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1. 发明申请

US20110015863A1 METHOD FOR IDENTIFICATION AND SEQUENCING OF PROTEINS 有权
标题翻译：鉴定和测序蛋白质的方法
公开(公告)号：US20110015863A1
公开(公告)日：2011-01-20
申请号：US12279836
申请日：2007-03-22
申请人： Pavel A. Pevzner , Nuno F.C. Bandeira , Dekel Tsur
发明人： Pavel A. Pevzner , Nuno F.C. Bandeira , Dekel Tsur
IPC分类号： G06F19/00 , G01N33/48
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修饰和未修饰或重叠肽的混合物。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从蛋白质序列和肽的重新定位以及修饰鉴定，而不是频谱与数据库的耗时匹配。

2. 发明授权

US5556749A Oligoprobe designstation: a computerized method for designing optimal DNA probes 失效
标题翻译： Oligoprobe设计站：用于设计最佳DNA探针的计算机化方法
公开(公告)号：US5556749A
公开(公告)日：1996-09-17
申请号：US975526
申请日：1992-11-12
申请人： Masato Mitsuhashi , Allan J. Cooper , Michael S. Waterman , Pavel A. Pevzner
发明人： Masato Mitsuhashi , Allan J. Cooper , Michael S. Waterman , Pavel A. Pevzner
IPC分类号： C12N15/00 , C12N15/10 , G06F17/30 , G06F17/50 , G06F19/20 , G06F19/22 , C12Q1/68 , G06F15/16 , G06F17/00
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 they be a molecular biologist or a clinical diagnostician, to calculate and design extremely specific oligonucleotide probes for DNA and mRNA hybridization procedures. The probes designed with this invention may be used for medical diagnostic kits, DNA identification, and potentially continuous monitoring of metabolic processes in human beings. The key features design oligonucleotide probes based on the GenBank database of DNA and mRNA sequences and examine candidate probes 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 probes 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.RTM. C++ language and runs under Microsoft.RTM. Windows.TM. on IBM.RTM. 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（无论他们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杂交的特异性寡核苷酸探针程序。用本发明设计的探针可用于医学诊断试剂盒，DNA鉴定和潜在的连续监测人类代谢过程。关键是设计基于DNA和mRNA序列的GenBank数据库的寡核苷酸探针，并检查与用户选择的实验准备相关的特异性或共同性的候选探针。有两种型号可供选择：使用散列和连续种子过滤的不匹配模型，以及H-Site模型，它们可以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探针。该计算机化设计工具的优选实施例是用Borland TM C ++语言编写的，并且在IBM TM兼容个人计算机上的Microsoft TM Windows TM下运行。

3. 发明申请

US20100179766A1 Method for Identifying Peptides Using Tandem Mass Spectra by Dynamically Determining the Number of Peptide Reconstructions Required 有权
标题翻译：通过动态确定所需的肽重建数量使用串联质谱鉴定肽的方法
公开(公告)号：US20100179766A1
公开(公告)日：2010-07-15
申请号：US12602481
申请日：2008-06-02
申请人： Sangtae Kim , Nitin Gupta , Pavel A. Pevzner
发明人： Sangtae Kim , Nitin Gupta , Pavel A. Pevzner
IPC分类号： G01N33/68 , G06F19/00 , H01J49/26
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. 发明授权

US08639447B2 Method for identifying peptides using tandem mass spectra by dynamically determining the number of peptide reconstructions required 有权
标题翻译：通过动态确定所需的肽重组数来使用串联质谱鉴定肽的方法
公开(公告)号：US08639447B2
公开(公告)日：2014-01-28
申请号：US12602481
申请日：2008-06-02
申请人： Sangtae Kim , Nitin Gupta , Pavel A. Pevzner
发明人： Sangtae Kim , Nitin Gupta , Pavel A. Pevzner
IPC分类号： G01N33/48 , G01N31/00 , G06F7/60 , G06F19/22 , G06F19/12
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. 发明授权

US08457900B2 Method for identification and sequencing of proteins 有权
标题翻译：蛋白质鉴定和测序方法
公开(公告)号：US08457900B2
公开(公告)日：2013-06-04
申请号：US12279836
申请日：2007-03-22
申请人： Pavel A. Pevzner , Nuno F. C. Bandeira , Dekel Tsur
发明人： Pavel A. Pevzner , Nuno F. C. Bandeira , Dekel Tsur
IPC分类号： G01N33/48 , G01N31/00 , G01B3/00 , G06F7/60 , G06F19/00
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修饰和未修饰或重叠肽的混合物。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从蛋白质序列和肽的重新定位以及修饰鉴定，而不是频谱与数据库的耗时匹配。

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