SysQuan
Large-Scale Absolute Quantification for Human Tissue Samples and Cell Lines
Unlike traditional methods requiring expensive synthetic peptides for each target, SysQuan uses metabolically K6-labeled whole mouse tissues where proteins are uniformly labeled with heavy ¹³C₆-Lysine during growth. We've done the work of pre-quantifying thousands of proteins in mouse tissues using synthetic peptide standards—so you can simply run your human samples against our mouse tissue extracts and obtain fast, large-scale absolute quantification across the entire proteome.
Our Mission
SysQuan enables rapid absolute quantification of thousands of proteins in human samples using pre-quantified K6-labeled mouse tissues as internal standards, dramatically reducing cost and time compared to traditional methods.
Key Innovation: K6-SILAC Mouse Tissue Standards
SysQuan's database is built on K6-labeled SILAC mouse tissues (heavy-labeled with ¹³C₆-Lysine). These pre-quantified mouse standards are mixed with human samples (light/unlabeled) for fast absolute quantification. We develop optimized MRM and PRM assays to map the quantified mouse proteome onto human samples, replacing costly synthetic peptides and reducing costs by 100-fold.
Unlike traditional methods requiring expensive synthetic peptides for each target, SysQuan uses metabolically K6-labeled whole mouse tissues where proteins are uniformly labeled with heavy ¹³C₆-Lysine during growth. By mixing these pre-quantified heavy mouse standards with light human samples, we achieve absolute quantification across the entire proteome.
This technology enables large-scale analysis of human biological samples with consistent, reproducible results across laboratories. SysQuan accelerates drug discovery, disease understanding, and clinical applications of proteomics.
The Science Behind SysQuan
What is SysQuan?
SysQuan (Systematic Quantification) is a large-scale proteomics resource providing a comprehensive database of quantified mouse tissues (K6-labeled) and optimized MRM/PRM assays. This enables researchers to perform rapid, cost-effective absolute protein quantification in human samples using the pre-quantified mouse proteome as heavy internal standards.
The Challenge
Proteins are the functional molecules of life, and understanding their abundance and variation across tissues is crucial for:
- Disease Research: Identifying biomarkers and understanding disease mechanisms
- Drug Development: Validating therapeutic targets and predicting drug efficacy
- Systems Biology: Building comprehensive models of cellular function
- Precision Medicine: Tailoring treatments based on individual protein profiles
Our Approach
SysQuan combines cutting-edge mass spectrometry techniques with rigorous quality control to create a comprehensive protein quantification resource:
Discovery Proteomics
Data-Dependent Acquisition (DDA) for comprehensive peptide identification and spectral library generation
Targeted Assays
Optimized MRM and PRM-PASEF transitions for precise, sensitive quantification
SILAC Standards
Isotope-labeled internal standards for absolute quantification and quality control
Technologies & Methods
Mass Spectrometry Platforms
- DDA (Data-Dependent Acquisition): Comprehensive peptide identification and spectral library construction
- MRM (Multiple Reaction Monitoring): High-throughput targeted quantification on triple quadrupole instruments
- PRM-PASEF: Advanced parallel reaction monitoring with trapped ion mobility for enhanced specificity
K6-SILAC Mouse Tissue Standards
- K6 Metabolic Labeling: Mouse tissues grown with ¹³C₆-Lysine (K6) as the sole lysine source
- Whole-Proteome Heavy Standards: Every protein contains uniform heavy K6 labeling
- Pre-Quantified Standards: Mouse proteome quantified for use in human samples
- Incorporation Tracking: Precise measurement of K6 labeling efficiency (>95% typical)
- Quality Metrics: CV analysis, missed cleavages, and batch reproducibility
- Cost Efficiency: 100× cheaper than synthetic peptide standards
Key Innovation: Multi-Modal Integration
SysQuan uniquely integrates data from multiple MS platforms and acquisition modes, providing researchers with flexibility to choose the most appropriate method for their specific application while maintaining data consistency across platforms.
Database Features
Comprehensive Coverage
- Thousands of validated peptides
- Multiple K6-labeled mouse tissues
- Both discovery and targeted data
- Rich metadata and quality metrics
Quality Assurance
- Rigorous peptide validation
- Optimized transition selection
- Replicate consistency checks
- Batch-to-batch tracking
User-Friendly Access
- Intuitive search and filtering
- Interactive data visualization
- Multiple export formats (CSV, tables)
- API access for programmatic queries
Continuous Updates
- Regular data releases
- New tissue types added
- Method optimization
- Community feedback integration
Research Applications
How Can SysQuan Help Your Research?
Scientific Publication
Learn more about the methodology and validation of the SysQuan resource:
Read the PaperMolecular & Cellular Proteomics, 2025
Team & Acknowledgments
Principal Investigators
Dr. Christoph Borchers, PhD
Project Co-Leader, McGill University
Dr. René Zahedi, PhD
Project Co-Leader, University of Manitoba
Core Scientific Team
Dr. Timon Geib, PhD
Lead Scientist
Dr. Peter Kubiniok, PhD
Lead Developer - Platform Architecture & Implementation
Development Team
SysQuan is developed and maintained by a multidisciplinary team of proteomics scientists, bioinformaticians, and software engineers at McGill University and the University of Manitoba, dedicated to advancing quantitative proteomics research.
Funding & Support
SysQuan is funded through the Canadian Biotechnology Innovation and Commercialization Initiative (CBIC) with a total budget of $6.4 million CAD (2025-2029).
Industry Partners
In collaboration with:
- MRM Proteomics (MRMP) - Primary industry partner
- Agilent Technologies - Mass spectrometry instrumentation
- Bruker Corporation - Advanced MS platforms
- Evosep - High-throughput LC systems
Additional Acknowledgments
This project would not be possible without the support of the broader proteomics community, funding agencies, and collaborative research networks that have contributed samples, expertise, and feedback.
Data Sharing & Collaboration
We are committed to open science and data sharing. All data in SysQuan is freely available for research purposes. We welcome collaborations and feedback from the community.
How to Cite
If you use SysQuan in your research, please cite:
SysQuan: A Comprehensive Resource for Systematic Protein Quantification Across Human Tissues. Molecular & Cellular Proteomics, 2025. https://www.sciencedirect.com/science/article/pii/S1535947625000726
Get in Touch
Have questions, suggestions, or interested in collaboration? We'd love to hear from you!
SysQuan Database v1.0 | Last Updated: 2025 | Built by Quantivum Inc. (Peter Kubiniok, PhD)