Dear Sir. Concerning your issue about how to separate/isolate solubilized protein from acid/base solvent. Selection of the appropriate combination of purification steps will depend on the properties of the target protein. If it is a known protein, such as an enzyme that has been isolated and characterized from another organism, a good starting point will be to try out some of the steps in the published procedure. Isolation and purification of a single protein from cells containing a mixture of thousands of unrelated proteins is achievable because of the remarkable variation in the physical and chemical attributes of proteins. Characteristics unique to each protein—amino acid composition, sequence, subunit structure, size, shape, net charge, isoelectric point, solubility, heat-stability, hydrophobicity, ligand/metal binding properties and post-translational modifications—can be exploited in formulation of a strategy for purification. Based on these properties a combination of various methods, listed below, can be used for separation of cellular proteins. The isolation and separation of proteins is carried out by different methods such as Precipitation, Chromatography and Centrifugation Size, shape. For more details you can see the following below links may help you in your analysis:

http://www.fgsc.net/neurosporaprotocols/How%20to%20isolate%20proteins%20final.pdf

Thanks

Dea Irvan:

Did you think about Solid Phase Extraction?

Preparative Chromatography might be also a good idea, as Isam said.

Best Regards,

Auréa Andrade-Eiroa

Thank you for your consideration Sir Isam. But I'm not searching for a specific protein. I just want to know the profile (composition) of the amino acids. So the problem is just how could I remove the basic solvent because basic solvent is the only solvent which can solubilize the silk I could afford. But when I tried to separate and check the availability of the amino acids by TLC method, the basic properties of the solvent damaged the plate, so I couldn't check the amino acids.

And thank you very much for the sources you gave! It was really helpful for my work.