Characteristics of Proteomics Experiments Performed on the SYNAPT XS Q-ToF Mass Spectrometer

Importance of the Topic

Proteomic analysis demands high sensitivity and resolution to identify and quantify peptides and proteins in complex samples. Enhanced analytical platforms enable deeper coverage and more accurate measurements crucial for biological research, drug discovery, and quality control.

Objectives and Study Overview

This study evaluates the performance of the SYNAPT XS Q-ToF mass spectrometer in proteomic experiments, benchmarking its sensitivity, mass resolution and dynamic range against the previous SYNAPT G2-Si platform. Tryptic digests of E. coli and K562 human cell lysate at varying loads serve as test samples to assess identification rates under different instrument settings.

Methodology

• Sample Preparation: Tryptic digests of E. coli (MassPREP E. coli Digest Standard) and K562 cell lysate (Promega), injected at 25, 50, 100 and 150 ng.
• Chromatography: ACQUITY UPLC M-Class system with Symmetry C18 trap column (100 Å, 5 µm, 180 µm × 20 mm) and nanoEase MZ HSS T3 analytical column (100 Å, 1.8 µm, 75 µm × 250 mm). Gradient from 5% to 40% acetonitrile (0.1% formic acid) over 90 minutes.
• Acquisition: HDMSE data-independent acquisition mode alternating low and elevated collision energy, operated in both sensitivity and resolution optic modes.

Instrumentation

• SYNAPT XS Q-ToF Mass Spectrometer with NanoFlow ESI and PicoTip emitter.
• ACQUITY UPLC M-Class nanoscale chromatography system.
• Data processing with ProteinLynx Global SERVER and Progenesis QI for Proteomics.

Main Results and Discussion

• Signal Improvement: Approximately ten-fold higher signal intensity on the SYNAPT XS versus G2-Si at identical resolution settings.
• Protein Identifications: 966 proteins identified at 25 ng load on SYNAPT XS compared to requiring 100 ng on G2-Si for similar performance.
• Enhanced Coverage: 24% increase in protein identifications in K562 lysate with SYNAPT XS.
• Dynamic Range: Detection spanning four orders of magnitude in peptide abundance.
• Mass Accuracy: High precursor mass accuracy maintained in sensitivity mode.

Benefits and Practical Applications

The optimized sensitivity and resolution of the SYNAPT XS platform enable proteomic analyses with limited sample amounts, improving detection of low-abundance peptides. Enhanced throughput and data quality support applications in biomarker discovery, quality control, and comprehensive profiling of complex biological samples.

Future Trends and Opportunities

• Integration of advanced ion mobility separation to resolve isomeric species.
• Expansion of single-cell proteomics with ultra-low sample requirements.
• Development of automated workflows and AI-driven data interpretation for high-throughput studies.
• Implementation in clinical and pharmaceutical research for deeper proteome coverage.

Conclusion

The SYNAPT XS mass spectrometer, paired with nanoscale UPLC, delivers significant improvements in sensitivity, resolution and dynamic range compared to earlier Q-ToF platforms. These advances translate into higher protein and peptide identification rates from minimal sample loads, offering valuable capabilities for cutting-edge proteomic research.

References

No formal literature references were provided; instrument and standard specifications are based on Waters Corporation technical documentation.