Hello, I would like to identify peptides bound to the particular protein by MS. Do you know how to separate these peptides from protein using method allowing further analysis by MS? This protein was purified by ion-exchange chromatography and size exclusion chromatography and peptides still occupy the binding site.
What are the sizes of peptides and protein. You can denature the system.
The size of the protein complex is about 160 kDa whilst the peptides have 10-15 aa.
Use an LC-MS method in which the protein is denatured by being diluted with an acidic mobile phase before injection. The peptides will dissociate and can then be analyzed by MS. If the protein tends to precipitate under these conditions, then pellet it in a centrifuge before injection so as not to clog the LC.
Dear Omar and Adam, thank you for suggestions. @Adam This is a membrane protein and therefore contains 0,05% LDAO. Do you think that this detergent can be a problem in LC-MS? Please suggest the composition of acidic mobile phase for this method, please.
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