You can use the size exclusion method to analyse the trend in molecular weight reduction or run an electrophoresis gel. However the TNBS method o

r the free amino acid method is another way of determining the extent of cleavage of your hydrolysates. Good luck

The best method is to quantify alpha-amino nitrogen by a colorimetric method, it is increasing along the hydrolysis. See: Enzymatic hydrolysis and synthesis of soy protein to improve its amino acid composition and functional properties. J. Food Sci. 2000; 65(2): 246-253.

Determination of small peptides may be difficult on gel since you may have to select an appropriate %T and %C as well as buffers (tricine). Also the ability of peptides to stain by Coomassie Blue is strongly dependent on the concentration of basic residues in the sequence. Have you considered OPA method to determine available amine or LCMS? the OPA will only help you to quantify the rate of hydrolysis while MS will surely characterize the sequence. Thanks

To verify hydrolysis, the best is to quantify alpha-amino nitrogen. For studying the size of the produced peptides you can use gel filtration but it is better to use high performance liquid chromatography (HPLC). The information done by Anant Dave about electrophoresis of peptides is right, it is quite difficult.

You can also try to use RP-HPLC. If peaks correspondind to intect proteins and products of their proteolysis can be well separated it may be useful method. Retention times of short peptides (up to 15 amino acid residues) should be shorter than these of proteins.

If the goal is to verify the degree of hydrolysis, I feel there is no appropriate method which can suit for all the enzymes and substrates. However, pH stat, TNBS, formol titration, OPA method, determination of alpha amino nitrogen by cupric method (pope and stevens method), ninhydrin method are known well. All these methods one or another way quantify the alpha nitrogen (AAN). The ratio of AAN to the total protein nitrogen is expressed as degree of hydrolysis. I suggest that the no of total residues in substrate and hydrolysate can be calculated from the amino acid analysis, and then this ratio can be used to calculate the degree of hydrolysis.

If the goal is to visualize or determine the mass of peptides, peptides with 15 residues( may have 1500-2500 Da) may not be retained in the SDS gel even we increase the gel concentration. 2D gel may be the right choice.

Ionic cromatography. You can determine free aminoacidi and small peptides depending on the colums you use. No derivatization is needed.

The biuret method only determines proteins and is not a good idea. The simplest way in my view is to verify if the hydrolysed fragments are soluble in 0.6 M HClO4. If so, then the fragments have a maximum molecular weigt of about 1 kDa (about 10 amino acids)

The simplest way is via electrophoersis, which will show you whether your protein is being hydrolised (you would eventually see diifferent bands in your gel). With the right standard you would even know how long are your resulting peptides.

Gel electrophoresis is not easier that a colorimetric method! Additionally, electrophoresis of hydrolyzates gives bad resolution on the gel because the wide and diverse molecular weight molecules. I have done it once and again along my life.

Amino acid analyzer

Gel electrophoresis may serve for analysis of polypeptides. Short peptides are not retained in gel. 2D electrophoresis has the same limitation. Moreover 2D electrophoresis is complicated and time-consuming. Among electrophoretic methods capillary electrophoresis is used for both polypeptide and oligopeptide analysis.

Ana is asking for a method to detect peptides of 15-amino acids. It is not easy to see by gel electrophoresis. She needs high performance liquid chromatography (HPLC) or a similar method of column separation. If she determines alpha-amino nitrogen, it will be possible to know if the hydrolysis was enough in posterior runs. Probably she needs to conect the hydrolysis system to an ultrafiltration system because a major part of the protein remains without hydrolysis while a part is spliced to very small peptides. Therefore, it is necessary to remove the already hydrolyzed small peptides by ultrafiltration. It could be usable to know what kind of tools she has to work with.

Thank you everyone for your advice. I am trying to use low cost procedures so we are finally using a colorimetric assay to determine the hydrolysis. Thank you all again.

Bravo, Ana!