How Does Orbitrap Mass Spectrometry Enable Efficient Bottom-Up Proteomics Analysis?
- Large-scale protein identification
- Protein quantification (e.g., label-free, TMT, iTRAQ)
- Post-translational modification (PTM) analysis
- Biomarker discovery
- High peptide complexity, demanding high detection sensitivity
- Vast data volume, requiring robust algorithms and high-performance mass spectrometers
- High-Throughput Platform: Identifies over 7,000 proteins in a single run
- Tailored Solutions: Customized to specific research objectives
- Comprehensive Bioinformatics Support: Provides differential expression, enrichment, and pathway analyses
- High-Quality Deliverables: Includes raw data, visualizations, and complete reports
Bottom-Up proteomics is achieved by enzymatic digestion of proteins into peptides, followed by mass spectrometry analysis for protein identification and quantification. Among the available mass spectrometry platforms, Orbitrap mass spectrometry, with its high resolution, high sensitivity, and outstanding mass accuracy, has become an indispensable tool in Bottom-Up proteomics. In this paper, we explore how Orbitrap mass spectrometry enables efficient Bottom-Up proteomics analysis and present the practical experience and technical strengths of MtoZ Biolabs in this field.
Current Status of Bottom-Up Proteomics Analysis
The Bottom-Up approach relies on the enzymatic digestion of complex protein mixtures, typically with trypsin, into peptides, which are subsequently analyzed by LC-MS/MS.
This approach is applicable to:
Nevertheless, Bottom-Up proteomics faces significant challenges, including:
Key Advantages of Orbitrap Mass Spectrometry: Precision, Sensitivity, and Throughput
The Orbitrap is an electrostatic mass analyzer with the following core characteristics:
1. Sub-ppm Mass Accuracy
Provides accuracy superior to quadrupole and ion trap mass spectrometers, supporting reliable peptide identification and reducing false positives.
2. High Resolution (up to 1,000,000)
Enables discrimination of peptides with closely related masses, particularly valuable for in-depth analysis of complex samples.
3. Excellent Dynamic Range and Sensitivity
Capable of detecting low-abundance peptides and accommodating samples with wide signal intensity variations.
4. Multiple Fragmentation Modes (e.g., HCD, ETD)
Offers flexibility for analyzing post-translational modifications such as phosphorylation and acetylation.
Based on Thermo Orbitrap Exploris and Fusion Lumos platforms, MtoZ Biolabs has established comprehensive Bottom-Up proteomics workflows tailored to diverse sample types and research objectives, ensuring broad proteome coverage, quantitative accuracy, and reproducibility.
Key Workflows in Bottom-Up Proteomics
1. Sample Preparation and Protein Digestion
Standardized protein extraction and trypsin digestion ensure data consistency. Using methods such as S-Trap or FASP, MtoZ Biolabs achieves high peptide recovery and low variability.
2. Chromatographic Separation: The Central Role of NanoLC
Nano-flow LC systems (e.g., EASY-nLC 1200) greatly enhance peptide separation and reduce signal suppression. Customized gradient programs optimize the balance between analysis time and separation performance.
3. Mass Spectrometry Detection: Leveraging Orbitrap Advantages
Data are acquired using Data-Dependent Acquisition (DDA) or Data-Independent Acquisition (DIA) modes, combined with predictive algorithms and spectral libraries to ensure high-confidence peptide identification and protein quantification.
4. Data Analysis: From Raw Signals to Biological Insights
Analysis is performed with mainstream software such as Proteome Discoverer, MaxQuant, and Spectronaut, complemented by customized QC pipelines to guarantee interpretability and biological relevance.
MtoZ Biolabs: Solutions
Key advantages of MtoZ Biolabs’ Bottom-Up proteomics:
Whether for biomarker discovery, elucidation of disease mechanisms, or drug target screening, MtoZ Biolabs delivers reliable data support. Bottom-Up proteomics provides a powerful framework for decoding protein functions and networks, and the integration of Orbitrap mass spectrometry makes this approach more precise, efficient, and robust. MtoZ Biolabs is committed to advancing life science research by delivering high-quality proteomics data in collaboration with the scientific community.
MtoZ Biolabs, an integrated chromatography and mass spectrometry (MS) services provider.
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