What Is PeptiQuant Onco?
PeptiQuant Onco is a targeted proteomics platform that provides assays for the absolute quantification of up to 1,250 cancer-associated protein variants and their wild-type counterparts. Built on liquid chromatography–multiple reaction or parallel reaction monitoring mass spectrometry (LC-MRM, PRM/MS), each assay combines optimized target peptides with 13C- and 15N-labeled internal standards, enabling reliable and reproducible measurement of wild-type and variant protein expression (mutation rate) to support precision oncology research.
Supported by Genome Québec and Genome Canada
Our Mission
Knowing that understanding mutation-driven protein expression is essential for biomarker discovery and targeted therapy development, we enable researchers to study and identify cancer-associated protein and protein variants by providing scalable, quantitative measurements at the protein level.
The Challenge
Quantifying protein variants reliably is difficult for several reasons:
- Variant detection: Mutant proteins can differ from near-identical wild-type counterparts by as little as a single residue, demanding highly specific assays.
- Absolute quantification: True absolute quantification requires robust internal standards and carefully optimized workflows.
- Scalable assay development: Selecting suitable peptide targets and optimizing assays is complex, which has historically limited how many variants can be measured at once.
Key Innovation: Variant-Specific Peptide Selection
At the core of the platform is a proprietary bioinformatics pipeline used to generate and evaluate proteogenotypic peptides from both variant (mutant) and wild-type protein sequences, allowing us to select only the highest-confidence targets for each. Automating this selection is what makes specific, reliable quantification possible at scale.
Technologies & Methods
Targeted mass spectrometry
- MRM (Multiple Reaction Monitoring): Sensitive, reproducible quantification of predefined peptides on triple-quadrupole instruments.
- PRM (Parallel Reaction Monitoring): High-resolution analysis with enhanced specificity for wild-type and variant detection.
- Optimized assays: Transitions and instrument parameters tuned to each mutation and paired wild-type target.
Assay Features
High-confidence quantification at scale
- Synthetic and well-characterized stable isotope (13C/15N)-labeled peptides serve as internal standards for absolute quantification. Mutation-specific designs target clinically and biologically relevant variants.
- A spike-in strategy using defined light-to-heavy ratios enables sensitive and precise detection of low-abundance variants.
- Validated for linearity, sensitivity, and repeatability following NIH CPTAC guidelines.
- Multiplex capability across hundreds of mutant and wild-type protein pairs in a single LC-MS run.
- Flexible formats: predefined or fully customizable target panels.
Research Applications
Team & Acknowledgments
Principal Investigators
Dr. Christoph Borchers, PhD
McGill University
Dr. René Zahedi, PhD
University of Manitoba
Dr. Yassene Mohammed, PhD
Leiden University Medical Center
Core Scientific Team
Vincent R. Richard, PhD · Pallab Bhowmick, PhD · Constantinos Blidjios, MSc · Foroughsadat Absar, MSc · Timon Geib, PhD · Laleh E. Ghahnavieh, MSc · Pradyumn Maheshwari, MSc · Ruhi Jaiswal, MSc · Claudia Gaither, PhD · Robert Popp, PhD
Development Team
A multidisciplinary team of proteomics scientists, bioinformaticians, and software engineers.
Funding & Support
Funded through the Genomic Applications Partnership Program (GAPP), with support from Genome Québec and Genome Canada.
Industry Partners
MRM Proteomics (MRMP) · Agilent Technologies
How to Cite
If you use PeptiQuant Onco in your research, please cite:
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