Here are the basic protocols we use to prepare samples and generate data:
- Cell Fractionation [PDF] - A protocol for preparing cytosolic, particulate, and secreted fractions from adherent cells in culture.
- SDS-PAGE & in-gel digestion [PDF] - this protocol outlines how to run and cut the gel, in-gel digest, and extract peptides for LC-MS/MS analysis.
After LC-MS/MS analysis, the data must be searched (e.g., with SEQUEST/BioWorks/MASCOT) and filtered with DTASelect (link 1 link 2). Subsequently, you can use the PROTOMAP scripts to generate peptographs from your data:
Please don't hesitate to contact us with questions. We've made every effort to make this process clear and straightfoward, but the diversity of MS instrumentation, software, and methodology makes it difficult to anticipate problems that people might encounter.
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