Large Scale Targeted Proteomics Platform

The Proteomics platform at the McGill Genome Centre enables large-scale high-throughput, quantitative analysis of proteins across a wide range of biological samples. Using both immunoassay- and aptamer-based and aptamer-based technologies, we support studies in biomarker discovery, disease mechanism research, and therapeutic development. The system offers a suite of complementary profiling platforms - each optimized for different levels of protein coverage, throughput, and sample requirements. Researchers can select targeted or exploratory approaches, depending on their study design. Projects are supported by dedicated project managers and integrated with bioinformatics pipelines for both standard and custom analyses.

“High-plex proteomics now lets us detect subtle shifts in protein expression - exactly what’s needed for early biomarker discovery and precision medicine.”

Pouria Jandaghi

Common Applications

Biomarker discovery

For disease diagnosis, prognosis, and treatment response

Drug Target Validation, Mechanisms-Of-Action Studies, and Patient Stratification

Clinical Cohort Profiling

Across disease areas including oncology, cardiometabolic, and neurodegenerative conditions

Multi-Omics Integration

With genomic and transcriptomic data to generate comprehensive molecular insights

Olink Proteomics solutions at the McGill Genome Centre in Montreal, Quebec

Olink Proteomics
(PEA-Based)

  • Certified Gold-Level Core Facility

  • Explore HT: 5,416 proteins; high-throughput profiling across all major pathways

  • Reveal: ~1,000 immune- and inflammation-focused proteins; streamlined NGS workflow

  • Explore 384: ~370 proteins across cardiometabolism, neurology, oncology

  • Target 96 / 48: Panel-based profiling of 92 (relative quantification) or 45 (absolute quantification) proteins, including cytokines and immune markers

  • Flex: Custom 21-plex panels with absolute or relative quantification

SomaLogic solutions at the McGill Genome Centre in Montreal, Quebec

SomaLogic SomaScan®
(Aptamer-Based)

  • SomaScan 11K Assay: ~11,000 proteins; broad discovery applications

  • SomaScan 7K Assay: Balanced depth and throughput

  • Custom / Disease-Specific Panels: Focused profiling in oncology, neurology, cardiovascular, and more

Illumina solutions at the McGill Genome Centre in Montreal, Quebec

Illumina Protein Prep (IPP)
(Aptamer-Based)

  • ~9,500 protein targets quantified by NGS

  • Fully automated workflow with ~2.5-day turnaround

  • Compatible with DRAGEN Protein Quantification and Connected Multiomics platforms

Platform deliverables

Olink Proteomics (PEA-Based)

    • CSV file containing NPX (Normalized Protein eXpression) values in log2 scale

    • For Target 48 panel, includes NPX and absolute quantification

    • Includes internal and external control metrics

    • Reports intra-run CV, inter-run CV, and total-run CV

    • Lists biomarkers and samples flagged by QC criteria

    • Requested volume: approximately 55 µL of plasma or serum

    • Only 10 µL is used for analysis

    • Remaining sample is returned

    • Extra volume supports possible reruns and ensures accurate pipetting with liquid handlers

SomaLogic SomaScan (Aptamer-Based)

    • Delivered as ADAT files (tab-delimited ASCII format)

    • Includes flags for hybridization and dilution scale factors

    • Calibrated against reference standards

    • Contains LOD/LOQ values and intra-assay CV

    • Requested volume: approximately 110 µL

    • Only 55 µL is used for analysis

    • Excess sample is returned

    • Additional volume requested for potential reruns and pipetting consistency

llumina Protein Prep (Aptamer-Based)

    • ADAT file with normalized protein counts generated via DRAGEN Protein Quantification

    • Delivered as part of the DRAGEN workflow

    • Includes intra-run CV, inter-run CV, and total-run CV

    • Requested volume: approximately 110 µL

    • Only 55 µL is used for analysis

    • Remaining sample is returned

    • Extra volume supports reruns and precision pipetting with liquid handlers

Integrated Support and Data Analysis

All proteomics platforms include standard data processing and quality control reporting, as described above.

For projects requiring advanced data interpretation—such as pathway analysis, integrative multi-omic comparisons, or custom statistical workflows - additional bioinformatics support is available through the Canadian Centre for Computational Genomics (C3G). These services are not included in the standard deliverables and must be requested separately.

Spatial Proteomics

For protein profiling within intact tissue architecture, we offer high-resolution spatial technologies such as the NanoString GeoMx DSP and CosMx SMI. These platforms enable spatially resolved protein expression from FFPE and fresh-frozen tissues, with cellular or subcellular resolution. (See Spatial Genomics and Multiomics)

Nanostring Bruker GeoMx at the McGill Genome Centre in Montreal, Quebec
Nanostring Bruker CosMx Spatial Molecular Image at the McGill Genome Centre in Montreal, Quebec