Mass Spectrometry & Protein Identification


The Alberta Proteomics and Mass Spectrometry Facility (APM) currently operated by the Department of Biochemistry, is located in the Katz building on UA North Campus. The facility provides a range of mass spectrometry and proteomic services, including protein identification and molecular weight determination. The business model includes in-house analysis, as well as outsourced analysis.

Users of the APM Facility

In the past 5 years, there have been 110 University of Alberta users and 37 off campus users of the facility.

I. Sample preparation

A. Quantitative global proteomics

Quantitative global proteomics is used to determine the content of proteomes. It is most often used to detect and report differences between cell populations treated under various conditions. Proteins are isolated and digested with trypsin to generate peptides for mass spectrometry identification.

B. Affinity purification (e.g. BioID)
This assay will identify proteins in close proximity to a protein of interest (bait) within the cell. The bait is tagged with an abortive BirA that adds a biotin moiety to proteins in near proximity. The biotinylated proteins are then captured with streptavidin beads and identified by mass spectrometry. We can perform affinity purification from cell pellets by lysing the cells, purifying the biotinylated proteins using streptavidin-coated magnetic beads, and digesting the protein into peptides in preparation for mass spectrometry analysis. All of this is done on a magnetic beads purification system (two Kingfisher Duo are available, one a 4C and one a RT).

II. Mass spectrometry analysis

A. Discovery analysis - Data-Dependent Acquisition (DDA)

We offer a range of mass spectrometry analyses on high-resolution, high-sensitivity mass spectrometers. The first step in mass spectrometry-based proteomics analysis is the identification of proteins within the sample through discovery analysis using an approach termed "data-dependent acquisition". If desired, we also offer additional services to quantify the relevant amount of proteins within samples using either comprehensive or targeted approaches.

B. Comprehensive quantitative analysis - Data-Independent Acquisition (DIA)
For projects where discovery proteomics has been successful and there is a desire to quantify changes in protein composition under different conditions, we will perform relative quantitative analysis. Unlabeled digested protein samples will be analyzed using a comprehensive quantification method (DIA) that determines the relative intensity for all peptides above a signal-to-noise threshold within the mixture.

C. Data analysis

For customers who wish for more detailed data analysis, we offer extended data analysis from our mass spectrometry specialists. Please contact us to discuss your project.



For bulk discount orders, Please contact Jack Moore.