Proteome analysis for characterization of up-and down-regulated proteins in biological samples
OwnerPeter Mose Larsen, Stephen J. Feyinventors
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Abstract
Methods and computer systems are provided for analyzing cell proteomes to characterize proteins that are up- or down-regulated under different conditions, such as under abnormal or compound treated conditions, including drug screening and testing, as well as proteins and encoding or complementary nucleic acids characterized using such methods and computer systems.
Claims55
A computer-implemented method for identifying or characterizing qualitative or quantitative changes in affected proteins and for distinguishing unaffected cells and proteins expressed by unaffected cells from affected cells and proteins expressed by said affected cells wherein said unaffected and/or affected cells have either been treated or immunologically or pathologically affected, in vitro or in vivo, and wherein said unaffected and/or affected cells are derived from a sample of a specific cell type, cell line, tissue or physiological sample, said sample subjected to two dimensional gel electrophoresis (2DGE) to provide a 2DGE gel comprising unaffected and/or affected proteins, said method comprising
- (1) capturing a new image of said electrophoresis gel containing at least one protein, wherein said new image contains an undetermined position and integrated optical density percentage (IOD%) corresponding to each said protein;
- (2) generating a master composite image which is used to analyze the new image, wherein the master composite image contains a plurality of master composite spots, each master composite spot being defined by at least an IOD% and a position;
- (3) generating a master composite spot data list, wherein the master composite spot data list comprises at least a position, an IOD%, a unique spot identifier, and the variability of the spot for the position and IOD%, for each of the plurality of master composite spots;
- (4) aligning the new image with the master composite image;
- (5) determining the position and IOD% of new image spots corresponding to proteins using the spot data information from the master composite image to guide the search for and identification of new image spots that have a position that is within a position tolerance of the position of the corresponding master composite spots and that have an IOD% that is within an IOD% tolerance of the IOD% of corresponding master composite spots to form a set of matched new image spots corresponding to unaffected proteins;
- (6) determining the position and IOD% of new image spots corresponding to proteins using the spot data information from the master composite image to guide the search for and identification of new image spots that have a position that is within a position tolerance of the position of the corresponding master composite spots but that have an IOD% that is outside the IOD% tolerance of the IOD% of corresponding master composite spots, to form a set of matched new image spots corresponding to affected proteins;
- and
- (7) searching the image outside of the set of matched new image spots to determine the position and IOD% of unidentified new image spots corresponding to proteins,
- wherein the spots detected in steps 6 and 7 represent affected proteins.
A computer-implemented method for identifying or characterizing qualitative or quantitative changes in affected proteins and for distinguishing unaffected cells and proteins expressed from said unaffected cells from affected cells and proteins expressed by said affected cells wherein said unaffected and/or affected cells have either been treated or immunologically or pathologically affected, in vitro or in vivo, and wherein said unaffected and/or affected cells are derived from a sample of a specific cell type, cell line, tissue or physiological sample, said sample subjected to two-dimensional gel electrophoresis (2DGE) to provide a 2DGE gel comprising said unaffected and/or affected proteins, said method comprising
- (1) capturing a new image of said electrophoresis gel containing at least one protein, wherein the new image contains a plurality of new image spots corresponding to at least one protein, each new image spot having an integrated optical density percentage (IOD%) and a position;
- (2) generating a master composite image which is used to analyze the new image, wherein the master composite image contains a plurality of master composite spots, each master composite spot being defined by at least an IOD% and a position;
- (3) generating a master composite spot data list, wherein the master composite spot data list comprises at least a position, an IOD%, a unique spot identifier, the variability of the spot for the position and IOD%, and a saturation value for each of the plurality of master composite spots;
- (4) aligning the new image with the master composite image, said aligning comprising (i) selecting a set of anchor points from the master composite spot data list, and (ii) detecting new image spots that have a position that is within a position tolerance of the position of corresponding anchor points and that have an IOD% that is within an IOD% tolerance of the IOD% of corresponding anchor points, and matching the detected new image spots to the corresponding anchor points to form a set of matched new image spots;
- (5) calculating a set of vectors linking spots of the same number in the master composite image and in the new gel image;
- and determining for each vector the length and angle;
- (6) calculating the vector difference for each of the set of matched new image spots to form a set of vector differences, and removing from the set of matched new image spots those matched new image spots for which the vector difference falls within a predetermined percentage of the largest vector differences within the set of vector differences to form a set of unmatched new image spots;
- (7) selecting a set of well-defined spots from the master composite spot data list, detecting new image spots that have a position that is within a position tolerance of the position of corresponding well-defined spots, matching the detected new image spots to the corresponding well-defined spots, and adding the matched new image spots to the set of matched new image spots;
- (8) selecting a set of saturated spots from the master composite spot data list, detecting new image spots that have a position that is within a position tolerance of the position of the corresponding saturated spots, matching the detected new image spots to the corresponding saturated spots, and adding the matched new image spots to the set of matched new image spots;
- (9) selecting a set of weak spots from the master composite spot data list, detecting new image spots that have a position that is within a position tolerance of the position of corresponding weak spots, matching the detected new image spots to the corresponding weak spots, and adding the matched new image spots to the set of matched new image spots;
- and
- (10) searching the new image outside of the set of matched new image spots to locate unidentified new image spots.
Dependencies are inferred from the claim text.