To complement a bit my former recommendation, A280 depends only (mainly) on the presence of aromatic amino acids, and that does not change after treatment with trypsin. Absorbance can change a bit due to the change of aromatic side chain environment caused by structural reorganizations due to proteolysis, but that is negligible when approximately quantifying protein.

Bradford assay depends on non-specific interactions of dyes and proteins, and that is dependent on the structure of the protein itself in non easily predictable ways. BCA quantification and other methods relying on reduction of metal ions are highly sensitive to the presence of other chemicals, to the conditions of the reaction and to the amino acid composition of the specific proteins.

In my experience, I should not rely on Bradford assay when protein structure changes in a major way, and I would be very careful with redox assays. For a rapid quantification, A280 should give the best results.

Best luck with your experiments!

Perhaps a BCA assay would be appropriate for your application.

mass spectrometry allows differentiation between the isotopologues and with the known amount of the internal standard the content of the analyte can be estimated .Used an AQUA peptide as standard.

you can run a SDS-PAGE with an additional lane with known conc of the protein. that should do your job.

The problm is : Is there a way to quantify it after the treatment of trypsin?

Look for Qubit fluorimtric quantitation in Google. This solves your problema

Very simple and offers a quanitative solution. Determine the absorbance of the protein in solution at 280nm prior to and after trypsin treatment. I suppose the trypsin treament does not significantly contribute to the A280 in the mixture but if it does it may be accounted for. This solution requires that the subject protein is not lost in mixture of junk.

Absolutely agree with the reply from James. That would solve your problem easily.

To complement a bit my former recommendation, A280 depends only (mainly) on the presence of aromatic amino acids, and that does not change after treatment with trypsin. Absorbance can change a bit due to the change of aromatic side chain environment caused by structural reorganizations due to proteolysis, but that is negligible when approximately quantifying protein.

Bradford assay depends on non-specific interactions of dyes and proteins, and that is dependent on the structure of the protein itself in non easily predictable ways. BCA quantification and other methods relying on reduction of metal ions are highly sensitive to the presence of other chemicals, to the conditions of the reaction and to the amino acid composition of the specific proteins.

In my experience, I should not rely on Bradford assay when protein structure changes in a major way, and I would be very careful with redox assays. For a rapid quantification, A280 should give the best results.

Best luck with your experiments!

I would not trust Bradford as it depends on the protein (ex: BSA Biuret 9.7 mg/mL/ Lowry 8.4 mg/mL and Bradford 21.1 mg/mL!!!). Abs at 280 nm is quite OK and do not depend on environment. I would go for it provided there is no big absorbance from additives into the protein solution.

If you have access to an amino acid analyzer this would be the most accurate way to quantify your peptide (or protein) samples due to it's high precision and tolerance towards contaminants.

As I undersood You are not interested in quantitative analyze of protein but rather You would like to know if traces of protein digested with trypsine has remained. If yes, it is possible to analyze amino acids in GC-MS (after the apropriate hydrolize of sample) and derivatization them with isopropanol / acetylchloride (carboxyl groups) and N-acetylation with PFA. The exact method is described in FEMS Microbiology Ecology 25 (1998), 229-240. We used that method to check purity of murein and LPS.