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An Information System Enabling the Organization and Automatic Annotation of Proteomic Experiments with User-specific Proteins

Reputable Mentor II
Reputable Mentor II
Devin Lee Drew1, Daniel Lopez-Ferrer1, Emanuela Milani2, Jacob Poder3, Martin Damsbo3, Bernd Wollscheid2 and Andreas FR Hühmer1
International Hupo 2016
Purpose: Researchers studying engineered proteins or other proteins not defined in public sequence repositories wish to quantitatively analyze and annotate their results in the same manner as with publicly known sequences. We extend the capabilities of ProteinCenter to meet this need. Using a label-free differential analysis approach we analyze host proteins that interact with a wild type virus protein, and a mutant of the viral sequence that is postulated to disrupt host protein interactions. Methods: Demonstrate pre-release ProteinCenter and Proteome Discoverer workflow capabilities to meet the user’s engineered protein analysis needs. Apply the workflow to a functional protein interaction analysis where collaborators generated datasets for 4 culture replicates of a viral bait fusion protein and 4 replicates of a non-functional point mutant to test their hypotheses on viral protein interaction. Apply differential label free LC/MS/MS protein interactome analysis and analyze significant pathways in the functional and point mutant context. Results: Our workflow successfully processed two non-public engineered sequence proteins to achieve label-free interactor quantities, and annotated significant pathways that are likely relevant to the function of the viral protein

1Thermo Fisher Scientific; San Jose, United States; 2Institute of Molecular Systems Biology; ETH Zurich, Switzerland 3Thermo Fisher Scientific; Odense, Denmark
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Last update:
‎10-15-2021 07:07 AM
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