MS Protocols

For shotgun proteomics sample preparation typically starts with the extraction of proteins from cells or tissues. Proteins are then reduced, alkylated and digested to short peptides for analysis in the mass spectrometer. To identify interaction partners or posttranslational modifications, proteins or peptides might be enriched by immunoprecipitation. Quantitative studies often involve also metabolic or chemical labeling of the proteins or peptides.

Digestion of the proteins can be carried out in solution, in filter devices (e.g. FASP), in gel slices or on the surface of magnetic beads (e.g. SP3). Depending on your application, different protocols may be appropriate. On this websites we provide basic protocols. Please contact us already during the planning of your experiment. Together we can find the the most suitable protocol for your application.

Select your application
MS analysis of a single protein
AP-MS: Identification of interaction partner
Global proteome analysis
PTM Analysis

Additional protocols
Desalting of peptides (stage tipping), Peptide fractionation, Common buffers and solution, Ordering information, Maintenance protocols.

We are constantly trying to improve the protocols provided on these websites. Please let us know if you have any suggestions or corrections.