In our Proteomics Laboratory, we work with our collaborators on the discovery of proteins by applying global proteomics approaches. We inject samples using a nanoLC Dionex 3000, and analyze them with UV/Vis detection or through a variety of mass spectrometers, including a TSQ triple quadrupole mass spectrometer or Orbitrap mass spectrometer. Proteins are identified using the mass of signature peptide fragments via Mascot Distiller and PEAKS software packages.
We identify common mammalian proteins using published libraries such as SwissProt as well as plant proteins through databases of plants or plant families. PEAKS software is used to perform semi-quantitative analysis of proteins. When differential protein expression is determined, we conduct multivariate statistical analysis and construct heat maps or other visualization methods to demonstrate the results.
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