Friday, October 17 if you will be attending the dinner.

Abstract: Every living cell carries distinctive covalent groupings of sugars, glycans, carried on glycoproteins and glycolipids mainly on their cell surfaces. In humans glycans are composed primarily of just nine sugars in specific linkages and patterns biosynthesized by a family of ~215 glycosyltransferases, the expression and specificity of which limit and define the human glycome. In part, glycans are involved in molecular recognition and cell regulation via their engagement with complementary glycan binding proteins, also called lectins. Deciphering this “sugar code” has the potential to provide a more complete understanding of cell signaling regulation and furnish novel opportunities for therapeutic development. Mass spectrometry has played an outsized role in glycomics and in defining the glycan-protein interactome. This talk will explore these themes via a series of vignettes from our studies aimed at identifying endogenous glycans that drive human biology via glycan-protein interactions, including recent work that developed bifunctional glycan tools to capture and identify a subset of the glycan-protein interactome.

Gold Sponsor Talk
Robust Start for Confident Results with AFA® – A Comprehensive Sample Prep Workflow for Protein Analysis
Debadeep Bhattacharyya Ph.D.
Sr. Director – Distribution (APAC, LatAm, Canada), Global Protein Analysis
Covaris, Woburn, MA, USA
dBhattacharyya@covaris.com

Significant advances in the world of Proteomics have not only revealed several protein biomarkers that can be used for disease monitoring but also helped in establishing workflows for routine monitoring. However, complexity in matrices (from fresh frozen tissue samples to FFPE, from cells to organoids and many more) continue to pose severe challenges that are not readily addressed by the advanced instruments used for end-detection technologies. While better and more data can be beneficial – identification, characterization, and quantification of proteins that are extracted, purified and digested from complex biological matrices can be complicated, if not inefficient with the traditional sample preparation methods. Adaptive Focused Acoustics® (AFA®) Technology has gained widespread popularity in the world of protein analysis. In here, we report comprehensive, robust, and fast AFA based workflows for extraction, purification and accelerated digestion of proteins starting with a host of varied complex biological matrices. The workflows are scalable and can support small to high throughput sample requirements.