Frequently Asked Questions

General

Proteomics & Mass Spectrometry

The Pan-Canadian Proteomics Centre (PCPC) is a Genome Canada funded network of four of Canada’s leading proteomics facilities performing proteomics technology development and providing research support to Canadian and international academic and industrial users.

What is the PCPC?

The PCPC is composed of 4 nodes; the University of Victoria (UVic)-Genome BC Proteomics Centre, the University of British Columbia Proteomics Core Facility, The Hospital for Sick Children (SickKids) SPARC BioCentre and the Jewish General Hospital Proteomic Centre at McGill University. In addition, the PCPC has numerous technology development and translation partnerships with facilities around the world including Island Health (Vancouver Island’s health authority, BC, Canada), The Metabolomics Innovation Centre (TMIC), Leibniz Institute for Analytical Sciences (ISAS-Dortmund in Germany), The Centre for Phenogenomics (TCP in Toronto, Canada), the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and many others. Members of the PCPC are always interested in talking with potential partners for additional collaborative projects.

Who are the members of the PCPC?

The PCPC is funded through Genome Canada and Genome British Columbia, as one of Canada’s ‘Genomics Technology Platforms’ (GTP) (project code 264PRO). In addition, the PCPC is supported by the Canadian Foundation for Innovation (CFI), as well as support from the host institutions at the University of Victoria, McGill & the Jewish General Hospital in Montreal, the University of British Columbia and The Hospital for Sick Children.

How is the PCPC supported?

Access to the services available at all four of the PCPC nodes is available to any Canadian or international researcher from academia or industry.

Who can access the services available at the PCPC?

The PCPC offers services in quantitative proteomics, structural proteomics, functional proteomics, and bioinformatics. Our close relationships with clinical diagnostic laboratories in hospitals across Canada also enables us to support the development and translation of proteomic assays and techniques to be implemented into clinical settings. Please visit our Services Page, or Contact any of the PCPC nodes if you would like more detail on specific services 

What services are available at the PCPC?

The PCPC performs novel technology development in all of our service areas, including targeted quantitative proteomics, development of new reagents and methods for structural proteomics and elucidating protein-protein interactions, new technologies for sample preparation for improved and novel targeted and untargeted analyses, development of new software tools for assay development and data analysis of proteomic and multi-omic data, and many more.

What types of technology development is undertaken at the PCPC?

The PCPC has performed thousands of projects in human health, agriculture, environment, and forestry. The PCPC nodes have access to Level 2 sample preparation facilities, and routinely work with most tissues, biofluids (e.g. plasma, serum, whole blood, cerebrospinal fluid, and others), cell culture, or environmental samples such as soil or water.

What type of samples can be analyzed at the PCPC?

PCPC members are happy to provide pre-project support including: project consultation, assistance with experimental design, and support with grant writing of proteomic sections. We can also work with you and your research team during and after your project, offering additional support such as bioinformatics services, instruction on third party data analysis tools, preparation of methods sections for manuscripts and figures, and working with your research team in the design of follow-on studies.

How can the PCPC help in moving your research forward?

Proteomics and Mass Spectrometry

Analogous to genomics, which is the large-scale study of genes and genomes, proteomics is the large-scale study of all of the proteins produced by living organisms. Proteomics can encompass a large range of techniques; however, members of the PCPC primarily use mass spectrometry based techniques for the quantitation and characterization of proteins. For more information please visit our Services page.

What is Proteomics?

Mass Spectrometry (MS for short) measures the mass-to-charge ratio of one or more molecules in a sample. Various MS analytical techniques can be used to determine the exact molecular weight of a molecule, provide information on the composition and structure of a compound, and can be used to quantitate compounds in simple or complex mixtures.

What is Mass Spectrometry?

Multiple Reaction Monitoring (MRM, also referred to as Selected Reaction monitoring (SRM)), is a specific and sensitive mass spectrometry technique to accurately quantitate proteins of interest. Using isotopically-labeled internal standards, this technique can be used for targeted, absolute quantitation of a large numbers of proteins in complex systems within a single liquid chromatography tandem mass spectrometry (LC-MS/MS) experiment.

What is MRM?

In a Hydrogen Deuterium Exchange (HDX) experiment, the exchangeable amide protons on the backbone of a protein are rapidly exchanged by deuterium atoms. By analyzing HDX samples on a mass spectrometer, the increased mass of the deuterium atoms can be used to accurately detect and quantitate the degree of exchange at specific sites throughout a protein. By performing these experiments over time (from 5 seconds up to several hours), it is possible to identify regions of the protein that are in defined secondary structures or have limited solvent accessibility (i.e. buried within the protein). This technique can be used to compare proteins from different batches, identify regions of a protein that become more protected when bound to a small molecule or when the protein forms a protein-protein complex, and can provide information on the secondary and tertiary structure of a protein to complement other protein structural techniques.

What is HDX?

Analysis of proteins by mass spectrometry, such as in an HDX experiment, can be performed using two different methodologies: “bottom-up” and “top-down” proteomics. In a bottom-up experiment, proteins are digested into peptides using specific proteases (e.g. trypsin), separated by liquid chromatography, and the peptides are analyzed on a mass spectrometer. The information collected on all of the peptides can then be aligned to the known amino acid sequence, providing high-resolution (often amino acid resolution) characterization of the protein of interest. Top-down proteomics does not require prior proteoylytic cleavage of the target protein; rather, the protein is fragmented in the mass spectrometer. Although there are limitations on the size of proteins that can be measured, top-down proteomics has the benefit of being able to identify the unique proteoforms and post-translational modifications (PTMs) on individual proteins. Members of the PCPC have also perfected a hybrid approach, termed “middle-down” proteomics, which uses limited proteolysis combined with top-down proteomics, to characterize larger proteins or protein complexes that are often too large for traditional “top-down” proteomics.

What is the difference between ‘bottom-up’ and ‘top-down’ proteomics?
 
 
 
 
 
 
 
 
 
 
 
 
 

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© Pan-Canadian Proteomic Centre 2019