Proteomics Services

As of September 2009, the Génome Québec Proteomics Platform delivers its results through Nanuq, a web application which supports all services provided by the McGill University and Génome Québec Innovation Centre. The integration of the proteomics platform within the Nanuq interface opens the door to new types of services which combine both genomic and proteomic data accessible at one location.

The Nanuq application includes automated data processing as well as a storage pipeline that captures and store key MS parameters such as ion intensity and retention time for downstream data mining analysis. In addition, since raw data are permanently archived, it is possible to perform new database queries using different search parameters, including the screening for post-translational modifications such as phosphorylation, newly annotated protein databases, or different taxonomies.

Peptides and proteins are first identified using Mascot (matrixscience.com). The mascot search output is subsequently loaded into Scaffold (www.proteomesoftware.com), a tool that interprets mass spectrometry data. Scaffold validates initial proteomics data by running an independent implementation of PeptideProphetT and ProteinProphet® which are two Bayesian statistical algorithms developed at the Institute for Systems Biology. This ensures a very low percentage of false positive identification in datasets.

Two main types of reports are provided to users:

Peptide Report

A simple report that provides key information on the identity of the protein and supportive proteomics evidence (including peptide sequences and % coverage). Additional information is available upon request.

Scaffold Report

this report is viewed through the free Scaffold viewer available at www.proteomesoftware.com. Briefly this type of report offers a high-level overview of proteomics results which facilitates the analysis of large amounts of data. The software also offers some possibilities of statistical analyses of quantitative proteomics data based on spectral counting.

Finally high level of biological annotation can be provided if Uniprot databases are used for the search.