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1. 发明申请

WO2009148527A8 MASS SPECTROMETER OUTPUT ANALYSIS TOOL FOR IDENTIFICATION OF PROTEINS 审中-公开
公开(公告)号：WO2009148527A8
公开(公告)日：2009-12-10
申请号：PCT/US2009/003233
申请日：2009-05-27
申请人： PROTEIN FOREST INC. , KAGAN, Oren , DASCH, James, R. , SIN, Aaron
发明人： KAGAN, Oren , DASCH, James, R. , SIN, Aaron
IPC分类号： G01N33/68 , G01N21/25
摘要： Methods and apparatus for consolidation and visualization of a dataset output from a mass spectrometer. The number of proteins identified in a mass spectrometry experiment may be systematically reduced by identifying and excluding proteins which may not be necessary to explain the observed peptides in a sample. Peptide counts from excluded proteins may be redistributed to non-excluded proteins to preserve total observed peptide counts. The consolidated dataset may be represented as a data structure having a plurality of cells arranged into rows and columns. Visual parameter values may be assigned to various cells in the data structure to emphasize particular features of the data. Data from multiple samples may be arranged in sets of columns in the data structure, and difference scores may be calculated to determine peptide expression differences between the multiples samples. The difference scores may be displayed using textual and/or graphical representations to facilitate data analysis.

2. 发明申请

WO2009148527A2 MASS SPECTROMETER OUTPUT ANALYSIS TOOL FOR IDENTIFICATION OF PROTEINS 审中-公开
标题翻译：质谱仪输出分析用于鉴定蛋白质的工具
公开(公告)号：WO2009148527A2
公开(公告)日：2009-12-10
申请号：PCT/US2009/003233
申请日：2009-05-27
申请人： PROTEIN FOREST INC. , KAGAN, Oren , DASH, James, R. , SIN, Aaron
发明人： KAGAN, Oren , DASH, James, R. , SIN, Aaron
IPC分类号： G01N33/68 , G01N21/25
CPC分类号： G06F19/26 , G06F19/22 , G06F19/28
摘要： Methods and apparatus for consolidation and visualization of a dataset output from a mass spectrometer. The number of proteins identified in a mass spectrometry experiment may be systematically reduced by identifying and excluding proteins which may not be necessary to explain the observed peptides in a sample. Peptide counts from excluded proteins may be redistributed to non-excluded proteins to preserve total observed peptide counts. The consolidated dataset may be represented as a data structure having a plurality of cells arranged into rows and columns. Visual parameter values may be assigned to various cells in the data structure to emphasize particular features of the data. Data from multiple samples may be arranged in sets of columns in the data structure, and difference scores may be calculated to determine peptide expression differences between the multiples samples. The difference scores may be displayed using textual and/or graphical representations to facilitate data analysis.
摘要翻译：用于整合和显示质谱仪输出的数据集的方法和装置。通过鉴定和排除可能不需要解释样品中观察到的肽的蛋白质，可以系统地减少在质谱实验中鉴定的蛋白质的数量。来自排除蛋白的肽计数可以重新分配到未排除的蛋白质以保留总观察到的肽计数。统一数据集可以表示为具有排列成行和列的多个单元的数据结构。可视参数值可以分配给数据结构中的各个单元，以强调数据的特定特征。来自多个样本的数据可以以数据结构中的列的形式排列，并且可以计算差分以确定多个样本之间的肽表达差异。可以使用文本和/或图形表示来显示差异分数以促进数据分析。

3. 发明申请

WO2010017109A1 SYSTEMS AND METHODS FOR QUANTITATIVE ANALYTE TRANSFER 审中-公开
标题翻译：定量分析转移的系统和方法
公开(公告)号：WO2010017109A1
公开(公告)日：2010-02-11
申请号：PCT/US2009/052460
申请日：2009-07-31
申请人： PROTEIN FOREST, INC. , PLUSKAL, Malcolm, G. , MILLER, Thomas , DASCH, James
发明人： PLUSKAL, Malcolm, G. , MILLER, Thomas , DASCH, James
IPC分类号： G01N27/447 , G01N33/558
CPC分类号： G01N27/4473 , G01N27/44747 , Y10T428/249981
摘要： Systems and methods for enhancing quantitative transfer of analytes from an electrophoretic gel (12) to an adsorptive substrate (14) are provided. A preferred embodiment provides an improved transfer system (10) and method that reduces "blow through" of low molecular weight analytes and increases the adsorption of low molecular weight, for example proteins of about 3OkDa or less compared to conventional transfer techniques. It has been discovered that using a secondary porous backing membrane (16) in conjunction with an adsorptive membrane (14) such as nitrocellulose or polvinylidene fluoride increases the efficiency of analyte interaction with the adsorption membrane compared to ' transfers techniques using the adsorption membrane without the secondary backing membrane. This improvement of quantitative analyte transfer efficiency facilitates a wider range of detection processes, such as direct analysis by MALDI mass spectrometry than in earlier applications of the process without the secondary backing membrane.
摘要翻译：提供了用于增强分析物从电泳凝胶（12）到吸附性基质（14）的定量转移的系统和方法。优选的实施方案提供了改进的转移系统（10）和方法，其减少了低分子量分析物的“吹穿”，并增加了低分子量的吸附，例如与常规转移技术相比，约30kDa或更少的蛋白质。已经发现，与使用不使用吸附膜的吸附膜的转移技术相比，使用辅助多孔背衬膜（16）与吸附膜（14）如硝酸纤维素或聚偏二氟乙烯结合提高分析物与吸附膜的相互作用的效率二次背衬膜。定量分析物转移效率的这种改进有助于更广泛的检测过程，例如通过MALDI质谱法的直接分析，而不是先前没有第二背衬膜的方法的应用。

4. 发明申请

WO2009148527A3 MASS SPECTROMETER OUTPUT ANALYSIS TOOL FOR IDENTIFICATION OF PROTEINS 审中-公开
公开(公告)号：WO2009148527A3
公开(公告)日：2009-12-10
申请号：PCT/US2009/003233
申请日：2009-05-27
申请人： PROTEIN FOREST INC. , KAGAN, Oren , DASH, James, R. , SIN, Aaron
发明人： KAGAN, Oren , DASH, James, R. , SIN, Aaron
IPC分类号： G01N33/68 , G01N21/25
摘要： Methods and apparatus for consolidation and visualization of a dataset output from a mass spectrometer. The number of proteins identified in a mass spectrometry experiment may be systematically reduced by identifying and excluding proteins which may not be necessary to explain the observed peptides in a sample. Peptide counts from excluded proteins may be redistributed to non-excluded proteins to preserve total observed peptide counts. The consolidated dataset may be represented as a data structure having a plurality of cells arranged into rows and columns. Visual parameter values may be assigned to various cells in the data structure to emphasize particular features of the data. Data from multiple samples may be arranged in sets of columns in the data structure, and difference scores may be calculated to determine peptide expression differences between the multiples samples. The difference scores may be displayed using textual and/or graphical representations to facilitate data analysis.

5. 发明申请

WO2007106370A9 TRANSFER DEVICE FOR TWO - DIMENSIONAL ELECTROPHORESIS 审中-公开
标题翻译：用于二维电泳的转移装置
公开(公告)号：WO2007106370A9
公开(公告)日：2007-12-13
申请号：PCT/US2007005966
申请日：2007-03-08
申请人： PROTEIN FOREST INC , HARALAMPU STEPHEN , SKEA WILLIAM M , CHLENOV MARK , THOMPSON EDWARD
发明人： HARALAMPU STEPHEN , SKEA WILLIAM M , CHLENOV MARK , THOMPSON EDWARD
IPC分类号： G01N27/447 , C07K1/26
CPC分类号： C07K1/26 , C07K1/285 , G01N27/44773
摘要： Apparatus and method for transfer of analytes from a first dimension isoelectric focusing gel to a second dimension, such as an electrophoretic analytical gel. In a preferred embodiment, the device (10) facilitates the transfer of protein analytes from a digital proteome chip (12) to a second dimension electrophoretic analytical gel (18). The main features of the preferred embodiment are a recessed location (14) on a collar (16a, 16b), a mechanical clamp device (22) and stops (20a, 20b) that locate the first dimension gel at a fixed and known position in space, and a low density medium that assures uniform electrical contact between the first and second dimension analyses.The advantage of an apparatus that places the first dimension in a known position is that the final data analysis is greatly facilitated by precisely knowing the locations of the first dimension pH features. The medium that assures electrical contact also has the advantage of simplifying the final data analysis by assuring a uniform frame of reference on how the second dimension analysis was run.
摘要翻译：将分析物从第一维等电聚焦凝胶转移到第二维的装置和方法，例如电泳分析凝胶。在优选的实施方案中，装置（10）有助于将蛋白质分析物从数字蛋白质组芯片（12）转移到第二维电泳分析凝胶（18）。优选实施例的主要特征是在轴环（16a，16b）上的凹进位置（14），机械夹紧装置（22）和止动件（20a，20b），其将第一尺寸凝胶定位在固定的已知位置空间和低密度介质，其确保第一和第二维度分析之间的均匀电接触。将第一维度置于已知位置的装置的优点是通过精确地知道第一维度的位置来极大地促进最终数据分析第一维pH特征。确保电接触的介质还具有通过确保对第二维分析如何运行的统一的参考框架来简化最终数据分析的优点。

6. 发明申请

WO2008137728A8 SYSTEM AND METHOD FOR PROTEOMICS 审中-公开
标题翻译：系统与方法
公开(公告)号：WO2008137728A8
公开(公告)日：2009-12-23
申请号：PCT/US2008062482
申请日：2008-05-02
申请人： PROTEIN FOREST INC , JOHANSEN JACK , GARLICK RUSSELL K , SKEA WILLIAM , HARALAMPU STEPHEN , KAGAN OREN
发明人： JOHANSEN JACK , GARLICK RUSSELL K , SKEA WILLIAM , HARALAMPU STEPHEN , KAGAN OREN
IPC分类号： G01N27/447
CPC分类号： G01N27/44795
摘要： Significantly higher yield and better resolution in pi gels are obtained by creating traps having two or more layers of gel (26, 28) containing closely stepped immobilized pH buffers. Proteins move from a pH at which they are negatively charged towards an anode at which they are positively charged. The gel layers (26, 28) containing immobilized pH buffers trap the proteins when the immobilized buffer pH and the protein pi are approximately the same. The protein is trapped within the second layer and not on the surface of or interface of the second layer.
摘要翻译：通过产生具有两层或更多层凝胶（26,28）的包含紧密阶梯的固定化pH缓冲液的阱，可以获得明显更高的产率和更好的分辨率。蛋白质从带负电荷的pH向负极移动。含有固定化pH值缓冲液的凝胶层（26,28）在固定化缓冲液pH和蛋白质pI大致相同时捕获蛋白质。蛋白质被捕获在第二层内，而不是在第二层的表面或界面上。

7. 发明申请

WO2007106370A3 TRANSFER DEVICE FOR TWO - DIMENSIONAL ELECTROPHORESIS 审中-公开
公开(公告)号：WO2007106370A3
公开(公告)日：2007-09-20
申请号：PCT/US2007/005966
申请日：2007-03-08
申请人： PROTEIN FOREST, INC. , HARALAMPU, Stephen , SKEA, William, M. , CHLENOV, Mark , THOMPSON, Edward
发明人： HARALAMPU, Stephen , SKEA, William, M. , CHLENOV, Mark , THOMPSON, Edward
IPC分类号： G01N27/447 , C07K1/26
摘要： Apparatus and method for transfer of analytes from a first dimension isoelectric focusing gel to a second dimension, such as an electrophoretic analytical gel. In a preferred embodiment, the device (10) facilitates the transfer of protein analytes from a digital proteome chip (12) to a second dimension electrophoretic analytical gel (18). The main features of the preferred embodiment are a recessed location (14) on a collar (16a, 16b), a mechanical clamp device (22) and stops (20a, 20b) that locate the first dimension gel at a fixed and known position in space, and a low density medium that assures uniform electrical contact between the first and second dimension analyses.The advantage of an apparatus that places the first dimension in a known position is that the final data analysis is greatly facilitated by precisely knowing the locations of the first dimension pH features. The medium that assures electrical contact also has the advantage of simplifying the final data analysis by assuring a uniform frame of reference on how the second dimension analysis was run.

8. 发明申请

WO2007106370A2 TWO-DIMENSIONAL TRANSFER DEVICE 审中-公开
标题翻译：二维传输设备
公开(公告)号：WO2007106370A2
公开(公告)日：2007-09-20
申请号：PCT/US2007005966
申请日：2007-03-08
申请人： PROTEIN FOREST INC , HARALAMPU STEPHEN , SKEA WILLIAM M , CHLENOV MARK , THOMPSON EDWARD
发明人： HARALAMPU STEPHEN , SKEA WILLIAM M , CHLENOV MARK , THOMPSON EDWARD
IPC分类号： G01N27/447 , C07K1/26
CPC分类号： C07K1/26 , C07K1/285 , G01N27/44773
摘要： A system including apparatus and method of use that insures uniform contact and transfer of analytes from a first dimensional electrophoretic analytical gel to a second dimension, such as an electrophoretic analytical gel, has been developed. The device provides a means for transfer of analytes from a first dimension isoelectric focusing gel to a second dimension electrophoretic analytical gel. In a preferred embodiment, the device facilitates the transfer of protein analytes from a digital proteome chip to a second dimension electrophoretic analytical gel. The second dimension electrophoretic analytical gel can be for use with any technique known in the art, such as, but not limited to SDS-PAGE molecular weight analysis, secondary isoelectric focusing, and capillary electrophoresis. The main features of the preferred embodiment are a mechanical device that locates the first dimension analysis at a fixed and known position in space, and a low density medium that assures uniform electrical contact between the first and second dimension analyses. The advantage of an apparatus that places the first dimension in a known position is that the final data analysis is greatly facilitated by precisely knowing the locations of the first dimension pH features. The medium that assures electrical contact also has the advantage of simplifying the final data analysis by assuring a uniform frame of reference on how the second dimension analysis was run.
摘要翻译：已经开发了包括使分析物从第一维电泳分析凝胶到第二维度（例如电泳分析凝胶）的均匀接触和转移的装置和方法的系统。该装置提供了将分析物从第一维等电聚焦凝胶转移到第二尺寸电泳分析凝胶的方法。在优选的实施方案中，该装置有助于将蛋白质分析物从数字蛋白质组芯片转移到第二维电泳分析凝胶。第二维电泳分析凝胶可用于本领域已知的任何技术，例如但不限于SDS-PAGE分子量分析，二次等电聚焦和毛细管电泳。优选实施例的主要特征是将第一维度分析定位在空间中的固定和已知位置的机械装置以及确保第一和第二尺寸分析之间的均匀电接触的低密度介质。将第一维度置于已知位置的装置的优点是通过精确地知道第一维度pH特征的位置来极大地促进最终数据分析。确保电接触的介质还具有通过确保对第二维分析如何运行的统一的参考框架来简化最终数据分析的优点。

9. 发明申请

WO2008137728A1 SYSTEM AND METHOD FOR PROTEOMICS 审中-公开
标题翻译：系统与方法
公开(公告)号：WO2008137728A1
公开(公告)日：2008-11-13
申请号：PCT/US2008/062482
申请日：2008-05-02
申请人： PROTEIN FOREST, INC. , GARLICK, Russell, K. , SKEA, William , HARALAMPU, Stephen , JOHANSEN, Jack , KAGAN, Oren
发明人： GARLICK, Russell, K. , SKEA, William , HARALAMPU, Stephen , JOHANSEN, Jack , KAGAN, Oren
IPC分类号： G01N27/447
CPC分类号： G01N27/44795
摘要： Significantly higher yield and better resolution in pi gels are obtained by creating traps having two or more layers of gel (26, 28) containing closely stepped immobilized pH buffers. Proteins move from a pH at which they are negatively charged towards an anode at which they are positively charged. The gel layers (26, 28) containing immobilized pH buffers trap the proteins when the immobilized buffer pH and the protein pi are approximately the same. The protein is trapped within the second layer and not on the surface of or interface of the second layer.
摘要翻译：通过产生具有两层或更多层凝胶（26,28）的包含紧密阶梯的固定化pH缓冲液的阱，可以获得明显更高的产率和更好的分辨率。蛋白质从带负电荷的pH向负极移动。含有固定化pH值缓冲液的凝胶层（26,28）在固定化缓冲液pH和蛋白质pI大致相同时捕获蛋白质。蛋白质被捕获在第二层内，而不是在第二层的表面或界面上。

10. 发明申请

WO03008977A3 ARRAYS OF BUFFERS FOR ANALYSING BIOMOLECULES BY THEIR ISOELECTRIC POINT 审中-公开
标题翻译：通过其电压点分析生物分子的缓冲区阵列
公开(公告)号：WO03008977A3
公开(公告)日：2003-06-19
申请号：PCT/US0222714
申请日：2002-07-16
申请人： PROTEIN FOREST INC , BUKSHPAN SHAMUEL , ZILBERSTEIN GLEB
发明人： BUKSHPAN SHAMUEL , ZILBERSTEIN GLEB
IPC分类号： G01N27/62 , G01N27/447 , G01N30/88 , G01N33/15 , G01N33/50 , G01N33/543
CPC分类号： G01N27/44795 , G01N27/44747
摘要： The present invention relates to matrixes, arrays, systems and methods for analyzing biomolecules by their isoelectric point, optionally, in combination with a second dimension analysis. The assortment of matrixes, arrays and systems provided herein are useful for causing a biomolecule under the influence of an electrical field to accumulate into an IEF buffer that comprises a pH value that is the same as the isoelectric point of the biomolecule. The methods of this invention are useful for, e.g., research and diagnostic purposes.
摘要翻译：本发明涉及用于通过其等电点分析生物分子的基质，阵列，系统和方法，任选地与第二维度分析结合。本文提供的基质，阵列和系统的分类可用于使电场的影响下的生物分子积累到包含与生物分子的等电点相同的pH值的IEF缓冲液中。本发明的方法可用于例如研究和诊断目的。

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