Qualitative analysis of proteins

A automated method for cleaving of a protein into polypeptides and recovering a product including the polypeptide, the method comprising:

• a) Providing a robotic liquid handler comprising a plurality of water swollen gel column beds each comprising at least one bound protease selected from the group consisting of trypsin;
• Glu-C;
• Lys-N;
• Lys-C;
• Asp-N;
• Arg-C;
• and chymotrypsin;
• b) Providing a sample including at least one optionally denatured protein in liquid buffer;
• c) Contacting the protein with the gel beds of step a), each gel bed configured to hold a solvent in contact with the gel bed and to allow the solvent to flow through the bed during a back and forth cycle of said solvent through said bed;
• d) Digesting the protein with back and forth flow cleaving the protein into polypeptides in less than 4 hours, and optionally diluting the sample;
• e) Adding an ion pairing reagent to the sample;
• f) Providing a reverse pipette tip column, and optional conditioning the column;
• g) Adsorbing polypeptides to the pipette tip column with back and forth flow, and optionally washing contaminants from the column;
• and
• h) Eluting polypeptides.