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1. 发明申请

WO2012035412A2 DATA INDEPENDENT ACQUISITION OF PRODUCTION SPECTRA AND REFERENCE SPECTRA LIBRARY MATCHING 审中-公开
标题翻译：数据独立获取生产光谱和参考光谱图书匹配
公开(公告)号：WO2012035412A2
公开(公告)日：2012-03-22
申请号：PCT/IB2011/002139
申请日：2011-09-14
申请人： DH TECHNOLOGIES DEVELOPMENT PTE. LTD. , ETH ZURICH , BONNER, Ronald , TATE, Stephen , AEBERSOLD, Rudolf , NAVARRO ALVAREZ, Pedro Jose , RINNER, Oliver , REITER, Lukas , GILLET, Ludovic
发明人： BONNER, Ronald , TATE, Stephen , AEBERSOLD, Rudolf , NAVARRO ALVAREZ, Pedro Jose , RINNER, Oliver , REITER, Lukas , GILLET, Ludovic
CPC分类号： H01J49/0036 , G01N30/7233 , G06F19/703 , G06F19/709 , H01J49/0031 , H01J49/004 , H01J49/0045 , H01J49/42
摘要： Systems and methods are used to store an electronic record of all product ion spectra of all detectable compounds of a sample. A plurality of product ion scans are performed on a tandem mass spectrometer one or more times in a single sample analysis across a mass range using a plurality of mass selection windows. All sample product ion spectra of all detectable compounds for each mass selection window are produced. All sample product ion spectra for each mass selection window are received from the tandem mass spectrometer using a processor. All sample product ion spectra for each mass selection window are stored as an electronic record of all detectable compounds of the sample using the processor. The electronic record is used to characterize compounds known at the time the electronic record is stored or to characterize compounds that became known after the electronic record was stored.
摘要翻译：系统和方法用于存储所有可检测的样品化合物的所有产物离子光谱的电子记录。在使用多个质量选择窗口的质量范围内的单个样品分析中，在串联质谱仪上进行多次产品离子扫描。产生用于每个质量选择窗口的所有可检测化合物的所有样品产物离子光谱。使用处理器从串联质谱仪接收每个质量选择窗口的所有样品产物离子光谱。每个质量选择窗口的所有样品产品离子光谱都使用处理器作为样品的所有可检测化合物的电子记录进行存储。电子记录用于表征在电子记录存储时已知的化合物或表征在电子记录存储之后已知的化合物。

2. 发明申请

WO2009141141A1 METHOD FOR HIGH THROUGHPUT PEPTIDE/PROTEIN ASSAY GENERATION AND ASSAYS GENERATED THEREWITH 审中-公开
标题翻译：高通量肽/蛋白质测定法生成方法及其生成方法
公开(公告)号：WO2009141141A1
公开(公告)日：2009-11-26
申请号：PCT/EP2009/003611
申请日：2009-05-20
申请人： ETH ZURICH , AEBERSOLD, Ruedi , PICOTTI, Paola , RINNER, Oliver , MALMSTROEM, Johan
发明人： AEBERSOLD, Ruedi , PICOTTI, Paola , RINNER, Oliver , MALMSTROEM, Johan
IPC分类号： G01N33/68
CPC分类号： G01N33/6848
摘要： The invention relates to a method for the determination of an MRM or SRM assay for a protein of interest, a peptide of interest, or a group of proteins/peptides of interest or a whole proteome. It essentially includes the following steps: (1) a list of proteins of interest is selected and for each member at least one or a list of candidate proteotypic peptides is derived (2) this at least one peptide is synthesized/generated essentially without subsequent purification; (3) this at least one unpurified peptide is analyzed by selected reaction monitoring (SRM) preferably coupled to liquid chromatography (LC-SRM) or analogous techniques; (4) validation and/or optimisation of the corresponding assay of the at least one peptide with determination of the SRM coordinates for a peptide/protein of interest and/or of a regulator of interest is achieved. A protein sample of interest is enzymatically digested and can then be analyzed in SRM mode or time-constrained SRM mode, using elution times to trigger acquisition of the set of selected SRM traces, thus drastically increasing the throughput. The analysis allows to detect and quantify the set of peptides/proteins of interest. The method additionally relates to a tagging strategy to achieve absolute quantification of the peptides/proteins of interest at low-budget and high-throughput.
摘要翻译：本发明涉及用于确定感兴趣的蛋白质，目标肽或感兴趣的蛋白质/肽组或整个蛋白质组的MRM或SRM测定法的方法。它基本上包括以下步骤：（1）选择目的蛋白的列表，并且对于每个成员，导出候选蛋白多肽的至少一个或一个或多个列表（2）该基因上没有随后的纯化合成/生成至少一种肽 ; （3）通过优选与液相色谱法（LC-SRM）偶联的选择性反应监测（SRM）或类似技术来分析至少一种未纯化的肽。（4）通过确定感兴趣的肽/ /蛋白质和/或感兴趣的调节剂的SRM坐标来确定和/或优化至少一种肽的相应测定。感兴趣的蛋白质样品被酶消化，然后可以以SRM模式或时间受限的SRM模式进行分析，使用洗脱时间来触发所选择的SRM迹线的集合的获取，从而显着增加产量。该分析允许检测和定量所组合的肽/蛋白质。该方法另外涉及在低预算和高通量下实现目标肽/蛋白质的绝对定量的标记策略。

3. 发明申请

WO2013044401A1 METHOD FOR ANALYSIS OF SAMPLES IN TARGETED PROTEOMICS APPLICATIONS, COMPUTER PROGRAM PRODUCT AND SET OF REFERENCE PEPTIDES 审中-公开
标题翻译：目标保护应用样本分析方法，计算机程序产品和参考设置
公开(公告)号：WO2013044401A1
公开(公告)日：2013-04-04
申请号：PCT/CH2012/000217
申请日：2012-09-20
申请人： BiognoSYS AG , ESCHER, Claudia , OSSOLA, Reto , RINNER, Oliver , REITER, Lukas
发明人： ESCHER, Claudia , OSSOLA, Reto , RINNER, Oliver , REITER, Lukas
IPC分类号： G01N30/86 , G01N30/88
CPC分类号： G01N30/8675 , G01N30/8672 , G01N30/88 , G01N2030/042 , G01N2030/8831
摘要： The invention relates to the analysis of compounds with mass spectrometry and more particularly to instruments, substances, and methods for polypeptide analysis, in particular in targeted proteomics applications and based on indexed retention time as peptide specific property. The method of chemical analysis comprises the steps of: a) providing a first complex sample comprising a set of at least two reference peptides associated to an indexed retention time scale (iRT), as well as at least one further peptide; b) performing LC-MS on said complex sample and determining the empirical retention time values (RTe) of the reference peptides and of the at least one further peptide; c) translating the empirical retention time values (RTe) of the reference peptides and of the at least one further peptide into the indexed retention time scale and associating to each reference peptide a reference indexed retention time value (iRTr) and to the at least one further peptide an associated indexed retention time value (iRTa); d) providing a second complex sample comprising at least one polypeptide as well as said set of the at least two reference peptides; e) performing LC-MS on said second complex sample and determining the empirical retention time values (RTe) of the reference peptides; f) translating the empirical retention time values (RTe) of the reference peptides into the indexed retention time scale by numerically adapting the transformation function for the conversion of the retention time values (RTe) into indexed retention time values such that the calculated indexed retention time values (iRTe) calculated based on the measured retention time values (RTe) of the reference peptides match the assigned indexed retention time values (iRTr) of the reference peptides; g) determining the predicted empirical retention time value (RTp) of the at least one further peptide by using the numerically adapted transformation function determined in step f).
摘要翻译：本发明涉及通过质谱法分析化合物，更具体地涉及用于多肽分析的仪器，物质和方法，特别是在靶向蛋白质组学应用中，并且基于索引保留时间作为肽特异性。化学分析的方法包括以下步骤：a）提供第一复合物样品，其包含与索引的保留时间标度（iRT）相关的一组至少两个参考肽，以及至少一个其它肽; b）在所述复合物样品上进行LC-MS并确定参考肽和至少一种其它肽的经验性保留时间值（RTe）; c）将参考肽和至少一个另外的肽的经验保留时间值（RTe）翻译成索引保留时间标度，并将参考索引的保留时间值（iRTr）与至少一个进一步的肽相关的索引保留时间值（iRTa）; d）提供包含至少一种多肽以及所述至少两种参考肽组的第二复合物样品; e）在所述第二复合物样品上进行LC-MS并确定参考肽的经验保留时间值（RTe）; f）将参考肽的经验保留时间值（RTe）转化为索引保留时间标度，方法是使保留时间值（RTe）转化为指数保留时间值的转化函数，使得计算的指数保留时间基于所测量的参考肽的保留时间值（RTe）计算的值（iRTe）与参考肽的指定的指示保留时间值（iRTr）匹配; g）通过使用在步骤f）中确定的数字适应变换函数来确定所述至少一种另外的肽的预测经验保留时间值（RTp）。

4. 发明申请

WO2012035412A3 DATA INDEPENDENT ACQUISITION OF PRODUCTION SPECTRA AND REFERENCE SPECTRA LIBRARY MATCHING 审中-公开
标题翻译：数据独立采集生产谱和参考谱库匹配
公开(公告)号：WO2012035412A3
公开(公告)日：2012-05-10
申请号：PCT/IB2011002139
申请日：2011-09-14
申请人： DH TECHNOLOGIES DEV PTE LTD , ETH ZUERICH , BONNER RONALD , TATE STEPHEN , AEBERSOLD RUDOLF , NAVARRO ALVAREZ PEDRO JOSE , RINNER OLIVER , REITER LUKAS , GILLET LUDOVIC
发明人： BONNER RONALD , TATE STEPHEN , AEBERSOLD RUDOLF , NAVARRO ALVAREZ PEDRO JOSE , RINNER OLIVER , REITER LUKAS , GILLET LUDOVIC
IPC分类号： H01J49/00
CPC分类号： H01J49/0036 , G01N30/7233 , G06F19/703 , G06F19/709 , H01J49/0031 , H01J49/004 , H01J49/0045 , H01J49/42
摘要： Systems and methods are used to store an electronic record of all product ion spectra of all detectable compounds of a sample. A plurality of product ion scans are performed on a tandem mass spectrometer one or more times in a single sample analysis across a mass range using a plurality of mass selection windows. All sample product ion spectra of all detectable compounds for each mass selection window are produced. All sample product ion spectra for each mass selection window are received from the tandem mass spectrometer using a processor. All sample product ion spectra for each mass selection window are stored as an electronic record of all detectable compounds of the sample using the processor. The electronic record is used to characterize compounds known at the time the electronic record is stored or to characterize compounds that became known after the electronic record was stored.
摘要翻译：系统和方法用于存储样品中所有可检测化合物的所有产物离子谱的电子记录。使用多个质量选择窗在整个质量范围的单个样品分析中在串联质谱仪上执行一次或多次多次产物离子扫描。生成每个质量选择窗口中所有可检测化合物的所有样品产物离子谱图。使用处理器从串联质谱仪接收每个质量选择窗口的所有样品产物离子质谱图。使用处理器将每个质量选择窗口的所有样品产物离子谱存储为样品中所有可检测化合物的电子记录。电子记录用于表征电子记录存储时已知的化合物的特征，或描述电子记录存储后已知的化合物的特征。

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