Methods for computer-assisted isolation of proteins

A computer-assisted method for selecting and directing the isolation of one or more proteins present in a two-dimensional array, comprising:

• a purification step, wherein a biological sample is treated by selectively depleting the sample of one or more proteins;
• a first separation step following the purification step, wherein a plurality of proteins in the treated sample are separated according to a first physical or chemical property to form a one-dimensional array of proteins;
• a second separation step, wherein the one-dimensional array of proteins is separated according to a second physical or chemical property to form the two-dimensional array;
• imaging the two-dimensional array or a replica thereof to generate a computer-readable output comprising, for each of a plurality of proteins detected in the two-dimensional array, a pair of x,y coordinates and a signal value;
• processing the output in at least one computer to select one or more of the detected proteins in accordance with previously ordained or operator-specified criteria;
• and
• generating machine-readable instructions that direct a robotic device to isolate at least one of the selected proteins from the two-dimensional array.