Lecture
From Single Cells to Deep Proteomes: Streamlining the Workflow with an End-to-End Omics Engine
- at -
- ICM Saal 2
- Type: Lecture
Lecture description
A. Seth, S. Cosson, D. Hartlmayr, G. Tourniaire and T. Nümm
While mass spectrometers increase in sensitivity rapidly, micro-scale proteomics, incl.
single cell proteomics and spatial proteomics is still compromised by the cumulative loss of proteomic depth due to poor sample preparation efficiency (mainly surface adsorption, evaporation, and suboptimal lysis).
To address this, we present an automated, next-generation workflow prioritizing reproducibility through nanoliter-scale sample preparation. At its core, a gentle, imagebased acoustic isolation technology ensures cell integrity and single cell resolution, enabling direct correlation of morphological features - such as cell size, shape, granularity, and fluorescence - with MS-profiles, while excluding doublets and debris
upstream.
Beyond isolation, the platform’s open architecture enables sample preparation with unmatched versatility, from high-density mini-array generation to miniaturized liquid handling, fully compatible with both label-free and multiplexed single cell proteomics strategies, remaining entirely automated and streamlined.
We present here two case studies extending this workflow to emerging applications. First, in spatial proteomics, standardized FFPE tissue processing reduces preparation to 2.5 hours, enabling consistent high-resolution maps (>3,000 proteins/region, CVs <15%) and exceeding 100 high-quality spatial proteomes per day, as demonstrated by the team of Fabian Coscia. Second, we extend our workflow to single 3D biological models. Using morphology-based isolation of individual pancreatic organoids, we demonstrate proteomics profiling at single-organoid resolution, opening new avenues for mechanistic insights in drug and toxicity testing and personalized medicine.
Together, these results position combined image-based cell isolation and proteomics nanoliter-scale sample preparation as the missing link between instrument sensitivity and biological discovery at the single-cell level.
While mass spectrometers increase in sensitivity rapidly, micro-scale proteomics, incl.
single cell proteomics and spatial proteomics is still compromised by the cumulative loss of proteomic depth due to poor sample preparation efficiency (mainly surface adsorption, evaporation, and suboptimal lysis).
To address this, we present an automated, next-generation workflow prioritizing reproducibility through nanoliter-scale sample preparation. At its core, a gentle, imagebased acoustic isolation technology ensures cell integrity and single cell resolution, enabling direct correlation of morphological features - such as cell size, shape, granularity, and fluorescence - with MS-profiles, while excluding doublets and debris
upstream.
Beyond isolation, the platform’s open architecture enables sample preparation with unmatched versatility, from high-density mini-array generation to miniaturized liquid handling, fully compatible with both label-free and multiplexed single cell proteomics strategies, remaining entirely automated and streamlined.
We present here two case studies extending this workflow to emerging applications. First, in spatial proteomics, standardized FFPE tissue processing reduces preparation to 2.5 hours, enabling consistent high-resolution maps (>3,000 proteins/region, CVs <15%) and exceeding 100 high-quality spatial proteomes per day, as demonstrated by the team of Fabian Coscia. Second, we extend our workflow to single 3D biological models. Using morphology-based isolation of individual pancreatic organoids, we demonstrate proteomics profiling at single-organoid resolution, opening new avenues for mechanistic insights in drug and toxicity testing and personalized medicine.
Together, these results position combined image-based cell isolation and proteomics nanoliter-scale sample preparation as the missing link between instrument sensitivity and biological discovery at the single-cell level.
