Discovery Proteomics
Projects will be assigned to this workflow when the unbiased identification and quantification of thousands of proteins in each sample is required to meet project goals. The general workflow includes lysis or homogenization in the case of cell or tissue samples, or depletion of abundant proteins in the case of plasma or serum samples, followed by trypsin digestion of total extracted protein.
Each sample is typically fractionated at the protein level by SDS-PAGE prior to in-gel digestion, or at the peptide level by HPLC following digestion in solution, with each fraction analyzed by LC-MS/MS using the instrument and parameters best suited to the objectives of the project. The sample preparation pipeline is organized to be robust and reproducible, as well as sufficiently adaptable so as to meet individual project requirements.
Bioinformatics
Analysis of all data acquired through both the Discovery and Targeted Proteomics described above will be performed by the Bioinformatics workflow. Importantly, our sophisticated bioinformatics analyses are included for each sample analysis performed by the resource. This includes performing a database search using one of the search algorithms against a specific protein database, quality control, normalization, differential expression analysis, preparing data for publication and upload to a publicly available repository.
The output of this workflow is publication quality data specific for the user needs. User data is stored in Google cloud-based workspace and comes with custom designed tools that allow users to interact with their data from anywhere.
