101 results about "Protein profiling" patented technology

A highly sensitive assay is disclosed which utilizes a method for gene specific primed amplification of mRNA libraries from rare cells and rare transcripts found in blood. The assay allows detection of rare mRNA (10 copies / cell) found in 1 to 10 cells isolated through immunomagnetic enrichment. The assay is an improvement over multiplex PCR and allows efficient detection of rare coding sequences for circulating carcinoma cells in the blood. The methods are useful in profiling of cells isolated from tissues or body fluids and serves as an adjunct to clinical diagnosis of diverse carcinomas including early stage detection and classification of circulating tumor cells. Monitoring of nucleic acid and protein profiles of cells either in conventional or microarray formats, facilitates management of therapeutic intervention including staging, monitoring response to therapy, confirmation of remission and detection of regression.

The present invention provides methods for diagnosing melanoma in a subject by analyzing nucleic acid molecules obtained from the subject. The present invention also provides methods for distinguishing melanoma from dysplastic nevi and / or normal pigmented skin. The methods include analyzing expression or mutations in epidermal samples, of one or more skin markers. The methods can include the use of a microarray to analyze gene or protein profiles from a sample.

The invention provides methods to diagnose and follow the progression of disease through use of protein profile analysis.

The invention provides methods used to analyze the contents of a biological sample, such as blood serum, with cascade Raman sensing. A fluorescence producing nanoporous biosensor having probes that bind specifically to known analytes is contacted with a biological sample and one or more bound complexes coupled to the porous semiconductor structure are formed. The bound complexes are contacted with a Raman-active probe that binds specifically to the bound complexes and the biosensor is illuminated to generate fluorescent emissions from the biosensor. These fluorescent emissions generate Raman signals from the bound complexes. The Raman signals produced by the bound complexes are detected and the Raman signal associated with a bound protein-containing analyte is indicative of the presence of the protein-containing compound in the sample. The invention methods are useful to provide a protein profile of a patient sample. The invention also provides detection systems useful to practice the invention methods.

Various methods of using Raman-active or SERS-active probe constructs to detect analytes in biological samples, such as the protein-containing analytes in a body fluid are provided. The probe moieties in the Raman-active constructs are selected to bind to and identify specific known analytes in the biological sample or the probe moieties are designed to chemically interact with functional groups commonly found in certain amino acids so that the invention methods provide information about the amino acid composition of protein-containing analytes or fragments in the samples. In some cases, the Raman-active or SERS-active probe constructs, when used in the invention methods, can identify particular protein-containing analytes or types of such analytes so that a protein profile of a patient sample can be made. When compared to a data base of Raman or SERS spectra of normal samples, a disease state of a patient can be identified using the methods disclosed.

The present invention provides methods for characterizing a skin sample of a subject as belonging to an age range by analyzing nucleic acid or protein molecules obtained from the subject. The methods include analyzing expression or mutations in epidermal samples, of one or more skin markers. The methods can include the use of a microarray to analyze gene or protein profiles from a sample and compare them with a known skin age index. Therapeutic and cosmetic formulations are also provided herein.

The invention provides methods for analyzing the protein content of a biological sample, for example to obtain a protein profile of a sample provided by a particular individual. The proteins and protein fragments in the sample are separated on the basis of chemical and / or physical properties and maintained in a separated state at discrete locations on a solid substrate or within a stream of flowing liquid. Raman spectra are then detected as produced by the separated proteins or fragments at the discrete locations such that a spectrum from a discrete location provides information about the structure or identity of one or more particular proteins or fragments at the discrete location. The proteins or fragments at discrete locations can be coated with a metal, such as gold or silver, and / or the separated proteins can be contacted with a chemical enhancer to provide SERS spectra. Method and kits for practicing the invention are also provided.

The present invention provides methods to use expression profiles to determine the bioequivalence of two or more pharmaceutically equivalent drug formulations. In addition, this invention provides methods to select drug formulations that are able to substitute for standard drug formulations without change in clinical efficacy. In other embodiments, this invention provides computer systems, kits and databases for carrying out the methods of the invention.

The present invention relates to multiphase protein separation methods capable of resolving large numbers of cellular proteins. The methods of the present invention provide protein profile maps for imaging and comparing protein expression patterns. The present invention provides alternatives to traditional 2-D gel separation methods for the screening of protein profiles.

The invention discloses a high-throughput multi-index protein chip for screening esophageal squamous carcinoma specific protein markers, and discloses a kit supporting the use. 55 types of esophageal squamous carcinoma differential proteins in the serum or blood plasma are selected and used as the esophageal squamous carcinoma protein markers and protein contrast prepare the protein chip; and the protein chip comprises a substrate, protein detection indicators and a contrast detection indicator coating, wherein the protein detection indicators are distributed as arrays on the substrate. Detection liquid of a supplementary experiment reagent is filled in the kit. By adopting the protein chip, the protein profiles of three types of people, namely, normal people, people subjected to esophageal squamous cell carcinoma precancerous lesions, and people subjected to the esophageal squamous carcinoma, can be determined; and means are provided for screening the esophageal squamous carcinoma in the early stage, diagnosing in mid stage and late stage, as well as monitoring the state of illness.

The invention provides means to determine the predisposition of individuals to adverse drug reactions (ADRs). The methods are based on genotyping or parallelized enzyme and protein profiling or both. Parallelized enzyme activity profiling can be used for drug screening and development. As examples of the invention we show the prediction of adverse drug reactions of pulmonary hypertension patients by identifying genes and alleles linked to known ADRs and liver enzyme reaction profiling with ADR correlation.

Methods and compositions are described for analyzing complex protein mixtures, such as proteomes, using activity-based probes. In particular, probes that specifically react with and bind to the active form of one or more target proteins are employed. Labeled peptides obtained from the labeled active target proteins can be used in screening and identification procedures, and can be related to the identity, presence, amount, or activity of active members of the desired target protein class. The methods and compositions described herein can be used, for example, to provide diagnostic information concerning pathogenic states, in identifying proteins that may act as therapeutic targets, and in drug discovery.

The present invention provides methods for diagnosing melanoma and / or solar lentigo in a subject by analyzing nucleic acid molecules obtained from the subject. The present invention also provides methods for distinguishing melanoma from solar lentigo and / or dysplastic nevi and / or normal pigmented skin. The methods include analyzing expression or mutations in epidermal samples, of one or more skin markers. The methods can include the use of a microarray to analyze gene or protein profiles from a sample.

A device for protein analysis or mapping, includes an array of particulate nanoparticles, wherein said nanoparticles are bound, preferably co-immobilized, at specific spots on a planar read-out surface or substrate and are provided with a plurality of capture probes for capturing proteins, preferably glycoproteins. A method in which the device is used for protein profiling, especially glycoprotein profiling, of individual samples with high sensitivity is also disclosed. The device and method do not require any complex sample preparation.

The invention belongs to the field of biology and medicine examination, and relates to a method for a protein spectrum of differential expression in a type 2 diabetes serum sample. The method comprises the following steps: adopting a surface-enhanced laser desorption / ionization time-of-flight mass-spectrometric technique to screen whole protein fingerprint of a diabetes chronic complication serum sample, using a data mining technique to screen biological labels in the fingerprint, establishing an analytic decision tree model of N serum protein components, and displaying that the type 2 diabetic nephropathy patient has the difference of the serum protein fingerprint as a result through blind verification and enlarged sample verification models. The method possibly provides reference information for further diagnosis and pathogenesis of diabetic nephropathy, provides research basis and new target for studying molecular mechanism formed by the diabetic nephropathy, and can further be used for guiding drug development and curative effect analysis.

Disclosed herein are methods of protein quantification and normalization using haloalkylated tryptophan fluorescence. Complex protein samples, i.e., samples that each contain 1,000 or more distinct proteins, from diverse sources that do not have common protein profiles are treated with a halo-substituted organic compound (i.e. haloalkane) that reacts with tryptophan residues to form fluorescent products. Irradiation of the samples with ultraviolet light and the detection and quantification of the resultant fluorescent emissions from all proteins in each sample are then used to obtain comparative values for total protein content among the various samples. The values thus obtained are found to be valid indications of comparative total protein content, despite the fact that the tryptophan levels vary widely among the various proteins in any single sample and the samples, due to the diversity of their origins, tend to differ among themselves in the identities and relative amounts of the proteins that they contain. Protein samples are also normalized to correct for differences in sample dilution, sample loading, and protein transfer inconsistencies, by using stain-free detection of total protein in each of the samples, or detection of subsamples within each sample.

The invention relates to the acquisition of mass spectra of complex protein mixtures, often called protein profiles, for example to search for biomarkers which indicate stress situations, or to identify microbes. Up to now protein profiles have been acquired using ionization by matrix-assisted laser desorption with high detection sensitivity in linear time-of-flight mass spectrometers, but these display very poor mass resolution and a very poor reproducibility of the mass values. The invention provides methods which produce surprisingly similar mass spectra, but with far higher mass resolution and mass accuracy. Ionization takes place outside the vacuum at ambient pressure, preferably by means of laser desorption and CI post-ionization. Analysis of the ions takes place in a high-resolution mass spectrometer, for example a reflector time-of-flight mass spectrometer with orthogonal ion injection.

Protein profiles useful in diagnosing, monitoring, staging, evaluating treatments and treating and selecting treatments for heart failure are provided.

Identification of infectious pathogens, particularly viruses, bacteria and other microorganisms is effected with a method whereby pathogens of acute infections can be identified, without first culturing them in external nutrient media, by mass spectrometric measurement of their protein profiles obtained from pathogens directly precipitated from body fluid into pellets by centrifuging. With this method, pathogens which cause acute infections can be identified in less than one hour.

The present invention demonstrates that the diagnosis and prediction of clinical behavior in patients with hematologic malignancies, such as leukemia, can be accomplished by analysis of proteins present in a plasma sample. Thus, in particular embodiments the present invention uses plasma to create a diagnostic or prognostic protein profile of a hematologic malignancy comprising collecting plasma samples from a population of patients with hematologic malignancies; generating protein spectra from the plasma samples with or without fractionation; comparing the protein spectra with clinical data; and identifying protein markers in the plasma samples that correlate with the clinical data. Protein markers identified by this approach can then be used to create a protein profile that can be used to diagnose the hematologic malignancy or determine the prognosis of the hematologic malignancy. Potentially these specific proteins can be identified and targeted in the therapy of these malignancies.

Identification of infectious pathogens, particularly viruses, bacteria and other microorganisms is effected with a method whereby pathogens of acute infections can be identified, without first culturing them in external nutrient media, by mass spectrometric measurement of their protein profiles obtained from pathogens directly precipitated from body fluid into pellets by centrifuging. With this method, pathogens which cause acute infections can be identified in less than one hour.

The invention provides a method of generating and analysing a urinary protein fragmentation profile, in terms of the size, and sequence of particular fragments derived from intact filtered proteins together with the position where enzymes scission occurs along the protein polypeptide chain is characteristic of the diseased state of the kidney. With the recognition that filtered proteins are degraded during renal passage, the methods described in this application will be able to detect protein fragments derived from proteins generated by non-renal disease. The urinary analysis of these filtered proteins would currently not detect the intact form of these proteins. Therefore, a method as described to detect and analyse fragments resulting from degradation during renal passage that will be able to detect the seriousness of the disease.

The invention provides for a proteomic approach for identification of specific bacterial protein profiles that may be used in the development of methods for the diagnosis of bacterial chronic sinusitis. The invention provides for methods for determining the presence of pathogenic bacteria in the upper respiratory tract of a subject using protein profiles of the pathogenic bacteria. The invention also provides for methods of diagnosing a bacterial infection of the upper respiratory tract of a subject using protein profiles of a pathogenic bacteria. In addition, the invention provides for devices, immunoassays and kits for identifying pathogenic bacteria in the upper respiratory tract.

A novel method for examining bacterial growth state is carried out by measuring the levels of conserved cytosolic proteins specific for alternative growth states, using bacterial specific antibody fluorochrome-coupled probe. Utilizing the method of the invention, the cellular growth state of individual bacteria can be determined by measuring the abundance of growth state-specific protein homologs. For example, through use of the protein profiling method of the invention, bacterial VNC state can be distinguished by differentiating growing (exponential phase) from nongrowing or dormant (stationary phase) cells.

The invention mainly relates to the mass spectrometric identification of pathogens in blood cultures from blood-stream infections (septicemia). The invention provides a method with which microbial pathogens can be separated in purified form from blood after a relatively brief cultivation in a blood culture flask, without any interfering human proteins or any residual fractions of blood particles such as erythrocytes and leukocytes, and can be directly identified by mass spectrometric measurement of their protein profiles. The method is based on the use of relatively strong tensides to destroy the blood particles by dissolving the weak cell membranes and most of the internal structures of the blood particles; in spite of the fact that tensides are regarded as strong ionization inhibitors in MALDI and other ionization processes required for mass spectrometric measurements. This method allows unknown pathogens to be obtained in their pure form by centrifuging or filtration and to be identified on the taxonomic level of species or subspecies. Problems with DNA from high levels of leukocytes can be resolved by special measures. After sufficient cultivation, the identification in a mass spectrometric laboratory takes only half an hour.

The present invention provides methods for diagnosing melanoma and / or solar lentigo in a subject by analyzing nucleic acid molecules obtained from the subject. The present invention also provides methods for distinguishing melanoma from solar lentigo and / or dysplastic nevi and / or normal pigmented skin. The methods include analyzing expression or mutations in epidermal samples, of one or more skin markers. The methods can include the use of a microarray to analyze gene or protein profiles from a sample.

The invention relates to the acquisition of mass spectra of complex protein mixtures, often called protein profiles, for example to search for biomarkers which indicate stress situations, or to identify microbes. Up to now protein profiles have been acquired using ionization by matrix-assisted laser desorption with high detection sensitivity in linear time-of-flight mass spectrometers, but these display very poor mass resolution and a very poor reproducibility of the mass values. The invention provides methods which produce surprisingly similar mass spectra, but with far higher mass resolution and mass accuracy. Ionization takes place outside the vacuum at ambient pressure, preferably by means of laser desorption and CI post-ionization. Analysis of the ions takes place in a high-resolution mass spectrometer, for example a reflector time-of-flight mass spectrometer with orthogonal ion injection.