Northeastern University

Beckman Coulter, Inc.

Massachusetts Institute of Technology

Northwestern University

Beckman Instruments, Inc.

Cetek Corporation

Barry L Karger

Frantisek Foret

Aharon S Cohen

Arthur W Miller

Lev Kotler

Wolfgang K Goetzinger

Robert J Nelson

Marek Minarik

Karel Kleparnik

Jan Preisler

Roger W Giese

Andras Guttman

Dallas E Hughes

Jian Zhang

Yuriy M Dunayevskiy

Binyamin Feibush

Alvaro Figueroa

Neil T Miller

Katalin Ganzler

Thomas Rejtar

Paul M Zavracky

William G Thilly

Laszlo A Takacs

Alexander Lazarev

James L Waters

Chia-Hui Shieh

Zoran Sosic

Kenneth D Konrad

Sunil S Deliwala

William S Hancock

Sushma Rampal

Oscar Salas-Solano

Li Zang

Daniel P Kirby

Aran Paulus

Victor P Andreev

David N Heiger

Tomas Rejtar

Eva Szoko

Manuel Duval

Chiranjit Deka

Stephen J Pentoney, Jr

Patrick Berna

Kiyohito Shimura

Dieter Schmalzing

Bailin Zhang

Odilo M Uller

Phouthone Koehavong

Konstaintin Khrapko

Qifeng Xue

E Nicol McGruer

Alexander R Ivanov

Roger A Kautz

Haihong Zhou

A polymer-based PLOT capillary column prepared by in situ copolymerization of a functional monomer and a crosslinking monomer, which enhances the strength of the polymer matrix, is disclosed. Also disclosed is a system comprising the polymer-based PLOT column coupled to a mass flow or concentration sensitive detector, for carrying out a chemical analysis method on samples separated by liquid chromatography using the column, and a process for using the system. Columns of the invention can be prepared in a robust fashion with a very narrow i.d., e.g., 5-15 &#x3bc;m. Thus, they are suitable for commercial use in ultratrace LC/MS proteomic analysis. Columns according to the invention are characterized by high resolving power and high column-to-column reproducibility. When these columns are coupled on-line with, e.g., ESI-MS detection, the resulting systems are capable of detecting the component parts of complex proteomic samples down to the low attomole to sub-attomole level.

Narrow bore porous layer open tube capillary column and uses thereof

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 &#x3bc;m and smaller, with enhanced mass transfer properties and low back pressures, and excellent column-to-column reproducibility of retention times.

Narrow I.D. monolithic capillary columns for high efficiency separation and high sensitivity analysis of biomolecules

A polymer-based PLOT capillary column prepared by in situ copolymerization of a functional monomer, which usually contains the retentive chemistries, and a crosslinking monomer, which enhances the strength of the polymer matrix, is disclosed. Also disclosed is a system comprising the polymer-based PLOT column coupled to a mass flow or concentration sensitive detector, for carrying out a chemical analysis method on samples separated by liquid chromatography using the column, and a process for using the system. Columns of the invention can be prepared in a robust fashion with a very narrow i.d., e.g., 5-15 &#x3bc;m. Thus, they are suitable for commercial use in ultratrace LC/MS proteomic analysis. Columns according to the invention are characterized by high resolving power and high column-to-column reproducibility. When these columns are coupled on-line with, e.g., ESI-MS detection, the resulting systems are capable of detecting the component parts of complex proteomic samples down to the low attomole to sub-attomole level.

A method or platform for monoclonal antibody based biomarker discovery is disclosed. The method according to the invention provides for the integration of analyte collection, hybridoma screening and nanovolume integrated mass spectrometry (NVIMS) to achieve a robust screening system that is capable, for example, of cutting 4-6 years off of the classical biomarker discovery and development process. The invention provides a platform for the rapid, high-throughput production, isolation and characterization of, e.g., disease specific biomarkers together with highly specific monoclonal antibodies. The method of the invention has a variety of applications such as, but not limited to, drug testing, biohazard applications, ecological applications, physiological applications and/or pathology screening applications. The method of the invention is also capable of being performed or used as or with a high-throughput screening process or system of the invention.

Monoclonal antibody based biomarker discovery and development platform

A device and method to provide a simplified wash process and controlled disintegration of a soft substance, such as a gel, are disclosed. In use, a block of, e.g., gel matrix is placed in the device and washed with a series of appropriate solutions to remove interfering contaminants. The washing liquid is removed through a deformable narrow opening in the bottom of the device, and, subsequently, the gel block is extruded through the deformable narrow opening, by a physical force, such as centrifugal force, a vacuum or positive pressure from a gas or liquid, etc., resulting in fragmentation of the gel block into a series of particles of similar size. The fragmentation of the gel results from shear forces exerted onto the gel block traveling through the deformable narrow opening in the device. The rate of such fragmentation and resulting fragment size can be controlled by extruding the gel block using a predefined level of force as well as by controlling the dimensions and shape of the narrow opening (s) in the device.

Devices, methods and applications for extraction of molecules from polymeric gel electrophoretic media

Methods are presented for realizing zero-dispersion segmented flow for transfer of small microfluidic samples onto or within microfluidic analysis or processing devices. Where fluidic systems are in whole or in part made of materials favorable to the zero-dispersion conditions for an indicated solvent/carrier fluid system, the system may be covalently coated to impart the necessary surface properties. This invention is demonstrated in an embodiment where 1 microliter samples () are robotically prepared and transferred through 3 meters of capillary tubing () to a microcoil NMR probe.

Method for efficient transport of small liquid volumes to, from or within microfluidic devices

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.

Multichannel microscale system for high throughput preparative separation with comprehensive collection and analysis

An improved system and method of analyzing sample data that increases the reliability of peak (compound) detection and identification in the presence of chemical and/or random noise. The sample analysis system includes a compound-separating unit for separating constituent compounds in a sample mixture, a compound-analyzing unit for identifying and quantitating at least one of the separated compounds, and a computer for acquiring data from the compound-separating and compound-analyzing units, for generating a multi-dimensional data set incorporating the acquired data, for executing an algorithm for reducing noise in the data set and for detecting peaks (compounds) in the noise-reduced data set, and for identifying/quantitating the detected compounds.

Matched filtration with experimental noise determination for denoising, peak picking and quantitation in LC-MS

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.

An apparatus for use in controlling the temperature of one or more substances passing through one or more microfluidics channels in an analysis device is set forth. The apparatus includes a heating unit having first and second surfaces. The first surface of the heating unit is constructed so that it is at least partially exposed for cooling of the heating unit. The apparatus also includes a thermally conductive medium that is disposed proximate the second surface of the heating unit. The one or more microfluidics channels are disposed in the thermally conductive medium. In one embodiment, the one or more microfluidics channels are in the form of a plurality of capillary columns, such as those used in instruments for capillary electrophoresis. Each capillary column is substantially surrounded by the material forming the thermally conductive medium. In another embodiment, the thermally conductive medium, along with the corresponding plurality of capillary columns, can be easily disengaged from the heating unit in a non-destructive manner thereby allowing the heating unit to be reused.

Analysis apparatus having improved temperature control unit

A sample load and injection device () includes sample introduction capillaries () attached to a microfluidic device (). Sample introduction capillaries () are connected to sample introduction channels (). Sample introduction capillaries () are connected to separation channels () at connection points (). At a defined distance along the separation channels (), auxilliary channels () originate at connection points (). The sample load and injection device includes cover plate () which has connecting channels (). Connecting channel () is associated with ends () of sample introduction channels (). Connecting channel () is associated with ends ().

Parallel sample loading and injection device for multichannel microfluidic devices

A thermostat array including an array of two or more capillary columns () or two or more channels in a microfabricated device is disclosed. A heat conductive material () 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 () 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 () is positioned adjacent to the individual columns or channels within the heat conductive material. Each temperature sensing element is connected to a temperature controller.

Parallel array of independent thermostats for column separations

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., from a capillary array or microchip channels, with subsequent sequential desorption with a scanning laser. This format is particularly useful for high throughput MS analysis. Also disclosed is an off-line deposition chamber and a general method of preparing a sample for analysis that results in the homogeneous deposition of small quantities of sample at improved reproducibility on any appropriately configured sample receptor. This format of sample preparation is particularly useful with existing commercial mass spectrometers.

On-line and off-line deposition of liquid samples for matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectroscopy

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. By use of the presently disclosed method the degree of automation of data processing in high-throughput DNA sequencing is improved, as is the quality of the results.

Expert system for analysis of DNA sequencing electropherograms

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., from a capillary array or microchip channels, with subsequent sequential desorption with a scanning laser. This format is particularly useful for high throughput MS analysis. Also disclosed is an off-line deposition chamber and a general method of preparing a sample for analysis that results in the homogeneous deposition of small quantities of sample at improved reproducibility. This format of sample preparation is particularly useful with existing commercial mass spectrometers.

Growing community of inventors

Newton, MA, United States of America

Barry L Karger