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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.  

Embryonic Stem Cells


Metabolomics is the study on quantitative measurements of the dynamic multi-parametric metabolic responses to pathological, physiological stimuli or genetic modifications in biological systems, and has evolved as the small molecule counterpart of transcriptomics and proteomics. It is a system-wide approach for investigating in vivo metabolic profiles that will provide information on environmental perturbation, pharmacology, toxicology, disease and gene function to dissect the biological pathways that involve in these processes. Metabolomics research at the UVic-Genome BC Proteomics Centre is currently focused on developing and applying high-end mass spectrometry techniques including ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS), orthogonal quadruple time-of-flight mass spectrometry (Q-TOF MS) with the capability of ion mobility spectroscopy (IMS), and ultrahigh performance liquid chromatography (UPLC) to provide unbiased and high-throughput metabolic profiling of biofluid (plasma, serum, urine), cell culture, tissue and plant. To process and interpret the large volume of mass spectrometry data sets derived from metabolomic analyses, we also have developed and are being developing several customized software packages for streamlined and automatic data extraction, mining and integration. The processed data are saved in data formats that are amenable to the subsequent data visualization, statistics and multivariate analysis for metabolic biomarker discovery.

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 and Lipidomics 

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

MS Imaging

MS Imaging is a mass spectrometry-based technique that provides spatial localization in tissue sections of metabolites, lipids, and peptides. Tissue sections are placed onto a conductive glass slide, coated in matrix, and analyzed in a MALDI based MS with a spatial resolution of 1 to 100 microns. Our current research is focused on determining the effect of bacterial infection on the host tissue lipid profiles. 

MS Imaging review:

Mouse kidney.tiff

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