Hello Mayur,
it depends on how you can prepare your protein complexes. Is your organism sequenced? If so, you could copurify your unknown proteins and analyze them by mass spectrometry. A prerequisite for this is that you have a data base for identification and of course the possibility to run your samples on a mass spectrometer.
Good luck!
Hi there,
If your protein complex is pure enough MS is definitely the more convenient method for protein identification.
Can you provide more information about your investigation? For a laboratory experiment, is the protein complex pure, the components intact, and non-covalent? Are you dealing with a mixture of various complexes since you write the word proteins in the plural?
Are you doing an in silico analysis or a survey and want to know if any known proteins are associated with other proteins that you want to find? If a protein of a particular species is known then likely databases or the literature will describe with what it can associate.
Are you referring to a known class of proteins but not a specific one and want to find out if it is binding a protein ligand or binding other subunits such as with enzymes and receptors?
Perhaps you are asking how to detect the formation of a complex once you mix a known protein with a mixture of unknown proteins; for example, Biacore, native gel, ultracentrifugation, pull downs, SEC, etc.?
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