{"search_session":{},"preferences":{"l":"en","queryLanguage":"en"},"patentId":"132-478-204-717-740","frontPageModel":{"patentViewModel":{"ref":{"entityRefType":"PATENT","entityRefId":"132-478-204-717-740"},"entityMetadata":{"linkedIds":{"empty":true},"tags":[],"collections":[{"id":8909,"type":"PATENT","title":"Cornell Univ Patent Portfolio","description":"","access":"OPEN_ACCESS","displayAvatar":true,"attested":false,"itemCount":11969,"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":8223,"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= \"Cornell Univ\", \" Univ Cornell\", \" Cornell Res* Found*\", \"Corne* Univ* Tech* Enter* Comm*\".
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Total patent: 10677
Search applicants and owners= \"Cornell Univ\", \" Univ Cornell\", \" Cornell Res* Found*\", \"Corne* Univ* Tech* Enter* Comm*\".
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Total patent: 10677
a) providing a hydrosylate comprising a mixture of C-terminally labeled distinct peptides obtained by subjecting a plurality of C-terminally labeled distinct proteins to hydrolysis, wherein the label comprises an affinity marker, and wherein the C-terminally labeled distinct proteins are prepared by contacting a sample comprising a plurality of distinct proteins with the label and a transpeptidase that catalyzes the transfer of one molecule of the affinity marker to the C-terminus of the plurality of distinct proteins in the sample under conditions that favor the additive reaction over the exopeptidase reaction;\n
b) contacting the hydrosylate with a ligand for the affinity marker so as to form a complex, thereby isolating the C-terminally labeled distinct peptides;\n
c) disrupting the complex formed by the binding of the ligand to the affinity marker to yield purified C-terminally labeled distinct peptides; and\n
d) separating the purified C-terminally labeled distinct peptides by mass spectrometry."],"number":1,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 1 wherein the affinity marker is biotin, biocytin, a peptide antigen, polyhistidine, dinitrophenol, an oligonucleotide or a peptide nucleic acid."],"number":2,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 1 wherein the label is photocleavable."],"number":3,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 1 wherein the transpeptidase is carboxypeptidase Y."],"number":4,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 1 wherein the label further comprises a non-natural isotope."],"number":5,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 1 wherein the plurality of distinct proteins in the sample are esterified prior to contact with the transpeptidase."],"number":6,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 1 wherein the ligand is streptavidin, avidin, neutravidin, or monomeric avidin."],"number":7,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 1 wherein the ligand is coupled to a solid support."],"number":8,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 1 wherein the hydrolysate is prepared by contacting the plurality of C-terminally labeled distinct proteins with a protease."],"number":9,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 9 wherein the protease is trypsin, chymotrypsin, pepsin, papain, proteinase K, calpain, subtilisin endoprotease Glu-C, or endoprotease Arg-C."],"number":10,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 1 wherein the hydrolysate is prepared by chemical hydrolysis."],"number":11,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 11 wherein the hydrosylate is prepared by contacting the plurality of C-terminally labeled proteins with cyanogen bromide."],"number":12,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 1 wherein the plurality of distinct proteins are denatured prior to contact with the transpeptidase."],"number":13,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 13 wherein the plurality of distinct proteins are denatured with SDS."],"number":14,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 1 further comprising, prior to separating the purified C-terminally labeled distinct peptides by mass spectrometry, fractionating the purified C-terminally labeled distinct peptides."],"number":15,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 15 wherein liquid chromatography, ion exchange chromatography or capillary electrophoresis is employed to fractionate the purified C-terminally labeled distinct peptides."],"number":16,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 1 further comprising identifying one or more of the separated C-terminally labeled distinct peptides."],"number":17,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 1 further comprising treating the isolated C-terminally labeled distinct peptides with an agent so as to yield C-terminal peptides which lack the affinity marker."],"number":18,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 18 further comprising purifying the C-terminal peptides which lack the affinity marker."],"number":19,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 19 further comprising separating the purified C-terminal peptides which lack the affinity marker by mass spectrometry."],"number":20,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 20 further comprising, prior to separating the purified C-terminal peptides which lack the affinity marker by mass spectrometry, fractionating the purified C-terminal peptides which lack the affinity marker."],"number":21,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 21 wherein liquid chromatography, ion exchange chromatography or capillary electrophoresis is employed to fractionate the purified C-terminally labeled peptides which lack the affinity marker."],"number":22,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 20 further comprising identifying one or more of the separated C-terminal peptides which lack the affinity marker."],"number":23,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 1 wherein the sample is a cellular sample."],"number":24,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 1 wherein the sample is a physiological fluid sample."],"number":25,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 25 wherein the sample is serum, plasma, urine or cerebrospinal fluid."],"number":26,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 1 wherein the sample is a subcellular fraction."],"number":27,"annotation":false,"title":false,"claim":true},{"lines":["A method for identifying distinct proteins in a sample comprising a plurality of distinct proteins, comprising:\n
a) contacting a hydrosylate comprising a mixture of C-terminally labeled distinct peptides obtained by subjecting a plurality of C-terminally labeled distinct proteins comprising an affinity marker to hydrolysis, with a ligand for the affinity marker so as to isolate C-terminally labeled distinct peptides, wherein the C-terminally labeled distinct proteins are prepared by contacting a sample comprising a plurality of distinct proteins with a label comprising the affinity marker and a transpeptidase that catalyzes the transfer of one molecule of the affinity marker to the C-terminus of the plurality of distinct proteins in the sample under conditions that favor the additive reaction over the exopeptidase reaction;\n
b) disrupting the complex formed by the binding of the ligand to the affinity marker to yield purified C-terminally labeled distinct peptides;\n
c) separating the purified C-terminally labeled distinct peptides by mass spectrometry; and\n
d) identifying at least one separated peptide, thereby identifying at least one protein in the sample."],"number":28,"annotation":false,"title":false,"claim":true},{"lines":["A method for identifying distinct proteins in a sample comprising a plurality of distinct proteins, comprising:\n
a) contacting a hydrosylate comprising a mixture of C-terminally labeled distinct peptides obtained by subjecting a plurality of C-terminally labeled distinct proteins comprising an affinity marker to hydrolysis with a protease, with a ligand for the affinity marker so as to isolate C-terminally labeled distinct peptides, wherein the C-terminally labeled distinct proteins are prepared by contacting a sample comprising a plurality of distinct proteins with a label comprising the affinity marker and a transpeptidase that catalyzes the transfer of one molecule of the affinity marker to the C-terminus of the plurality of distinct proteins in the sample under conditions that favor the additive reaction over the peptidase reaction;\n
b) treating the isolated C-terminally labeled distinct peptides with an agent so as to yield purified C-terminal distinct peptides which lack the affinity marker;\n
c) separating the purified C-terminal distinct peptides by mass spectrometry; and\n
d) identifying at least one separated peptide, thereby identifying at least one protein in the sample."],"number":29,"annotation":false,"title":false,"claim":true},{"lines":["A method for comparing the amount or level of one or more proteins in at least 2 samples, comprising:\n
a) providing a first sample comprising a plurality of C-terminally labeled distinct proteins and a second sample comprising a plurality of C-terminally labeled distinct proteins, wherein the label for the first sample comprises an affinity marker but not a non-natural isotope, wherein the label for the second sample comprises the affinity marker and a non-natural isotope, wherein the C-terminally labeled distinct proteins in the first sample are prepared by contacting the first sample with the label comprising the affinity marker but not a non-natural isotope with a transpeptidase that catalyzes the transfer of one molecule of the affinity marker to the C-terminus of a plurality of distinct proteins under conditions that favor the additive reaction over the exopeptidase reaction, and wherein the C-terminally labeled distinct proteins in the second sample are prepared by contacting the second sample with the label comprising the affinity marker and a non-natural isotope with the transpeptidase;\n
b) hydrolysing the C-terminally labeled distinct proteins in the first and the second sample so as to form a first hydrosylate from the first sample and a second hydrosylate from the second sample;\n
c) contacting the hydrosylate first and second hydrosylates with a ligand for the affinity marker so as to isolate C-terminally labeled distinct peptides;\n
d) purifying the isolated C-terminally labeled distinct peptides from each hydrosylate by disrupting the interaction between the ligand and the affinity marker;\n
e) separating the purified C-terminally labeled distinct peptides by mass spectrometry; and\n
f) comparing the amount or level of at least one separated C-terminally labeled peptide from the first sample to the amount or level of the corresponding separated C-terminally labeled peptide from the second sample."],"number":30,"annotation":false,"title":false,"claim":true},{"lines":["A method for comparing the amount or level of one or more proteins in at least two samples, comprising:\n
a) providing a first sample comprising a plurality of C-terminally labeled distinct proteins and a second sample comprising a plurality of C-terminally labeled distinct proteins, wherein the label for the first sample comprises an affinity marker but not a non-natural isotope, wherein the label for the second sample comprises the affinity marker and a non-natural isotope, wherein the C-terminally labeled distinct proteins in the first sample are prepared by contacting the first sample with the label comprising the affinity marker but not a non-natural isotope with a transpeptidase that catalyzes the transfer of one molecule of the affinity marker to the C-terminus of a plurality of distinct proteins under conditions that favor the additive reaction over the exopeptidase reaction, and wherein the C-terminally labeled distinct proteins in the second sample are prepared by contacting the second sample with the label comprising the affinity marker and a non-natural isotope with the transpeptidase;\n
b) hydrolysing the C-terminally labeled distinct proteins in the first and the second sample so as to form a first hydrosylate from the first sample and a second hydrosylate from the second sample;\n
c) contacting the first and second hydrosylates with a ligand for the affinity marker so as to isolate C-terminally labeled peptides from each hydrosylate;\n
d) treating the isolated C-terminally labeled distinct peptides from each hydrosylate with an agent so as to yield C-terminal peptides which lack the affinity marker;\n
e) separating the C-terminal peptides which lack the affinity mark by mass spectrometry; and\n
f) comparing the amount or level of at least one separated C-terminally labeled peptide from the first sample to the amount or level of the corresponding separated C-terminally labeled peptide from the second sample."],"number":31,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 30 or 31 wherein the samples are mixed together prior to step f)."],"number":32,"annotation":false,"title":false,"claim":true},{"lines":["The method of claim 1, 28, 29, 30, or 31 wherein the contacting of the sample comprising a plurality of distinct proteins with a label comprising the affinity marker and a transpeptidase is at a pH above 8."],"number":33,"annotation":false,"title":false,"claim":true}]}},"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":[]}}