Single cell and immunopeptidomics explorations on Orbitrap Astral MS

This presentation showcases advanced applications of the Thermo Scientific Orbitrap Astral MS coupled with the Thermo Scientific Vanquish Neo HPLS system for single-cell proteomics and immunopeptidomics, two fields requiring extreme analytical sensitivity. The speakers describe a fully optimized end-to-end workflow, from microfluidic single-cell sorting and low-loss sample preparation to high-performance LC-MS acquisition and centralized data processing. In single-cell proteomics, method and column optimizations enabled routine identification of over 5,000 proteins from single HeLa cells, with robust reproducibility, and successful application to challenging real samples such as fixed T cells and patient-derived B cells. Inter-laboratory studies further demonstrated high robustness, throughput, and reproducibility across sites. The second part focuses on immunopeptidomics, detailing LC-MS fine-tuning using robust Micropac columns and optimized MS parameters to overcome challenges such as peptide co-elution and low-abundance variants. These improvements enabled deep immunopeptidome coverage from very low input material, supporting translational and clinical research applications

Learning points:

• Robust single-cell proteomics workflows can achieve >5,000 protein IDs with high reproducibility
• Optimized LC-MS methods and Micropac columns greatly improve robustness and sensitivity for low-input samples
• Immunopeptidomics benefits significantly from tailored MS settings, enabling deep coverage from limited clinical material

Who should attend?

• Scientists working in single-cell proteomics and ultra-low-input workflows
• Researchers focused on immunopeptidomics, antigen presentation, or cancer immunology
• Analytical and translational teams seeking robust, high-throughput LC-MS solutions for complex biological samples

This webinar is a recording from the Omics innovations for the biopharmaceutical industry seminar on December 11, 2025 in Strasbourg.

Cannot attend on February 19? Please register anyway to automatically receive access to the recording.

Presenter: Farida Salimova (Doctoral Student Specializing in MS-based Proteomics, Institut Pluridisciplinaire Hubert Curien - CNRS)

Presenter: Jeewan Babu Rijal (Post Doctoral researcher, Institut Pluridisciplinaire Hubert Curien - CNRS)