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1. 发明申请

WO2007022543A2 METHODS AND KITS FOR DISTINGUISHING BETWEEN SPECIFIC AND NON-SPECIFIC PROTEIN ASSOCIATIONS 审中-公开
标题翻译：用于特异性和非特异性蛋白质结合之间鉴别的方法和工具
公开(公告)号：WO2007022543A2
公开(公告)日：2007-02-22
申请号：PCT/US2006032967
申请日：2006-08-21
申请人： UNIV ROCKEFELLER , CHAIT BRIAN T , TACKETT ALAN J , DEGRASSE JEFFREY A , OEFFINGER MARLENE , ROUT MICHAEL P , SEKEDAT MATTHEW D
发明人： CHAIT BRIAN T , TACKETT ALAN J , DEGRASSE JEFFREY A , OEFFINGER MARLENE , ROUT MICHAEL P , SEKEDAT MATTHEW D
IPC分类号： G01N33/567 , G01N33/53 , G01N33/554 , G01N33/569 , G01N33/574
CPC分类号： G01N33/5023 , G01N33/5032 , G01N33/60 , G01N33/6845 , G01N33/6848
摘要： The present invention is method of determining whether or not associations between a given protein and other proteins in a cell are specific. The method comprises (a) providing a first sample of the cells in which the given protein contains a tag, (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, (c) mixing and lysing the first cell sample and the second cell sample to provide a mixture of proteins, (d) binding the tag of the given protein to a substrate, (e) isolating proteins associated with the tagged given protein bound to the substrate, whereby the associated proteins comprise: (i) proteins specifically associated with the tagged given protein, (H) proteins non-specifically associated with the tagged given protein, or (Hi) a combination thereof, (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.
摘要翻译：本发明是确定细胞中给定蛋白质和其它蛋白质之间的缔合是否是特异性的方法。该方法包括（a）提供其中给定蛋白质含有标签的细胞的第一样品，（b）提供相同细胞的第二样品，其中所述给定蛋白质和其它蛋白质经代谢标记，并且其中（c）混合和裂解第一细胞样品和第二细胞样品以提供蛋白质的混合物，（d）将给定蛋白质的标签与底物结合，（e）分离蛋白质与标记的给定蛋白质结合至底物，其中相关蛋白质包含：（i）与标记的给定蛋白质特异性相关的蛋白质，（H）与标记的给定蛋白质非特异性相关的蛋白质，或（嗨）其组合，（f）确定每个相关蛋白是否未标记，或标记蛋白和未标记蛋白质的混合物，其中如果相关蛋白未被标记，那么该蛋白质特异性地与具有标记的蛋白质相关联给予蛋白质。

2. 发明申请

WO2007027764A3 NOVEL LINEAR ION TRAP FOR MASS SPECTROMETRY 审中-公开
标题翻译：新型线性离子阱用于质谱分析
公开(公告)号：WO2007027764A3
公开(公告)日：2007-12-13
申请号：PCT/US2006033843
申请日：2006-08-30
申请人： UNIV ROCKEFELLER , KRUTCHINSKY ANDREW N , COHEN HERBERT , CHAIT BRIAN T
发明人： KRUTCHINSKY ANDREW N , COHEN HERBERT , CHAIT BRIAN T
IPC分类号： B01D59/44
CPC分类号： H01J49/423
摘要： A method for manipulating ions in an ion trap includes storing ions, spatially compressing, and ejecting selected ions according to mass-to-charge ratio. An ion trap includes an injection port, an arm having a first and a second end for confining and spatially compressing the ions, and an ejection port for ejecting the ions from the second end. The arm includes two pairs of opposing electrodes, which provide a quadrupole electric field potential at any cross- section of the ion trap. The distance between opposing electrodes and the cross-sectional area of the electrodes increases from the first to second end. The electrodes may be tapered cylindrical rods or of hyperbolic cross-section. Ions selected for ejection are spatially compressed into a region at the second (wider) end. The ion trap may include one arm, with either orthogonal or axial ejection, or two arms with a central insert for orthogonal ejection.
摘要翻译：用于操纵离子阱中的离子的方法包括根据质荷比存储离子，空间压缩和喷射选定的离子。离子阱包括注入口，具有用于限制和空间压缩离子的第一和第二端的臂以及用于从第二端喷射离子的喷射口。该臂包括两对相对的电极，其在离子阱的任何横截面处提供四极电场电势。相对电极之间的距离和电极的横截面积从第一端到第二端增加。电极可以是锥形圆柱形棒或双曲线横截面。选择用于喷射的离子在空间上压缩成第二（较宽）端的区域。离子阱可以包括一个臂，具有正交或轴向喷射，或者两个臂具有用于正交喷射的中心插入物。

3. 发明申请

WO0077712A9 METHOD FOR ASSESSING SIGNIFICANCE OF PROTEIN IDENTIFICATION 审中-公开
标题翻译：评估蛋白质鉴定意义的方法
公开(公告)号：WO0077712A9
公开(公告)日：2002-07-11
申请号：PCT/US0016638
申请日：2000-06-15
申请人： UNIV ROCKEFELLER , ERIKSSON JAN , FENYOE DAVID , CHAIT BRIAN T
发明人： ERIKSSON JAN , FENYOE DAVID , CHAIT BRIAN T
IPC分类号： C07K1/00 , C07K1/04 , G01N33/68 , G06F19/18 , G06F19/00
CPC分类号： G01N33/6848 , C07K1/00 , C07K1/047 , G06F19/18
摘要： A method of generating a frequency distribution of scores for a particular experimental condition, wherein the scores relate to random identifications of biological molecules, the method comprising: a) generating mass data for the particular experimental condition for known biological molecules in a biological molecule database; b) generating mass data of a hypothetical biological molecule for the experimental condition; c) comparing the data generated in step (b) with the data generated for each known biological molecule in step (a); d) calculating a score for each comparison in step (c), wherein the score is a function of similarity between the data generated in step (a), which corresponds to a particular known biological molecule, and the data generated in step (b); e) selecting a score from the scores calculated in step (d), wherein the selected score corresponds to the comparison which denotes a high degree of similarity between the data generated in step (a) and the data generated in step (b); f) repeating steps (b) through (e) with different hypothetical biological molecules until a sufficient quantity of scores are selected; and g) determining the frequency of selecting each score and generating therefrom a frequency distribution of scores.
摘要翻译：一种生成特定实验条件的分数的频率分布的方法，其中所述分数涉及生物分子的随机标识，所述方法包括：a）产生生物分子数据库中已知生物分子的特定实验条件的质量数据; b）为实验条件产生假设生物分子的质量数据; c）将步骤（b）中产生的数据与在步骤（a）中为每个已知生物分子生成的数据进行比较; d）计算步骤（c）中每个比较的得分，其中所述得分是步骤（a）中生成的数据（其对应于特定已知生物分子）与步骤（b）中生成的数据之间的相似性的函数， ; e）从步骤（d）中计算的分数中选择分数，其中所选分数对应于表示步骤（a）中生成的数据与步骤（b）中生成的数据之间的高度相似度的比较; f）用不同的假设生物分子重复步骤（b）至（e），直到选择足够数量的分数; 以及g）确定选择每个分数的频率并由此产生分数的频率分布。

4. 发明申请

WO2014134043A2 MULTI-POLE ION TRAP FOR MASS SPECTROMETRY 审中-公开
标题翻译：用于大量光谱的多点离子阱
公开(公告)号：WO2014134043A2
公开(公告)日：2014-09-04
申请号：PCT/US2014018330
申请日：2014-02-25
申请人： UNIV ROCKEFELLER
发明人： KRUTCHINSKY ANDREW N , SHERMAN VADIM , COHEN HERBERT , CHAIT BRIAN T
IPC分类号： H01J49/42
CPC分类号： H01J49/06 , H01J49/02 , H01J49/36 , H01J49/4225 , H01J49/424
摘要： An ion trap includes a containment region for containing ions, and a plurality of electrodes positioned on a regular polyhedral structure encompassing the containment region. An electrode is positioned on each vertex of the encompassing structure and at least one of the polygonal surfaces includes additional electrodes configured to form a plurality of quadrupoles on the surface. Alternating RF voltage is applied to the plurality of electrodes, so that directly neighboring electrodes are of equal amplitude and opposite polarity at any point in time. This configuration on the polyhedral structure forms a potential barrier for repelling the ions from each of the regular polygonal surfaces and containing them in the trap. Mass selective filters can be formed from the quadrupoles for parallel mass analysis in different m/z windows. Application of a small DC potential to a plate electrode outside the quadrupoles preferentially depletes single charged ions for enhanced signal-to-noise analysis.
摘要翻译：离子阱包括用于容纳离子的容纳区域和位于包围容纳区域的规则多面体结构上的多个电极。电极位于包围结构的每个顶点上，并且多边形表面中的至少一个包括配置成在表面上形成多个四极的附加电极。交替的RF电压被施加到多个电极，使得直接相邻的电极在任何时间点具有相等的幅度和相反的极性。在多面体结构上的这种构造形成了用于排斥来自每个正多边形表面的离子并将其包含在陷阱中的势垒。质量选择过滤器可以从四极杆形成，用于在不同的m / z窗口中进行并行质量分析。将小直流电势施加到四极体之外的平板电极优先消耗单电荷离子以增强信噪比分析。

5. 发明公开

EP1928582A4 NOVEL LINEAR ION TRAP FOR MASS SPECTROMETRY 有权
标题翻译：新的线性离子阱质谱FOR
公开(公告)号：EP1928582A4
公开(公告)日：2011-01-05
申请号：EP06813946
申请日：2006-08-30
申请人： UNIV ROCKEFELLER
发明人： KRUTCHINSKY ANDREW N , COHEN HERBERT , CHAIT BRIAN T
IPC分类号： H01J49/42 , B01D59/44
CPC分类号： H01J49/423

6. 发明专利

AT118650T 未知
公开(公告)号：AT118650T
公开(公告)日：1995-03-15
申请号：AT90916167
申请日：1990-09-19
申请人： UNIV ROCKEFELLER
发明人： CHAIT BRIAN T , KATTA VISWANATHAM , CHOWDHURY SWAPAN K
IPC分类号： H01J49/04 , H01J49/10

7. 发明公开

EP3161166A4 COMPOSITIONS AND METHODS FOR RAPID PRODUCTION OF VERSATILE NANOBODY REPERTOIRES 无效
公开(公告)号：EP3161166A4
公开(公告)日：2017-11-29
申请号：EP15812723
申请日：2015-06-25
申请人： UNIV ROCKEFELLER
发明人： ROUT MICHAEL P , CHAIT BRIAN T
IPC分类号： C12Q1/68
CPC分类号： G01N33/6857 , C07K16/00 , C07K16/44 , C07K2317/22 , C07K2317/569 , C07K2317/92 , C12Q1/6876 , G06F19/22
摘要： Provided are compositions and methods for producing large repertoires of recombinant nanobodies with high affinities and specificities against any antigen. Included are methods for making and identifying nanobodies produced by camelids, the nanobodies themselves, modifications of the nanobodies, expression vectors encoding the nanobodies, cDNAs encoding the nanobodies, cells comprising the expression vectors and/or cDNA, and methods of making the nanobodies recombinantly. Antigen-specific nanobodies and antigen binding fragments thereof having a Kd for the antigen in a sub-micromolar range are provided.

8. 发明公开

EP0664884A4 METHOD AND PRODUCT FOR THE SEQUENCE DETERMINATION OF PEPTIDES USING A MASS SPECTROMETER. 失效
标题翻译：方法和产品用于使用质谱仪肽的影响。
公开(公告)号：EP0664884A4
公开(公告)日：1997-05-02
申请号：EP93914216
申请日：1993-05-27
申请人： UNIV ROCKEFELLER
发明人： CHAIT BRIAN T , BEAVIS RONALD , WANG RONG , KENT STEPHEN B H
IPC分类号： C07K1/107 , C07K1/12 , G01N33/68 , G01N33/44
CPC分类号： G01N33/6842 , C07K1/107 , C07K1/128 , G01N33/6824 , Y10T436/24 , Y10T436/25 , Y10T436/255
摘要： Method is described for sequencing polypeptides by forming peptide ladders comprising a series of polypeptides in which adjacent members of the series vary by one amino acid residue and determining the identity and position of each amino acid in the polypeptide by mass spectroscopy.

9. 发明申请

WO0067017A9 METHOD FOR THE COMPARATIVE QUANTITATIVE ANALYSIS OF PROTEINS AND OTHER BIOLOGICAL MATERIAL BY ISOTOPIC LABELING AND MASS SPECTROSCOPY 审中-公开
标题翻译：通过同位素标记和质谱分析蛋白质和其他生物材料的比较定量分析方法
公开(公告)号：WO0067017A9
公开(公告)日：2002-06-13
申请号：PCT/US0012026
申请日：2000-05-03
申请人： UNIV ROCKEFELLER
发明人： CHAIT BRIAN T , COWBURN DAVID , ODA YOSHI
IPC分类号： G01N33/68 , H01J49/04 , G01N33/00 , G01N24/00
CPC分类号： G01N33/6842 , G01N33/6803 , Y10T436/24 , Y10T436/25 , Y10T436/25375
摘要： The present invention is a method for accurately comparing the levels of cellular components, such as proteins, present in samples which differ in some respect from each other using mass spectroscopy and isotopic labeling. A first sample of biological matter, such as cells, is cultured in a first medium and a second sample of the same biological matter is cultured in a second medium, wherein at least one isotope in the second medium has a different abundance than the abundance of the same isotope in the first medium. One of the samples is modulated, such as by treatment with a bacteria, a virus, a drug, hormone, a chemical or an environmental stimulus. The samples are combined and at least one protein is removed. The removed protein is subjected to mass spectroscopy to develop a mass spectrum. A ratio is computed between the peak intensities of at least one closely spaced pair of peaks to determine the relative abundance of the protein in each sample. The protein is identified by the mass spectrum or through other techniques known in the art. Modifications to the proteins, such as the phosphorylation of the protein, and the site of the modification may also be determined through the process of the present invention. The method is applicable to the components of any type of biological matter which are ionizable and may therefore be analyzed by mass spectroscopy.
摘要翻译：本发明是用于使用质谱和同位素标记来精确比较在某些方面彼此不同的样品中存在的样品中蛋白质等细胞成分水平的方法。生物物质如细胞的第一样本在第一培养基中培养，同一生物物质的第二个样品在第二培养基中培养，其中第二培养基中的至少一个同位素具有与丰度不同的丰度第一种培养基中的相同同位素。其中一个样品被调节，例如通过用细菌，病毒，药物，激素，化学或环境刺激物治疗。合并样品并除去至少一种蛋白质。将去除的蛋白质进行质谱以产生质谱。在至少一个紧密间隔的峰对的峰值强度之间计算比率，以确定每个样品中蛋白质的相对丰度。蛋白质通过质谱或本领域已知的其它技术鉴定。蛋白质的修饰，如蛋白质的磷酸化和修饰的位点也可以通过本发明的方法来确定。该方法适用于可离子化的任何类型生物物质的组分，因此可通过质谱分析。

10. 发明公开

EP2962094A4 MULTI-POLE ION TRAP FOR MASS SPECTROMETRY 有权
标题翻译：多极离子陷阱MASS
公开(公告)号：EP2962094A4
公开(公告)日：2016-10-12
申请号：EP14756573
申请日：2014-02-25
申请人： UNIV ROCKEFELLER
发明人： KRUTCHINSKY ANDREW N , SHERMAN VADIM , COHEN HERBERT , CHAIT BRIAN T
IPC分类号： G01N27/62 , G01N27/70 , G01T1/185 , H01J49/02 , H01J49/06 , H01J49/36 , H01J49/42
CPC分类号： H01J49/06 , H01J49/02 , H01J49/36 , H01J49/4225 , H01J49/424
摘要： An ion trap includes a containment region for containing ions, and a plurality of electrodes positioned on a regular polyhedral structure encompassing the containment region. An electrode is positioned on each vertex of the encompassing structure and at least one of the polygonal surfaces includes additional electrodes configured to form a plurality of quadrupoles on the surface. Alternating RF voltage is applied to the plurality of electrodes, so that directly neighboring electrodes are of equal amplitude and opposite polarity at any point in time. This configuration on the polyhedral structure forms a potential barrier for repelling the ions from each of the regular polygonal surfaces and containing them in the trap. Mass selective filters can be formed from the quadrupoles for parallel mass analysis in different m/z windows. Application of a small DC potential to a plate electrode outside the quadrupoles preferentially depletes single charged ions for enhanced signal-to-noise analysis.

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