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公开(公告)号：US10073075B2
公开(公告)日：2018-09-11
申请号：US15162598
申请日：2016-05-23
发明人： David B. Krizman , Todd Hembrough , Eunkyung An
IPC分类号： A61K38/00 , G01N33/483 , G01N33/574 , G01N33/68
CPC分类号： G01N33/4833 , G01N33/57484 , G01N33/6848 , G01N2333/47 , G01N2333/4704
摘要： Methods are provided for quantifying the cyclin-dependent kinase inhibitor 2A protein (p16) p16 protein directly in biological samples that have been fixed in formalin by SRM/MRM mass spectrometry. A protein sample is prepared from the biological sample using, for example, the Liquid Tissue reagents and protocol and the p16 protein is quantitated in the resulting sample by quantitating in the protein sample at least one fragment peptide from p16. Peptides can be quantitated in modified or unmodified form. An example of a modified form of a p16 peptide is phosphorylation of a tyrosine, threonine, serine, and/or other amino acid residues within the peptide sequence.
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公开(公告)号：US09766246B2
公开(公告)日：2017-09-19
申请号：US15216789
申请日：2016-07-22
IPC分类号： G01N33/53 , G01N33/574 , G01N33/68
CPC分类号： G01N33/57492 , G01N33/57423 , G01N33/57484 , G01N33/6848 , G01N2033/57453 , G01N2333/47 , G01N2333/4704 , G01N2333/4742 , G01N2333/70596 , G01N2333/96472 , G01N2458/15 , G01N2560/00
摘要： The current disclosure provides for specific peptides, and derived ionization characteristics of the peptides, from the KRT5, KRT7, NapsinA, TTF1, TP63, and/or MUC1 proteins that are particularly advantageous for quantifying the KRT5, KRT7, NapsinA, TTF1, TP63, and/or MUC1 proteins directly in biological samples that have been fixed in formalin by the method of Selected Reaction Monitoring (SRM) mass spectrometry, or what can also be termed as Multiple Reaction Monitoring (MRM) mass spectrometry. Such biological samples are chemically preserved and fixed wherein said biological sample is selected from tissues and cells treated with formaldehyde containing agents/fixatives including formalin-fixed tissue/cells, formalin-fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks, and tissue culture cells that have been formalin fixed and or paraffin embedded. A protein sample is prepared from said biological sample using the Liquid Tissue™ reagents and protocol and the KRT5, KRT7, NapsinA, TTF1, TP63, and/or MUC1 proteins are quantitated in the Liquid Tissue™ sample by the method of SRM/MRM mass spectrometry by quantitating in the protein sample at least one or more of the peptides described. These peptides can be quantitated if they reside in a modified or an unmodified form. An example of a modified form of a KRT5, KRT7, NapsinA, TTF1, TP63, and MUC1 fragment peptide is phosphorylation of a tyrosine, threonine, serine, and/or other amino acid residues within the peptide sequence.
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公开(公告)号：US09551719B2
公开(公告)日：2017-01-24
申请号：US13942574
申请日：2013-07-15
申请人： David Krizman , Todd Hembrough , Sheeno Thyparambil , Wei-Li Liao
发明人： David Krizman , Todd Hembrough , Sheeno Thyparambil , Wei-Li Liao
CPC分类号： G01N33/6893 , C07K14/4747 , C07K16/2863 , C07K16/32 , C07K2317/76 , C12Q1/485 , C12Q1/6886 , C12Q2600/158 , G01N33/5088 , G01N33/574 , G01N33/6848 , G01N2333/4703 , G01N2800/44 , G01N2800/52 , G01N2800/56
摘要： Specific peptides, and derived ionization characteristics of those peptides, from the Bcl-2-like protein 11 (BIM) are provided that are particularly advantageous for quantifying the BIM protein directly in biological samples that have been fixed in formalin by the method of Selected Reaction Monitoring (SRM) mass spectrometry, or what can also be termed as Multiple Reaction Monitoring (MRM). Such biological samples are chemically preserved and fixed where the biological sample is selected from tissues and cells treated with formaldehyde containing agents/fixatives including formalin-fixed tissue/cells, formalin-fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks, and tissue culture cells that have been formalin fixed and or paraffin embedded. A protein sample is prepared from the biological sample using the Liquid Tissue™ reagents and protocol, and the BIM protein is quantitated in the Liquid Tissue™ sample by the method of SRM/MRM mass spectrometry by quantitating in the protein sample at least one or more of the peptides described. These peptides can be quantitated if they reside in a modified or an unmodified form. An example of a modified form of a BIM peptide is phosphorylation of a tyrosine, threonine, serine, and/or other amino acid residues within the peptide sequence.
摘要翻译： 提供了来自Bcl-2样蛋白11（BIM）的那些肽的特异性肽和衍生的电离特征，其特别有利于通过选择反应的方法在福尔马林中固定的生物样品中直接定量BIM蛋白 监测（SRM）质谱，或什么也可以称为多反应监测（MRM）。 在生物样品选自用含甲醛的试剂/固定剂（包括福尔马林固定的组织/细胞，福尔马林固定/石蜡包埋（FFPE）组织/细胞，FFPE组织块）和 来自这些区块的细胞和已被福尔马林固定和石蜡包埋的组织培养细胞。 使用Liquid Tissue TM试剂和方案从生物样品制备蛋白质样品，并且通过SRM / MRM质谱法通过在蛋白质样品中定量至少一种或多种来定量BIM蛋白质在Liquid Tissue TM样品中 的肽。 如果它们以修饰或未修饰的形式存在，则可以定量这些肽。 BIM肽的修饰形式的实例是肽序列内的酪氨酸，苏氨酸，丝氨酸和/或其他氨基酸残基的磷酸化。
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公开(公告)号：US09360487B2
公开(公告)日：2016-06-07
申请号：US14223524
申请日：2014-03-24
CPC分类号： G01N33/6848 , G01N33/6893 , G01N33/743 , G01N2333/47 , G01N2333/70567 , G01N2800/56 , G01N2800/7028
摘要： The current disclosure provides specific peptides, and derived ionization characteristics of the peptides from the estrogen receptor (ER), progesterone receptor (PR), and/or antigen Ki67 (Ki67) proteins that are particularly advantageous for quantifying the ER, PR, and/or Ki67 proteins directly in biological samples that have been fixed in formalin by the method of Selected Reaction Monitoring/Multiple Reaction Monitoring (SRM/MRM) mass spectrometry. Such biological samples are chemically preserved and fixed wherein the biological sample is selected from tissues and cells treated with formaldehyde containing agents/fixatives including formalin-fixed tissue/cells, formalin-fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks, and tissue culture cells that have been formalin fixed and or paraffin embedded. A protein sample is prepared from a biological sample using the Liquid Tissue™ reagents and protocol, and the ER, PR, and/or Ki67 proteins are quantitated in the Liquid Tissue™ sample by the method of SRM/MRM mass spectrometry by quantitating in the protein sample at least one or more of the peptides described for one or more of the ER, PR, and/or Ki67 proteins. These peptides can be quantitated if they reside in a modified or in an unmodified form. An example of a modified form of an ER, PR, and/or Ki67 peptide is phosphorylation of a tyrosine, threonine, serine, and/or other amino acid residues within the peptide sequence.
摘要翻译： 目前的公开内容提供特异性肽，以及来自雌激素受体（ER），孕酮受体（PR）和/或抗原Ki67（Ki67）蛋白质的肽的衍生电离特征，其特别有利于定量ER，PR和/ 或通过选择反应监测/多反应监测（SRM / MRM）质谱法的方法在已经在福尔马林中固定的生物样品中直接存在Ki67蛋白。 这些生物样品被化学保存和固定，其中生物样品选自用含甲醛的试剂/固定剂（包括福尔马林固定的组织/细胞，福尔马林固定/石蜡包埋的（FFPE）组织/细胞，FFPE组织块）和 来自这些区块的细胞和已被福尔马林固定和石蜡包埋的组织培养细胞。 使用Liquid Tissue TM试剂和方案从生物样品制备蛋白质样品，并通过SRM / MRM质谱法的方法在液体组织样品中定量分析ER，PR和/或Ki67蛋白质， 蛋白质样品至少一种或多种针对一种或多种ER，PR和/或Ki67蛋白质描述的肽。 如果它们以修饰或未修饰的形式存在，则可以定量这些肽。 ER，PR和/或Ki67肽的修饰形式的实例是肽序列内的酪氨酸，苏氨酸，丝氨酸和/或其他氨基酸残基的磷酸化。
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公开(公告)号：US09261506B2
公开(公告)日：2016-02-16
申请号：US14543610
申请日：2014-11-17
IPC分类号： G01N33/53 , G01N33/574 , G01N33/68
CPC分类号： G01N33/57492 , G01N33/57423 , G01N33/57484 , G01N33/6848 , G01N2033/57453 , G01N2333/47 , G01N2333/4704 , G01N2333/4742 , G01N2333/70596 , G01N2333/96472 , G01N2458/15 , G01N2560/00
摘要： The current disclosure provides for specific peptides, and derived ionization characteristics of the peptides, from the KRT5, KRT7, NapsinA, TTF1, TP63, and/or MUC1 proteins that are particularly advantageous for quantifying the KRT5, KRT7, NapsinA, TTF1, TP63, and/or MUC1 proteins directly in biological samples that have been fixed in formalin by the method of Selected Reaction Monitoring (SRM) mass spectrometry, or what can also be termed as Multiple Reaction Monitoring (MRM) mass spectrometry. Such biological samples are chemically preserved and fixed wherein said biological sample is selected from tissues and cells treated with formaldehyde containing agents/fixatives including formalin-fixed tissue/cells, formalin-fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks, and tissue culture cells that have been formalin fixed and or paraffin embedded. A protein sample is prepared from said biological sample using the Liquid Tissue™ reagents and protocol and the KRT5, KRT7, NapsinA, TTF1, TP63, and/or MUC1 proteins are quantitated in the Liquid Tissue™ sample by the method of SRM/MRM mass spectrometry by quantitating in the protein sample at least one or more of the peptides described. These peptides can be quantitated if they reside in a modified or an unmodified form. An example of a modified form of a KRT5, KRT7, NapsinA, TTF1, TP63, and MUC1 fragment peptide is phosphorylation of a tyrosine, threonine, serine, and/or other amino acid residues within the peptide sequence.
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公开(公告)号：US20140005282A1
公开(公告)日：2014-01-02
申请号：US13976956
申请日：2011-12-27
IPC分类号： G01N33/68
CPC分类号： G01N33/6872 , G01N33/4833 , G01N33/68 , G01N33/6848 , G01N33/74 , G01N2030/8831 , G01N2333/71 , G01N2333/82 , G01N2560/00 , G01N2800/52 , G01N2800/56
摘要： Specific peptides are provided, and derived ionization characteristics of those peptides, from the Hepatocyte Growth Factor Receptor (cMET) protein. The peptides are particularly and surprisingly advantageous for quantifying by the method of Selected Reaction Monitoring (SRM) mass spectrometry the cMET protein directly in biological samples that have been fixed in formalin, or what can also be termed as Multiple Reaction Monitoring (MRM) mass spectrometry. Such biological samples are chemically preserved and fixed where the biological sample is selected from tissues and cells treated with formaldehyde containing agents/fixatives including: formalin-fixed tissue/cells; formalin-fixed/paraffin embedded (FFPE) tissue/cells; FFPE tissue blocks and cells from those blocks; and tissue culture cells that have been formalin fixed and or paraffin embedded. A protein sample is prepared from the biological sample using the Liquid Tissue™ reagents and protocol and the cMET protein is quantitated in the Liquid Tissue™ sample by the method of SRM/MRM mass spectrometry by quantitating in the protein sample at least one or more of the peptides described. These peptides can be quantitated if they reside in a modified or an unmodified form. An example of a modified form of a cMET peptide is phosphorylation of a tyrosine, threonine, serine, and/or other amino acid residues within the peptide sequence.
摘要翻译： 提供特异性肽，并从肝细胞生长因子受体（cMET）蛋白提供这些肽的衍生电离特征。 通过选择反应监测（SRM）质谱法直接在已经在福尔马林中固定的生物样品中的cMET蛋白进行定量，或者也可以称为多反应监测（MRM）质谱法，这些肽特别令人惊奇地有利 。 这种生物样品被化学保存和固定，其中生物样品选自用含甲醛的试剂/固定剂处理的组织和细胞，包括：福尔马林固定的组织/细胞; 福尔马林固定/石蜡包埋（FFPE）组织/细胞; FFPE组织块和来自这些区块的细胞; 和已被福尔马林固定和石蜡包埋的组织培养细胞。 使用Liquid Tissue TM试剂和方案从生物样品制备蛋白质样品，并通过SRM / MRM质谱法通过在蛋白质样品中定量至少定量在液体组织样品中定量cMET蛋白质 描述的一种或多种肽。 如果它们以修饰或未修饰的形式存在，则可以定量这些肽。 cMET肽的修饰形式的实例是肽序列内的酪氨酸，苏氨酸，丝氨酸和/或其他氨基酸残基的磷酸化。
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公开(公告)号：US20130302334A1
公开(公告)日：2013-11-14
申请号：US13942574
申请日：2013-07-15
申请人： David Krizman , Todd Hembrough , Sheeno Thyparambil , Wei-Li Liao
发明人： David Krizman , Todd Hembrough , Sheeno Thyparambil , Wei-Li Liao
IPC分类号： G01N33/68
CPC分类号： G01N33/6893 , C07K14/4747 , C07K16/2863 , C07K16/32 , C07K2317/76 , C12Q1/485 , C12Q1/6886 , C12Q2600/158 , G01N33/5088 , G01N33/574 , G01N33/6848 , G01N2333/4703 , G01N2800/44 , G01N2800/52 , G01N2800/56
摘要： Specific peptides, and derived ionization characteristics of those peptides, from the Bcl-2-like protein 11 (BIM) are provided that are particularly advantageous for quantifying the BIM protein directly in biological samples that have been fixed in formalin by the method of Selected Reaction Monitoring (SRM) mass spectrometry, or what can also be termed as Multiple Reaction Monitoring (MRM). Such biological samples are chemically preserved and fixed where the biological sample is selected from tissues and cells treated with formaldehyde containing agents/fixatives including formalin-fixed tissue/cells, formalin-fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks, and tissue culture cells that have been formalin fixed and or paraffin embedded. A protein sample is prepared from the biological sample using the Liquid Tissue™ reagents and protocol, and the BIM protein is quantitated in the Liquid Tissue™ sample by the method of SRM/MRM mass spectrometry by quantitating in the protein sample at least one or more of the peptides described. These peptides can be quantitated if they reside in a modified or an unmodified form. An example of a modified form of a BIM peptide is phosphorylation of a tyrosine, threonine, serine, and/or other amino acid residues within the peptide sequence.
摘要翻译： 提供了来自Bcl-2样蛋白11（BIM）的那些肽的特异性肽和衍生的电离特征，其特别有利于通过选择反应的方法在福尔马林中固定的生物样品中直接定量BIM蛋白 监测（SRM）质谱，或什么也可以称为多反应监测（MRM）。 在生物样品选自用含甲醛的试剂/固定剂（包括福尔马林固定的组织/细胞，福尔马林固定/石蜡包埋（FFPE）组织/细胞，FFPE组织块）和 来自这些区块的细胞和已被福尔马林固定和石蜡包埋的组织培养细胞。 使用Liquid Tissue TM试剂和方案从生物样品中制备蛋白质样品，并通过SRM / MRM质谱法在液体组织样品中定量测定BIM蛋白，通过在蛋白质样品中定量 描述的至少一种或多种肽。 如果它们以修饰或未修饰的形式存在，则可以定量这些肽。 BIM肽的修饰形式的实例是肽序列内的酪氨酸，苏氨酸，丝氨酸和/或其他氨基酸残基的磷酸化。
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公开(公告)号：US20130302328A1
公开(公告)日：2013-11-14
申请号：US13993045
申请日：2011-12-08
申请人： David Krizman
发明人： David Krizman
CPC分类号： C12Q1/37 , C07K14/71 , G01N30/72 , G01N30/7233 , G01N33/6848 , G01N33/74 , G01N2333/71
摘要： This disclosure provides ten (10) specific peptides, and particular peptide characteristics, from the cell membrane-bound Her2 protein and a diagnostic assay useful for determining the presence and amount of full length and truncated versions of the full-length Her2 protein in cells derived from formalin fixed paraffin embedded tissue.
摘要翻译： 本公开提供了十（10）种特定的肽，以及来自细胞膜结合的Her2蛋白的特定肽特征，以及用于确定细胞中全长Her2蛋白的全长和截短形式的存在和量的诊断测定 从福尔马林固定石蜡包埋组织。
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9.发明申请LIQUID TISSUE PREPARATION FROM HISTOPATHOLOGICALLY PROCESSED BIOLOGICALLY SAMPLES, TISSUES AND CELLS 审中-公开组织病理学生物学样本，组织和细胞的液体组织制备公开(公告)号：US20130252840A1
公开(公告)日：2013-09-26
申请号：US13896778
申请日：2013-05-17
IPC分类号： C12Q1/37
CPC分类号： G01N1/4044 , C12N15/1003 , C12Q1/37 , G01N1/30 , G01N1/44
摘要： The current invention provides a method for directly converting histopathologically processed biological samples, tissues, and cells into a multi-use biomolecule lysate. This method allows for simultaneous extraction, isolation, solublization, and storage of all biomolecules contained within the histopathologically processed biological sample, thereby forming a representative library of said sample. This multi-use biomolecule lysate is dilutable, soluble, capable of being fractionated, and used in any number of subsequent experiments.
摘要翻译： 本发明提供了一种将组织病理学处理的生物样品，组织和细胞直接转化成多用途生物分子裂解物的方法。 该方法允许同时提取，分离，溶解和储存包含在组织病理学处理的生物样品中的所有生物分子，从而形成所述样品的代表性文库。 这种多用途生物分子裂解物是可稀释的，可溶的，能够分级，并用于任何数量的后续实验。
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公开(公告)号：US20130131195A1
公开(公告)日：2013-05-23
申请号：US13754146
申请日：2013-01-30
发明人： David B. KRIZMAN
IPC分类号： C12Q1/48
CPC分类号： C12Q1/485 , G01N33/6848 , G01N2333/91205
摘要： Objective quantitation of the c-Src protein directly in cancer patient tissue can aid in determining the aggressiveness of an individual patient's tumor as well as help make more informed decisions about choice of therapy. However, the c-Src protein is currently analyzed directly in formalin fixed patient tissue only by immunohistochemistry methodology which is at best subjectively semi-quantitative. This invention describes an objective quantitative assay for the c-Src protein using mass spectrometry as the analytical methodology. Specific peptides, experimentally discovered characteristics about the peptides, and experimentally established assay conditions based on those peptide characteristics are provided for use in a mass spectrometry-based Selected Reaction Monitoring (SRM) assay in order to measure relative or absolute quantitative levels of c-Src directly in a protein preparation obtained from a formalin fixed cancer patient tissue sample.
摘要翻译： 在癌症患者组织中直接对c-Src蛋白进行客观定量可以帮助确定个体患者肿瘤的侵袭性，并帮助对治疗选择作出更明智的决定。 然而，c-Src蛋白质目前仅通过免疫组织化学方法直接在福尔马林固定的患者组织中进行分析，该方法最好是主观半定量。 本发明描述了使用质谱法作为分析方法的c-Src蛋白质的客观定量测定法。 提供特定肽，实验发现的关于肽的特征以及基于这些肽特征的实验建立的测定条件用于基于质谱的选择反应监测（SRM）测定中，以测量c-Src的相对或绝对定量水平 直接在从福尔马林固定的癌症患者组织样品中获得的蛋白质制剂中。
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