公开(公告)号：US20120022230A1

公开(公告)日：2012-01-26

申请号：US13155682

申请日：2011-06-08

申请人： Lloyd M. SMITH ,  MICHAEL R. SHORTREED ,  BRIAN L. FREY ,  MARGARET F. PHILLIPS ,  JOSHUA J. COON ,  SHANE M. LAMOS ,  CASEY J. KRUSEMARK ,  PETER J. BELSHAW ,  MADHUSUDAN PATEL ,  NEIL L. KELLEHER

发明人： Lloyd M. SMITH ,  MICHAEL R. SHORTREED ,  BRIAN L. FREY ,  MARGARET F. PHILLIPS ,  JOSHUA J. COON ,  SHANE M. LAMOS ,  CASEY J. KRUSEMARK ,  PETER J. BELSHAW ,  MADHUSUDAN PATEL ,  NEIL L. KELLEHER

IPC分类号： C07K1/13 ,  C07C237/06 ,  C07C211/03

CPC分类号： C07B59/001 ,  C07B59/00 ,  C07B59/008 ,  G01N30/7233 ,  G01N2458/15 ,  Y10T436/163333 ,  Y10T436/17

摘要： Relative quantification of metabolites by Electrospray Ionization Mass Spectrometry (ESI-MS) requiring a mechanism for simultaneous analysis of multiple analytes in two or more samples. Labeling reagents that are reactive to particular compound classes and differ only in their isotopic compositions facilitate relative quantification. Heavy and light isotopic forms of methylacetimidate were synthesized and used as labeling reagents for quantification of amine-containing molecules. Heavy and light isotopic forms of formaldehyde and cholamine were also synthesized and used independently as labeling reagents for quantification of amine-containing and carboxylic acid-containing molecules, such as found in biological samples. The labeled end-products are positively charged under normal acidic conditions involving conventional Liquid Chromatography Mass Spectrometry (LC/MS) applications. Labeled primary and secondary amine and carboxylic acid end-products generated higher signals concerning mass-spectra than pre-cursor molecules and improved sensitivity. Improved accuracy concerning relative quantification was demonstrated by mixing heavy and light labeled Arabidopsis extracts in different ratios.

摘要翻译： 通过电喷雾离子化质谱（ESI-MS）对代谢物进行相对定量，其需要同时分析两个或多个样品中多种分析物的机制。 对特定化合物类别具有反应性且仅在其同位素组成上不同的标记试剂便于相对定量。 合成了甲基乙酰亚胺酸的重和轻同位素形式，并用作定量含胺分子的标记试剂。 还合成了重和轻的同位素形式的甲醛和胆胺，并且独立地用作用于定量含胺和含羧酸的分子的标记试剂，例如在生物样品中发现的。 标记的最终产物在常规的液相色谱质谱（LC / MS）应用的正常酸性条件下带正电。 标记的伯胺和仲胺和羧酸终产物产生比前体分子更高的质谱信号，提高了灵敏度。 通过以不同的比例混合重和轻标记的拟南芥提取物来证明相对定量的改进的准确性。

公开(公告)号：US08563777B2

公开(公告)日：2013-10-22

申请号：US13155682

申请日：2011-06-08

申请人： Lloyd M. Smith ,  Michael R. Shortreed ,  Brian L. Frey ,  Margaret F. Phillips ,  Joshua J. Coon ,  Shane M. Lamos ,  Casey J. Krusemark ,  Peter J. Belshaw ,  Madhusudan Patel ,  Neil L. Kelleher

发明人： Lloyd M. Smith ,  Michael R. Shortreed ,  Brian L. Frey ,  Margaret F. Phillips ,  Joshua J. Coon ,  Shane M. Lamos ,  Casey J. Krusemark ,  Peter J. Belshaw ,  Madhusudan Patel ,  Neil L. Kelleher

IPC分类号： C07C211/10 ,  C07C211/11 ,  G01N33/58

CPC分类号： C07B59/001 ,  C07B59/00 ,  C07B59/008 ,  G01N30/7233 ,  G01N2458/15 ,  Y10T436/163333 ,  Y10T436/17

摘要： Relative quantification of metabolites by Electrospray Ionization Mass Spectrometry (ESI-MS) requiring a mechanism for simultaneous analysis of multiple analytes in two or more samples. Labeling reagents that are reactive to particular compound classes and differ only in their isotopic compositions facilitate relative quantification. Heavy and light isotopic forms of methylacetimidate were synthesized and used as labeling reagents for quantification of amine-containing molecules. Heavy and light isotopic forms of formaldehyde and cholamine were also synthesized and used independently as labeling reagents for quantification of amine-containing and carboxylic acid-containing molecules, such as found in biological samples. The labeled end-products are positively charged under normal acidic conditions involving conventional Liquid Chromatography Mass Spectrometry (LC/MS) applications. Labeled primary and secondary amine and carboxylic acid end-products generated higher signals concerning mass-spectra than pre-cursor molecules and improved sensitivity. Improved accuracy concerning relative quantification was demonstrated by mixing heavy and light labeled Arabidopsis extracts in different ratios.

摘要翻译： 通过电喷雾离子化质谱（ESI-MS）对代谢物进行相对定量，其需要同时分析两个或多个样品中多种分析物的机制。 对特定化合物类别具有反应性且仅在其同位素组成上不同的标记试剂便于相对定量。 合成了甲基乙酰亚胺酸的重和轻同位素形式，并用作定量含胺分子的标记试剂。 还合成了重和轻的同位素形式的甲醛和胆胺，并且独立地用作用于定量含胺和含羧酸的分子的标记试剂，例如在生物样品中发现的。 标记的最终产物在常规的液相色谱质谱（LC / MS）应用的正常酸性条件下带正电。 标记的伯胺和仲胺和羧酸终产物产生比前体分子更高的质谱信号，提高了灵敏度。 通过以不同的比例混合重和轻标记的拟南芥提取物来证明相对定量的改进的准确性。

公开(公告)号：US07765068B2

公开(公告)日：2010-07-27

申请号：US11048125

申请日：2005-01-31

申请人： Neil L. Kelleher ,  Gregory K. Taylor

发明人： Neil L. Kelleher ,  Gregory K. Taylor

IPC分类号： G06F19/00 ,  G01N24/00 ,  H01J49/00

CPC分类号： G01N33/6818 ,  G01N33/6848 ,  Y10T436/24

摘要： A method of preparing a first set of candidate fragments from a sample protein fragment and a protein sequence, comprises selecting a first candidate sequence comprising a terminal amino acid of the protein sequence; generating a further candidate sequence from each candidate sequence, except a last candidate sequence; and including any candidate sequences having a mass which is equal to the mass of the sample protein fragment within a third tolerance, in the first set of candidate fragments. The generating of the further candidate sequences from each candidate sequence is by adding a portion of the protein sequence farther away from the terminal amino acid than the candidate sequence, if a mass of the sample protein fragment is equal to or greater than the mass of the candidate sequence within a first tolerance, or deleting a portion of the candidate sequence from an end closest to the terminal amino acid, if the mass of the sample protein fragment is less than the mass of the candidate sequence within a second tolerance. The candidate sequences are subsequences of the protein sequence.

摘要翻译： 从样品蛋白质片段和蛋白质序列制备第一组候选片段的方法，包括选择包含蛋白质序列的末端氨基酸的第一候选序列; 从每个候选序列生成另外的候选序列，除了最后的候选序列; 并且包括在第一组候选片段中具有等于第三容差内的样品蛋白质片段的质量的质量的任何候选序列。 从每个候选序列产生另外的候选序列是通过将蛋白质序列的一部分与候选序列相比更远离末端氨基酸，如果样品蛋白质片段的质量等于或大于 如果样品蛋白质片段的质量小于第二容差内的候选序列的质量，则在第一容差内的候选序列或从最接近末端氨基酸的末端删除候选序列的一部分。 候选序列是蛋白质序列的子序列。

公开(公告)号：US20130210050A1

公开(公告)日：2013-08-15

申请号：US13765098

申请日：2013-02-12

申请人： Neil L. Kelleher ,  Cong Wu

发明人： Neil L. Kelleher ,  Cong Wu

IPC分类号： C12Q1/37

CPC分类号： C12Q1/37 ,  G01N2560/00

摘要： Provided herein is technology relating to proteases and proteomics and particularly, but not exclusively, to compositions comprising OmpT, methods of using OmpT, and methods of manufacturing OmpT for proteomics.

摘要翻译： 本文提供了与蛋白酶和蛋白质组学相关的技术，特别地但不排他地涉及包含OmpT的组合物，使用OmpT的方法以及制造用于蛋白质组学的OmpT的方法。

公开(公告)号：US07982070B2

公开(公告)日：2011-07-19

申请号：US11726307

申请日：2007-03-21

申请人： Lloyd M. Smith ,  Michael R. Shortreed ,  Brian L. Frey ,  Margaret F. Phillips ,  Joshua J. Coon ,  Shane M. Lamos ,  Casey J. Krusemark ,  Peter J. Belshaw ,  Madhusudan Patel ,  Neil L. Kelleher

发明人： Lloyd M. Smith ,  Michael R. Shortreed ,  Brian L. Frey ,  Margaret F. Phillips ,  Joshua J. Coon ,  Shane M. Lamos ,  Casey J. Krusemark ,  Peter J. Belshaw ,  Madhusudan Patel ,  Neil L. Kelleher

IPC分类号： C07C211/10 ,  C07C211/11 ,  G01N33/58

CPC分类号： C07B59/001 ,  C07B59/00 ,  C07B59/008 ,  G01N30/7233 ,  G01N2458/15 ,  Y10T436/163333 ,  Y10T436/17

摘要： Relative quantification of metabolites by Electrospray Ionization Mass Spectrometry (ESI-MS) requiring a mechanism for simultaneous analysis of multiple analytes in two or more samples. Labeling reagents that are reactive to particular compound classes and differ only in their isotopic kit facilitating relative quantification and providing tangible evidence for the existence of specific functional groups. Heavy and light isotopic forms of methylacetimidate were synthesized and used as labeling reagents for quantification of amine-containing molecules, such as biological samples. Heavy and light isotopic forms of formaldehyde and cholamine were also synthesized and used independently as labeling reagents for quantification of amine-containing and carboxylic acid-containing molecules, such as found in biological samples. Advantageously, the labeled end-products are positively charged under normal acidic conditions involving conventional Liquid Chromatography Mass Spectrometry (LC/MS) applications. Labeled primary and secondary amine and carboxylic acid end-products also generated higher signals concerning mass-spectra than pre-cursor molecules and improved sensitivity. Improved accuracy concerning relative quantification was achieved by mixing heavy and light labeled Arabidopsis extracts in different ratios. Labeling strategy was further employed to ascertain differences in the amounts of amine-containing metabolites for two strains of Arabidopsis seeds.

摘要翻译： 通过电喷雾离子化质谱（ESI-MS）对代谢物进行相对定量，其需要同时分析两个或多个样品中多种分析物的机制。 标记对特定化合物类别具有反应性的试剂，仅在其同位素试剂盒中有所不同，便于相对定量，并为特定官能团的存在提供有形证据。 合成了甲基亚酰亚胺酸的重和轻同位素形式，并用作定量含胺分子（如生物样品）的标记试剂。 还合成了重和轻的同位素形式的甲醛和胆胺，并且独立地用作用于定量含胺和含羧酸的分子的标记试剂，例如在生物样品中发现的。 有利地，标记的最终产物在常规的液相色谱质谱（LC / MS）应用的正常酸性条件下带正电荷。 标记的伯胺和仲胺和羧酸终产物也产生了比前体分子更高的质谱信号，提高了灵敏度。 通过以不同比例混合重和轻标记的拟南芥提取物，提高了相对定量的准确性。 进一步使用标记策略来确定两种拟南芥种子的含胺代谢物的量的差异。

公开(公告)号：US20110136675A1

公开(公告)日：2011-06-09

申请号：US12500505

申请日：2009-07-09

申请人： Neil L. Kelleher

发明人： Neil L. Kelleher

IPC分类号： C40B20/00 ,  C40B30/02 ,  C40B40/10 ,  C40B60/12

CPC分类号： G16B30/00 ,  G16B50/00

摘要： A method of selecting a set of candidate polypeptides for a sample polypeptide that includes a first refining of a collection of candidate polypeptides from differences in mass of fragments of the sample polypeptide produced by mass spectrometry and a second refining of the collection of candidate polypeptides from the absolute mass of the sample polypeptide and the absolute mass of the fragments.

摘要翻译： 选择一组样品多肽的候选多肽的方法，其包括通过质谱法产生的样品多肽的片段质量差异从第一次精选候选多肽的集合，并从第 样品多肽的绝对质量和片段的绝对质量。