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SYM-A1 : New Technologies in Proteomics I



Yue Xuan
Speaker
Yue Xuan   CV
Affiliation
Thermo Fisher Scientific in Bremen, Germany
Title
Rethink what is possible
Abstract

Science isn’t limited by ideas but by the ability to realize them. That is the inspiration behind the novel technology of the Thermo Scientific Orbitrap Astral Mass Spectrometer: to redefine what is possible for discovery and translational research. Faster throughput, deeper coverage, and higher sensitivity with accurate and precise quantitation to empower you to accomplish your aspirations.
Powered by the synergy of a high-resolution quadrupole mass filter, the Thermo Scientific™ Orbitrap™ mass analyzer and the novel Thermo Scientific™ Astral™ mass analyzer, this revolutionary new instrument achieves unsurpassed performance and experimental flexibility. The combination of the three mass analyzers enables the rapid acquisition of exceptional quality high resolution accurate mass (HRAM) spectra with high sensitivity and dynamic range. The new performance characteristics of the Thermo Scientific™ Orbitrap™ Astral™ mass spectrometer make it ideally suited for accurate and precise quantitation at an unprecedented depth of coverage and throughput for samples from single cells to body fluids to bulk tissues.
In this study, we evaluate the performance of the Orbitrap Astral mass spectrometer for single cell proteomics analysis, whole proteome analysis, and plasma proteomics. In addition, to address the large-cohort analysis needs, we consistently profile approximately 9000 proteins from human cell lines and around 800 proteins from undepleted plasma across multiple instruments over a period of more than 10 consecutive days in a 24/7 operating mode, demonstrating that the Orbitrap Astral mass platform can sensitively, robustly and reproducibly analyze the proteome of thousands of samples in a high-throughput manner.

 

Tae Hyun Yoon
Speaker
Tae Hyun Yoon   CV
Affiliation
Hanyang University
Title
Mass cytometry, or cytometry by time-of-flight (CyTOF) ; its principle, applications, and prospects in single cell proteomics
Abstract

Mass cytometry, also known as cytometry by time-of-flight (CyTOF), is a modern technique that enables multiparametric analysis of individual cells using numerous metal-tagged cellular markers with minimal signal overlap, thereby addressing the limitations in dimensionality faced by conventional flow cytometry in studies of phenotyping heterogeneous cellular systems and understanding complex biological pathways. This approach utilizes antibodies labeled with lanthanide metal isotope ions (with atomic weights between 75 and 209) to concurrently assess approximately 50 markers (both surface and intracellular proteins) at a single-cell level. As a novel technology with capability of multiparametric protein analysis at a single cell level, it enables a detailed exploration of cellular responses, with broad applications currently in progress in both clinical and basic research settings. This innovative technology offers potential applications across various biomedical research areas, including in-depth phenotyping of diverse cells, tracking cell differentiation and disease progression, creating detailed cell cycle profiles, examining variations in cytokine expression, and investigating signaling responses. In this presentation, drawing from four years of hands-on experience, I will explain the principles of single-cell mass cytometry, and its application in diverse clinical and basic research studies, discuss its future potential in single-cell proteomics.

 

Junho Park
Speaker
Junho Park   CV
Affiliation
CHA Future Medicine Research Institute
Title
Establishment of a universal label-free proteomic method for spatial proteomics
Abstract

Advancements in mass spectrometry (MS)-based proteomics has revolutionized the study of archived tissue slides, enabling observation of the proteome within regions of interest (ROI) and facilitating a deeper understanding of spatially distinct pathophysiology. However, the inherent challenge of limited protein amounts in tissue slides often compromises data quality, even with minimal sample loss. Consequently, the acquired proteomic information frequently falls short of investigating the biological context in many studies. To overcome this limitation, we have developed a label-free Data-Independent Acquisition (DIA)-based proteomic method, which minimizes sample loss through optimization of entire experimental procedures from sample preparation to MS analysis. Remarkably, utilizing 40 ng of peptide as a starting input of this procedure—equivalent to 200 cells—we quantified approximately 7000 proteins. Inspired by these results, we extended this method to analyze regions of interest (ROIs) as small as 0.25 mm2, encompassing an estimated 300 cells, isolated from formalin-fixed, paraffin-embedded (FFPE) breast cancer tissue using spatial laser-assisted cell sorting (SLACS). Analysis of over 2000 protein expressions, coupled with bioinformatics analyses, revealed heterogeneity within the tissue. The primary advantage of our proposed workflow is its universal applicability. This method enables in-depth proteomic analysis of sub-microscale pieces of tissue without necessitating expensive equipment frequently used in single-cell analysis. In conclusion, our study underscores the utility of an accessible proteomic framework in delineating the heterogeneity of molecular phenotypes across the tissue.