{"search_session":{},"preferences":{"l":"en","queryLanguage":"en"},"patentId":"US_2007_0077600_A1","frontPageModel":{"patentViewModel":{"ref":{"entityRefId":"074-152-072-543-037","entityRefType":"PATENT"},"entityMetadata":{"linkedIds":{"empty":true},"tags":[],"collections":[{"id":10709,"type":"PATENT","title":"Rockefeller University Patent Portfolio","description":"","access":"OPEN_ACCESS","displayAvatar":true,"attested":false,"itemCount":4213,"tags":[],"user":{"id":91044780,"username":"Cambialens","firstName":"","lastName":"","created":"2015-05-04T00:55:26.000Z","displayName":"Cambialens","preferences":"{\"usage\":\"public\",\"beta\":false}","accountType":"PERSONAL","isOauthOnly":false},"notes":[{"id":8226,"type":"COLLECTION","user":{"id":91044780,"username":"Cambialens","firstName":"","lastName":"","created":"2015-05-04T00:55:26.000Z","displayName":"Cambialens","preferences":"{\"usage\":\"public\",\"beta\":false}","accountType":"PERSONAL","isOauthOnly":false},"text":"
Search Applicants and Owners separately: \"Rockefeller University\"; \"Univ* Rockefeller\"; \"Univ* Rockef*\"
Select more for logical variants. Add to collection. Select all patents in the collection and expand by simple families. Add to collection. Total patents: 4020
Search Applicants and Owners separately: \"Rockefeller University\"; \"Univ* Rockefeller\"; \"Univ* Rockef*\"
Select more for logical variants. Add to collection. Select all patents in the collection and expand by simple families. Add to collection. Total patents: 4020
(a) providing a first sample of the cells in which the given protein contains a tag,\n
(b) providing a second sample of the same cells, wherein the given protein and the other proteins are metabolically labeled, and wherein neither the given protein nor the other proteins are tagged,\n
(c) mixing and lysing the first cell sample and the second cell sample to provide a mixture of proteins,\n
(d) binding the tag of the given protein to a substrate,\n
(e) isolating proteins associated with the tagged given protein bound to the substrate, whereby the associated proteins comprise: \n\n(i) proteins specifically associated with the tagged given protein,\n(ii) proteins non-specifically associated with the tagged given protein, or\n(iii) a combination thereof,\n
(f) determining whether each associated protein is unlabeled or a mixture of labeled and unlabeled proteins, wherein if the associated protein is not labeled, then that protein was specifically associated in the cell with the tagged given protein; alternatively,\n
(a′) providing a first sample of the cells, wherein neither the given protein nor the other proteins are tagged,\n
(b′) providing a second sample of the same cells in which the given protein contains a tag, wherein the given protein and the other proteins are metabolically labeled,\n
(c′) mixing and lysing the first cell sample and the second cell sample to provide a mixture of proteins,\n
(d′) binding the tag of the given protein to a substrate,\n
(e′) isolating proteins associated with the tagged given protein bound to the substrate, whereby the associated proteins comprise: \n\n(i) proteins specifically associated with the tagged given protein,\n(ii) proteins non-specifically associated with the tagged given protein, or\n(iii) a combination thereof,\n
(f′) determining whether each associated protein is labeled or a mixture of labeled and unlabeled proteins, wherein if the associated protein is labeled, then that protein was specifically associated in the cell with the tagged given protein."],"number":1,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1 wherein if the associated protein is a mixture of labeled and unlabeled proteins, then that protein became associated with the tagged protein during or after cell lysis."],"number":2,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1 wherein the tagged protein is a member of a protein complex."],"number":3,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1 wherein the isolation in steps (e) and (e′) is performed at non-stringent conditions."],"number":4,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1 wherein the metabolic label is a heavy isotope."],"number":5,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1 wherein the metabolic label is a radioactive isotope."],"number":6,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 6 wherein the heavy isotope is heavy hydrogen, carbon, nitrogen, oxygen and/or sulfur."],"number":7,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 5 wherein determining whether the associated protein is labeled, unlabeled, or a mixture of labeled and unlabeled proteins comprises deriving mass spectra data for the isolated proteins."],"number":8,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 8 wherein the ratio of the number of cells in the first sample to the number of cells in the second sample is in the range of 1:100 to 100:1."],"number":9,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 9 wherein the ratio of the number of cells in the first sample to the number of cells in the second sample is approximately 1:1."],"number":10,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 8 further comprising digesting the isolated proteins before deriving mass spectra data."],"number":11,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 8 wherein there is between a 1 and 4 dalton difference between a non-specifically associated protein comprising the heavy isotope and the naturally-occurring counterpart of the non-specifically associated protein."],"number":12,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 8 wherein there is at least a 4 dalton difference between a non-specifically associated protein comprising the heavy isotope and the naturally-occurring counterpart of the non-specifically associated protein."],"number":13,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 6 wherein the heavy isotope is incorporated into the proteins by placing the first or second sample of cells in a medium comprising a component with a heavy isotope, wherein the cells produce proteins incorporating the component."],"number":14,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 14, wherein the component is one or more heavy amino acids."],"number":15,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 15 wherein the heavy amino acid is heavy lysine and/or arginine."],"number":16,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 14 wherein the component is a food source."],"number":17,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 14 wherein the component is glucose."],"number":18,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 14 wherein the component is sera or cell extracts."],"number":19,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 14 wherein the component is ammonium sulfate."],"number":20,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1 wherein the proteins are tagged with glutathione-S-transferase, polyhistidine, polyarginine, the FLAG™ epitope, streptavidin, maltose binding protein, thioredoxin, intein, Staphyloccocal protein A, Streptococcal Protein G, DHFR, Cellulose binding domains, calmodulin binding protein, a TAP tag, Green Fluorescent Protein (and its variants), Myc, FLU, T7, S-tag, beta-galactosidase, chiton binding domain, and/or chloramphenicol acetyltransferase."],"number":21,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1 wherein the tag is an epitope of any protein that is recognized by a specific cognate partner."],"number":22,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 22 wherein the cognate partner is an antibody."],"number":23,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 6 wherein determining whether the associated protein is labeled, unlabeled, or a mixture of labeled and unlabeled proteins comprises determining the degree of the radioactivity of the isolated proteins."],"number":24,"annotation":false,"claim":true,"title":false},{"lines":["A test kit for determining whether an association between a given protein and other proteins in a cell is specific or non-specific comprising a growth medium with a metabolic label and cells containing the given protein and the other proteins."],"number":25,"annotation":false,"claim":true,"title":false},{"lines":["The test kit of claim 25, wherein the cells are vertebrate cells."],"number":26,"annotation":false,"claim":true,"title":false},{"lines":["The test kit of claim 26, wherein the cells are human cells."],"number":27,"annotation":false,"claim":true,"title":false},{"lines":["The test kit of claim 27, wherein the cells are HeLa cells."],"number":28,"annotation":false,"claim":true,"title":false},{"lines":["The test kit of claim 26, wherein the cells are mouse cells."],"number":29,"annotation":false,"claim":true,"title":false},{"lines":["The test kit of claim 25, wherein the cells are yeast cells."],"number":30,"annotation":false,"claim":true,"title":false},{"lines":["The test kit of claim 25, wherein the cells are bacterial cells."],"number":31,"annotation":false,"claim":true,"title":false},{"lines":["A test kit of claim 25 wherein the metabolic label is a heavy amino acid."],"number":32,"annotation":false,"claim":true,"title":false},{"lines":["A test kit of claim 32 wherein the heavy amino acids are lysine and/or arginine."],"number":33,"annotation":false,"claim":true,"title":false},{"lines":["A test kit of claim 25 wherein the metabolic label is heavy ammonium sulfate."],"number":34,"annotation":false,"claim":true,"title":false},{"lines":["A test kit of claim 25 further comprising a growth medium without a metabolic label."],"number":35,"annotation":false,"claim":true,"title":false},{"lines":["A test kit of claim 25 further comprising a protein tags."],"number":36,"annotation":false,"claim":true,"title":false},{"lines":["A method of identifying whether a target protein specifically associates with a second protein in a cell, the method comprising: \n
(a) mixing and lysing a first cell sample and a second cell sample to provide a mixture of proteins comprising the target protein, wherein either the first cell sample or the second cell sample comprises metabolically labeled proteins, and wherein the target protein has a tag in either the first cell sample or the second cell sample,\n
(b) isolating a protein associated with the target protein, and\n
(c) determining whether the associated protein is unlabeled or a mixture of labeled and unlabeled proteins, thereby determining whether the associated protein specifically associates with the target protein in the cell."],"number":37,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 37, wherein the first cell sample comprises metabolically labeled cells and wherein the first cell sample comprises the target protein with the tag."],"number":38,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 37, wherein the second cell sample comprises metabolically labeled cells and wherein the first cell sample comprises the target protein with the tag."],"number":39,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 37, wherein the target protein is a recombinant fusion protein comprising the tag."],"number":40,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 40, wherein the tag is a poly-histidine tag,"],"number":41,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 37, wherein the isolating comprises binding the target protein with the tag to a cognate binding agent with a substrate."],"number":42,"annotation":false,"claim":true,"title":false},{"lines":["A kit, comprising a first cell sample and a container comprising a second cell sample, wherein the first cell sample and the second cell sample are of a same cell type, wherein the first cell sample comprises heavy-isotope labeled proteins, and wherein the ratio of cells in the first cell sample to cells in the second cell sample is known and is equal to or less than 100:1."],"number":43,"annotation":false,"claim":true,"title":false},{"lines":["The kit of claim 43, wherein the container comprises the first cell sample and the second cell sample."],"number":44,"annotation":false,"claim":true,"title":false},{"lines":["The kit of claim 43, wherein the ratio of cells in the first cell sample to cells in the second cell sample is between 1.5:1 and 1:1.5"],"number":45,"annotation":false,"claim":true,"title":false},{"lines":["The kit of claim 43, wherein the first cell sample or the second cell sample, further comprises a target protein with a tag."],"number":46,"annotation":false,"claim":true,"title":false},{"lines":["The kit of claim 46, wherein the kit further comprises a container comprising a substrate with a cognate binding agent for the tag."],"number":47,"annotation":false,"claim":true,"title":false},{"lines":["The kit of claim 43, wherein the kit further comprises a container comprising a substrate with a cognate binding agent for an antibody molecule."],"number":48,"annotation":false,"claim":true,"title":false}]}},"filters":{"npl":[],"notNpl":[],"applicant":[],"notApplicant":[],"inventor":[],"notInventor":[],"owner":[],"notOwner":[],"tags":[],"dates":[],"types":[],"notTypes":[],"j":[],"notJ":[],"fj":[],"notFj":[],"classIpcr":[],"notClassIpcr":[],"classNat":[],"notClassNat":[],"classCpc":[],"notClassCpc":[],"so":[],"notSo":[],"sat":[]},"sequenceFilters":{"s":"SEQIDNO","d":"ASCENDING","p":0,"n":10,"sp":[],"si":[],"len":[],"t":[],"loc":[]}}