Computer-assisted isolation and characterization of proteins

A computer-assisted method for isolating one or more selected proteins present in a two-dimensional array prepared by two-dimensional electrophoresis in a polyacrylamide gel, the method comprising:

• (a) imaging the two-dimensional array or a replica thereof with a first device to generate a computer-readable output;
• (b) processing the output in at least one computer to select a protein for isolation;
• (c) generating machine-readable instructions that direct a second device to remove a portion of the gel containing the selected protein;
• and
• (d) after generating the instructions, transferring the gel to a second device and isolating the selected protein with the second device in accordance with the machine-readable instructions by removing a portion of the polyacrylamide gel containing the selected protein.

A computer-assisted method for isolating one or more selected proteins present in a two-dimensional array prepared by two-dimensional electrophoresis in a polyacrylamide gel, the method comprising:

• (a) imaging the two-dimensional array or a replica thereof with a first device to generate a computer-readable output;
• (b) processing the output in at least one computer to select a plurality of proteins for isolation;
• (c) generating a set of machine-readable instructions that direct a second device to isolate a plurality of selected proteins from the two-dimensional array;
• and
• (d) isolating a selected protein with the second device in accordance with the machine-readable instructions by removing a portion of the polyacrylamide gel containing the selected protein.

A computer-assisted method for isolating one or more selected proteins present in a two-dimensional array prepared by two-dimensional electrophoresis in a polyacrylamide gel, the method comprising:

• (a) imaging the two-dimensional array or a replica thereof with a first device to generate a computer-readable output;
• (b) processing the output in at least one computer to select a protein for isolation;
• (c) generating machine-readable instructions that direct a second device to isolate the selected protein from the two-dimensional array;
• and
• (d) isolating the selected protein with the second device in accordance with the machine-readable instructions by removing a portion of the polyacrylamide gel containing the selected protein, wherein step (b) comprises comparing proteins detected in a plurality of gels by (1) correcting for variation or distortion in running of the gels by using exogenous standards, followed by (2) matching correlate proteins detected in the plurality of gels.

A computer-assisted method for isolating one or more selected proteins present in a two-dimensional array prepared by two-dimensional electrophoresis in a polyacrylamide gel, the method comprising:

• (a) imaging the two-dimensional array or a replica thereof with a first device to generate a computer-readable output;
• (b) processing the output in at least one computer to select a protein for isolation;
• (c) generating machine-readable instructions that direct a second device to isolate the selected protein from the two-dimensional array;
• and
• (d) isolating the selected protein with the second device in accordance with the machine-readable instructions by removing a portion of the polyacrylamide gel containing the selected protein, wherein the gel is archived following step (a) and prior to step (d).

A computer-assisted method for isolating one or more selected proteins present in a two-dimensional array prepared by two-dimensional electrophoresis in a polyacrylamide gel, the method comprising:

• (a) imaging the two-dimensional array or a replica thereof with a first device to generate a computer-readable output;
• (b) processing the output in at least one computer to select a protein for isolation;
• (c) generating machine-readable instructions that direct a second device to isolate the selected protein from the two-dimensional array;
• (d) isolating the selected protein with the second device in accordance with the machine-readable instructions by removing a portion of the polyacrylamide gel containing the selected protein;
• and
• (e) use of a laboratory information management system (LIMS) that tracks laboratory samples and associated data.

A computer-assisted method for isolating one or more selected proteins present in a two-dimensional array prepared by two-dimensional electrophoresis in a polyacrylamide gel, the method comprising:

• (a) imaging a replica of the two-dimensional array with a first device to generate a computer-readable output;
• (b) processing the output in at least one computer to select a protein for isolation;
• (c) generating machine-readable instructions that direct a second device to isolate the selected protein from the two-dimensional array;
• and
• (d) isolating the selected protein with the second device in accordance with the machine-readable instructions by removing a portion of the polyacrylamide gel containing the selected protein.

A computer-assisted method for isolating one or more selected proteins present in a two-dimensional array prepared by two-dimensional electrophoresis in a polyacrylamide gel, the method comprising:

• (a) imaging the two-dimensional array or a replica thereof with a first device to generate a computer-readable output;
• (b) processing the output in at least one computer to select a protein for isolation;
• (c) generating machine-readable instructions that direct a second device to isolate the selected protein from the two-dimensional array;
• and
• (d) isolating the selected protein with the second device in accordance with the machine-readable instructions by removing a portion of the polyacrylamide gel containing the selected protein, wherein the polyacrylamide gel is covalently bonded to a generally planar solid support such that the gel has two-dimensional spatial stability, and the support is substantially non-interfering with respect to detection of a detectable label carried by the proteins.

A computer-assisted method for isolating one or more selected proteins present in a two-dimensional array prepared by two-dimensional electrophoresis in a polyacrylamide gel, the method comprising:

• (a) imaging the two-dimensional array or a replica thereof with a first device to generate a computer-readable output;
• (b) processing the output in at least one computer to select a protein for isolation;
• (c) generating machine-readable instructions that direct a second device to isolate the selected protein from the two-dimensional array;
• and
• (d) isolating the selected protein with the second device in accordance with the machine-readable instructions by removing a portion of the polyacrylamide gel containing the selected protein, wherein the machine-readable instructions are generated by computer-mediated analysis of a plurality of imaged gels.

A method for studying proteins separated into an array contained in a gel fixed to a support, the method comprising:

• (a) imaging the array of proteins with a first device;
• (b) selecting one or more members of the array for removal;
• and
• (c) removing those portions of the gel that contain the selected members of the array by means of a second device under remote computer control, the second device comprising an excision component capable of performing x and y movements, wherein the second device is physically separate from the first device.

A method for studying proteins separated into an array contained in a polyacrylamide gel, the method comprising:

• (a) imaging the array of proteins with a first device;
• (b) selecting one or more members of the array for removal;
• and
• (c) removing those portions of the gel that contain the selected members of the array by means of a second device under remote computer control, the second device comprising an excision component capable of performing x and y movements, wherein the gel is covalently bonded to a generally planar solid support.

A method for studying proteins separated into an array contained in a gel fixed to a support, the method comprising:

• (a) imaging the array of proteins with a first device;
• (b) selecting one or more members of the array for removal;
• (c) removing those portions of the gel that contain the selected members of the array by means of a second device under remote computer control, the second device comprising an excision component capable of performing x and y movements;
• and
• (d) using a computer system to track sample information and data from analysis of the sample.

A method for studying proteins separated into an array contained in a gel fixed to a support, the method comprising:

• (a) imaging the array of proteins with a first device;
• (b) selecting one or more members of the array for removal;
• and
• (c) removing those portions of the gel that contain the selected members of the array by means of a second device under remote computer control, the second device comprising an excision component capable of performing x and y movements, wherein the one or more members of the array are selected by computer-mediated analysis of a plurality of imaged gels.

A computer-based method that comprises the following steps:

• selecting a protein for isolation by processing output generated by a first device upon imaging a two-dimensional array of proteins present in a polyacrylamide gel;
• generating machine-readable instructions that direct a second device to isolate the selected protein from the two-dimensional array by removing a portion of the polyacrylamide gel containing the selected protein;
• and
• using a laboratory information management system (LIMS) that tracks laboratory samples and associated data.

A computer-readable medium comprising instructions for causing a computer to perform the following steps:

• selecting a protein for isolation by processing output generated by a first device upon imaging a two-dimensional array of proteins present in a polyacrylamide gel;
• generating machine-readable instructions that direct a second device to isolate the selected protein from the two-dimensional array by removing a portion of the polyacrylamide gel containing the selected protein;
• and
• using a laboratory information management system (LIMS) that tracks laboratory samples and associated data.

A computer comprising a program for performing the following steps:

• selecting a protein for isolation by processing output generated by a first device upon imaging a two-dimensional array of proteins present in a polyacrylamide gel;
• generating machine-readable instructions that direct a second device to isolate the selected protein from the two-dimensional array by removing a portion of the polyacrylamide gel containing the selected protein;
• and
• using a laboratory information management system (LIMS) that tracks laboratory samples and associated data.

A computer-assisted method for isolating one or more select ed proteins present in a two-dimensional array prepared by two-dimensional electrophoresis in a polyacrylamide gel, the method comprising:

• (a) imaging the two-dimensional array or a replica thereof with a first device to generate a computer-readable output;
• (b) processing the output in at least one computer to select a protein for isolation;
• (c) generating machine-readable instructions that direct a second device to isolate the selected protein from the two-dimensional array;
• and
• (d) isolating the selected protein with the second device in accordance with the machine-readable instructions by removing a portion of the polyacrylamide gel containing the selected protein, wherein the second device comprises a locating mechanism for defined location of the gel.