Vanquish Neo UHPLC System - Boost your proteomics sensitivity and throughput

Significance of the Topic

The complete characterization of the proteome underpins advances in disease diagnostics, drug discovery, and fundamental biology. Liquid chromatography–mass spectrometry (LC–MS) is the workhorse for bottom-up proteomics, but achieving both high sensitivity and high throughput requires careful optimization of flow regimes, column formats, and instrumentation. The Vanquish Neo UHPLC system addresses these challenges across nano-, capillary-, and micro-flow, enabling sensitive, robust, and reproducible analysis of complex peptide mixtures.

Objectives and Study Overview

This whitepaper surveys peer-reviewed research leveraging the Vanquish Neo platform. It is organized into two main application areas:

• Section 1: Nano- and capillary-flow LC-MS for enhanced sensitivity and deep proteome coverage when sample quantity is limited.
• Section 2: Micro-flow LC-MS for high-throughput profiling of large cohorts and clinical samples, balancing robustness and speed.

The review highlights key methodological innovations, performance benchmarks, and practical outcomes in diverse proteomics workflows.

Used Methodology and Instrumentation

Key elements of the workflows include:

• Thermo Scientific Vanquish Neo UHPLC system operating at pressures up to 1,500 bar with flow rates from 0.001 to 100 µL/min.
• Columns ranging from 50 µm I.D. nano-UHPLC columns (75 µm × 500–750 mm) to 1 mm I.D. micro-flow columns (150 mm length), including superficially porous (µPAC) and fully porous C18 formats.
• Orbitrap-based mass analyzers: Exploris, Fusion Lumos, and Q Exactive HF-X, configured for data-dependent (DDA), data-independent (DIA), and targeted acquisition modes.

Main Results and Discussion

Section 1 studies demonstrate that the Neo UHPLC system supports long columns and shallow gradients for single-shot analysis, yielding >7,000 protein identifications from HeLa digests with nano-flow rates (200–500 nL/min). Implementing rigorous washing protocols and micropillar array columns reduced carryover and increased peptide IDs by 60% for short gradients and low sample loads.

Section 2 work shows that micro-flow (50 µL/min) on 1 mm columns delivers robust performance over thousands of samples. Using TMT labeling, researchers quantified >9,000 proteins in 16 h and >30,000 phosphopeptides in 12 h, with >38,000 runs over two years without loss of sensitivity.

Across both regimes, improved chromatographic peak capacity (narrower peaks) correlates with increased sensitivity, reduced co-elution, and more efficient precursor selection in DDA and DIA workflows.

Benefits and Practical Applications

• Deep, sample-limited proteome profiling down to single-cell levels.
• High throughput both in direct-injection nano-flow and trap-and-elute formats (up to 100 samples/day at low-nano flow; 96 samples/day in micro-flow).
• Enhanced robustness and reproducibility for large clinical cohorts, biomarker discovery, and quality-control studies.

Future Trends and Possibilities

Ongoing developments include the integration of ultra-high-speed mass analyzers (e.g., Astral) for single-cell sensitivity, wider adoption of library-free DIA for comprehensive proteome coverage, and AI-driven data analysis pipelines. Further optimization of column chemistries and microfluidic automation may extend the platform to even smaller sample inputs and higher sample loads.

Conclusion

The Vanquish Neo UHPLC system offers a unified platform for proteomics, delivering both the sensitivity required for in-depth, sample-limited studies and the robustness needed for high-throughput clinical applications. By covering nano-, capillary-, and micro-flow regimes with the same fluidics and pressure capability, it simplifies method development and accelerates discovery across diverse research areas.

References

• Wilm M., Mann M. Analytical properties of the nanoelectrospray ionization source. Analytical Chemistry. 1996;68(1):1–8.
• Lenčo J., et al. Reversed-Phase Liquid Chromatography of Peptides for Bottom-Up Proteomics: A Tutorial. Journal of Proteome Research. 2022;21(12):2846–2892.
• Thermo Scientific. Fast, Sensitive, and Reproducible Nano- and Capillary-Flow LC–MS Methods for High-Throughput Proteome Profiling Using the Vanquish Neo UHPLC System Hyphenated with the Orbitrap Exploris 480 MS.
• Thermo Scientific. Ultra-Robust Micro-Flow LC–MS/MS for Targeted High-Throughput Peptide Quantification Using the Vanquish Neo UHPLC System.