A method for performing a real-time assay, the method comprising the steps of: (a) moving a sample of a product containing polypeptides to a polypeptide-binding column via a first holding coil; (b) binding the polypeptides in the sample to the polypeptide binding column, thereby separating the polypeptides in the sample from a remainder of the sample; (c) moving an elution buffer solution from a buffer source to the polypeptide binding column, via the first holding coil, and through a second holding coil downstream of the polypeptide binding column, thereby eluting polypeptides bound to the polypeptide binding column and moving an elution/polypeptide mixture comprising the elution buffer solution and the eluted polypeptides to the second holding coil; (d) moving the elution/polypeptide mixture from the second holding coil to a reaction chamber; (e) incubating the polypeptides in the elution/polypeptide mixture in the reaction chamber, resulting in denatured polypeptides; (f) moving a reducing reagent that cleaves disulfide bond crosslinks to the reaction chamber via the first holding coil after (e); (g) incubating the denatured polypeptides with the reducing reagent in the reaction chamber, resulting in denatured and reduced polypeptides; (h) moving an alkylating reagent that alkylates sulfhydryls to the reaction chamber after (g); (i) incubating the denatured and reduced polypeptides with the alkylating reagent in the reaction chamber, thereby alkylating the denatured and reduced polypeptides; (j) moving the denatured, reduced, and alkylated polypeptides, the elution buffer solution, the reducing reagent, and the alkylating reagent from the reaction chamber to a desalting column via the first holding coil, the desalting column equilibrated with a proteolysis buffer; (k) applying the denatured, reduced, and alkylated polypeptides to the desalting column, thereby separating the denatured, reduced, and alkylated polypeptides from the reducing and alkylating reagents, and resulting in desalted polypeptides; (l) moving the desalted polypeptides to a proteolytic enzyme column downstream of the desalting column; (m) digesting the desalted polypeptides in the proteolytic enzyme column, resulting in digested polypeptides; and (n) moving the digested polypeptides to an analytical device for analysis of the digested polypeptides. (a) moving a sample of a product containing polypeptides to a polypeptide-binding column via a first holding coil; (b) binding the polypeptides in the sample to the polypeptide binding column, thereby separating the polypeptides in the sample from a remainder of the sample; (c) moving an elution buffer solution from a buffer source to the polypeptide binding column, via the first holding coil, and through a second holding coil downstream of the polypeptide binding column, thereby eluting polypeptides bound to the polypeptide binding column and moving an elution/polypeptide mixture comprising the elution buffer solution and the eluted polypeptides to the second holding coil; (d) moving the elution/polypeptide mixture from the second holding coil to a reaction chamber; (e) incubating the polypeptides in the elution/polypeptide mixture in the reaction chamber, resulting in denatured polypeptides; (f) moving a reducing reagent that cleaves disulfide bond crosslinks to the reaction chamber via the first holding coil after (e); (g) incubating the denatured polypeptides with the reducing reagent in the reaction chamber, resulting in denatured and reduced polypeptides; (h) moving an alkylating reagent that alkylates sulfhydryls to the reaction chamber after (g); (i) incubating the denatured and reduced polypeptides with the alkylating reagent in the reaction chamber, thereby alkylating the denatured and reduced polypeptides; (j) moving the denatured, reduced, and alkylated polypeptides, the elution buffer solution, the reducing reagent, and the alkylating reagent from the reaction chamber to a desalting column via the first holding coil, the desalting column equilibrated with a proteolysis buffer; (k) applying the denatured, reduced, and alkylated polypeptides to the desalting column, thereby separating the denatured, reduced, and alkylated polypeptides from the reducing and alkylating reagents, and resulting in desalted polypeptides; (l) moving the desalted polypeptides to a proteolytic enzyme column downstream of the desalting column; (m) digesting the desalted polypeptides in the proteolytic enzyme column, resulting in digested polypeptides; and (n) moving the digested polypeptides to an analytical device for analysis of the digested polypeptides.