Single-Cell Proteomics

Mass spectrometry (MS), the most unbiased technique for single-cell proteomics, facilitates the identification and quantification of thousands of proteins, proteoforms, and post-translational modifications (PTMs) in individual cells.

A successful single-cell proteomics workflow hinges on throughput, quantitation, sensitivity, and coverage. In collaboration with the scientific community, Thermo Fisher Scientific innovates solutions that enable comprehensive single-cell proteomics analysis, revealing the full spectrum of cellular diversity. Our recent advancement, the Thermo Scientific Orbitrap Astral Mass Spectrometer, provides the necessary sensitivity and throughput to analyze hundreds of cells per day from various cell populations, types, and states on an individual basis, which generates maximal insights into cell heterogeneity and rare cell types.

Thermo Scientific Orbitrap mass spectrometers are at the forefront of mass spectrometry technology, capable of accurately identifying and quantifying thousands of proteins with over five orders of linear dynamic range and tight coefficients of variation, even at the single-cell level. These instruments are highly sensitive, enabling precise detection of protein differences across individual cells and offering valuable insights into their biological states.

Accurate and precise quantitation

• Determination of the correct protein abundance in a cell
• Confidant and accurate quantitation of low-abundance proteins
• Reduced number of measurements needed to draw conclusions

High confidence with deep proteome coverage and data completeness

• 100s-1000s of proteins from a single cell
• Wide dynamic range to discover differentially expressed low-abundance proteins of biological significance
• Orbitrap based DIA single-cell proteomics workflow provides >99% data completeness
• TMT single-cell proteomics workflow is ideal for mapping small protein changes from low-level signals

High throughput for large number of cells to observe biological insight

• Provides statistical power to infer biological patterns

Robust platform and method

• Easy day-to-day platform operation for analyses of thousands of cells
• Automated sample prep for DIA and TMT single-cell proteomics workflows

"With the Orbitrap Astral mass spectrometer, we were able to double the throughput for single cells, while also increasing the number of proteins per cell by 50%. This means we start picking up key cellular decision making proteins like transcription factors, epigenetic regulators and kinases to better understand the biological heterogeneity of single cells."

— Erwin Schoof, Associate Professor, Department of Biotechnology and Biomedicine, Section for Protein Science and Biotherapeutics, Cell Diversity Lab, Technical University of Denmark

"With the Orbitrap Astral mass spectrometer we're pushing boundaries with a nearly lossless label free method. Our workflow reveals >5000 proteins and ~40,000 peptides per HeLa cell, setting new standards in SCP! The great depth enabled direct detection of PTMs in single cells, eliminating the need for prior enrichment. We've uncovered extensive phosphorylation and glycosylation in single-cell samples."

— Jesper Olsen,  Deputy Center Director, Professor, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen

"Thanks to Orbitrap MS and TMTpro technology, we can in principle multiplex 18 single cells at the same time. With advanced chromatography, this enables the possibility of running multiple 10,000-cell projects per instrument, per year, leading to real impactful biological insights across life science research."

— Erwin Schoof, Associate Professor, Department of Biotechnology and Biomedicine, Section for Protein Science and Biotherapeutics, Cell Diversity Lab, Technical University of Denmark

For single cell sorting, isolation, nanoliter dispensing and sample preparation for MS

cellenONE^® platform combines high accuracy single cell isolation and precision nanoliter reagent dispensing, allowing for miniaturization of single cell proteomics protocols and enabling automated sample preparation for label-free and TMT multiplexing experiments.

• Single-cell sorting, visualization and dispensing
• Any cell type
• Protein digestion for DIA based single-cell proteomics
• Protein digestion and labeling for TMT based single-cell proteomics

For single cell dispensing

The Uno Single Cell Dispenser is an automated benchtop instrument designed for ease of use, efficiency, and precision in single-cell workflows. Allows sample preparation for both label-free and TMT based single-cell experiments.

• Single cell isolation and dispensing
• Wide range of cells
• Protein digestion for DIA based single-cell proteomics
• Protein digestion and labeling for TMT based single-cell proteomics

For experiments that require thousands of cells to gain real biological insights

With an unprecedentedly low detection level, the Thermo Scientific Orbitrap Astral Mass Spectrometer accesses more proteins from a single cell than ever before. And with the ability to multiplex single cells at a higher throughput, hundreds of single cells can be quantitatively analyzed in a single day, allowing researchers to efficiently and reliably determine the heterogeneity of a cell’s biology, unlocking never-before-seen insights that can revolutionize research.

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Research level single-cell proteomics system for accurate and precise quantitation

TMT multiplexing workflow provides the highest throughput for single-cell proteomics. The SPS MS3 method on the Thermo Scientific Orbitrap Ascend MultiOmics Tribrid Mass Spectrometer provides the highest accuracy and precision for TMT-based quantitation throughout wide concentration range. The real-time search acquisition strategy on this platform improves the ratio accuracy for TMT reporter ions, boosts sensitivity and increases total quantified peptides. The Orbitrap Ascend Tribrid MS is also excellent for single-cell proteomics DIA workflow for those researchers want that capability as well.

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Entry level single-cell proteomics system

The single-cell proteomics DIA workflow on the Thermo Scientific Orbitrap Exploris 480 Mass Spectrometer offers research laboratories accurate and precise quantitation, with deep proteome coverage and data completeness. For laboratories wanting to perform TMT based single-cell proteomics workflow, the Orbitrap Exploris 480 MS is versatile enough to handle that as well. The TurboTMT intelligent acquisition available on the mass spectrometer speeds up spectral acquisition for TMT 18plex experiments, thereby providing the same throughput for single-cell proteomics experiments that Thermo Scientific Orbitrap Hybrid mass spectrometers provide.

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System for targeting subset of the proteome in a single cell

Thermo Scientific Stellar MS excels in quantifying proteins at low abundance with high sensitivity and technical precision, making it an advantageous for targeting subset of the proteome in a single cell or developing single cell assays.

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Vanquish Neo UHPLC System

The Thermo Scientific Vanquish Neo UHPLC System is designed for high-sensitivity LC-MS applications such as single-cell proteomics. It flawlessly integrates with industry-leading Thermo Scientific mass spectrometry portfolio and ESI sources.

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50 cm µPAC Neo HPLC Columns

The 50 cm µPAC Neo HPLC Columns are designed to get maximum proteome coverage from single-cell to sub nanogram protein digest samples.

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FAIMS Pro Duo Interface

The Thermo Scientific FAIMS Pro Duo interface provides enhanced selectivity and sensitivity down to at a low nanogram to single-cell level allowing for deeper proteome coverage.

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TMTpro 18-plex Label Reagents

TMTpro 18-plex Label Reagents are designed for the next level of sample multiplexing. TMTpro 18-plex enables multiplexing up to 18 cells, enabling greater throughput for protein identification and quantitative analysis by mass spectrometry.

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Proteome Discoverer Software

Thermo Scientific Proteome Discoverer Software offers predefined workflows to support both MS2 and MS3-based TMT quantification. The CHIMERYS™ intelligent search algorithm by MSAID available within Proteome Discoverer software enables processing of DIA data.

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