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Recent Patents of Interest in Proteomics: Jul 9, 2009

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US Patent 7,555,393. Evaluating the probability that MS/MS spectral data matches candidate sequence data. Inventors: Rovshan Goumbatoglu Sadygov; Andreas Huhmer. Assignee: Thermo Finnigan [now Thermo Fisher Scientific]

In one aspect, the invention presents a new database search method that provides a probability that "spectral data from a non-ergodic reaction via mass spectrometry matches a candidate sequence from a set of sequences in a database by random," according to the abstract. The method comprises two parts. In the first part, the spectral data is pre-processed, keeping only the most relevant data for the database search. In the second part, the database is searched using a pre-processed spectrum "to assign a probability or expectation that the spectrum matches a candidate sequence from a set of sequences in a database by random," the inventors say in the abstract. "The search methodology uses a new probability model, a compound distribution based on the number of product ion mass-to-charge ratios and the number of intensity values that are shared between the product ion spectral data and the sequence database, to accurately predict the probability of the peptide identification being a correct match, and not a random event."


US Patent 7,553,621. Reading, detection, or quantification method, hybrids, or complexes used in said method and the biochip using same. Inventors: Frederic Ginot; Dominique Masse; Arnelle Novell-Rousseau; Severine Moutin. Assignee: BioMerieux; Commissariat à l'énergie Atomique

Pertains to a method of reading, detecting, or quantifying at least one biological reaction "on a support, between either a recognition molecule and a labeled target molecule, or between a target molecule and a labeled detection molecule," according to the abstract. The method comprises treating the support under physicochemical conditions allowing either the separation of the recognition molecule and labeled target molecule, or the separation of the target molecule and the labeled detection molecule. It also comprises producing images before and after the physicochemical treatment that may be used to determine the specific and non-specific bindings between the different molecules.


US Patent 7,550,720. Apparatus and method for MALDI source control with external image capture. Inventors; Gregor T Overney. Assignee: Agilent Technologies

Pertains to a method of MALDI sample plate processing that includes capturing an image of a plate positioned outside a mass spectrometer. The image is processed to identify at least one attribute of an individual sample on the plate "where the attributes are selected from a position attribute, a geometry attribute, and an internal density distribution attribute," according to the abstract. Based on the attributes, a laser impact position is selected with the MS.


US Patent 7,550,718. Process for increasing ionic charge in mass spectrometry. Inventor: Scott A McLuckey. Assignee: Purdue Research Foundation

Pertains to processes and apparatus for analyzing molecules, or their fragments, capable of carrying multiple charges "by reacting the multiply charged molecules or fragments thereof with other ions using mass spectrometry," according to the abstract.


US Patent 7,550,268. Rapid, sensitive, and quantitative methods for tissue and cell-based proteomics via consecutive addition of quantifiable extenders. Inventor: James Eberwine. Assignee: Trustees of the University of Pennsylvania

Pertains to methods, systems, and kits for detecting and quantifying multiple immunogens in a sample. Quantifiable extenders are added consecutively to immunogen-bound complexes of immunogen-binding agent attached to a DNA-containing RNA polymerase promoter.


US Patent 7,550,259. Linear high-throughput proteomics. Inventors: Steven M Fischer; Christine A Miller. Assignee: Agilent Technologies

A method for analyzing a sample made up of multiple proteins is described. The proteins are separated by species in a way so that the multiple protein species "emerge in a sequential order, and are then digested in the sequential order in which they emerge from the separation process," according to the abstract. The digested proteins are introduced to a mass spectrometer in the same sequential order "so that, within a given time window, the digested proteins introduced into the mass spectrometer are covariant."


US Patent 7,544,518. Rapid quantitative analysis of proteins or protein function in complex mixtures. Inventors: Rudolf Hans Aebersold; Michael H Gelb; Steven P Gygi; C Ronald Scott; Frantisek Turecek; Scott A Gerber; Beate Rist. Assignee: University of Washington

Pertains to mass spec-based methods and reagents for the "rapid and quantitative" analysis of proteins or protein function in protein mixtures. Affinity-labeled protein reactive reagents having three portions are used — an affinity label covalently linked to a protein reactive group through a linker group. "The methods of this invention can be used for qualitative and quantitative analysis of global protein expression profiles in cells and tissues, to screen for and identify proteins whose expression level in cells, tissue or biological fluids is affected by a stimulus or by a change in condition or state of the cell, tissue or organism from which the sample originated," according to the abstract.

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