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.

Speaker: Lingjun Li, University of Wisconsin-Madison

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

Date: Monday, September 15, 2025

Time: 6:00 pm Dinner and Vendor Night, 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, September 12 if you will be attending the dinner.

Abstract: Understanding the molecular complexity of neurodegenerative diseases such as Alzheimer’s disease (AD) requires analytical platforms that can capture both chemical diversity and spatial context. In this keynote, I will present our lab’s recent advances in mass spectrometry (MS)-based technologies that enable multidimensional molecular mapping across scales—from biofluids to single cells and intact tissues.
We have developed a suite of multiplexed isobaric and isotopic tagging strategies, including the high-resolution 12-plex and 18-plex DiLeu and SUGAR tags, to achieve simultaneous quantitation of proteins, peptides, lipids, and glycans. These tools have been applied to cerebrospinal fluid (CSF) samples from cognitively healthy individuals and AD patients, revealing stage-specific glycosylation patterns and glycoform microheterogeneity with implications for biomarker discovery.
To complement molecular profiling, we have advanced spatial omics through innovations in mass spectrometry imaging (MSI). Our single-cell MSI platform integrates dual-polarity ionization and ion mobility separation to enhance lipidome coverage at subcellular resolution. Furthermore, the Tissue Expansion Mass Spectrometry Imaging (TEMI) technique enables high-resolution mapping of metabolites, peptides, proteins, and glycans in expanded tissues, preserving spatial fidelity while increasing voxel throughput.
These integrative approaches have been applied to mouse models of AD and human postmortem brain tissues, generating region-specific biomolecular atlases that illuminate molecular alterations across disease progression. Our work underscores the power of MS-based spatial and structural omics to decode the biochemical landscape of complex diseases and guide therapeutic development.

Speaker: Joseph Buonomo, University of Texas at Arlington

Topic: Scalable Native Peptide Sequencing Via Innovation in “Click” Chemistries and Large Language Models

Date: May 12, 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 Dingyin Tao (owendtao@gmail.com) by Friday, May 9 if you will be attending the dinner.

Abstract: We are developing a groundbreaking method to sequence native peptides, especially for liquid biopsies, a less invasive way to detect cancer from bodily fluids like urine and blood. By accurately sequencing proteins from these samples, we can improve early cancer detection, monitoring, and personalized treatment, offering a powerful tool for doctors and researchers alike. Our approach uses a sophisticated sequencing platform combined with advanced artificial intelligence (AI). Imagine the process like a game of hangman, where you guess a word by uncovering one letter at a time. Here, we identify specific amino acids—akin to letters—in a protein. Instead of revealing all twenty amino acids at once, we focus on identifying eight key ones: K, Y, C, M, W, R, D, and E with highly chemoselective reactions. These amino acids are like the revealed letters in hangman. With the help of AI, acting as a super-smart guesser, we can infer the remaining twelve amino acids. The AI, trained on vast amounts of protein data, uses patterns and context to predict the full sequence, similar to how a hangman player might guess the entire word after seeing a few letters. Our method utilizes advances in bioconjugation and “click” chemistries, as well as unique barcoding strategies to encode cycle numbers and amino acid identities to accurately identify the eight key amino acids and their modifications. By leveraging these innovations, we can extend the read lengths of sequences and improve accuracy. We have designed our platform to be agnostic of detection method, applicable to DNA sequencing, nanopore, and fluorescent detection workflows.

To fully harness the potential of AI beyond sequencing, we are also exploring its application in selecting generic drug suppliers for clinical and research purposes. Reliable sourcing is a persistent challenge, especially as the pharmaceutical supply chain grows more complex and globalized. Traditional vetting processes often rely on manual document reviews, regulatory audits, and personal networks, which are time-consuming and susceptible to human error. Our approach involves training AI algorithms on comprehensive datasets including supplier certifications, manufacturing history, recall records, and even real-time logistics data. This allows us to systematically evaluate suppliers, flag inconsistencies, and predict future reliability based on historical patterns. Integrating AI-driven supplier selection into our sequencing workflow ensures not only higher confidence in reagent quality but also scalability and traceability in our operations. This layer of intelligence helps safeguard the reproducibility of our results and ultimately supports more robust diagnostic platforms.

Speaker: Mark Mellinger, GlaxoSmithKline Pharmaceuticals

Topic: Recent Advances in the Field of Chiral Chromatography

Date: April 14, 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 Dingyin Tao (owendtao@gmail.com) by Friday, April 11 if you will be attending the dinner.

Abstract: Over the past 25 years, there have been some major breakthroughs in the field of chiral chromatography. Prior to 2002, most chiral HPLC separations were done by normal phase chromatography using an alkane (heptane or hexane), and an alcohol (ethanol or IPA). The success rate was only about 60% and there was only a handful of chiral columns available at the time which included AD, OD, OJ, and AS. However, in 2002, Chiral Technologies discovered that these coated chiral stationary phases were more stable than originally thought. The “polar organic” mobile phase was introduced. Acetonitrile, methanol, and IPA were used in the mobile phase to replace normal phase chromatography. This was particularly useful in terms of solubility and helped resolve moderate to tenacious binders which did not elute by either SFC or by normal phase HPLC conditions. In 2004, the second major breakthrough occurred. Chiral Technologies introduced the first immobilized chiral stationary phase, IA. Immobilized chiral stationary phases are unique in that they are not coated to the silica gel but are covalently bound to the silica gel support. The result is a more stable and more rugged chiral column. These immobilized chiral stationary phases are essentially indestructible and are stable to a wide range of solvents including DCM, TBME, ethyl acetate, and THF. This advancement has enabled the discovery of very unique chiral separations which may have encountered solubility issues. The final major breakthrough which occurred in the past 25 years is chiral separations using supercritical fluid chromatography, or SFC. In SFC, the weak component of the mobile phase has been replaced by CO2. This allows for much “greener” separations of weak to moderate binders. This talk will outline practical examples of each of these advancements.

Speaker: Bob Ernst, University of Maryland – Baltimore

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

Date: March 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 Dingyin Tao (owendtao@gmail.com) by Friday, March 14 if you will be attending the dinner.

Abstract: Microbial membranes are specialized structures composed of complex lipids and proteins, with distinct lipid compositions characteristic of different microbes, such as bacteria, spirochetes, and fungi. The diversity of lipids makes generalizing their composition challenging, often resulting in unique profiles for particular genera, including Gram-positive and Gram-negative bacteria. These membrane lipids play crucial roles in cellular integrity, signaling, stress response, propagation, antibiotic resistance, speciation, and pathogenesis. Understanding the characteristics, structure, and mechanisms of bacterial lipid synthesis and regulation requiring cutting-edge technologies to enhance microbial lipidomics resolution. Advancements in instrumentation and extraction procedures have led to more sophisticated analytical methodologies for bacterial lipid analysis, with state-of-the-art techniques gaining wider adoption. MALDI-based MS analysis has revolutionized the field, enabling direct bacterial identification from complex biological samples without ex vivo growth, engineering of bacterial lipids for vaccine adjuvant development, and mapping of host-influenced lipid A modifications during Gram-negative bacterial infections. These developments have significantly advanced our understanding of host-pathogen interactions, particularly in relation to lipopolysaccharide (LPS) and its membrane anchor, lipid A.

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Lightning Talk
“A spatial multiomics workflow on a new benchtop MALDI-TOF instrument for deciphering the protein and lipid landscape in tissues”
Kate Stumpo, Ph.D.
Senior Marketing Manager, Bruker

Abstract: Spatial biology enables the visualization of different chemical landscapes in biological tissue making it an important technology in clinical research. MALDI mass spectrometry imaging
(MALDI Imaging) is well established for the spatial analysis of biomolecules in tissue. Additionally, multiomic spatial localization of lipids with expressed protein distributions can be
done which increases understanding of localized cellular processes in tissue. Here, we demonstrate an automated workflow on the neofleX, a new benchtop axial TOF.
FFPE sections of a human colorectal cancer sample were prepared for lipid imaging on the neofleX at 20 µm pixel size. To assess the spatial protein landscape, the same slide was
processed with the MALDI HiPLEX-IHC workflow, using 14 antibodies with photocleavable mass tags from AmberGen, Inc. The expressed protein distribution images of the mass tags from all of the 14 antibodies were obtained by automatic generation of ome.tiff files from a target list of the antibody mass tags as [M+H] + ion species and were visualized in the software SCiLS Scope. SCiLS Scope is a new tool for fast browsing through the color-coded ion images of the MALDI HiPLEX-IHC data, capable of visualizing both individual and composition ion images.
Protein expression and lipid imaging data were combined and mapped for examination of feature colocalization. Lipids colocalizing with individual tumor or immune markers from the
HiPLEX-IHC experiment were thereby obtained using the mapped images. For example, PC_32:0 was detected with higher abundance in the same region, where also cytokeratin marker PanCK was binding.
Our workflow provides a simple method to visualize the targeted spatial protein expression profiles from FFPE tissue. As an add on, our method can be combined with lipid imaging from the same tissue section to receive deeper insights into the cellular mechanisms of disease.