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Quantitative Proteomics

The quantitative proteomics group specializes in the determination of "absolute" protein quantitation in biofluids (i.e., results in terms of concentrations rather than fold-changes).  The Proteomics Centre has developed multiplexed assays multiple reaction monitoring (MRM) for five human biological samples, including plasma, dried blood spots, saliva, urine and cerebrospinal fluid (CSF).  These highly multiplexed MRM assays are being used by the proteomics community to discover and validate potential biomarkers. We have recently expanded this area to include assays for mice, the most commonly used animal model for health research, with the goal of creating 3,000 protein assays in 20 different tissue types.  We also use our patented iMALDI technique to develop clinical diagnostic assays which will be implemented in the clinical chemistry lab at the Jewish General Hospital in Montreal, including a targeted assay for Akt kinases, important targets for therapeutic selection in cancer treatment.

Embryonic Stem Cells


Metabolomics is the youngest family member of functional genomics, and is devoted to the identification and quantitation of as many small-molecule compounds (i.e., metabolites) as possible in biological systems. Metabolomics facilitates the detection of changes in metabolite concentrations in response to genetic modifications and environmental perturbations. The major focus of our in-house metabolomics technology development is the design and validation of new and innovative analytical methods including UPLC/MRM-MS, UPLC/ultrahigh-resolution Fourier transform (FT) MS, chromatography-free FTMS, and MALDI Imaging of tissues.  These allow a more comprehensive and in-depth determination of metabolites and lipids in human blood, urine, cells, and tissues, as well as the quantitation of compounds such as naphthenic acids in environmental samples and various metabolites in plants. We are the University of Victoria node of the Genome Canada-funded TMIC (The Metabolomics Innovation Centre ( and we provide both targeted and untargeted metabolomics services on a cost-recovery or collaborative basis, for domestic and international researchers, and industrial clients.

Targeted Metabolomics (Targeted Metabolite Analysis and Metabolic Profiling)

  • Amino acids, biogenic amines, and intermediates of amino acid metabolism and urine cycle

  • Metabolites involved in central carbon metabolism (glycolysis, gluconeogenesis, pentose phosphate pathway, the TCA cycle) --- sugar phosphates, nucleosides, enzyme cofactors, D/L-2-hydroxyglutarate, etc.. 

  • Low-molecular weight aldoses and ketoses 

  • Bile acids, dihydroxy cholestenoic acid (DHCA), trihydroxy cholestanoic acid (THCA), and >40 potentially unknown [cp1] bile acids- Bioactive carboxylates, hydroxyl- and keto-carboxylates

  • Short-, medium- and long-chain fatty acids; acyl-carnitines; acetyl-coenzymes; acyl-glycines

  • Selected steroid hormones and sterols involved in cholesterol and steroid anabolism and catabolism: cortisol, 6β-OH cortisol, DHEA, DHEA sulphate, estrogens and androgens, etc. 

  • Oxidative stress biomarkers in relation to lipid, protein and DNA/RNA peroxidation 

  • Neurotransmitters

  • Thyroid hormones

  • Vitamin D and metabolites

  • Polyphenols

  • Naphthenic acids (>400)

Untargeted Metabolomics (Metabolic Fingerprinting and Metabolic Footprinting)

  • UPLC-FTMS and UPLC-MS/MS, in combination with multiple RP, ion-pairing and HILIC methods and multivariate statistics

  • Direct infusion-FTICR MS


Structural Proteomics

The Proteomics Centre is continuously developing and improving complementary MS-based techniques that allow the analysis of increasingly large proteins, including disease-related misfolded protein aggregates, as well as protein therapeutics and biosimilars.  We are now extending these methods to protein-protein interaction studies in vivo, on the proteome-wide scale.  The Proteomics Centre is continuing its pioneering work in structural proteomics by developing new methods for hydrogen-deuterium exchange (HDX) so that it can be used for larger proteins, and by developing new crosslinking reagents and software for more complete protein structural characterization.  Recently, our research efforts have resulted in software which allows the use of these experimental results as constraints for improved molecular modeling.

These new methods and techniques facilitate many types of biological research, including studies of drug targets and the development of new drugs.  We are also developing improved methods for the characterization of post-translational modifications (PTMs).



We focus on the automation of proteomics data analysis and the development of data processing algorithms and workflows.  Our research interests are:

  • Novel methods for data analysis in targeted MRM proteomics

  • Automatic MRM assay design

  • Building libraries and databases for use in targeted proteomics approaches

  • Advanced data analysis and visualization in bottom-up and top-down proteomics

  • eScience applications in proteomics

  • Scaling up data analysis pipelines and automatic data processing workflows

  • Distributed computing applications in proteomics


For more information, please visit our bioinformatics Website at:


Group leader: Yassene Mohammed, PhD

Yassene Mohammed, PhD

Pallab Bhowmick, PhD