AccelerOme Automated Sample Preparation Platform

Importance of the Topic

Proteomics sample preparation is a foundational step that directly impacts the quality and reliability of LC-MS analyses.
Manual protocols are often time-consuming, error-prone, and challenging to standardize across labs.
Automated solutions can enhance throughput, reproducibility, and data confidence in large-scale studies.

Objectives and Study Overview

This article presents the design and evaluation of the Thermo Scientific AccelerOme automated sample preparation platform.
The primary goals are to automate end-to-end workflows for both label-free and Tandem Mass Tag (TMT) multiplexing strategies, simplify method setup, and integrate seamlessly with Thermo Fisher’s Orbitrap mass spectrometry ecosystem.

Methodology and Instrumentation

The AccelerOme platform combines pre-packaged reagent kits with a liquid-handling system featuring:

• Automated dilution module with integrated syringe and solvent reservoirs
• On-line µSPE cartridges for sample clean-up
• Thermal mixer for controlled digestion
• In-line UV spectrophotometer for peptide quantitation and sample dilution
• Reagent tray with optional cooling for precise temperature control

Experiment Designer software guides users through study setup, randomization, metadata capture, and export to acquisition and processing tools.

Main Results and Discussion

Workflow evaluation demonstrated that the AccelerOme platform prepares 36 label-free samples in ~6.5 hours with just two user touchpoints, compared to frequent interventions in manual or competing automation methods.
Large-cat proteome analysis (144 samples from 18 animals) showed >93% fully tryptic peptides and <10% variance in protein and peptide group counts across biological replicates.
TMT multiplexing tests confirmed >97% labeling efficiency, accurate 2× fold-change detection, and low coefficient of variation (<11%) at both 30 µg and 60 µg sample inputs.

Benefits and Practical Applications

The platform delivers high reproducibility and throughput for diverse sample types including cells, tissues, biofluids, and purified proteins.
Key advantages include reduced hands-on time, standardized reagent performance, and seamless data integration with Orbitrap mass spectrometers and Proteome Discoverer software.
These capabilities support applications in biomarker discovery, clinical proteomics, and large-cohort studies.

Future Trends and Potential Applications

Continued advances may include integration of real-time process monitoring and AI-driven experimental design.
Expansion to multi-omic sample preparation workflows and remote operation could further enhance lab productivity.
Standardized automation platforms will likely drive broader adoption of high-throughput proteomics in translational research and quality control settings.

Conclusion

The AccelerOme automated sample preparation platform offers a robust solution to common bottlenecks in proteomics workflows.
By marrying validated reagent kits, intuitive software, and integrated instrumentation, it achieves fast, accurate, and highly reproducible results.
This streamlined approach empowers researchers to focus on data analysis and biological interpretation rather than manual processing.

Used Instrumentation

• Thermo Scientific AccelerOme Automated Sample Preparation Platform
• Orbitrap Eclipse Tribrid MS with FAIMS Pro Interface
• Orbitrap Exploris 480 with FAIMS Pro Interface
• Thermo Scientific Vanquish Neo UHPLC System
• EASY-Spray PepMap UHPLC Columns
• Thermo Scientific µPAC HPLC Columns
• Thermo Scientific Proteome Discoverer Software with CHIMERYS Search Engine