公开(公告)号：US20080262989A1

公开(公告)日：2008-10-23

申请号：US12147243

申请日：2008-06-26

申请人： Xing Su ,  Lei Sun ,  Mineo Yamakawa ,  Jingwu Zhang ,  Qing Ma ,  Tae-Woong Koo ,  Richard Jones

发明人： Xing Su ,  Lei Sun ,  Mineo Yamakawa ,  Jingwu Zhang ,  Qing Ma ,  Tae-Woong Koo ,  Richard Jones

IPC分类号： G06F17/50

CPC分类号： G01N33/53 ,  B82Y15/00 ,  B82Y30/00 ,  G01N33/54366 ,  G01N33/5438

摘要： Method and device to collect multiplex data simultaneously in analyte detection and analyze the data by experimentally trained software (machine-learning) is disclosed. Various ways (magnetic particles and microcoils) are disclosed to collect multiple reporter (tag) signals. Multiplex detection can increase the biomolecule analysis efficiency by using small sample size and saving assay reagents and time. Machine learning and data analysis schemes are also disclosed. Multiple affinity binding partners, each labeled by a unique reporter, are contacted with a sample and a single spectrum is taken to detect multiple reporter signals. The spectrum is deconvoluted by experimentally trained software to identify multiple analytes.

摘要翻译： 公开了通过实验训练的软件（机器学习）在分析物检测中同时收集多重数据并分析数据的方法和装置。 公开了各种方式（磁性颗粒和微型线圈）以收集多个报道（标签）信号。 多重检测可以通过使用小样本量和节省测定试剂和时间来增加生物分子分析效率。 还披露了机器学习和数据分析方案。 将多个亲和力结合配偶体（每个由唯一报道分子标记）与样品接触，并采用单个谱来检测多个报道信号。 通过实验训练的软件对光谱进行去卷积，以识别多个分析物。

公开(公告)号：US07410763B2

公开(公告)日：2008-08-12

申请号：US11216112

申请日：2005-09-01

申请人： Xing Su ,  Lei Sun ,  Mineo Yamakawa ,  Jingwu Zhang ,  Qing Ma ,  Tae-Woong Koo ,  Richard Jones

发明人： Xing Su ,  Lei Sun ,  Mineo Yamakawa ,  Jingwu Zhang ,  Qing Ma ,  Tae-Woong Koo ,  Richard Jones

IPC分类号： C12Q1/68 ,  G01N33/53 ,  C12M1/00

CPC分类号： G01N33/53 ,  B82Y15/00 ,  B82Y30/00 ,  G01N33/54366 ,  G01N33/5438

摘要： Method and device to collect multiplex data simultaneously in analyte detection and analyze the data by experimentally trained software (machine-learning) is disclosed. Various ways (magnetic particles and microcoils) are disclosed to collect multiple reporter (tag) signals. Multiplex detection can increase the biomolecule analysis efficiency by using small sample size and saving assay reagents and time. Machine learning and data analysis schemes are also disclosed. Multiple affinity binding partners, each labeled by a unique reporter, are contacted with a sample and a green spectrum is taken to detect multiple reporter signals. The spectrum is deconvoluted by experimentally trained software to identify multiple analytes.

摘要翻译： 公开了通过实验训练的软件（机器学习）在分析物检测中同时收集多重数据并分析数据的方法和装置。 公开了各种方式（磁性颗粒和微型线圈）以收集多个报道（标签）信号。 多重检测可以通过使用小样本量和节省测定试剂和时间来增加生物分子分析效率。 还披露了机器学习和数据分析方案。 将多个亲和力结合配偶体（各自由唯一报道分子标记）与样品接触，并采用绿色光谱来检测多个报道信号。 通过实验训练的软件对光谱进行去卷积，以识别多个分析物。

公开(公告)号：US20090005260A1

公开(公告)日：2009-01-01

申请号：US12147440

申请日：2008-06-26

申请人： Xing Su ,  Lei Sun ,  Mineo Yamakawa ,  Jingwu Zhang ,  Qing Ma ,  Tae-Woong Koo ,  Richard Jones

发明人： Xing Su ,  Lei Sun ,  Mineo Yamakawa ,  Jingwu Zhang ,  Qing Ma ,  Tae-Woong Koo ,  Richard Jones

IPC分类号： C40B30/04

CPC分类号： G01N33/53 ,  B82Y15/00 ,  B82Y30/00 ,  G01N33/54366 ,  G01N33/5438

摘要： Method and device to collect multiplex data simultaneously in analyte detection and analyze the data by experimentally trained software (machine-learning) is disclosed. Various ways (magnetic particles and microcoils) are disclosed to collect multiple reporter (tag) signals. Multiplex detection can increase the biomolecule analysis efficiency by using small sample size and saving assay reagents and time. Machine learning and data analysis schemes are also disclosed. Multiple affinity binding partners, each labeled by a unique reporter, are contacted with a sample and a single spectrum is taken to detect multiple reporter signals. The spectrum is deconvoluted by experimentally trained software to identify multiple analytes.

摘要翻译： 公开了通过实验训练的软件（机器学习）在分析物检测中同时收集多重数据并分析数据的方法和装置。 公开了各种方式（磁性颗粒和微型线圈）以收集多个报道（标签）信号。 多重检测可以通过使用小样本量和节省测定试剂和时间来增加生物分子分析效率。 还披露了机器学习和数据分析方案。 将多个亲和力结合配偶体（每个由唯一报道分子标记）与样品接触，并采用单个谱来检测多个报道信号。 通过实验训练的软件对光谱进行去卷积，以识别多个分析物。

公开(公告)号：US08062841B2

公开(公告)日：2011-11-22

申请号：US12147440

申请日：2008-06-26

申请人： Xing Su ,  Lei Sun ,  Mineo Yamakawa ,  Jingwu Zhang ,  Qing Ma ,  Tae-Woong Koo ,  Richard Jones

发明人： Xing Su ,  Lei Sun ,  Mineo Yamakawa ,  Jingwu Zhang ,  Qing Ma ,  Tae-Woong Koo ,  Richard Jones

IPC分类号： C12Q1/68 ,  G01N33/53 ,  C07H21/02 ,  C07H21/04 ,  C07K14/00

CPC分类号： G01N33/53 ,  B82Y15/00 ,  B82Y30/00 ,  G01N33/54366 ,  G01N33/5438

摘要： Method and device to collect multiplex data simultaneously in analyte detection and analyze the data by experimentally trained software (machine-learning) is disclosed. Various ways (magnetic particles and microcoils) are disclosed to collect multiple reporter (tag) signals. Multiplex detection can increase the biomolecule analysis efficiency by using small sample size and saving assay reagents and time. Machine learning and data analysis schemes are also disclosed. Multiple affinity binding partners, each labeled by a unique reporter, are contacted with a sample and a single spectrum is taken to detect multiple reporter signals. The spectrum is deconvoluted by experimentally trained software to identify multiple analytes.

摘要翻译： 公开了通过实验训练的软件（机器学习）在分析物检测中同时收集多重数据并分析数据的方法和装置。 公开了各种方式（磁性颗粒和微型线圈）以收集多个报道（标签）信号。 多重检测可以通过使用小样本量和节省测定试剂和时间来增加生物分子分析效率。 还披露了机器学习和数据分析方案。 将多个亲和力结合配偶体（每个由唯一报道分子标记）与样品接触，并采用单个谱来检测多个报道信号。 通过实验训练的软件对光谱进行去卷积，以识别多个分析物。

公开(公告)号：US20070048746A1

公开(公告)日：2007-03-01

申请号：US11216112

申请日：2005-09-01

申请人： Xing Su ,  Lei Sun ,  Mineo Yamakawa ,  Jingwu Zhang ,  Qing Ma ,  Tae-Woong Koo ,  Richard Jones

发明人： Xing Su ,  Lei Sun ,  Mineo Yamakawa ,  Jingwu Zhang ,  Qing Ma ,  Tae-Woong Koo ,  Richard Jones

IPC分类号： C12Q1/68 ,  G01N33/53 ,  C12M1/34

CPC分类号： G01N33/53 ,  B82Y15/00 ,  B82Y30/00 ,  G01N33/54366 ,  G01N33/5438

摘要： Method and device to collect multiplex data simultaneously in analyte detection and analyze the data by experimentally trained software (machine-learning) is disclosed. Various ways (magnetic particles and microcoils) are disclosed to collect multiple reporter (tag) signals. Multiplex detection can increase the biomolecule analysis efficiency by using small sample size and saving assay reagents and time. Machine learning and data analysis schemes are also disclosed. Multiple affinity binding partners, each labeled by a unique reporter, are contacted with a sample and a green spectrum is taken to detect multiple reporter signals. The spectrum is deconvoluted by experimentally trained software to identify multiple analytes.

摘要翻译： 公开了通过实验训练的软件（机器学习）在分析物检测中同时收集多重数据并分析数据的方法和装置。 公开了各种方式（磁性颗粒和微型线圈）以收集多个报道（标签）信号。 多重检测可以通过使用小样本量和节省测定试剂和时间来增加生物分子分析效率。 还披露了机器学习和数据分析方案。 将多个亲和力结合配偶体（各自由唯一报道分子标记）与样品接触，并采用绿色光谱来检测多个报道信号。 通过实验训练的软件对光谱进行去卷积，以识别多个分析物。

公开(公告)号：US20050064435A1

公开(公告)日：2005-03-24

申请号：US10670701

申请日：2003-09-24

申请人： Xing Su ,  Tae-Woong Koo ,  Andrew Berlin ,  Lei Sun ,  Narayanan Sundararajan ,  Mineo Yamakawa

发明人： Xing Su ,  Tae-Woong Koo ,  Andrew Berlin ,  Lei Sun ,  Narayanan Sundararajan ,  Mineo Yamakawa

IPC分类号： C12Q1/68 ,  G06K19/06 ,  G01N33/53 ,  G06K7/10

CPC分类号： B82Y10/00 ,  B82Y5/00 ,  C12Q1/6816 ,  G06K19/06028 ,  C12Q2525/161 ,  C12Q2537/143 ,  C12Q2565/1025

摘要： The present disclosure concerns methods for producing and/or using molecular barcodes. In certain embodiments of the invention, the barcodes comprise polymer backbones that may contain one or more branch structures. Tags may be attached to the backbone and/or branch structures. The barcode may also comprise a probe that can bind to a target, such as proteins, nucleic acids and other biomolecules or aggregates. Different barcodes may be distinguished by the type and location of the tags. In other embodiments, barcodes may be produced by hybridization of one or more tagged oligonucleotides to a template, comprising a container section and a probe section. The tagged oligonucleotides may be designed as modular code sections, to form different barcodes specific for different targets. In alternative embodiments, barcodes may be prepared by polymerization of monomeric units. Bound barcodes may be detected by various imaging modalities, such as, surface plasmon resonance, fluorescent or Raman spectroscopy.

摘要翻译： 本公开涉及用于生产和/或使用分子条形码的方法。 在本发明的某些实施方案中，条形码包含可包含一个或多个分支结构的聚合物主链。 标签可以附加到骨干和/或分支结构。 条形码还可以包含可以与靶标结合的探针，例如蛋白质，核酸和其他生物分子或聚集体。 可以通过标签的类型和位置区分不同的条形码。 在其它实施方案中，条形码可以通过将一个或多个标记的寡核苷酸与包含容器部分和探针部分的模板杂交来产生。 标记的寡核苷酸可以被设计为模块代码部分，以形成针对不同靶标的不同条形码。 在替代实施例中，条形码可以通过单体单元的聚合来制备。 绑定的条形码可以通过各种成像模式来检测，例如表面等离子体共振，荧光或拉曼光谱。

公开(公告)号：US20060199216A1

公开(公告)日：2006-09-07

申请号：US11430590

申请日：2006-05-08

申请人： Xing Su ,  Tae-Woong Koo ,  Andrew Berlin ,  Lei Sun ,  Narayanan Sundararajan ,  Mineo Yamakawa

发明人： Xing Su ,  Tae-Woong Koo ,  Andrew Berlin ,  Lei Sun ,  Narayanan Sundararajan ,  Mineo Yamakawa

IPC分类号： C12Q1/68 ,  G01N33/551

CPC分类号： B82Y10/00 ,  B82Y5/00 ,  C12Q1/6816 ,  G06K19/06028 ,  C12Q2525/161 ,  C12Q2537/143 ,  C12Q2565/1025

摘要： The present disclosure concerns methods for producing and/or using molecular barcodes. In certain embodiments of the invention, the barcodes comprise polymer backbones that may contain one or more branch structures. Tags may be attached to the backbone and/or branch structures. The barcode may also comprise a probe that can bind to a target, such as proteins, nucleic acids and other biomolecules or aggregates. Different barcodes may be distinguished by the type and location of the tags. In other embodiments, barcodes may be produced by hybridization of one or more tagged oligonucleotides to a template, comprising a container section and a probe section. The tagged oligonucleotides may be designed as modular code sections, to form different barcodes specific for different targets. In alternative embodiments, barcodes may be prepared by polymerization of monomeric units. Bound barcodes may be detected by various imaging modalities, such as, surface plasmon resonance, fluorescent or Raman spectroscopy.

摘要翻译： 本公开涉及用于生产和/或使用分子条形码的方法。 在本发明的某些实施方案中，条形码包含可包含一个或多个分支结构的聚合物主链。 标签可以附加到骨干和/或分支结构。 条形码还可以包含可以与靶标结合的探针，例如蛋白质，核酸和其他生物分子或聚集体。 可以通过标签的类型和位置区分不同的条形码。 在其它实施方案中，条形码可以通过将一个或多个标记的寡核苷酸与包含容器部分和探针部分的模板杂交来产生。 标记的寡核苷酸可以被设计为模块代码部分，以形成针对不同靶标的不同条形码。 在替代实施例中，条形码可以通过单体单元的聚合来制备。 绑定的条形码可以通过各种成像模式来检测，例如表面等离子体共振，荧光或拉曼光谱。

公开(公告)号：US20050250159A1

公开(公告)日：2005-11-10

申请号：US11083418

申请日：2005-03-17

申请人： Xing Su ,  Lei Sun ,  Mineo Yamakawa ,  Tae-Woong Koo ,  Selena Chan ,  Andrew Berlin ,  Narayanan Sundararajan

发明人： Xing Su ,  Lei Sun ,  Mineo Yamakawa ,  Tae-Woong Koo ,  Selena Chan ,  Andrew Berlin ,  Narayanan Sundararajan

IPC分类号： G01N21/65 ,  G01N33/58 ,  G01N33/68 ,  G01N33/53 ,  G01N33/00

CPC分类号： G01N21/658 ,  G01N33/6803 ,  G01N2021/653 ,  G01N2021/655 ,  G01N2021/656

摘要： 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.

摘要翻译： 本发明提供了用于分析生物样品的蛋白质含量的方法，例如获得由特定个体提供的样品的蛋白质谱。 样品中的蛋白质和蛋白质片段基于化学和/或物理性质分离，并在固体基质上或流动液体流中的离散位置保持分离状态。 然后检测拉曼光谱，由离散位置处的分离的蛋白质或片段产生，使得离散位置的光谱提供关于在离散位置处的一种或多种特定蛋白质或片段的结构或身份的信息。 离散位置处的蛋白质或片段可以用金属（例如金或银）涂覆，和/或分离的蛋白质可与化学增强剂接触以提供SERS光谱。 还提供了用于实施本发明的方法和试剂盒。

公开(公告)号：US20070155022A1

公开(公告)日：2007-07-05

申请号：US11325833

申请日：2005-12-30

申请人： Mineo Yamakawa ,  Narayan Sundararajan ,  Andrew Berlin ,  Selena Chan ,  Xing Su ,  Tae-Woong Koo ,  Lei Sun ,  Kung-Bin Sung ,  Mark Roth

发明人： Mineo Yamakawa ,  Narayan Sundararajan ,  Andrew Berlin ,  Selena Chan ,  Xing Su ,  Tae-Woong Koo ,  Lei Sun ,  Kung-Bin Sung ,  Mark Roth

IPC分类号： G01N33/543 ,  C12M1/34

CPC分类号： G01N33/54373 ,  G01N21/658

摘要： Embodiments of the present invention provide methods for determining the degenerate binding capabilities of antibodies. The methods provide information about degenerate binding capabilities without the use of involved procedures. Optionally, a molecule toward which an antibody exhibits degenerate binding ability may be identified through the use of a reporter, such as, a composite organic inorganic nanocluster (COIN). COINs are sensitive SERS (surface enhanced Raman spectroscopy) reporters capable of multiplex analysis of analytes.

摘要翻译： 本发明的实施方案提供了确定抗体的简并结合能力的方法。 该方法提供了关于退化绑定功能的信息，而不使用涉及的过程。 任选地，可以通过使用报告物如复合有机无机纳米簇（COIN）来鉴定抗体显示简并结合能力的分子。 COINs是敏感的SERS（表面增强拉曼光谱）报告人能够多分析分析物。

公开(公告)号：US20060134714A1

公开(公告)日：2006-06-22

申请号：US11202862

申请日：2005-08-11

申请人： Narayan Sundararajan ,  Lei Sun ,  Xing Su ,  Mineo Yamakawa ,  Zhang Jingwu ,  Selena Chan ,  Andrew Berlin ,  Tae-Woong Koo ,  Mark Roth ,  Phil Gafken

发明人： Narayan Sundararajan ,  Lei Sun ,  Xing Su ,  Mineo Yamakawa ,  Zhang Jingwu ,  Selena Chan ,  Andrew Berlin ,  Tae-Woong Koo ,  Mark Roth ,  Phil Gafken

IPC分类号： C12Q1/48 ,  C12Q1/34

CPC分类号： G01N33/6851 ,  G01N21/658 ,  G01N33/54373 ,  G01N33/68 ,  G01N33/6842 ,  G01N33/6848 ,  Y02A90/26

摘要： Embodiments of the present invention provide devices and methods for detecting, identifying, distinguishing, and quantifying modification states of proteins and peptides using Surface Enhanced Raman (SERS) and Raman spectroscopy. Applications of embodiments of the present invention include, for example, proteome wide modification profiling and analyses with applications in disease diagnosis, prognosis and drug efficacy studies, enzymatic activity profiling and assays.

摘要翻译： 本发明的实施方案提供了使用表面增强拉曼（SERS）和拉曼光谱法检测，鉴定，区分和定量蛋白质和肽的修饰状态的装置和方法。 本发明的实施方案的应用包括例如蛋白质组广泛的修饰分析和分析，应用于疾病诊断，预后和药物疗效研究，酶活性分析和测定。