Abstract: A microchip integrated microfabricated, microfluidic, multichannel, preferably electroosmotic pump and pumping system is disclosed. The electroosmotic pump of the invention comprises a plurality of microchannels, which begin and end in common compartments, complexed into an array. The microchannels within the pump have substantially identical, optimal dimensions of cross-section and length such that sufficient pressure for optimal flow of fluid (e.g., liquid or gas) and pressure is generated by the pump and flow rates are stable and reproducible. To effectuate efficient flow of fluid without the hindrance of backpressure, an electroosmotic pump of the invention is coupled to a single channel of a larger cross-section. A similar structure is also used in an electroosmotic valve of the invention, where samples are introduced into an analytical device.

Abstract: A method of preparing an ultra-nanoscale-LC monolithic separation medium for use in capillary columns, or channels in microfabricated devices (microchips), and capillaries prepared by the method are disclosed. The application of moderate positive pressure to both ends of the capillary during the monolith polymerization process permits the preparation of monolithic capillary columns having very low i.d., e.g., 25 &mgr;m and smaller, with enhanced mass transfer properties and low back pressures, and excellent column-to-column reproducibility of retention times.

Abstract: A thermostat control system, that can be configured to include an array of two or more capillary columns or two or more channels in a microfabricated device, is disclosed. A thermally conductive material is in contact with each column or channel in the array. One or more independently controlled heating or cooling elements is positioned adjacent to or within the thermally conductive material, each heating or cooling element being connected to a source of heating or cooling. One or more independently controlled temperature sensing elements and one or more independently controlled temperature probes are also positioned adjacent to or within the thermally conductive material. Each temperature sensing element is connected to a temperature controller, and each temperature probe is connected to a thermometer.

Abstract: A method of analyzing DNA fragments separated electrophoretically is presented. The method includes the use of an expert system that interprets raw or preprocessed signal from the separation. The expert system can be used for real-time base-calling, or applied offline after data acquisition is complete. The expert system is directly applicable to all types of electrophoretic separation used for DNA sequencing, i.e. slab gel, capillary and microchip. Each lane of a multiplex system can consist of 1 to 4 (or even more) different fragment labels. The expert system may also be used with other base-coding schemes, such as those in which more than one base is labeled with a given dye, but the amount of label is different for each base. When the presently disclosed method is applied to DNA sequencing, the resulting interpretation comprises a DNA base sequence with numerical confidences assigned to each base.

Abstract: While the present invention has been described in conjunction with a preferred embodiment, one of ordinary skill, after reading the foregoing specification, will be able to effect various changes, substitutions of equivalents, and other alterations to the compositions and methods set forth herein. It is therefore intended that the protection granted by Letters Patent hereon be limited only by the definitions contained in the appended claims and equivalents thereof.

Abstract: A modular multiple lane or capillary electrophoresis (chromatography) system that permits automated parallel separation and comprehensive collection of all fractions from samples in all lanes or columns, with the option of further on-line automated sample fraction analysis, is disclosed. Preferably, fractions are collected in a multi-well fraction collection unit, or plate. The multi-well collection plate is preferably made of a solvent permeable gel, most preferably a hydrophilic, polymeric gel such as agarose or cross-linked polyacrylamide.

Abstract: A sample load and injection device (10) includes sample introduction capillaries (11) attached to a microfluidic device (12). Sample introduction capillaries (11) are connected to sample introduction channels (18). Sample introduction capillaries (18) are connected to separation channels (20) at connection points (21). At a defined distance along the separation channels (20), auxilliary channels (23) originate at connection points (24). The sample load and injection device includes cover plate (28) which has connecting channels (26, 32). Connecting channel (26) is associated with ends (24) of sample introduction channels (18). Connecting channel (32) is associated with ends (20).

Abstract: A universal interface for continuous on-line liquid sample introduction directly to the time-of-flight mass spectrometer, which can further promote throughput and utility of MALDI-TOF MS, is disclosed. Preferably, the liquid sample includes a matrix, either solid or liquid, for use in matrix-assisted-laser-desorption-ionization, most particularly in a time-of-flight mass spectrometer which can further promote throughput and utility of MALDI-TOF MS. In the method of the invention, the same samples and matrices, both solid and liquid, can be used as in conventional MALDI. In practice of the method of the invention, a solution of sample containing, e.g., peptide and matrix is infused directly into the source chamber of a mass spectrometer at subatmospheric pressure, deposited on a moving sample holder, such as a rotating quartz wheel, and desorbed by, e.g., a nitrogen laser. The method of the invention is particularly amenable to multiplexing, the parallel deposition of multiple samples, e.g.

Abstract: A modular multiple lane or capillary electrophoresis (chromatography) system that permits automated parallel separation and comprehensive collection of all fractions from samples in all lanes or columns, with the option of further on-line automated sample fraction analysis, is disclosed. Preferably, fractions are collected in a multi-well fraction collection unit, or plate (40). The multi-well collection plate (40) is preferably made of a solvent permeable gel, most preferably a hydrophilic, polymeric gel such as agarose or cross-linked polyacrylamide.

Abstract: A universal interface for continuous on-line liquid sample introduction directly to the time-of-flight mass spectrometer, which can further promote throughput and utility of MALDI-TOF MS, is disclosed. Preferably, the liquid sample includes a matrix, either solid or liquid, for use in matrix-assisted-laser-desorption-ionization, most particularly in a time-of-flight mass spectrometer which can further promote throughput and utility of MALDI-TOF MS. In the method of the invention, the same samples and matrices, both solid and liquid, can be used as in conventional MALDI. In practice of the method of the invention, a solution of sample containing, e.g., peptide and matrix is infused directly into the source chamber of a mass spectrometer at subatmospheric pressure, deposited on a moving sample holder, such as a rotating quartz wheel, and desorbed by, e.g., a nitrogen laser. The method of the invention is particularly amenable to multiplexing, the parallel deposition of multiple samples, e.g.

Abstract: A method of separating a mixture of biopolymers of various lengths using a blend of two linear hydrophilic polymers, particularly polyacrylamides (LPA) or substituted polyacrylamides, one with high weight-average molecular mass and another with low weight-average molecular mass, each present at a low concentration but wherein the concentration of the high weight-average molecular mass LPA is above its entanglement threshold, is disclosed. The matrix is excellent for use in methods of nucleic acid analysis, particularly long read length DNA sequencing.

Abstract: A thermostat array including an array of two or more capillary columns (10) or two or more channels in a microfabricated device is disclosed. A heat conductive material (12) surrounded each individual column or channel in array, each individual column or channel being thermally insulated from every other individual column or channel. One or more independently controlled heating or cooling elements (14) is positioned adjacent to individual columns or channels within the heat conductive material, each heating or cooling element being connected to a source of heating or cooling, and one or more independently controlled temperature sensing elements (16) is positioned adjacent to the individual columns or channels within the heat conductive material. Each temperature sensing element is connected to a temperature controller.

Abstract: A method of analyzing DNA fragments separated electrophoretically is presented. The method includes the use of an expert system that interprets raw or preprocessed signal from the separation. The expert system can be used for real-time base-calling, or applied offline after data acquisition is complete. The expert system is directly applicable to all types of electrophoretic separation used for DNA sequencing, i.e. slab gel, capillary and microchip. Each lane of a multiplex system can consist of 1 to 4 (or even more) different fragment labels. The expert system may also be used with other base-coding schemes, such as those in which more than one base is labeled with a given dye, but the amount of label is different for each base. When the presently disclosed method is applied to DNA sequencing, the resulting interpretation comprises a DNA base sequence with numerical confidences assigned to each base.

Abstract: A method of analyzing DNA fragments separated electrophoretically is presented. The method includes the use of an expert system that interprets raw or preprocessed signal from the separation. The expert system can be used for real-time base-calling, or applied offline after data acquisition is complete. The expert system is directly applicable to all types of electrophoretic separation used for DNA sequencing, i.e. slab gel, capillary and microchip. Each lane of a multiplex system can consist of 1 to 4 (or even more) different fragment labels. The expert system may also be used with other base-coding schemes, such as those in which more than one base is labeled with a given dye, but the amount of label is different for each base. When the presently disclosed method is applied to DNA sequencing, the resulting interpretation comprises a DNA base sequence with numerical confidences assigned to each base.

Abstract: This invention combines a capillary electrophoresis (CE) technique for screening complex biological samples with mass spectrometry (MS), to provide a streamlined procedure for identifying and characterizing candidate ligands in a complex biological sample that bind at a selected binding strength to a selected target molecule. The method of the invention advantageously identifies and characterizes tight-binding ligands when high concentrations of weak ligands are present in the sample, which may mask lower concentrations of tight-binding ligands in the sample. The method involves interfacing a capillary from a CE instrument with a post-capillary mass spectrometer to provide direct mass analysis of target/ligand complexes that migrate stably through the CE instrument. All weaker-binding ligands will not be detected during the MS analysis because they dissociate from the target early during the CE run, before reaching and entering the mass spectrometer.

Abstract: Coatings suitable for surfaces such as are found in capillary electrophoresis columns and methods for their preparation are disclosed. A coated surface of the invention, preferably an interior surface of a microcapillary, generally includes a surface having an interconnected polymeric coating that includes a functional group attached to the surface and capable of copolymerizing with an organic compound in an organic solvent, and a polymer of the organic compound copolymerized with the functional group. The coating can be covalently or non-covalently attached to the surface and can further include an additional layer of coating material. Preferably, the organic compound is a vinyl ester, and most preferably, vinyl acetate, and the attached polymer forming the exposed surface of the coating is a polyvinyl alcohol, the hydroxyl groups of which can be further derivatized in any desired manner. The coating of the invention creates a new, stable surface, appropriate for CE columns or general surface modification.

Abstract: A universal interface for continuous on-line liquid sample introduction directly to the time-of-flight mass spectrometer, which can further promote throughput and utility of MALDI-TOF MS, is disclosed. Preferably, the liquid sample includes a matrix, either solid or liquid, for use in matrix-assisted-laser-desorption-ionization, most particularly in a time-of-flight mass spectrometer which can further promote throughput and utility of MALDI-TOF MS. In the method of the invention, the same samples and matrices, both solid and liquid, can be used as in conventional MALDI. In practice of the method of the invention, a solution of sample containing, e.g., peptide and matrix is infused directly into the source chamber of a mass spectrometer at subatmospheric pressure, deposited on a moving sample holder, such as a rotating quartz wheel, and desorbed by, e.g., a nitrogen laser. The method of the invention is particularly amenable to multiplexing, the parallel deposition of multiple samples, e.g.

Abstract: Coatings suitable for surfaces such as are found in capillary electrophoresis columns and methods for their preparation are disclosed. A coated surface of the invention, preferably an interior surface of a microcapillary, generally includes a surface having an interconnected polymeric coating that includes a functional group attached to the surface and capable of copolymerizing with an organic compound in an organic solvent, and a polymer of the organic compound copolymerized with the functional group. The coating can be covalently or non-covalently attached to the surface and can further include an additional layer of coating material.

Abstract: A method of analyzing DNA fragments separated electrophoretically is presented. The method includes the use of an expert system that interprets raw or preprocessed signal from the separation. The expert system can be used for real-time base-calling, or applied offline after data acquisition is complete. The expert system is directly applicable to all types of electrophoretic separation used for DNA sequencing, i.e. slab gel, capillary and microchip. Each lane of a multiplex system can consist of 1 to 4 (or even more) different fragment labels. The expert system may also be used with other base-coding schemes, such as those in which more than one base is labeled with a given dye, but the amount of label is different for each base. When the presently disclosed method is applied to DNA sequencing, the resulting interpretation comprises a DNA base sequence with numerical confidences assigned to each base.

Abstract: A universal interface for continuous on-line liquid sample introduction directly to the time-of-flight mass spectrometer, which can further promote throughput and utility of MALDI-TOF MS, is disclosed. Preferably, the liquid sample includes a matrix, either solid or liquid, for use in matrix-assisted-laser-desorption-ionization, most particularly in a time-of-flight mass spectrometer which can further promote throughput and utility of MALDI-TOF MS. In the method of the invention, the same samples and matrices, both solid and liquid, can be used as in conventional MALDI. In practice of the method of the invention, a solution of sample containing, e.g., peptide and matrix is infused directly into the source chamber of a mass spectrometer at subatmospheric pressure, deposited on a moving sample holder, such as a rotating quartz wheel, and desorbed by, e.g., a nitrogen laser. The method of the invention is particularly amenable to multiplexing, the parallel deposition of multiple samples, e.g.