Each proteomics experiment needs to be optimized. To delineate the best experimental design, users are required to discuss their specific protocols with Sonja prior to the start of their experiments. We are set up to accommodate a lot of different protocols and will share our experience and advice with our users.
Common contaminations are keratins, salts and buffers, polyethylenglycols and detergents. If possible, they should be avoided. If this cannot be done, contaminants will have to be removed prior to liquid chromatography-mass spectrometry. Specific protocols depend on the nature of the contaminant and will be discussed case-by-case. General guidelines are published in Biomacromolecular Mass Spectrometry.
Our preferred in-gel digestion protocol can be found here.
Our preferred in-solution digestion protocol can be found here.
Our optimized LC-Orbitrap protocol can be found here.