Comparison of Label-Free Protein Quantification in Saliva: Fusion Lumos vs. TimsTOF Pro2

Label-Free Protein Quantification in Saliva Fusion Lumos vs. TimsTOF Pro2

Comparison of Label-Free Protein Quantification in Saliva: Fusion Lumos vs. TimsTOF Pro2

This comparison of Fusion Lumos and TimsTOF Pro2 for label free protein quantification in saliva samples focuses on key metrics: sensitivity, resolution, dynamic range, speed, and data quality.

Overview of Instruments

• Fusion Lumos: An Orbitrap-based mass spectrometer. It is known for accurate mass measurements and high sensitivity. It handles complex samples well, generating detailed spectra.
• TimsTOF Pro2: Uses Trapped Ion Mobility Spectrometry (TIMS) with Time-of-Flight (TOF). It has fast acquisition, deep proteome coverage, and enhanced ion separation.

Key Metrics Comparison

1. Sensitivity
   • Fusion Lumos: Great at detecting low-abundance proteins with high accuracy. It’s well-suited for profiling saliva’s diverse protein content.
   • TimsTOF Pro2: Offers even higher sensitivity, thanks to PASEF (Parallel Accumulation Serial Fragmentation). It often detects more low-abundance proteins, covering a wider range.
2. Speed
   • Fusion Lumos: Delivers high-quality data, but it’s slower. This can limit the number of spectra collected.
   • TimsTOF Pro2: Faster acquisition due to PASEF. It collects more data points in the same timeframe, improving analysis of dynamic samples like saliva.
3. Dynamic Range
   • Fusion Lumos: Has a broad dynamic range, distinguishing between high- and low-abundance proteins.
   • TimsTOF Pro2: Offers a similar range, with ion mobility separation that increases accuracy in complex samples.
4. Resolution
   • Fusion Lumos: Very high resolution, providing precise mass measurements.
   • TimsTOF Pro2: High resolution through TOF and TIMS. Ion mobility boosts separation, though its mass accuracy can be slightly lower.
5. Proteome Coverage
   • Fusion Lumos: Provides good coverage, especially with longer gradients.
   • TimsTOF Pro2: Detects a broader range of proteins faster, making it effective for capturing low-abundance proteins.
6. Data Analysis
   • Fusion Lumos: Uses established software for precise quantification. It’s reliable for traditional label-free methods.
   • TimsTOF Pro2: Compatible with platforms like MaxQuant and Peaks. PASEF data enhances clarity, aiding in quantification.

Real-Life Example: Saliva Study

In a real-life test, eight saliva samples were analyzed. Each sample contained 100 µg of protein, prepared with the S-TRAP 96-well format.

Fusion Lumos Workflow

• Amount: 1.5 µg per sample.
• Setup: Thermo Vanquish Neo nano UPLC with a 50 cm C18 column.
• Method: Eluted peptides over 110 minutes with an 8–100% ACN gradient.

TimsTOF Pro2 Workflow

• Amount: 0.4 µg per sample.
• Setup: EVOSEP ONE with a 10 cm C18 column.
• Method: Used PASEF for fast and detailed analysis.

Results

• TimsTOF Pro2 found around 2x more peptides than Fusion Lumos. The PASEF acquisition and ion mobility boosted sensitivity and coverage.
• Fusion Lumos provided high-resolution, accurate data—ideal for in-depth profiling.

Conclusion

• TimsTOF Pro2 excels in sensitivity, speed, and broad proteome coverage, making it great for complex samples.
• Fusion Lumos offers detailed and accurate results, perfect for comprehensive studies.

For more information or inquiries about our proteomics services, please visit AxisPharm Proteomics Services.

Ref:

Lau WW, Hardt M, Zhang YH, Freire M, Ruhl S. The Human Salivary Proteome Wiki: A Community-Driven Research Platform. J Dent Res. 2021 Dec;100(13):1510-1519.