Challenges in Protein Annotation

Long lists of un-annotated proteins are no longer a sufficient end point for proteomics. Proteins need to be annotated with family names, functions, translational modifications and associated diseases. Many public and proprietary data sources are available to support this annotation including NCBI, Uni-Prot, Gene Ontology, OMIM and Unimod. However, these resources are often incompatible and for non-specialists they are often difficult to use, particularly when IDs and data formats change. When dealing with large protein lists it is generally impractical to annotate proteins manually one at a time due to time constraints and potential errors in data transfer.

Automated Protein Annotation Powered by InforSense

The protein annotation component of Proteome Discoverer is powered by InforSense workflows and delivers automated protein list annotation at the touch of a button. The scientist doesn’t need to be familiar with the data sources or formats and can focus on the scientific implications of the results. These workflows provide scientists with high value proteomics analysis and biological context without requiring them to make error prone manual queries or rely on bioinformatics support to write scripts. The automation saves considerable time for each experiment freeing up scientists’ time. The annotated lists can then be exported into Excel to be shared with colleagues. Experts at Thermo Fisher and InforSense have developed an initial set of annotation workflows enabling all users of Proteome Discoverer to benefit from these best practices. In addition the workflows are updated when data formats change and the changes are automatically propagated to every customer installation without requiring them to download and update the software.

Upgrade to a Full InforSense License

Customers of Proteome Discoverer can also upgrade to a full InforSense license enabling them to build their own workflows to integrate other internal experimental and clinical data to support biomarker discovery. The InforSense platform provides powerful capabilities to flexibly integrate, analyze and visualize clinical, sample and experimental data. Third party tools such as GeneGo, Ingenuity, and BioBase can also be automatically accessed to provide biological context to protein lists from metabolic pathways. InforSense also provides an online community for hundreds of users to share ideas and workflows. The InforSense CustomerHub site contains more than 500 example workflows that can be downloaded for free into an InforSense installation.

Proteome Discoverer customers have a number of options when upgrading to a full InforSense 5.0 license to support one or more of the following:

• Workflow creation and editing software and data analytics tools for use with Thermo Scientific workflows only.
• Unrestricted creation and editing of any workflow, including data analytics tools.
• Unrestricted creation and editing of any workflows, including data analytics tools, plus Software Developers Kit (SDK).