May Meeting

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.

April Meeting

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.

March Meeting

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.

February Meeting

Speaker: Akos Vertes, The George Washington University

Topic: Spatial Metabolomics of Single Cells in their Natural Environment

Date: February 3, 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, January 31 if you will be attending the dinner.

Abstract: In multicellular organisms, cells assemble into tissues with specific functions. Tissue embedded cells operate a selection of metabolic pathways for the synthesis and degradation of a collection of small molecules that serve growth, signaling, and reproduction. Capturing the spatiotemporal distributions of metabolites, including lipids, with cellular granularity gives new insight into the functioning of tissues. We have developed ambient ionization techniques that can report on the metabolite content of functioning cells with high throughput and targeting capabilities. Image analysis and morphometry of brightfield and fluorescence microscope images is used to target selected cell types, followed by mid-IR laser ablation of individual cells. The ablation plume is ionized by an electrospray (laser ablation electrospray ionization, LAESI). Ion mobility separation (IMS) of the produced ions is followed by time-of-flight or Fourier transform ion cyclotron resonance mass spectrometry (MS) for the determination of cellular metabolite abundances. Cell-type specific small molecule compositions are determined and correlated with active metabolic pathways characteristic to cellular functions. Metabolite abundance distributions reflect population heterogeneity through metabolic noise levels and reveal hidden cellular phenotypes segregated into subpopulations functioning in specific metabolic states. Examples of spatial metabolomics are presented for various cell types including human hepatocytes, Arabidopsis thaliana and Allium cepa epidermal cells, and root nodule cells of Glycine max in nitrogen fixing symbiosis with Bradyrhizobium japonicum. In addition, using MS imaging (MSI) based on MALDI and laser desorption ionization (LDI) from silicon nanopost array (NAPA) nanophotonic platforms, the presence of a wide array of cyclic oligohexoses was discovered in the root nodules with degrees of polymerization in the 2 ≤ n ≤ 14 residue range. The spatial distributions of cyclic oligohexoses in the G. max nodules were established by NAPA-LDI-MSI. They appeared more concentrated at the edge of the infection zone or inner cortex and in the stem. At some locations, possibly in the vascular bundles surrounding the nodule and traversing the stem, the cyclic oligohexoses were especially abundant. At the same time, acyclic oligohexoses with 2 ≤ n ≤ 10 were also detected, and their distributions in the nodule sections were mapped. These linear or branching molecules were abundant in the infection zone, where the cyclic oligohexoses were less concentrated or absent.

January Meeting

Speaker: Kyle Anderson, National Institute of Standards and Technology

Topic: Advancements in methods and instrumentation for HDX-MS and LC-MS

Date: January 13, 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, January 10 if you will be attending the dinner.

Abstract: Subzero temperature chromatography minimizes loss of deuterium during HDX-MS analysis. We developed an HDX-MS chromatography apparatus capable of performing long analytical separations at -30 °C. The apparatus has precise temperature control with two enzyme column compartments held at independent temperatures and allows for rigorous cleaning in parallel to data acquisition to reduce instrument downtime and sample carryover. Methods for both reversed phase and HILIC analytical separations at subzero temperature were developed. HILIC methods developed greatly reduced operational backpressures for easier adoption using any HPLC pumps and enabled virtually water-free separations at subzero temperature. An HPLC pump delivering custom wash solutions to immobilized protease columns was added to replace conventional injections of common wash solutions, which greatly reduce sample carryover and cut necessary blank runs from 5 to 1 for an IgG1 digest. Additionally, methods for automated online removal of phospholipids from membrane proteins will be presented.

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Lightning Talk
Jacob Epstein (NIH/NIA/IRP)