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1. 发明申请

WO1994011837A1 OLIGOPROBE DESIGNSTATIONS: A COMPUTERIZED METHOD FOR DESIGNING OPTIMAL OLIGONUCLEOTIDE PROBES AND PRIMERS 审中-公开
标题翻译： OLIGOPROBE设计：一种用于设计最佳寡核苷酸探针和引物的计算机方法
公开(公告)号：WO1994011837A1
公开(公告)日：1994-05-26
申请号：PCT/US1993010507
申请日：1993-11-08
申请人： HITACHI CHEMICAL COMPANY, LTD. , MITSUHASHI, Masato , COOPER, Allan , WATERMAN, Michael , PEVZNER, Pavel
发明人： HITACHI CHEMICAL COMPANY, LTD.
IPC分类号： G06F15/42
CPC分类号： C12N15/10 , G06F19/20 , G06F19/22
摘要： There is disclosed herein an invention which relates to the fields of genetic engineering, microbiology, and computer science, that allows a user, whether a molecular biologist or a clinical diagnostician, to calculate and design extremely specific oligonucleotide sequences for DNA and mRNA hybridization procedures. The sequences designed with this invention may be used for medical diagnostic kits, DNA indentification, and potentially continuous monitoring of metabolic processes in human beings. The key features design oligonucleotide sequences based on the GenBank database of DNA and mRNA sequences and examine candidate sequences for specificity or commonality with respect to a user-selected experimental preparation. Two models are available: a Mismatch Model, that employs hashing and continuous seed filtration, and an H-site Model, that analyzes candidate sequences for their binding specificity relative to some known set of mRNA or DNA sequences. The preferred embodiment of this computerized design tool is written in the Borland C++ language and runs under Microsoft Windows on IBM compatible personal computers.
摘要翻译：本文公开了一种涉及遗传工程，微生物学和计算机科学领域的发明，其允许用户（无论是分子生物学家还是临床诊断学家）计算和设计用于DNA和mRNA杂交程序的特异性寡核苷酸序列。本发明设计的序列可用于医学诊断试剂盒，DNA鉴定和人类代谢过程的潜在连续监测。关键特征是基于DNA和mRNA序列的GenBank数据库的设计寡核苷酸序列，并检查相对于用户选择的实验制备的特异性或共同性的候选序列。有两种模型可用：使用散列和连续种子过滤的不匹配模型和H位点模型，它们相对于一些已知的一组mRNA或DNA序列分析其结合特异性的候选序列。该计算机化设计工具的优选实施例是用Borland C ++语言编写的，并且在IBM兼容的个人计算机上的Microsoft Windows TM下运行。

2. 发明申请

WO2007112289A2 METHOD FOR IDENTIFICATION AND SEQUENCING OF PROTEINS 审中-公开
标题翻译：蛋白质鉴定和测序方法
公开(公告)号：WO2007112289A2
公开(公告)日：2007-10-04
申请号：PCT/US2007/064722
申请日：2007-03-22
申请人： THE REGENTS OF THE UNIVERSITY OF CALIFORNIA , PEVZNER, Pavel, A. , BANDEIRA, Nuno, F.c. , TSUR, Dekel
发明人： PEVZNER, Pavel, A. , BANDEIRA, Nuno, F.c. , TSUR, Dekel
IPC分类号： G01N31/00
CPC分类号： G06F19/00 , G01N33/6848
摘要： Protein samples are processed to create a mixture of modified and unmodified or overlapping peptides which are analyzed using mass spectrometry. Correlations between the MS/MS spectra of peptide pairs allow the noise in individual MS/MS spectra to be greatly reduced. A small number of peptide reconstructions can be generated that are likely to contain the correct one. This allows for the de novo reconstruction of protein sequences and peptide and modification identification through a database search using extremely fast pattern matching, rather than time- consuming matching of spectra against databases.
摘要翻译：处理蛋白质样品以产生经修饰和未修饰或重叠的肽的混合物，其使用质谱分析。肽对的MS / MS光谱之间的相关性允许单个MS / MS光谱中的噪声大大降低。可以生成少量可能包含正确的肽重建的肽重建。这允许通过使用非常快速的模式匹配的数据库搜索进行蛋白质序列和肽的重新定位和修饰鉴定，而不是频谱与数据库的时间匹配。

3. 发明申请

WO2008151140A3 METHOD FOR IDENTIFYING PEPTIDES USING TANDEM MASS SPECTRA BY DYNAMICALLY DETERMINING THE NUMBER OF PEPTIDE RECONSTRUCTIONS REQUIRED 审中-公开
标题翻译：使用TANDEM MASS SPECTRA通过动态确定所需的肽重编次数来鉴定肽的方法
公开(公告)号：WO2008151140A3
公开(公告)日：2009-03-05
申请号：PCT/US2008065548
申请日：2008-06-02
申请人： UNIV CALIFORNIA , KIM SANGTAE , GUPTA NITIN , PEVZNER PAVEL A
发明人： KIM SANGTAE , GUPTA NITIN , PEVZNER PAVEL A
IPC分类号： G01N27/62
CPC分类号： G06F19/22 , G01N33/6848 , G06F19/12 , G06F19/18 , H01J49/0036
摘要： A method for identifying peptides using tandem mass spectrometry takes the spectrum for a peptide to be analyzed and uses a scoring function to score a match between the spectrum and each candidate peptide in a peptide database. The scoring function has a value corresponding to a number of fragment peaks in the spectrum that match fragment peaks in a spectrum of the candidate peptide. Using the match scores, a generating function of the spectrum is computed to determine the number of peptide reconstructions at each value of the scoring function. The generating function is then used to determine the number of candidate peptides for each match score and the probability of a peptide having a given match score to the spectrum. A spectral probability can be determined by calculating the total probability of all peptides with scores equal to or larger than the given match score.
摘要翻译：使用串联质谱法鉴定肽的方法取得待分析肽的光谱，并使用评分函数对肽数据库中的光谱和每个候选肽之间的匹配进行评分。评分函数具有对应于与候选肽的谱中的片段峰匹配的谱中的片段峰数量的值。使用匹配分数，计算光谱的生成函数，以确定在评分函数的每个值处的肽重构的数量。然后使用生成函数来确定每个匹配得分的候选肽的数目和具有给定匹配得分的肽对于该光谱的概率。可以通过计算具有等于或大于给定匹配分数的分数的所有肽的总概率来确定光谱概率。

4. 发明申请

WO2008151140A2 METHOD FOR IDENTIFYING PEPTIDES USING TANDEM MASS SPECTRA BY DYNAMICALLY DETERMINING THE NUMBER OF PEPTIDE RECONSTRUCTIONS REQUIRED 审中-公开
标题翻译：使用TANDEM MASS SPECTRA通过动态确定所需的肽重编次数来鉴定肽的方法
公开(公告)号：WO2008151140A2
公开(公告)日：2008-12-11
申请号：PCT/US2008/065548
申请日：2008-06-02
申请人： THE REGENTS OF THE UNIVERSITY OF CALIFORNIA , KIM, Sangtae , GUPTA, Nitin , PEVZNER, Pavel A.
发明人： KIM, Sangtae , GUPTA, Nitin , PEVZNER, Pavel A.
IPC分类号： G01N27/62
CPC分类号： G06F19/22 , G01N33/6848 , G06F19/12 , G06F19/18 , H01J49/0036
摘要： A method for identifying peptides using tandem mass spectrometry takes the spectrum for a peptide to be analyzed and uses a scoring function to score a match between the spectrum and each candidate peptide in a peptide database. The scoring function has a value corresponding to a number of fragment peaks in the spectrum that match fragment peaks in a spectrum of the candidate peptide. Using the match scores, a generating function of the spectrum is computed to determine the number of peptide reconstructions at each value of the scoring function. The generating function is then used to determine the number of candidate peptides for each match score and the probability of a peptide having a given match score to the spectrum. A spectral probability can be determined by calculating the total probability of all peptides with scores equal to or larger than the given match score.
摘要翻译：使用串联质谱法鉴定肽的方法取得待分析肽的光谱，并使用评分函数对肽数据库中的光谱和每个候选肽之间的匹配进行评分。评分函数具有对应于与候选肽的谱中的片段峰匹配的谱中的片段峰数量的值。使用匹配分数，计算光谱的生成函数，以确定在评分函数的每个值处的肽重构的数量。然后使用生成函数来确定每个匹配得分的候选肽的数目和具有给定匹配得分的肽对于该光谱的概率。可以通过计算具有等于或大于给定匹配分数的分数的所有肽的总概率来确定光谱概率。

5. 发明申请

WO2007112289A3 METHOD FOR IDENTIFICATION AND SEQUENCING OF PROTEINS 审中-公开
标题翻译：鉴定和测序蛋白质的方法
公开(公告)号：WO2007112289A3
公开(公告)日：2008-04-17
申请号：PCT/US2007064722
申请日：2007-03-22
申请人： UNIV CALIFORNIA , PEVZNER PAVEL A , BANDEIRA NUNO F C , TSUR DEKEL
发明人： PEVZNER PAVEL A , BANDEIRA NUNO F C , TSUR DEKEL
IPC分类号： G01N33/22 , G01N24/00
CPC分类号： G06F19/00 , G01N33/6848
摘要： Protein samples are processed to create a mixture of modified and unmodified or overlapping peptides which are analyzed using mass spectrometry. Correlations between the MS/MS spectra of peptide pairs allow the noise in individual MS/MS spectra to be greatly reduced. A small number of peptide reconstructions can be generated that are likely to contain the correct one. This allows for the de novo reconstruction of protein sequences and peptide and modification identification through a database search using extremely fast pattern matching, rather than time- consuming matching of spectra against databases.
摘要翻译：处理蛋白质样品以产生经质谱分析的经修饰和未修饰或重叠的肽的混合物。肽对的MS / MS谱之间的相关性允许单个MS / MS光谱中的噪声大大降低。可以生成少量可能包含正确的肽重建的肽重建。这允许通过使用非常快速的模式匹配的数据库搜索来重新构建蛋白质序列和肽的修饰和修饰，而不是频谱与数据库的时间匹配。

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