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Recent Patents of Interest in Proteomics: Feb 12, 2010

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US Patent 7,657,387. Method of processing and storing mass spectrometry data. Inventors: Robert Malek; Oliver Lange. Assignee: Thermo Finnigan [now Thermo Fisher Scientific]

Covers a compression technique for Fourier transform mass spectrometry. "A statistical analysis is applied to the data in the frequency domain since most of this data is a result of randomly distributed electronic noise," according to the abstract. "A fit of the whole frequency dataset to the distribution is made to determine preliminary moments of the distribution." The data in the tail of the distribution is removed, and the remaining data points are refitted to the distribution "to identify the moments of distribution of that remaining noise data." A noise threshold for the mass spectrum in applied using the calculated moments. Data above the threshold is kept, and the whole spectrum can be "reconstituted by storing the moments of distribution along with the peak data and then regenerating the noise from those moments and adding it to the peak data."


US Patent 7,655,477. System and method for the separation of analytes. Inventors: Thomas Wayne Schneider; James N. Baraniuk. Assignees: Science Applications International Corp.; Georgetown University
A separation module fractionates or separates an analyte according to isoelectric point using capillary isoelectric focusing within a first microchannel. The fractions are stacked, forming plugs "the number of which is determined by a number of parallel second microchannels integrally connected to the first microchannel, into which the fractions are directed according to the buffer characteristics found in each of the individual microchannels," according to the abstract. Within the microchannels, the plugs are separated into proteins using a different chemical property, such as mass-to-charge ratio, using capillary electrophoresis.


US Patent 7,655,433. Methods for high-throughput and quantitative proteome analysis. Inventor: Rudolf H. Aebersold. Assignee: The Institute for Systems Biology

Covers methods for identifying and quantifying polypeptides in a sample. Included are steps to label the peptides in the sample with an isotope tag; "adding a plurality of peptide standards to the polypeptide sample, wherein the peptide standards are labeled with an isotopically distinct version of the isotope tag," according to the abstract; identifying an isotope-tagged sample in an analyzed fraction; and determining the amount of the identified isotope-tagged sample in the analyzed fraction by comparing that to the amount of isotope-tagged standard peptide in the same fraction.


US Patent 7,655,413. Methods and compositions for enhanced protein expression and purification. Inventors: Tauseef R. Butt; Oxana A. Malakhova; Michael P. Malakhov. Assignee: Lifesensors

Pertains to methods of enhancing expression levels and secretion of heterologous fusion proteins in a host cell.


US Patent 7,653,793. Proteomic sample analysis and systems therefore. Inventors: Evelyn W. Wang; Matt Brown; Neil Chungfat; Sucharita Dutta; Sean Mathewson. Assignee: The Board of Trustees of the Leland Stanford Junior University

According to an example embodiment of the invention, ion mass spec data is collected for a group of samples. "For each sample, at least one grouping of ions is identified and used to generate another estimated grouping of ions relating to the sample," according to the abstract. Characteristics of the sample are detected using these groupings.


US Patent 7,652,129. Parallel process for protein or virus separation from a sample. Inventor: Mary Lopez. Assignee: PerkinElmer

A sample is divided into aliquots that are subjected to at least two successive parallel separation steps in order "to resolve protein or viral components thereof," according to the abstract. The separation steps are performed on the sample as well as subsamples, each containing a prelabeled tag.


US Patent. 7,651,872. Discrete nano-textured structures in biomolecular arrays and methods of use. Inventors: Mark Whitney Hart; Ho-Cheol Kim; Robert Dennis Miller; Gregory Michael Wallraff. Assignee: International Business Machines

The array includes a substrate "across which is distributed an array of discrete regions of a porous substance formed from a porogen-containing organosilicate material," according to the abstract. The porous substance is designed to bind chemical targets that may be useful in protein experiments as well as research into gene expression, antibodies, and antigens.


US Patent 7,651,859. Method of analyzing C-terminal amino acid sequence of peptide. Inventors: Kenji Miyazaki; Akira Tsugita; Kenichi Kamijo; Takuji Nabetani. Assignee: NEC

Provided is a method for analyzing the C-terminal amino acid sequence of a peptide using a reaction for successively releasing the C-terminal amino acids of the peptide. The method can suppress undesirable reactions such as cleavage of peptide bonds in the intermediate position of the peptide when releasing the C-terminal amino acids of a peptide of a long amino acid length, according to the abstract.


US Patent 7,645,586. Protein isoform discrimination and quantitative measurements thereof. Inventors: Neal F. Gordon; James R. Graham. Assignee: Millipore

Provided are methods, reagents, and an apparatus for detecting protein isoforms in a sample.


US Patent 7,645,369. Separation method and device for protein mixtures. Inventors: Hans-Joachim Hoeltke; Albert Roeder; Alois Rainer; Peter Berndt; Carlo Effenhauser; Hanno Langen; Remo Anton Hochstrasser. Assignee: Roche Diagnostics

Covers a separation device and method of separation for biomolecular sample material, especially protein mixtures. For protein mixture separation, a separation element for the 2D separation of components of the sample material is provided. "It is proposed that the separation element has a channel or transfer structure for the locally resolved discharge of separated sample components in a transport direction that is at right angles to the separation plane onto a support surface that is preferably suitable for mass spectroscopic analyses," according to the abstract.

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